Translating the Computable Plant
Multinational Arabidopsis
Steering Committee
Annual Report 2023-2024

MASC annual report 2023/24

Design and editing
Geraint Parry
MASC Secretary, Arabidopsis Events UK
https://www.arabidopsisevents.uk/
arabidopsisventsuk@gmail.com
Cover images taken from Open Access publications
Top: Ochoa et al (2023) Natural variation in Arabidopsis responses to Plasmodiophora brassicae
reveals an essential role for Resistance to Plasmodiophora brasssicae 1 (RPB1)
https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.16438
Middle: Li et al (2023) Nature Communications 14 (1), 2600, 5/5/2023
https://www.nature.com/articles/s41467-023-38096-2
Bottom: Nobori et al (2023) Multiplexed single-cell 3D spatial gene expression analysis in planttissue using PHYTOMap.
https://www.nature.com/articles/s41477-023-01439-4
Further information can be found on the MASC website: www.Arabidopsisresearch.org
Previous reports are also available online at:• MASC, The Multinational Arabidopsis Steering Committee:
https://arabidopsisresearch.org/index.php/en/publications• uNASC, The Nottingham Arabidopsis Stock Centre:
http://Arabidopsis.info/progreports.html
Published by the Multinational Arabidopsis Steering Committee (MASC) August 2024
MASC Inc is registered as a not-for-profit corporation in Canada under Corporatation Number
960778-1, subject to the regulations of the Canada Not-for-profit Corporations Act
Acknowledgements
MASC is grateful to all authors for their contribution to the MASC annual report 2023-4
This report has been written by the members of the MASC community including the MASC
directors, subcommittee chairs and co-chairs with support of subcommittee members, country
representatives, project or resource directors and the wider Arabidopsis community.
Throughout the report any references that are highlighted in green include an associated figure
from that open access article.

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annualContents
Members of MASC								01Activities of MASC								04Tribute to Phil Benfey								11MASC Subcommittee Reports						12MASC Project Reports							23MASC Country Reports							33MASC annual report 2023/24

The Multinational Arabidopsis
Steering Committee
Annual Report 2023/2024
MASC interim President
Siobhan Brady
sbrady@ucdavis.edu

Plant Immunity
Shahid Mukhtar
mshahid@clemson.edu

MASC Treasurer
Nicholas Provart
nicholas.provart@utoronto.ca

Proteomics
Klaas van Wijk
kv35@cornell.edu

MASC Secretary
Geraint Parryarabidopsiseventsuk@gmail.com

Systems and Synthetic Biology
Siobhan Brady
sbrady@ucdavis.edu

MASC Directors

MASC Project Resource Contacts

Shahid Mukhtar
mshahid@clemson.edu
Yuling Jiao
yuling.jiao@pku.edu.cn

ABRCDavid Somers
somers.24@osu.edu
Emma Kneeknee.2@osu.edu

MASC Subcommittee Contacts
Bioinformatics
Nicholas Provart
nicholas.provart@utoronto.ca
Epigenetics and Epigenomes
Robert Schmitz
schmitz@uga.edu
Xuehua Zhong
xuehua.zhong@wisc.edu
Metabolomics
Wolfram Weckwerth
wolfram.weckwerth@univie.ac.at
Takayuki Tohge
tohge@bs.naist.jp

BAR
Nicholas Provart
nicholas.provart@utoronto.ca
Global Plant Council
Isabel Mendoza
isabel@globalplantcouncil.org
GrameneMarcela Karey Tello-Ruiz
telloruiz@cshl.edu
NASC
Sean May
sean@Arabidopsis.org.uk

Phenotyping Resources
Natural Varation and Comparative Genomics Roland Pieruschkar.pieruschka@fz-juelich.de
J. Chris Pires
chris.pires@colostate.edu
RIKEN
Ya-Long Guo
Masatomo Kobayashi
yalong.guo@ibcas.ac.cn
kobayasi@rtc.riken.jp

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TAIR
Leonore Reiser
lreiser@phoenixbioinformatics.org

Estonia
Hanna Hõrak
hanna.horak@ut.ee

MASC Country/ Region
Representatives

FinlandAri Pekka Mahonen
aripekka.mahonen@helsinki.fi

Argentina
Gabriela Augeauge.gabriela@inta.gob.arFranceLoic Lepiniec
Loic.Lepiniec@versailles.inra.fr
Cécile Bousquet-Antonelli
insb.das5f@cnrs.fr

Australia
Monika Murcha
monika.murcha@uwa.edu.au
Austria
Marie-Theres Hauser
marie-theres.hauser@boku.ac.at
BelgiumMoritz K. Nowack
moritz.nowack@vib.be
BrazilWagner Araújo
wlaraujo@ufv.br
Adriano Nunes-Nesi
nunesnesi@ufv.br
CanadaDario Bonetta
dario.bonetta@uoit.ca
Nicholas Provart
nicholas.provart@utoronto.ca

Germany
Klaus Harterklaus.harter@zmbp.uni-tuebingen.de
GreeceStamatis Rigas
srigas@aua.gr
India
Jyothilakshmi Vadasseryjyothi.v@nipgr.ac.in
Sourav Datta
sdatta@iiserb.ac.in
IrelandCharles Spillane
charles.spillane@nuigalway.ie
IsraelAssaf Mosquna
assaf.mosquna@mail.huji.ac.il

Chile
Adrian A. Moreno
adrian.moreno@unab.cl

Italy
Alice Pajoro
alice.pajoro@cnr.it

China
Yuling Jiao
yuling.jiao@pku.edu.cn
Czech Republic
Viktor Žárský
viktor@natur.cuni.cz

Japan
Masatomo Kobayashi
kobayasi@rtc.riken.jp
Minami Matsui
minami@riken.jp
Motoaki Seki
motoaki.seki@riken.jp

Denmark
Michael Palmgren
palmgren@plen.ku.dk

New Zealand
Rowan Herridge
Rowan.Herridge@otago.ac.nz

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Norway
Thorsten Hamann
thorsten.hamann@ntnu.no
PolandRobert Malinowski
rmal@igr.poznan.pl
Saudi Arabia
Yunhe Jiang
yunhe.jiang@kaust.edu.sa
Singapore
Eunyoung Chae
dbsce@nus.edu.sg
South Korea
Inhwan Hwang
ihhwang@postech.ac.kr
Spain
Cristina Ferrandizcferrandiz@ibmcp.upv.es
SwedenMaria E. Eriksson
maria.erikson@plantphys.umu.se
Switzerland
Misako Yamazaki
misako.yamazaki@ieu.uzh.ch
Kentaro K. Shimizu
kentaro.shimizu@ieu.uzh.ch
TaiwanCheng-Hsun Hozcybele3@sinica.edu.tw
TurkeyBaris Uzilday
baris.uzilday@ege.edu.tr
United Kingdom
Geraint Parryarabidopsiseventsuk@gmail.com
United States of America
Joanna D. Friesner
jdfriesner@danforth.edu

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Activities of MASC
Thanks for being interested in the latest activities of the Multinational Arabidopsis Steering
Committee (MASC). The first task is to thank the many contributors who have submitted pieces
for this annual report. Without their input then MASC would be unable to prepare this document,
which aims to track of progress and challenges of the global Arabidopsis community.
MASC Inc is incorporated as a not-for-profit in Canada. This requires the official positions ofPresident, Treasurer and Secretary of which the current incumbents are Siobhan Brady, Nicholas
Provart and Geraint Parry respectively. These people have been in post since MASC Inc wasincorporated in 2017. In the next year, we will seek a new President and update members of our
Executive Board. We remain very much open to new ideas that will inform the future activities of
MASC.
The recent launch of the ‘Arabidopsis Community suported by NAASC’ has provided a
new exciting resource for the global community (https://www.arabidopsiscommunity.org/) This
organisation has arise from the activities of NAASC (the North America Arabidopsis Steering
Committee), is organised from the USA and are initiating many important activities that lower theboundaries to entry to ICAR (and other) meetings.
MASC looks forward to interacting where relevant with the ‘Arabidopsis Community’ totake a more global view with regard Arabidopsis research and researchers. This role for MASC is
exemplified both through the publication of this document and in the upcoming publication of the‘4th Decadal Vision: Arabidopsis Research in 2030: Translating the Computable Plant’ and throughoversight of the ICAR meetings.
In 2017 eight MASC Directors were elected for a range of term lengths. These directors
officially took up their positions at the MASC annual meeting that took place at ICAR2018 in Turku,
Finland. However over the past few years we have been unable to recruit new directors so at theend of 2024 there won’t be any current directors. Therefore MASC need to elect new directors
and the leadership team will make a renewed push to recruit both from existing MASC participants
and/or anyone currently ‘outside’ the organisation.
If you are interested in becoming a MASC Director please contact Geraint Parry(arabidopsiseventsuk@gmail.com). These roles are VERY light-touch, requiring very little work!
This is a current list of the MASC board of directors and the end of their term. You will
see that Shahid and Yuling will soon leave so we are looking to recruit a completely new set of
Directors.
- 2020-2024: Shahid Mukhtar (United States of America), Yuling Jiao (China)
The MASC coordinator/secretary position was established in 2002 and has been previously
supported by the NSF (USA), the DFG (Germany) and by the BBSRC. From 2020 MASC has
directly paid to support secretary activities, albeit for these limited roles:- Serving as executive secretary of MASC
- Collating, writing, and editing of the annual MASC progress report with input from MASC
members- Maintaining and updating the MASC web pages to inform the global research community about
various opportunities, collaborations, large-scale activities and research progress- Organising the MASC annual meeting

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From August 2020 Dr Geraint Parry has been engaged by MASC Inc to oversee its
activities, which remain at the minimum level (anticipated to be a total 12 hours in 2024) tomaintain the activity of the organisation. In 2022 and 2023 preparation of the report has been
aided by a UK-based PhD student. This is something we hope to repeat in 2025 and beyond. This
provides some good experience and may be undertaken by anyone who is looking for a different
experience outside of their standard research activities.
MASC operates through three groups who receive continuous input from the entire
Arabidopsis and plant community: MASC subcommittees, Arabidopsis community projects andresources and MASC country representatives.
The MASC subcommittees, proposed in 2002, were established to help tracking the
progress and advances made by the international Arabidopsis community. This report includes
contributions from five subcommittees: Bioinformatics, Epigenetics and Epigenomes, Natural
Variation and Comparative Genomics, Plant Immunity and Systems and Synthetic Biology.
Subcommittees have certain loose guidelines for their activities:- Subcommittee chairs are usually required for a 3-year minimum term to provide continuity- Chair/co-chair should confirm and represent the interests of subcommittee members- Submission of an annual report- Input at MASC annual meetings
We encourage subcommittee members to take a role in the organisation of workshops at
ICAR meetings. At ICAR2024 in San Diego the Bioinformatics subcommittee group organised a
concurrent session on ‘Our Community Effort to Reannotate the Arabidopsis Genome’ andthe Epigenetics and Epigenomics subcommittee organised a Concurrent session simply entitled‘Epigenetics’.
One strength of the global Arabidopsis research community comes in the form of the
genomic resources and seed stocks that are available for use. This document includes reports
the three major international stock centres (ABRC, NASC, RIKEN Stock Centre), from two majorinternational phenotyping projects, from Gramene and the Global Plant Council. Finally the report
includes submissions from TAIR and the BAR (Bio-Analytic Resource for Plant Biology).
Country reports provide the bulk of the MASC report and highlight the new resources andpublications that have been generated from different parts of the world. We are grateful to theCountry representatives who contributed to this report.
We are extremely grateful to all representative of subcommittees, projects, or countries as
they voluntarily give their time toward MASC activities. All MASC contributors are invited to attend
the remote MASC annual meeting that will take place on September 12th at 2pm GMT.
Overall, we very much encourage Arabidopsis researchers to become involved in MASC
activities, e.g. subcommittees, projects and resources or as country representatives. If this is ofinterest to you then please contact Geraint Parry. The future of the Arabidopsis community is up to
us. We encourage you to attend our annual meeting and to consider becoming one of our directors
or a member of our leadership.

MASC annual report 2023/24

5International Conference on Arabidopsis Research (ICAR)Over the past decade the flagship ICAR meeting has rotated though locations in Asia, North
America and Europe. However, the board of directors are more than happy to consider otherlocations if there is a need to take the ICAR meeting to previously under-represented regions orcountries.
ICAR 2024 took place in San Diego, USA at a meeting organised by Joanna Friesnerand NAASC. 538 in-person and 45 online delegates attended the meeting, which is an excellent
number considering the competition from other global plant science meetings occuring in lateJune 2024 (IPMB in Cairns Australia and ASPB in Hawaii). 47% of ICAR2024 attendees were
early career students (including 18 undergraduates!). Alongside the 4 Keynote speakers, 6
Plenary sessions there were a remarkable 37 Concurrent sessions that were organised thanks
to community suggestions. These sessions provided the opportunity for 310 oral presenters in
addition to 250 poster presentations.
NAASC was able to secure some excellent funding primarily from the US National Science
Foundation, but also from several additional sponsors, that supported the attendance of 86
early career and/or global South scientists with free registration. Three Global South attendees
were also provided free campus
accommodation to enable their
participation.
The adjacent graph showsthat the number of ICAR attendees
has stayed consistent over the past
two decades, with higher delegate
numbers at the Asian meetings(2023 JAPAN, 2019 CHINA, 2016
KOREA).
It is gratifying to observethat the past few years has seena higher proportion of delegateshaving submitted abstracts,
indicating that there is a morescientifically engaged set ofdelegates.
For obvious reasons ICAR
2021 was online-only and engaged~1000 delegates. The subsequent ICARs have also included a hybrid element. However thenumber of online delegates have declined over the past 3 years. (~200 in 2022, 55 in 2023, 45 in2024).
In 2023 both online and in-person registrations were a similar price but in 2022 and 2024
the online price was much lower than the in-person price. Organising a good quality hybrId
meeting has significant costs so future ICAR organisers will need to carefully consider both
economic and access reasons when organising a hybrid meeting. NAASC reports that the hybrid
cost component of ICAR 2024 was $22,000+ whereas virtual attendee revenue was slightly under$10,000. On the positive side, when several speakers canceled at the last minute due to illness or
travel challenges, they were able to be quickly converted to virtual speakers.

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Organisation of ICAR meetings relies upon a committed local organising committee who
might engage a conference management company to deal with the meeting details. Unlike mostmajor international meetings there is limited seed funding available from MASC to help with theorganisational costs of ICARs.
The locations for upcoming ICAR meetings:- 35th ICAR, Ghent, Belgium. June 16th-20th 2025. www.icar2025.com- 36th ICAR, TBC in Asia
- 37th ICAR, TBC in The Americas
The MASC Code of Conduct
The MASC directors in collaboration with Joanna Friesner (Executive Director of NAASC)
developed a code of conduct for ICAR events. This code includes advice about appropriately
dealing with harassment and unwanted reporting of conference materials. ICAR conferences will
provide a safe and productive environment that promotes equal opportunity and treatment for allparticipants that is free of harassment and discrimination and allows the sharing of unpublishedscientific findings. The code of conduct applies to all registered attendees, speakers, exhibitors,
staff, contractors, volunteers, and guests; and it applies both within the ICAR conference venues
and in associated events and locations where ICAR conference delegates are present.
The Code of Contact updated for ICAR2024 can be read here:
https://icar2024.weebly.com/advocacyconduct-code.html
The MASC website
http://Arabidopsisresearch.org/
The MASC website is hosted in Canada by Hostpapa, maintained by Geraint Parry andNick Provart.
This is an information resource for previous MASC related activities. These include:- Abstract books from ICAR meetings going back to the 10th ICAR in 1999.
http://Arabidopsisresearch.org/index.php/en/icar- Agenda and Minutes from MASC Annual meetings since 2001.
http://Arabidopsisresearch.org/index.php/en/archive- MASC Annual Reports since 1990
http://Arabidopsisresearch.org/index.php/en/publications- Documents and Articles related to Roadmap activities and related surveys
http://Arabidopsisresearch.org/index.php/en/publications
Secondly the website contains the most up-to-date information from each of the MASC
Subcommittees, Project and Country reports that are published in each MASC annual report. This
provides a quick reference for the latest tools and publications from each of those subcommittees,
resources or countries.

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7

Publication of the Fourth Roadmap
Over the past 30 years MASC has led in the preparation of the series of decadal Roadmap
documents that have advised on the future activities of the community. These roadmaps were
published in 1990 as ‘A Long range plan for the Genome Research project’; in 2002 as ‘Beyond
the Whole genome Sequence’ and in 2012 as ‘From Bench to Bountiful Harvests’.
The 4th Decadal Roadmap document has been recently prepared by Elizabeth Haswell,
Nicholas Provart and other members of MASC. This document is titled ‘Arabidopsis Researchin 2030: Translating the Computable Plant’ and will be soon submitted for publication in a peerreviewed journal.
The topics promoted in this document where synthesised following a workshop session
at ICAR2023 and a 2024 survey in which respondants were asked, among other questions, toidentify which of the 100 important questions for plant biology from Larson et al. (2023, New
Phytol. https://doi.org/10.1111/nph.18663) Arabidopsis researchers should focus on.
The Roadmap covers 8 broad topics:- Increasing computational approaches- Supporting research and training- Translating from Arabidopsis to crops – or “back-translating” into Arabidopsis to elucidate
mechanisms in other plants- Promoting accessibility and diversity atof conferences- Coordinating research efforts- Understanding/mitigating climate change and plant stress- Sustainably producing food, materials, and fuel- Emphasizing the importance of fundamental researchOnce the document is published MASC looks forward to receiving community feedback.

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Update on Arabidopsis Publications
Over the past decade the MASC report has performed a simple analysis of the number of
Arabidopsis publications as assesed through the PubMed database.

Global Analysis
In the 2018 report we reported thatthe number of Arabidopsis publications
had for the first time dipped below thenumber of publications that include‘Rice/ Orzya’. Over the past years thisdifference has increased and indeed thenumber of publications on Maize/Cornand Wheat/Triticum have now overtaken
those that feature Arabidopsis. Of course
there are many reasons for this but there
is little doubt that incredible technicalbreakthroughs and increase in knowledge
has allowed for an increase in research
publications in food crops.

Country Analysis

Number of Publications that feature different plant species.
PubMed search using the following terms: ARABIDOPSIS [Title/
Abstract] AND (“journal article”[Publication Type] OR “review”[Publication Type]) AND 20XX[DP], Rice [Title/Abstract] OR “Oryza”[Title/Abstract], Maize [Title/Abstract] OR “Corn” [Title/Abstract],
Wheat [Title/Abstract] OR “Triticum” [Title/Abstract].

The growth in Arabidopsis
publications over the last thirty years was first driven by the ‘Western World’ and over the past 15
years by China. The number of publications from Chinese researchers is still increasing and in
2023 represents over half the total number of global Arabidopsis publications. Elsewhere acrossthe globe the number of Arabidopsis publications in each country have flat-lined or are in decline.
This is clearest in the United Kingdom where the number of Arabidopsis publications has almost
halved from 2019-2023 (incidentally over this time-period the number of rice, corn or wheat
publications have slightly declined).
India and Singapore are the only
other countries with sustained increases inpublications over the past decade, albeit
from low numbers. We might expect tocontinue to observe this increase overcoming years as funders in these countries
understand the importance of Arabidopsis
research to provide a base of fundamental
discoveries that can then be applied to thelarge number of economically important
crops.
Number of publications that include Arabidopsis research from
China since 2007. This search term was used in Pubmed:
ARABIDOPSIS [Title/Abstract] AND CHINA AND (“journal
article”[Publication Type] OR “review”[Publication Type]) AND
20XX[DP].

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Number of publications that include Arabidopsis research from countries with over 100 publications in
2023. This search term was used in Pubmed:ARABIDOPSIS [Title/Abstract] AND COUNTRY AND (“journal
article”[Publication Type] OR “review”[Publication Type]) AND 20XX[DP].

Number of Publications that include Arabidopsis research from countries with between 50-100 publicationin 2023. This search term was used in Pubmed:ARABIDOPSIS [Title/Abstract] AND COUNTRY AND(“journal article”[Publication Type] OR “review”[Publication Type]) AND 20XX[DP].

Number of Publications that include Arabidopsis research from countries with fewer than 50-publicationsin 2023. This search term was used in Pubmed: ARABIDOPSIS [Title/Abstract] AND COUNTRY AND(“journal article”[Publication Type] OR “review”[Publication Type]) AND 20XX[DP].

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A Tribute to Philip N. Benfey, a Luminary in the
Field of Plant Biology
SM Brady, GM Coruzzi.
On September 26, 2023, the Arabidopsis research community
lost a visionary - Philip N. Benfey, Paul Kramer Professor at Duke
University.
Philip made critical advancements in our understanding ofroot developmental biology and in the generation of cell type andsingle cell-resolution resources. This work culminated in The RootCell Atlas - a pointillist view of the expression profile of every genewithin the root.
In addition to his extraordinary science, Philip was a leader
in the Arabidopsis community. He served as president of theMultinational Arabidopsis Steering Committee in 2005 and 2006,
as well as a member of the North American Arabidopsis Steering Committee from 2003-2007. He enabledfunctional genomics research as the chair of the Multinational Coordinated Arabidopsis thaliana Functional
Genomics Project.
Philip was recognized for his research achievements as a Member of the United States National
Academy of Sciences and as a Howard Hughes Medical Institute Investigator, a Pioneer of the ASPB,
amongst many other accolades. Importantly, Philip was an exceptional mentor, colleague and friend. His
untimely passing leaves a gaping hole in our plant community. We encourage all to learn more about Philip
Benfey’s legacy in the following tributes.
References and Links:
Remembering Philip N. Benfey: A visionary in plant biology and mentor extraordinaire.
N. Raikhel, JR Ecker, G Coruzzi. PNAS. 120(45), e2317677120
Philip N. Benfey (1953-2023): A “ring” master of plant development and cellular genomics.
GM Coruzzi, KD Birnbaum. Science. 382(6675): 1127.
Philip N. Benfey (1953-2023).
MJ Bennett, SM Brady, JR Dinneny, Y Helariutta, R. Sozzani. Developmental Cell. 58(22):2413-2415.
Arabidopsis Lifetime Achievement Award:
https://www.arabidopsiscommunity.org/news-events/benfey-arabidopsis-community-lifetime-achievement-award

ASPB Pioneer:

https://aspb.org/membership/aspb-pioneer-members/pioneer-philip-benfey/#testimonials

ASPB Members Remember Philip Benfey

https://blog.aspb.org/aspb-remembers-philip-benfey/

NYU Genome Symposium Tribute to Philip Benfey:

https://as.nyu.edu/departments/biology/events-news/news/philip-benfey.html (Video link)

MASC Philip Benfey Lifetime Achievement Awards
https://youtu.be/QCx1rPPg-Pw

Philip N. Benfey Memorial Symposium
https://youtu.be/QCx1rPPg-Pw

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MASC Subcommittee Reports
Bioinformatics 								13Natural Variation and Comparative Genomics

15

Epigenetics and Epigenomics					17Plant immunity								19Systems and Synthetic Biology					21MASCannualreportreport2023/24
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MASC Bioinformatics Subcommittee Report
Prepared by
Nicholas Provart, Leonore Reiser, Tanya Berardini and with input from MASC Bioinformatics
Subcommittee members and the wider Arabidopsis community.

TAIR: TAIR continues to add new gene function data on a weekly basis. This past year 1222 new/updated

locus summaries, 499 new/updated gene symbols, 1766 articles linked to 3677 genes, 14301 experimental
Gene Ontology (GO) and Plant Ontology (PO) annotations, 131 new/updated alleles, and 232 phenotypes
linked to germplasms were curated. TAIR regularly updates InterPro domain mapping for the Arabidopsis
proteins using bimonthly updates data from UniProt. TAIR also released a new version of its website in May
2024. The redesigned website is easier-to-navigate, more accessible, and is mobile friendly. Also, in terms ofmodernizing code, TAIR rolled out an instance of JBrowse2 for browsing Arabidopsis genomic data sets in a
track-based manner. Most of the tracks from TAIR’s still-operational JBrowse instance have been ported over.
One of the enhancements in JBrowse2 is being able to visualize synteny, such as that between the Arabidopsis
thaliana and Arabidopsis lyrata genomes. A paper by Reiser et al. (2024) describing these updates to TAIR
came out earlier this year. It also nicely gives a snapshot of the status of the Arabidopsis genome annotation
effort and describes efforts to modernize the backend code that powers TAIR.

BAR: The Bio-Analytic Resource for Plant Biology was designated a “global core biodata resource” last yearby the Global Biodata Coalition, one of just 52 such databases worldwide (https://globalbiodata.org/whatwe-do/global-core-biodata-resources/). The BAR contains data from not just Arabidopsis, but also Medicago
truncatula, rice, wheat, barley and 27 other plant species (with data for 3 others to be released soon). These
data include nucleotide and protein sequence data, gene expression data, protein-protein and protein-DNA
interactions, protein structures, subcellular localizations, and polymorphisms. The data are stored in morethan 200 relational databases holding 186 GB of data and are presented to the user via web apps. These web
apps provide data analysis and visualization tools that are hosted on the BAR. Some of the most popular
tools are eFP (“electronic fluorescent pictograph”) Browsers, ePlants, and ThaleMine (an Arabidopsis-specificinstance of InterMine). The BAR upgraded Thalemine to the current version (v5.1.0-20230710) based on
the InterMine 5.1.0 release, with data updates from many sources from mid-2023. The BAR released a highresolution gynoecium view for its Arabidopsis eFP Browser (Luna-García et al. 2024).
An Arabidopsis genome update is coming this year! In October 2022, Tanya Berardini of TAIR and
Nicholas Provart of the BAR organized a conference call for members of the Arabidopsis genome sequencing
and annotation community to develop a plan for producing a new structural annotation of the A. thaliana
Col-0 genome, to update the Araport11 version, released in June 2016. NCBI ran their annotation pipeline ona new consensus “telomere-to-telomere” assembly last year (https://www.ncbi.nlm.nih.gov/datasets/genome/
GCA_028009825.2/). TAIR has coordinated this effort with NCBI and with volunteers from labs around theworld who are adding/updating NORs, rDNAs and tandem repeats, and who are expertly curating of protein
coding genes, transposable elements, and lncRNAs. See TAIR’s website (https://conf.phoenixbioinformatics.
org/display/COM/A.+thaliana+Col-0+v12+reannotation+effort) for updates. The genome annotations will
be submitted to NCBI following completion of manual verification and quality checks later this summer. All
participants in the effort are working on a manuscript together.

Large-scale Data Sets and Methods of Note: Peleke et al. (2024) used deep learning to unravel the

cis-regulatory code of several model plant species, including Arabidopsis. The Mutwil Lab’s effort to harness
the power of ChatGPT is available at https://connectome.plant.tools. The Mutwil Lab used ChatGPT toprocess 101,341 Arabidopsis publications to extract – in a traceable way – 387,777 relationships between

MASC annual report 2023/24

13genes, molecules, compartments, organs etc. Check out the preprint by Fo et al. (2023)! ggPlantMap wasdeveloped by Jo and Kajala (2024)for “eFP” representations that can be generated with an open-source R
package. The eFP Browser representation also made its way into a nice toolkit called TBtools, with more than
130 functions for working with high-throughput data (Chen et al. 2020, 2023).

Pedagogy, Policy and Outreach:
The Plant Cell Atlas continues to organize workshops on single-cell approaches in plant biology. Keepan eye on http://www.plantcellatlas.org/ for updates! An inaugural Gordon Research Conference on SingleCell Approaches in Plant Biology kicked off last August to positive reviews from attendees. TAIR continues
its partnership with https://www.micropublication.org/, a platform for very short peer-reviewed reports.
Nicholas Provart’s Plant Bioinformatics course covering 33 online tools from labs around the world on
Cousera.org (https://www.coursera.org/learn/plant-bioinformatics/) was fully updated in June 2024.

References
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, and Xia R. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol Plant. 2020:13(8):1194–1202. https://doi.
org/10.1016/j.molp.2020.06.009
Chen C, Wu Y, Li J, Wang X, Zeng Z, Xu J, Liu Y, Feng J, Chen H, He Y, et al. TBtools-II: A “one for all, all forone” bioinformatics platform for biological big-data mining. Mol Plant. 2023:16(11):1733–1742. https://doi.
org/10.1016/j.molp.2023.09.010
Fo K, Chuah YS, Foo H, Davey EE, Fullwood M, Thibault G, and Mutwil M. PlantConnectome: knowledge networks encompassing &gt;100,000 plant article abstracts. 2023:2023.07.11.548541. https://doi.
org/10.1101/2023.07.11.548541
Jo L and Kajala K. ggPlantmap: an open-source R package for the creation of informative and quantitative
ggplot maps derived from plant images. J Exp Bot. 2024:erae043. https://doi.org/10.1093/jxb/erae043
Luna-García V, Bernal Gallardo JJ, Rethoret-Pasty M, Pasha A, Provart NJ, and de Folter S. A high-resolution gene expression map of the medial and lateral domains of the gynoecium of Arabidopsis. Plant Physiol.
2024:195(1):410–429. https://doi.org/10.1093/plphys/kiad658
Peleke FF, Zumkeller SM, Gültas M, Schmitt A, and Szymański J. Deep learning the cis-regulatory code forgene expression in selected model plants. Nat Commun. 2024:15(1):3488. https://doi.org/10.1038/s41467024-47744-0
Reiser L, Bakker E, Subramaniam S, Chen X, Sawant S, Khosa K, Prithvi T, and Berardini TZ. The Arabidopsis Information Resource in 2024. Genetics. 2024:227(1):iyae027. https://doi.org/10.1093/genetics/iyae027

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Natural Variation and Comparative Genomics Subcommittee Report
Prepared by
J. Chris Pires (Chair)jchrispires@gmail.com, Colorado State University
Ya-Long Guo (Co-Chair)yalong.guo@ibcas.ac.cn, Institute of Botany, Chinese Academy of Sciences

Recently developed Open Tools and Resources for Arabidopsis Researchers
Many new genomic resources have been produced in the Brassicaceae, see selected publications below
for examples.

Recent or Future activities of Subcommittee members.
Lots of species of the Brassicaceae family have been sequenced and studied in diverse aspects.
In particular, natural variation of the model species Arabidopsis produced many fascinating results.
Subcommittee members jointly organized the XX International Botanical Congress will be hold from 21-27
July 2024.

Selected Publications
Hendriks, K.P., Kiefer, C., Al-Shehbaz, I.A., Bailey, C.D., Hooft van Huysduynen, A., Nikolov, L.A.,
Nauheimer, L., Zuntini, A.R., German, D.A., Franzke, A., Koch, M.A., Lysak, M.A., Toro-Nunez, O.,
Ozudogru, B., Invernon, V.R., Walden, N., Maurin, O., Hay, N.M., Shushkov, P., Mandakova, T., Schranz,
M.E., Thulin, M., Windham, M.D., Resetnik, I., Spaniel, S., Ly, E., Pires, J.C., Harkess, A., Neuffer, B., Vogt, R.,
Brauchler, C., Rainer, H., Janssens, S.B., Schmull, M., Forrest, A., Guggisberg, A., Zmarzty, S., Lepschi, B.J.,
Scarlett, N., Stauffer, F.W., Schonberger, I., Heenan, P., Baker, W.J., Forest, F., Mummenhoff, K., and Lens, F.
2023. Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset. Curr Biol 33, 4052-4068.
This study involves a worldwide community of thousands of researchers working on Brassicaceae andits diverse members, which reveals a new genus-level family phylogeny, and will be an indispensable tool forstudies on biodiversity and plant biology.
Lan, Z., Song, Z., Wang, Z., Li, L., Liu, Y., Zhi, S., Wang, R., Wang, J., Li, Q., Bleckmann, A., Zhang, L.,
Dresselhaus, T., Dong, J., Gu, H., Zhong, S., and Qu, L.J. (2023). Antagonistic RALF peptides control anintergeneric hybridization barrier on Brassicaceae stigmas. Cell 186, 4773-4787.
This study uncover a ‘‘lock-and-key’’ system governing the hybridization breadth of interspecific/
intergeneric crosses in Brassicaceae. Manipulating this system holds promise for facilitating broad
hybridization in crops.
Jiang, J., Xu, Y.C., Zhang, Z.Q., Chen, J.F., Niu, X.M., Hou, X.H., Li, X.T., Wang, L., Zhang, Y., Ge, S., and Guo,
Y.L. (2024). Forces driving transposable element load variation during Arabidopsis range expansion. Plant
Cell 36, 840-862.
This study reveals the variation in TE genetic load during Arabidopsis expansion and highlights thecauses of TE load variation from the perspectives of both population genetics and quantitative genetics.

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Wlodzimierz, P., Rabanal, F.A., Burns, R., Naish, M., Primetis, E., Scott, A., Mandakova, T., Gorringe, N.,
Tock, A.J., Holland, D., Fritschi, K., Habring, A., Lanz, C., Patel, C., Schlegel, T., Collenberg, M., Mielke, M.,
Nordborg, M., Roux, F., Shirsekar, G., Alonso-Blanco, C., Lysak, M.A., Novikova, P.Y., Bousios, A., Weigel, D.,
and Henderson, I.R. (2023). Cycles of satellite and transposon evolution in Arabidopsis centromeres. Nature
618, 557-565.
This study identified rapid cycles of transposon invasion and purging through satellite
homogenization, which drive centromere evolution and ultimately contribute to speciation.
Lian, Q., Huettel, B., Walkemeier, B., Mayjonade, B., Lopez-Roques, C., Gil, L., Roux, F., Schneeberger, K.,
and Mercier, R. (2024). A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome
structure throughout the global species range. Nat Genet 56, 982-991.
This study present chromosome-level genome assemblies of 69 accessions from a global species range,these 69 new Arabidopsis genome assemblies will empower future genetic research.

Members of the subcommittee
Sureshkumar Balasubramanian sureshkumar.balasubramanian@monash.edu
Wolfgang Busch wbusch@salk.edu
Patrick Edger edgerpat@msu.edu

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Epigenetics and Epigenomics Subcommittee Report
Prepared byRobert Schmitz, schmitz@uga.edu, University of Georgia
Xuehua Zhong, xuehuazhong@wustl.edu, Washington University in St. Louis

Recent or Future activities of Subcommittee members.
2024International Conference on Arabidopsis Research, San Diego, CA, July, 2024
– Epigenetics– Epigenome and Epitranscriptome in Environmental Stress Signaling and Memor– Chromatin at Single-cell and Single-molecule Resolution
Plant Epigenetics - EpiPlant – Clermont-Ferrand, France, July, 2024
International Plant Molecular Biology (IPMB) Congress, Queensland, Australia, June 2024
– Epigenetics– Transposable Elements– Transcriptional and Post-transcriptional Regulation
2025
Keystone meeting on Plant Epigenetics and Gene Regulation, 2025
International Conference on Arabidopsis Research, Gent, Belgium, June, 2025
– Epigenetics

Selected Publications
Epiallelic variation of non-coding RNA genes and their phenotypic consequences.
Liu J, Zhong X. Nat Commun. 2024 Feb 14;15(1):1375. doi: 10.1038/s41467-024-45771-5.
Sequence and epigenetic landscapes of active and silent nucleolus organizer regions in Arabidopsis.
Fultz D, McKinlay A, Enganti R, Pikaard CS. Sci Adv. 2023 Nov 3;9(44):eadj4509. doi: 10.1126/sciadv.
adj4509.
An evolutionary epigenetic clock in plants.
Yao N, Zhang Z, Yu L, Hazarika R, Yu C, Jang H, Smith LM, Ton J, Liu L, Stachowicz JJ, Reusch TBH,
Schmitz RJ, Johannes F. Science. 2023 Sep 29;381(6665):1440-1445. doi: 10.1126/science.adh9443.
Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA
methylation.
Lee SC, Adams DW, Ipsaro JJ, Cahn J, Lynn J, Kim HS, Berube B, Major V, Calarco JP, LeBlanc C, Bhattacharjee S, Ramu U, Grimanelli D, Jacob Y, Voigt P, Joshua-Tor L, Martienssen RA. Cell. 2023 Sep 14;186(19):41004116.e15. doi: 10.1016/j.cell.2023.08.001.

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The plant nuclear lamina disassembles to regulate genome folding in stress conditions
Wang N, Wang Z, Tzourtzou S, Wang X, Bi X, Leimeister J, Xu L, Sakamoto T, Matsunaga S, Schaller A, Jiang
H, Liu C. Nat Plants. 2023 Jul;9(7):1081-1093. doi: 10.1038/s41477-023-01457-2.

Members of the subcommittee
Robert Schmitz, schmitz@uga.edu, University of Georgia
Xuehua Zhong, xuehuazhong@wustl.edu, Washington University in St. Louis

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Plant Immunity Subcommittee Report
Prepared by
Chair, Shahid Mukhtar
Clemson University
mshahid@clemson.edu
Members:
1- Dr. Yasuhiro Kadota, yasuhiro.kadota@riken.jp, RIKEN Center for Sustainable Resource Science (CSRS),
Yokohama, Japan
2- Dr. Karolina Mukhtar kmukhta@clemson.edu Clemson University, SC, USA
3- Dr. Farid El Kasmi, farid.el-kasmi@zmbp.uni-tuebingen.de, ZMBP – Center for Plant Molecular Biology,
University of Tuebingen, Tuebingen, Germany
4- Dr. Marc Nishimura, marc.nishimura@colostate.edu, Colorado State University, Fort Collins, CO, USA
3. Recently developed Open Tools and Resources for Arabidopsis Researchers

Please provide a list of resources that have been developed over the past 12 months thatare relevant to your subcommittee’s research area.
1. AlphaFold3; https://deepmind.google/technologies/alphafold/
2. AraPathogen2.0: An Improved Prediction of Plant–Pathogen Protein–Protein Interactions Empowered by
the Natural Language Processing Technique. http://zzdlab.com/arapathogen2/index.php
3. PPIntegrator: semantic integrative system for protein–protein interaction and application for host–pathogen datasets. https://github.com/YasCoMa/ppintegrator
4. Arabidopsis Developmental Atlas Viewer: http://neomorph.salk.edu:9000/#about
5. Deep-HPI-pred: An R-Shiny applet for network-based classification and prediction of Host-Pathogen
protein-protein interactions. https://github.com/tahirulqamar/Deep-HPI-pred

Recent or Future activities of Subcommittee members.
The 33rd International Conference on Arabidopsis Research held in Makuhari, Japan.
2023 Fall international conference of Korean Society of Plant Pathology (KSPP)
2023 Brazilian Symposium on Plant Molecular Genetics; Florianopolis, Brazil (5/30-6/2)
2023 The Plant & Animal Genome, Australia
2023 IS-MPMI Congress; Providence, RI, USA (7/16-7/20)
2024 The Plant & Animal Genome, San Diego, USA
2024 IPMB; Cairnes, Australia (6/24-6/28)
2025 IS-MPMI Congress; Cologne, Germany (7/13-7/17)
2025 The Plant & Animal Genome, San Diego, USA

Selected Publications
Saarenpää S, Shalev O, Ashkenazy H, Carlos V, Lundberg DS, Weigel D, Giacomello S. Spatial
metatranscriptomics resolves host-bacteria-fungi interactomes. Nature Biotechnology. 2023 Nov 20. doi:
10.1038/s41587-023-01979-2.
This article introduced spatial metatranscriptomics (SmT), a sequencing technique that utilizes
16S/18S/ITS/poly-d(T) multimodal arrays to simultaneously characterize both the host transcriptome andthe microbiome within tissues, achieving a resolution of 55 μm

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Nomura K, Andreazza F, Cheng J, Dong K, Zhou P, He SY. Bacterial pathogens deliver water- and solutepermeable channels to plant cells. Nature. 2023 Sep;621(7979):586-591. doi: 10.1038/s41586-023-06531-5.
AlphaFold2-enabled discovery that bacterial virulence proteins use a porin-like mechanism torelease water from host cells, hydrating the apoplast and generating the classic “water soaking” phenotype topromote pathogen success.
Xiao Y, Sun G, Yu Q, Gao T, Zhu Q, Wang R, Huang S, Han Z, Cervone F, Yin H, Qi T, Wang Y, Chai J. A
plant mechanism of hijacking pathogen virulence factors to trigger innate immunity. Science. 2024 Feb
16;383(6684):732-739. doi: 10.1126/science.adj9529.
Structural biology reveals that a plant polygalacturonase inhibitor protein functions by altering
pathogen polygalacturonase catalysis, creating a mixed-organism enzyme complex that produces immuneactivating products rather than inhibiting immunity.
Tang B, Feng L, Hulin MT, Ding P, Ma W. Cell-type-specific responses to fungal infection in plants revealedby single-cell transcriptomics. Cell Host Microbe. 2023 Oct 11;31(10):1732-1747.e5. doi: 10.1016/j.
chom.2023.08.019.
By creating an atlas of 95,040 Arabidopsis thaliana leaf cells infected by Colletotrichum higginsianum,
this work reveals cell-type-specific gene expression, with vasculature cells showing enriched intracellularimmune receptors and trajectory analysis highlighting varying interactions with the fungus.
Ngou BPM, Wyler M, Schmid MW, Kadota Y,
Shirasu K. Evolutionary trajectory of patternrecognition receptors in plants. Nat Commun.
2024 Feb 1;15(1):308. doi: 10.1038/s41467-02344408-3.
This work reveals that cell-surface
receptors involved in immunity and development
share a common origin. After diversification, theirectodomains, juxtamembrane, transmembrane,
and cytosolic regions have either diversified or
stabilised to recognise diverse ligands and activate
differential downstream responses.
.

Members of the subcommittee

Chair, Dr. Shahid Mukhtar mshahid@clemson.edu Clemson University, SC, USA
Members:
1- Dr. Yasuhiro Kadota, yasuhiro.kadota@riken.jp, RIKEN Center for Sustainable Resource Science (CSRS),
Yokohama, Japan
2- Dr. Karolina Mukhtar kmukhta@clemson.edu Clemson University, SC, USA
3- Dr. Farid El Kasmi, farid.el-kasmi@zmbp.uni-tuebingen.de, ZMBP – Center for Plant Molecular Biology,
University of Tuebingen, Tuebingen, Germany
4- Dr. Marc Nishimura, marc.nishimura@colostate.edu, Colorado State University, Fort Collins, CO, USA

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Systems and Synthetic Biology Subcommittee Report
Prepared by
Siobhan Brady, sbrady@ucdavis.edu, UC Davis

Recently developed Open Tools and Resources for Arabidopsis Researchers
Next-Gen GWAS: full 2D epistatic interaction maps retrieve part of missing heritability and improve
phenotypic prediction C Carré, JB Carluer, C Chaux, C Estoup-Streiff, N Roche, E Hosy, A Mas, ...
Genome Biology 25 (1), 76
PHYTOMap: (https://www.nature.com/articles/s41477-023-01439-4)
ggPlantmap: (https://pubmed.ncbi.nlm.nih.gov/38329371/)
ccPlantDB: https://academic.oup.com/nar/article/52/D1/D1629/7252671

Recent or Future activities of Subcommittee members.
1- Planning of the International Plant Systems Biology Meeting 2025 in Venice Italy.
2- Synthetic Biology UK 2024 27-28 November, Hinxton Hall, Cambridge, UK.
3- Plant SynBio Hackathon, August 2024

Selected Publications
The trans-regulatory landscape of gene networks in plants
NFC Hummel, A Zhou, B Li, K Markel, IJ Ornelas… - Cell Systems, June 2023
https://www.cell.com/cell-systems/pdf/S2405-4712(23)00146-1.pdf
Hummel et al. characterize the activity of more than 400 transcriptional effector domains from
Arabidopsis and annotate effector activity in a gene regulatory network to elucidate novel targets forengineering in synthetic biology.
Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors
M Li, T Yao, W Lin, WE Hinckley, M Galli, W Muchero, A Gallavotti, Jin-Gui Shen and Shao-shao Carol
Huang Nature Communications 14 (1), 2600, 5/5/2023
This paper presents the double DNA Affinity Purification-sequencing (dDAP-seq) techniquethat maps heterodimer binding sites on endogenous genomic DNA which is key for combinatorial gene
regulation, the next frontier in gene regulatory networks.
Jores T, Tonnies J, Mueth NA, Romanowski A, Fields S, Cuperus JT, Queitsch C. Plant enhancers exhibit bothcooperative and additive interactions among their functional elements. Plant Cell. 2024 Mar 21:koae088. doi:
10.1093/plcell/koae088.
Experimental evidence that plant enhancers exhibit cooperative and additive interactions.

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Guiziou S, Maranas CJ, Chu JC, Nemhauser JL. An integrase toolbox to record gene-expression during plantdevelopment. Nat Commun. 2023 Apr 3;14(1):1844. doi: 10.1038/s41467-023-37607-5.
Demonstration of history-dependent circuits for decoding the order of expression duringorganogenesis.
SHR and SCR coordinate root patterning and growthearly in the cell cycle
CM Winter, P Szekely, V Popov, H Belcher, R Carter,
M Jones, SE Fraser, ...
Nature 626 (7999), 611-616
https://www.nature.com/articles/s41586-023-06971-z
Using light sheet microscopy, the Benfey
lab shows that levels of short root and scarecrowtranscription factors early in the cell cycle determine
the orientation of the division plane, resulting in either
formative or proliferative cell division, revealing an
uncharacterized mechanism by which developmental
regulators directly coordinate patterning and growth.

Members of the subcommittee
Siobhan Brady
Gloria Coruzzi
Gabriel Krouk
Shahid Mukhtar
Nicola Patron

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Projects and Resources
Arabidopsis Biological Resource Center				24

Bio-Analytic Resource for Plant Biology 				

25Gramene: A comparative genomics and pathways resource forplants											27The Nottingham Arabidopsis Stock Centre 			29

RIKEN BioResource Research Center 				

30The Arabidopsis Information Resource (TAIR) 		

31

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2023/24
				MASCannual23

Arabidopsis Biological Resource Center
Prepared by
Emma Knee, knee.2@osu.edu
David Somers, somers.24@osu.edu, The Ohio State University

Recent activities and newly developed tools and/or resources of your project/resource
ABRC distributed 62,669 samples to 1,594 individuals located in 43 countries in 2023. This represents
a decrease in samples from the previous year which can be attributed to fewer large sets of seed stocks
being ordered. The number of researchers receiving samples is slightly higher and the number of countries
represented is approximately the same as the previous year. 59% of orders were shipped to researchers in theUS, 13% to Japan, 6% to Canada, and 5% to Korea. Other countries each accounted for less than 4% of totalorders. In addition to orders placed directly at the ABRC website, 1,608 individual samples were requested by
the European Arabidopsis Stock Center (NASC) to be distributed to their customers. ABRC also provided to
NASC bulk seed for 2,270 lines, and smaller aliquots of seed for 1,597 lines.
ABRC received donations of 263 seed stocks from the research community over the past year.
These included characterized mutant and transgenic lines as well as natural variants and close relativesof Arabidopsis. 20 non-seed resources were also added to the collection including multi-knock CRISPR
libraries, Arabidopsis clones, and cloning vectors. The majority of donations were received from the US.
Donations were also received from China, Hong Kong, and Israel. All stock information is available through
ABRC website (https://abrc.osu.edu/). ABRC no longer uploads stock data to TAIR but has made select stock
data available via an API allowing query by stock name or AGI. Contact ABRC to request API access.
The seed collection now numbers over 530,000 stocks. ABRC has ceased distribution of some nonseed stocks that were no longer ordered, so that the collection of non-seed stocks has decreased by 58%
to just over 189,000 stocks. The center also operates with a smaller staff than in previous years and has
streamlined operations. Quality control testing is mostly focused on monitoring seed germination rates andtargets 2000 to 3000 stocks per year. New seed lots are generated for stocks with lower than 81% germination.
The ABRC outreach program reached over 1000 individuals in 2023. Activities included tours of thecenter, presentations at local science fairs, and distribution of education kits and other stocks to students andeducators. Publications Planned future activities of your project/resource ABRC continues to seek additionalsources of funding in order to keep stock prices as low as possible. Stock distribution is projected to continue
at the current level and donations are projected to increase in the coming year based on communications wehave received from potential donors. Please consider donating any Arabidopsis resources your laboratory
has generated. We are particularly interested in receiving characterized mutants, especially lines withmultiply stacked mutations. We are happy to receive verified T-DNA insertion lines even if we already have a
confirmed line in the collection. We are also happy to receive seeds of close relatives of Arabidopsis and other
Brassicaceae. ABRC will continue to provide stocks to NASC and a reciprocal receipt of stocks from NASC is
hoped to resume following an extended hiatus.
Outreach activities will continue to focus on distribution of education kits and programming with local
partners. ABRC and NASC will staff a joint booth at ICAR 2024 in San Diego.

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Bio-Analytic Resource for Plant Biology (BAR)

BAR

https://bar.utoronto.ca

Prepared by
Nicholas Provart (director) nicholas.provart@utoronto.ca
BAR bioinformatics technician Asher Pasha, University of Toronto.

Recent activities and newly developed tools and/or resources of your project/resource•
eFP Arabidopsis Gynoecium view is added in collaboration with Stefan de Folter’s Lab•
BAR is designated one of just 52 Global Core Biodata Resources•
BAR FAIR-sharing page was created: https://fairsharing.org/FAIRsharing.8c6779•
BAR API is a new API to access data in BAR databases•
ThaleMine is updated to v5.1.0-20230710 with the latest datasets•
400+ interactions determined by TurboID using BIN2 were added to the Arabidopsis Interactions
Viewer/AIV2 database•
ASPB Plant Biology 2023 conference talk and booth in Savannah, GA, USA•
ICAR Conference 2023 in Chiba, Japan•ASPB Plant Biology 2024 conference talk and booth in Honolulu, HI, USA•
ePlant Barley is released as two separate apps. ePlant Barley legacy and ePlant Barley with version 3
gene IDs for the “seed atlas” dataset from the Pecinka Lab•
eFP Mangosteen is a new eFP Browser on the BAR, together with the Goh Lab•
eFP Wheat abiotic stress data are added, in collaboration with the Kagale Lab•
eFP Sorghum is updated with new views in collaboration with the Ware Lab at CSHL•
ePlant Medicago LCM data are added, in collaboration with the Frugoli Lab•
ePlant Eucalyptus is published, in collaboration with Jin Zhang’s Lab•
eFP Little Millet is published, in collaboration with the Soolanayakanahally Lab•
eFP Cacao with the Guiltinan Lab in online as of July 2024•
The BAR’s SequenceServer (Blast server) is updated with Mangosteen and Euphorbia sequences•
eFP Arabidopsis Gynoecium view is added in collaboration with Stefan de Folter’s Lab•
BAR is designated one of just 52 Global Core Biodata Resources•
BAR FAIR-sharing page was created: https://fairsharing.org/FAIRsharing.8c6779•
BAR API is a new API to access data in BAR databases•
ThaleMine is updated to v5.1.0-20230710 with the latest datasets•
400+ interactions determined by TurboID using BIN2 were added to the Arabidopsis Interactions
Viewer/AIV2 database•
ASPB Plant Biology 2023 conference talk and booth in Savannah, GA, USA•
ICAR Conference 2023 in Chiba, Japan•ASPB Plant Biology 2024 conference talk and booth in Honolulu, HI, USA•
ePlant Barley is released as two separate apps. ePlant Barley legacy and ePlant Barley with version 3
gene IDs for the “seed atlas” dataset from the Pecinka Lab•
eFP Mangosteen is a new eFP Browser on the BAR, together with the Goh Lab•
eFP Wheat abiotic stress data are added, in collaboration with the Kagale Lab•
eFP Sorghum is updated with new views in collaboration with the Ware Lab at CSHL•
ePlant Medicago LCM data are added, in collaboration with the Frugoli Lab•
ePlant Eucalyptus is published, in collaboration with Jin Zhang’s Lab•
eFP Little Millet is published, in collaboration with the Soolanayakanahally Lab•
eFP Cacao with the Guiltinan Lab in online as of July 2024•
The BAR’s SequenceServer (Blast server) is updated with Mangosteen and Euphorbia sequences

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Publications
Jiang, Y., N’Diaye, A., Koh, C. S., Quilichini, T. D., Shunmugam, A. S. K., Kirzinger, M. W., Konkin, D.,
Bekkaoui, Y., Sari, E., Pasha, A., Esteban, E., Provart, N. J., Higgins, J. D., Rozwadowski, K., Sharpe, A.
G., Pozniak, C. J., & Kagale, S. (2023). The coordinated regulation of early meiotic stages is dominated by
non‐coding RNAs and stage‐specific transcription in wheat. Plant Journal, 114(1), 209–224. https://doi.
org/10.1111/tpj.16125
Luna-García, V., Gallardo, J. J. B., Rethoret-Pasty, M., Pasha, A., Provart, N. J., & De Folter, S. (2023). A highresolution gene expression map of the medial and lateral domains of the gynoecium of Arabidopsis. Plant
Physiology, 195(1), 410–429. https://doi.org/10.1093/plphys/kiad658
Schnabel, E., Thomas, J., El-Hawaz, R., Gao, Y., Poehlman, W. L., Chavan, S., Pasha, A., Esteban, E., Provart,N., Feltus, F. A., & Frugoli, J. (2023). Laser Capture Microdissection Transcriptome Reveals Spatiotemporal
Tissue Gene Expression Patterns of Medicago truncatula Roots Responding to Rhizobia. Molecular Plantmicrobe Interactions, 36(12), 805–820. https://doi.org/10.1094/mpmi-03-23-0029-r
Wee, C., Pasha, A., Provart, N. J., Muhammad, N. a. N., Subbiah, V. K., Arita, M., & Goh, H. (2024). An eFP
reference gene expression atlas for mangosteen. Scientia Horticulturae, 327, 112846. https://doi.org/10.1016/j.
scienta.2024.112846
Fan, C., Lyu, M., Zeng, B., He, Q., Wang, X., Lu, M., Liu, B., Liu, J., Esteban, E., Pasha, A., Provart, N.
J., Wang, H., & Zhang, J. (2024). Profiling of the gene expression and alternative splicing landscapes of
Eucalyptus grandis. Plant, Cell & Environment/Plant, Cell and Environment, 47(4), 1363–1378. https://doi.
org/10.1111/pce.14814
Pahari, S., Vaid, N., Soolanayakanahally, R., Kagale, S., Pasha, A., Esteban, E., Provart, N., Stobbs, J. A., Vu,
M., Meira, D., Karunakaran, C., Boda, P., Prasannakumar, M. K., Nagaraja, A., & Jain, A. K. (2024). Nutri‐cereal tissue‐specific transcriptome atlas during development: Functional integration of gene expression
to identify mineral uptake pathways in little millet (Panicum sumatrense). Plant Journal. https://doi.
org/10.1111/tpj.16749
Kovacik, M., Nowicka, A., Zwyrtková, J., Strejčková, B., Vardanega, I., Esteban, E., Pasha, A., Kaduchová, K.,
Krautsova, M., Červenková, M., Šafář, J., Provart, N. J., Simon, R., & Pecinka, A. (2024). The transcriptome
landscape of developing barley seeds. the Plant Cell. https://doi.org/10.1093/plcell/koae095

Planned future activities of your project/resource•
Arabidopsis guard cell data under drought in eFP-Seq Browser•
ThaleMine data upgrade•
BAR server upgrade. We will move to new Dell PowerEdge R760 server in summer 2024•
New eFP Sorghum datasets with CSHL•
Collaborate with TAIR on MtDNA in Chromosome 2 of Arabidopsis for the Col-CC12/TAIR12
genome reannotation effort

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Gramene: A comparative genomics andpathways resource for plants

PLANTShttps://www.gramene.org
The Gramene project –rebranded Gramene Plants– (www.gramene.org) is a knowledgebase founded on
stewardship of plant genomes with a focus on cross-species comparison, using a single reference assembly
to anchor genomic and pathway data for model plants and major crops, aiming to support agriculturalresearchers.
Gramene’s Pan-Genome resources for four crop species were built on the Gramene infrastructure to extend
the depth of the reference genomes, linking genetic variation to agronomically important traits.
https://maize-pangenome.gramene.org/
https://oryza.gramene.org/
https://vitis.gramene.org/
http://www.sorghumbase.org/

Prepared by
Marcela Karey Tello-Ruiz, telloruiz@cshl.edu, Cold Spring Harbor Laboratory (CSHL)
Reviewed by Doreen Ware, ware@cshl.edu, doreen.ware@usda.gov, USDA ARS, CSHL; Andrew Olson,
olson@cshl.edu, CSHL; and Sunita Kumari, kumari@cshl.edu CSHL

Recent activities and newly developed tools and/or resources of your project/resource
Arabidopsis serves as one of the central model research organisms for Gramene Plants and Gramene’s
crop-specific pan-genome databases. Over the past year, we released two updates for Gramene (R67 inAugust 2023; R68 in November 2023) and five updates for the pan-genome resources: Oryza (R7 in August2023), Sorghum (R6 in June 2023 and R7 in March 2024), Grape (R3 in February 2024), and Maize (R4 in
February 2024). In total, 35 new genomes were added across the platforms: 22 in Gramene Plants, 1 inSorghumBase, 11 in Gramene Vitis, and 1 in Gramene Maize, with orthologs/homeologs assigned to A.
thaliana.
For genes in family trees, the Gramene search interface now displays the closest annotated homologwith a TAIR-curated description, thereby providing access to curated gene functions. Our collection of genefunctional annotations from the literature, sourced from NCBI’s GeneRIF and RAP-DB, has grown to a totalof 13,529 with 7,255 annotations for A. thaliana (an increase of 71 compared to the prior year) and 37 new
annotations for A. lyrata (see Figure 1).
Access to these curated annotations is deployed in the “Papers” tab of the Gramene search interface.
This tab presents a table of PubMed-linked publications associated with a given gene, and its annotations,
utilizing Trait Ontology (TO) or Plant Ontology (PO) terms, which are searchable. Additionally, users can
now submit additional gene functions through an embedded form in this tab, labeled “Add Papers” if noprior functional annotations were linked to curated publications (see Figure 1).
Arabidopsis thaliana is one of the plant outgroups included in phylogenetic analyses performed tosculpt gene family trees. It continues to be used as one of the reference dicot species for pairwise wholegenome alignments (WGAs) and synteny maps. Synteny maps with A. thaliana were created for the 11 new

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grapevine assemblies in Gramene Vitis, as well as for teosinte Til11 in Gramene Maize (see Figure 2). WGAs
between A. thaliana and 79 plant species (including A. lyrata and A. halleri) are available in Gramene Plants,
along with three additional WGAs for A. lyrata with Japonica rice, B73 maize, and Medicago, and two more
for A. halleri against rice and maize. Using the trees and WGAs, putative gene annotation artifacts (alsoknown as contiguous gene split models) calculated for Gramene R68 based on the corresponding Gene Tree
database, revealed 14 such putative split models in A. thaliana (31 in SorghumBase R6), 40 in A. halleri, and
43 in A. lyrata.
The electronic Fluorescent Pictograph (eFP) browsers from the Bio-Analytical Resources (BAR) wereadded to support curated RNA-seq-based gene expression data for Arabidopsis, sorghum, soybean, andmaize genes in the latest released versions of Gramene, SorghumBase, and Gramene Maize. Arabidopsis eFPs
are only available from the Gene Expression tab of the search interface in Gramene and SorghumBase. Thereare 26 eFP images based on the published studies of Arabidopsis which are categorized based on tissue type,growth and development, biological condition, chemical treatment, etc.
Gramene and its pan-genome sites continue to provide gene expression profiles for 18 baseline
experiments for A. thaliana and 1 for A. lyrata, curated in collaboration with the EBI Expression Atlas. In
addition, differential expression data for 611 experiments in Arabidopsis spp. and 13 single-cell experimental(SCE) studies in A. thaliana, also curated by Gramene in collaboration with the Expression Atlas are offereddirectly from the EBI Expression Atlas website.
We continue to host a CLIMtools portal where users can explore Genome x Environment (G x
E) associations for Arabidopsis and rice. In its version 2.0, the Arabidopsis CLIMtools portal (https://www.gramene.org/CLIMtools/arabidopsis_v2.0/) encompasses 473 climate variables in 2,999 Arabidopsis
accessions, RiboSNitch predictions, climate GWAS and TWAS, and hosts five R Shiny apps that provide
distinct views of the data: AraCLIM, CLIMGeno, GenoCLIM, PhenoCLIM, and T-CLIM. Publications
Planned future activities of your project/resource In the next year, Gramene Plants will replace temporary
SNP identifiers with standard reference SNP cluster IDs (rsIDs) for A. thaliana. In addition, we intend tointegrate GWAS results for various traits into the Gramene database. This will allow users to browse genomic
loci associated with phenotypes of interest.
The 13 SCE studies in the EBI Expression Atlas will be indexed and made available to the Gramene
user community in the future.

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The Nottingham Arabidopsis Stock Centre (NASC)
http://arabidopsis.info/

Prepared by
Sean May, Director Sean.May@nottingham.ac.uk
Marcos Castellanos-Uribe, Operations Manager.

Recent activities and newly developed tools and/or resources of your project/resource
Orders sent from NASC increased a little to 62,892 stocks total for the 2023 calendar year (compared
to ~60K for 2022). Community use has stabilised after the dip to 48K we saw in 2021 but has not yet returned
to pre-covid levels (>100K).
We know that it has become increasingly difficult in recent years to send seeds between laboratories.
We were ahead of that curve and have come through the painful birth of a much more complicated service
on our side. For you, ordering seeds through NASC can make this process a lot easier for your laboratory– we take care of the inspections, phytosanitary certificates, and bewilderingly variable international postal
regimes. So please consider donating your stocks to the centres, it may make your lives a lot easier to pass thisfrustrating work from your postdocs and technicians onto us.
Thank you to all those generous groups continuing to donate new stocks and populations of seed(>3200 in 2023 – more than 8 a day). We really appreciate every contact. Again, if you need help or advice
donating or exporting stocks to us, please don’t hesitate to get in touch with curators@arabidopsis.info.
For recipients, we send a tracking email with your order so please use this, and check that yourphone/email details at NASC are current just in case DHL need to contact you (please check your spam
folders). Delays in responding to emails can sometimes lead to local storage charges, which are often manytimes the (low) import costs. We apply for the phytosanitary certificate attached to your order and allocate
the correct content codes, but local requirements beyond that can vary (especially if you need import
documents). If in doubt, please check for any additional legal requirements at your local entry point/institute.
We are looking forward to the ICAR in sunny San Diego, with a new ‘crop’ of ‘thank you’ goodies toyou, the community, at our booth. Come see us - but if you miss out, just look at our twitter photos: https://twitter.com/NascArabidopsis and ask for specific conference goodies to be included in your seed order(assuming we still have some left by then).
For up-to-date details on stock donations or anything else that you wish to know, please visit the
NASC site, or contact us at any time. If we (NASC, ABRC, and RIKEN) can help you or promote yourresearch to the community by distributing seed on your behalf, then please don’t wait for us to find you –send an email, we can help.

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RIKEN BioResource Research Center
Prepared by
Masatomo Kobayashi (masatomo.kobayashi@riken.jp)

Recent activities and newly developed tools and/or resources of your project/resource
Together with RIKEN CSRS, RIKEN BRC sponsored 3 Keynotes and MASC Workshop in the
ICAR2023 that was held in Japan in June 2023. We intended to support face-to-face discussion among theattendees on “Arabidopsis for SDGs/4th Decadal Vision”.
The Exp-Plant Catalog (https://plant.rtc.riken.jp/resource/home/index.html) provides theinformation of plant resources provided from RIKEN BRC.
Following resources have been added to the Catalog during the past 12 months.
1.
We released following three callus cell lines established from suspension cell lines. Since the original
suspension cell lines are not suitable for overseas transport, we decided to provide the callus cell cultures thatare stably maintained on solid culture media for overseas users. Suspension cell cultures can be easily induced
from the callus cell cultures.
rpc00110: Grape YU-1-c
rpc00111: Arabidopsis YG1-c
rpc00112: Arabidopsis At tom-c
2.
The Exp-Plant Catalog now includes 85 lines of Arabidopsis mutant and transgenic seeds that havebeen newly deposited from Japanese scientists. Now the Catalog provides information of 524 individual lines
in total.
3.
The 201 F2 seed stocks established by crossing Arabidopsis natural accessions with Col and Ler are
now available from RIKEN BRC. These natural accessions include the group IDs, gr1 and gr2. Publications
Planned future activities of your project/resource The RIKEN BRC intends to support the researchcompatible with an increasingly inclusive and sustainable global society. For use in the studies on abiotic
stress responses, Experimental Plant Division has distributed the seeds of natural accessions and their F2progenies after crossing with Col and Ler. Now we start digging the value of natural accessions by genotype
and phenotype characterization. We will establish a new database and disseminate such information to theinternational research community.

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The Arabidopsis Information Resource
www.arabidopsis.org

Prepared by
Leonore Reiser, lreiser@arabidopsis.org, Phoenix Bioinformatics
Tanya Berardini, tberardi@arabidopsis.org , Phoenix Bioinformatics

Recent activities and newly developed tools and/or resources of your project/resource
Data: Genome Annotation
Tanya Berardini (TAIR) and Nick Provart (BAR) initiated the reannotation project via Zoom in
October 2022, enlisting the support of NCBI to run their annotation pipeline on a new consensus telomere
to telomere assembly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_028009825.2/). TAIR has
been coordinating the effort with a dedicated group of volunteers who have contributed a high quality,
gapless reference genome including the NORs, tandem repeats and expert curation of protein coding genes,
transposable elements, lncRNAs, and rDNAs Regular updates are being provided on the TAIR website(https://conf.phoenixbioinformatics.org/display/COM/A.+thaliana+Col-0+v12+reannotation+effort). The
genome annotations will be submitted to NCBI following completion of manual verification and quality
checks. All of the participants in the effort are working on a manuscript together.
Gene Function Annotation
We continue to add new gene function data on a weekly basis including: 1222 new/updated locus
summaries, 499 new/updated gene symbols, 1766 articles linked to 3677 genes, 14301 experimental Gene
Ontology (GO) and Plant Ontology (PO) annotations, 131 new/updated alleles, and 232 phenotypes linked
to germplasms. We regularly update InterPro domain mapping for the Arabidopsis proteins using thebimonthly updates data from UniProt.
We especially wish to acknowledge the contributions of individual authors who submitted their annotations
via our Generic Ontology Annotation Tool (GOAT:goat.phoenixbioinformatics.org). TAIR gene function
data and more is included in our quarterly data releases that are available from our website(https://www.
arabidopsis.org/download/index.jsp) and Zenodo archive (https://doi.org/10.5281/zenodo.7843882).
Software/Tools:
TAIR website update
After over a year of development and a short period of beta testing, we released a new version of theTAIR website on May 6, 2024. The website (frontend) update follows a complete rewrite of the ‘backend’
to a more modern technical platform. These changes were necessary as the legacy software was becoming
increasingly difficult and costly to maintain. The changes to the backend improved reliability and speed. The
redesigned website is more responsive, accessible, and mobile friendly. The updated searches include newfunctionalities such as embedding the bulk search/ download capabilities into the Gene and Protein searches.
We are continuing to iterate on the design and functionality of the TAIR website.
.

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JBrowse2: We also installed an instance of the open source genome browser JBrowse2; a significant
rewrite of the original JBrowse. Most of the tracks from JBrowse have been ported over. One of theenhancements in JBrowse2 is visualization of syntenic datasets which we plan to add over time. We arealso working with the JBrowse2 community to include some favorite features of the Seqviewer nucleotide
sequence view into JBrowse2.
Conferences:
TAIR hosted an update on the V12 genome annotation at the Arabidopsis Informatics workshop at
PAG31 in San Diego (January 2024) and will present more updates at Plant Biology 2024 in the AgBioData
Plant Bioinformatics Workshop Session (June 2024) and the Community Annotation workshop at ICAR
(July 2024).

Publications:Leonore Reiser, Erica Bakker, Sabarinath Subramaniam, Xingguo Chen, Swapnil Sawant, Kartik Khosa,
Trilok Prithvi, Tanya Z. Berardini (2024) The Arabidopsis Information Resource in 2024, Genetics, https://doi.org/10.1093/genetics/iyae027

Planned future activities of your project/resource
Data: We plan to submit the V12 genome annotation to NCBI and integrate the new version into TAIR’s
database and tools. We will continue to maintain an Apollo instance for refining gene models. For
data curation, we will continue to emphasize capturing information about new gene functions and areinvestigating integration of large language models into our curation pipeline.
Tools: We will continue to update and modify the design and functionality of the TAIR website based on user
feedback. We encourage community members to reach out to us via email (curator@arabidopsis.org) to share
their ideas/concerns/questions.
ThanksIn 2024 TAIR celebrates our 25th anniversary (est. Nov 1999). We are grateful to have
had the privilege of serving the plant science community for all of these years and thankeveryone for their continued support.

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Countries
ARGENTINA									34		AUSTRALIA 									36AUSTRIA										38BELGIUM										40BRAZIL											42CHILE											44CHINA											45CZECH REPUBLIC								47ESTONIA										49FINLAND										50FRANCE										51GREECE										53ITALY											54JAPAN											56NEW ZEALAND									58NORWAY										59POLAND										60PORTUGAL										61SPAIN											63SWEDEN										65SWITZERLAND									67UNITED KINGDOM								69UNITED STATES and NAASC						72MASCannualreportreport2023/24
2023/24
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ARGENTINA
Prepared by
Gabriela Auge, auge.gabriela@inta.gob.ar, Instituto de Agrobiotecnología yBiología Molecular (IABIMO) INTA-CONICET. Hurlingham, Argentina.
Rocío Tognacca, rtognacca@agro.uba.ar, Instituto de Fisiología, Biología Molecular y Neurociencias(IFIBYNE) UBA-CONICET. Buenos Aires, Argentina.

Please describe any new or updated experimental resources and/or software tools
available to Arabidopsis researchers that have been initiated or funded in your country in2023 or early 2024.
Moretti, B., Rodriguez Alvarez, S.N. & Grecco, H.E. Nfinder: automatic inference of cell neighborhood in
2D and 3D using nuclear markers. BMC Bioinformatics 24, 230 (2023). https://doi.org/10.1186/s12859-02305284-2
Nfinder enhances pipelines for tracking cell interactions and studying tissue-level spatiotemporalcorrelations.

Planned events for 2024 and 2025•
XIX Congreso Latinoamericano de Genética, Congreso Nacional de Genética 2024 de la Sociedad
Mexicana de Genética, LII Congreso Argentino de Genética, LVII Reunión Anual de la Sociedad de Genética
de Chile, II Congreso Paraguayo de Genética, IX Congreso de la Sociedad Uruguaya de Genética, V
Congreso de La Red Latinoamericana de Genética Humana-RELAGH. October 21-24, 2024. Guadalajara,
Mexico.
•Plant Biology Lectures Series 2024. 16-18 October 2024, Rosario, Argentina.
•
LX Reunión Anual de la Sociedad Argentina de Investigación Bioquímica y Biología Molecular(SAIB). November 5-8, 2024. Córdoba, Argentina.
•
2° Congreso Argentino de Semillas. November 28-29, 2024, Córdoba, Argentina.
•
XXXV Reunión Argentina de Fisiología Vegetal. September, 2025. Mar del Plata, Argentina.
•
XL Jornadas Argentinas de Botánica, September, 2025. Mar del Plata, Argentina.
•
4° Reunión Argentina de Biología de Semillas (RABioS), November, 2025. Concepción del Uruguay,
Argentina.
•
31° Reunión Argentina de Ecología. October, 2025.

Selected Publications
Leonardo A Arias, Sebastián D’Ippolito, Jésica Frik, Natalia L Amigo, Fernanda Marchetti, Claudia A
Casalongué, Gabriela C Pagnussat, Diego F Fiol, The DC1 Domain Protein BINUCLEATE POLLEN is
Required for POLLEN Development in Arabidopsis thaliana, Plant and Cell Physiology, Volume 63, Issue 12,
December 2022, Pages 1994–2007, https://doi.org/10.1093/pcp/pcac122
This study identified BNP, a gene coding for a DC1 domain protein, which is required for pollen
development and germination by interacting with VOZ1 and VOZ2.

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Torres, J. R., Botto, J. F., & Sanchez, D. H. (2024). Canonical transcriptional gene silencing may contribute tolong‐term heat response and recovery through MOM1. Plant, Cell & Environment, 47(1), 372-382. https://doi.org/10.1111/pce.14722
This study led by an early-career researcher shows that a canonical TGS factor may play a role in plant
acclimation and recovery from prolonged heat stress, despite the induced epigenetic disturbances.
Pereyra, M. E., Costigliolo Rojas, C., Jarrell, A. F., Hovland, A. S., Snipes, S. A., Nagpal, P., ... & Casal, J. J.
(2023). PIF4 enhances the expression of SAUR genes to promote growth in response to nitrate. Proceedingsof the National Academy of Sciences, 120(39), e2304513120. https://doi.org/10.1073/pnas.2304513120
This work from a group with proved tracking record of publications sheds light on a novel mechanismthat integrates nutrient and growth pathways during the promotion of plant stature, offering insights forgenetically modifying plant height without reducing nitrogen use efficiency.
Mammarella, M. F., Lucero, L., Hussain, N., Muñoz‐Lopez, A., Huang, Y., Ferrero, L., ... & Ariel, F. (2023).
Long noncoding RNA‐mediated epigenetic regulation of auxin‐related genes controls shade avoidance
syndrome in Arabidopsis. The EMBO Journal, 42(24), e113941. https://doi.org/10.15252/embj.2023113941
Another excellent paper from a highly prolific and highly collaborative group on the role of thelncRNA APOLO on the regulation of SAS by modulating auxin signaling in response to far-red light,
highlighting its potential as a bioactive molecule for agricultural applications.
Canal, María Victoria, Natanael Mansilla, Diana E. Gras, Agustín Ibarra, Carlos M. Figueroa, Daniel
H. Gonzalez, and Elina Welchen. “Cytochrome c levels affect the TOR pathway to regulate growth andmetabolism under energy‐deficient conditions.” New Phytologist 241, no. 5 (2024): 2039-2058. https://doi.
org/10.1111/nph.19506
This work led by an outstanding female researcher shows that CYTc-deficient plants adjust growthby reducing the TOR-pathway activation as a preventive signal to adjust growth in anticipation of energy
exhaustion.

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AUSTRALIA
Prepared by
Monika Murcha, monika.murcha@uwa.edu.au, The University of Western
Australia

Please describe any new or updated experimental resources and/or software tools
available to Arabidopsis researchers that have been initiated or funded in your country in2023 or early 2024.
PHYTOMap: Multiplexed single-cell 3D spatial gene expression analysis in plant tissue.
Nobori, T., Oliva, M., Lister, R., & Ecker, J. R. (2023). Multiplexed single-cell 3D spatial gene expression
analysis in plant tissue using PHYTOMap. Nat Plants, 9(7), 1026-1033. https://doi.org/10.1038/s41477-02301439-4

Planned events for 2024 and 2025
- Australian Society of Plant Scientists Hybrid Conference 28th Nov in Hobart, Tasmania, Australia.

Selected Publications
Ghifari, A. S., Ivanova, A., Berkowitz, O., Whelan, J., & Murcha, M. W. (2023). FTSH PROTEASE 3 facilitates
Complex I degradation through a direct interaction with the Complex I subunit PSST. Plant Cell, 35(8),3092-3108. https://doi.org/10.1093/plcell/koad128

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Huynh, S. D., Melonek, J., Colas des Francs-Small, C., Bond, C. S., & Small, I. (2023). A unique C-terminal
domain contributes to the molecular function of Restorer-of-fertility proteins in plant mitochondria. New
Phytol, 240(2), 830-845. https://doi.org/10.1111/nph.19166
Khan, M. A., Herring, G., Zhu, J. Y., Oliva, M., Fourie, E., Johnston, B., Zhang, Z., Potter, J., Pineda, L.,
Pflueger, J., Swain, T., Pflueger, C., Lloyd, J. P. B., Secco, D., Small, I., Kidd, B. N., & Lister, R. (2024).
CRISPRi-based circuits to control gene expression in plants. Nat Biotechnol. https://doi.org/10.1038/s41587024-02236-w
Pinto, S. C., Leong, W. H., Tan, H., McKee, L., Prevost, A., Ma, C., Shirley, N. J., Petrella, R., Yang, X.,
Koltunow, A. M., Bulone, V., Kanaoka, M. M., Higashyiama, T., Coimbra, S., & Tucker, M. R. (2024).
Germline beta-1,3-glucan deposits are required for female gametogenesis in Arabidopsis thaliana. Nat
Commun, 15(1), 5875. https://doi.org/10.1038/s41467-024-50143-0
Sureshkumar, S., Bandaranayake, C., Lv, J., Dent, C. I., Bhagat, P. K., Mukherjee, S., Sarwade, R., Atri, C.,
York, H. M., Tamizhselvan, P., Shamaya, N., Folini, G., Bergey, B. G., Yadav, A. S., Kumar, S., Grummisch,
O. S., Saini, P., Yadav, R. K., Arumugam, S., . . . Balasubramanian, S. (2024). SUMO protease FUG1, histone
reader AL3 and chromodomain protein LHP1 are integral to repeat expansion-induced gene silencing in
Arabidopsis thaliana. Nat Plants, 10(5), 749-759. https://doi.org/10.1038/s41477-024-01672-5

Major Funding Sources
Fundamental and translational research can be funded by the Australian Research Council (www.arc.gov.au)
Translational research is funded by the Grains Research Development Corporation (http://grdc.com.au)
Industry collaborations can be funded by the Australian Research Council Linkage Programs (www.arc.gov.
au)

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AUSTRIA
Prepared byMarie-Theres Hauser, marie-theres.hauser@boku.ac.at , University of

Natural Resources and Life Sciences, Vienna (BOKU)
J. Matthew Watson, james.watson@gmi.oeaw.ac.at, Gregor Mendel Instituteof Molecular Plant Biology

Planned events for 2024 and 2025
- Mendel Early Career Symposium 2024 16 - 17 May 2024 ,Vienna BioCenter, Austria, https://www.oeaw.
ac.at/gmi/news-events/events/mendel-early-career-symposium-2024- Plant Proteostasis Conference,Vienna 17 - 20 September 2024, Vienna Biocenter https://www.oeaw.ac.at/
gmi/news-events/events/international-plant-proteostasis-conference-2024- 4th International Plant Spectroscopy Conference (https://ipscvienna2024.plantspec.org/) will take place
24.-27.09.2024 in Vienna at BOKU
- Plant Chromosome Biology (https://plantcyto2025.univie.ac.at/) will take place 15.-17. 2025 Vienna
BioCenter, AUSTRIA- EMBO conference Plant Evolution: From Origins to Diversification on Land will take place 25-27.11.25 at
the Gregor Mendel Institute of Molecular Plant Biology (GMI) in Vienna, AUSTRIA
https://coming-soon.embo.org/w25-18

Selected Publications
Gabriele Bradamante, Vu Hoang Nguyen, Marco Incarbone, Zohar Meir, Heinrich Bente, Mattia Donà,
Nicole Lettner, Ortrun Mittelsten Scheid, Ruben Gutzat (2024) Two ARGONAUTE proteins loaded withtransposon-derived small RNAs are associated with the reproductive cell lineage in Arabidopsis. Plant Cell.
36(4):863-880. doi: 10.1093/plcell/koad295.
This publication reports that ARGONAUTE proteins AGO5 and AGO9, which carry small RNAs
from highly methylated transposons, mark sexually reproductive cells in Arabidopsis, indicating an early
segregating germline similar to animals.
Marco Incarbone Gabriele Bradamante, Florian Pruckner, Tobias Wegscheider, Wilfried Rozhon, Vu Nguyen,
Ruben Gutzat, Zsuzsanna Mérai, Thomas Lendl, Stuart MacFarlane, Michael Nodine, Ortrun Mittelsten
Scheid (2023) Salicylic acid and RNA interference mediate antiviral immunity of plant stem cells.Proc Natl
Acad Sci U S A. 120(42):e2302069120. doi: 10.1073/pnas.2302069120.
This study shows that, RNA interference (RNAi) amplified by an RNA-dependent RNA polymerase
activated by salicylic acid prevents viral proliferation in stem cells, providing a crucial mechanism for stem
cell immunity against several RNA viruses, despite their ability to suppress RNAi in other plant tissues.
Benjamin Jaegle, Rahul Pisupati, Luz Mayela Soto-Jiménez, Robin Burns, Fernando A Rabanal, Magnus
Nordborg (2023 ) Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity.
Genome Biol. 24(1):44.doi: 10.1186/s13059-023-02875-3.
The study found that most heterozygous SNP calls in Arabidopsis are artifacts, emphasizes caution
with short-read sequencing SNP data, and highlights that significant copy-number variation in genes
suggests future analyses with independently assembled genomes.

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Bhagyshree Jamge, Zdravko J Lorković, Elin Axelsson, Akihisa Osakabe, Vikas Shukla, Ramesh Yelagandula,
Svetlana Akimcheva, Annika Luisa Kuehn, Frédéric Berger (2023) Histone variants shape chromatin states in
Arabidopsis. Elife.:12:RP87714.doi: 10.7554/eLife.87714.
This study reveals that histone variants, particularly H2A variants, play a crucial role in organizing
chromatin states in Arabidopsis by interacting with histone modifications, and that the chromatin remodeler
DDM1 is essential for the exchange of histone variants, affecting chromatin state distribution.
Lorenzo Picchianti, Víctor Sánchez de Medina Hernández, Ni Zhan, Nicholas At Irwin, Roan Groh, Madlen
Stephani, Harald Hornegger, Rebecca Beveridge, Justyna Sawa-Makarska, Thomas Lendl, Nenad Grujic,
Christin Naumann, Sascha Martens, Thomas A Richards, Tim Clausen, Silvia Ramundo, G Elif Karagöz,
Yasin Dagdas (2023)
Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and autophagy.
EMBO J. 42(10):e112053. doi: 10.15252/embj.2022112053. Epub 2023 Feb 10.
This study reveals that UFMylation by UFM1 is crucial for ER homeostasis by triggering C53-mediatedautophagy in response to stalled translation and highlights the evolutionary conservation across eukaryotes,
excluding fungi and some algae.
Mattia Donà, Gabriele Bradamante, Zorana Bogojevic, Ruben Gutzat, Susanna Streubel, Magdalena
Mosiolek, Liam Dolan, Ortrun Mittelsten Scheid (2023) A versatile CRISPR-based system for lineage tracingin living plants Plant J. 115:1169-1184. doi: 10.1111/tpj.16378.
This publication uses CRISPR to trace cell lineages in living plants by correcting a frameshift mutation
to restore fluorescent protein expression, with Cas9 activity controlled by tissue-specific and inducible
promoters..
Jakob Weiszmann, Dirk Walther, Pieter Clauw, Georg Back, Joanna Gunis, Ilka Reichardt, Stefanie Koemeda,
Jakub Jez, Magnus Nordborg, Jana Schwarzerova, Iro Pierides, Thomas Nägele, Wolfram Weckwerth (2023)
Metabolome plasticity in 241 Arabidopsis thaliana accessions reveals evolutionary cold adaptation processes.
Plant Physiol. 193(2):980-1000. doi: 10.1093/plphys/kiad298.
The study used natural accessions and two temperatures to determine with machine learning tool thepredictive power of natural metabolic variation among accessions. They report that the plasticity of metabolic
regulation is predictable from the genome and epigenome and driven evolutionarily by growth habitats.
Ivan Kulich, Julia Schmid, Anastasia Teplova, Linlin Qi, Jiří Friml (2024) Rapid translocation of NGR
proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. Elife:12:RP91523.
doi: 10.7554/eLife.91523.
The study found that localization of the NEGATIVE GRAVITROPIC RESPONSE OF ROOTS
1 (NGR1) on the statolith surface and plasma membrane (PM) domains is indispensable for NGR1
functionality. A rapid, NGR-dependent translocation of PIN-activating AGCVIII kinase D6PK towards
lower PMs of gravity-perceiving cells might be the reason for the rapid redirection of auxin fluxes following
gravistimulation.

Major Funding Sources
European Research Council 				Austrian Science Fund (FWF)				
Vienna Science and Technology Fund (WWTF)
Austrian Research Promotion Agency (FFG)		

https://erc.europa.eu/
https://www.fwf.ac.at/https://www.wwtf.at/https://www.ffg.at/en

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BELGIUM
Prepared byMoritz K. Nowack moritz.nowack@vib.be VIB-UGent Center for Plant Systems
Biology, Ghent, Belgium
Please describe any new or updated experimental resources and/or software tools
available to Arabidopsis researchers that have been initiated or funded in your country in 2023 or early 2024.
- Plant single cell RNAseq atlas
https://bioit3.irc.ugent.be/plant-sc-atlas/- Updated collection of GoldenGate and Gateway vectors
https://gatewayvectors.vib.be/- Centralized resource for plant post-translational modifications(PTMs)
https://www.psb.ugent.be/webtools/ptm-viewer/- Updated versions of PLAZA
https://bioinformatics.psb.ugent.be/plaza/
Planned events for 2024 and 2025
35th ICAR, Ghent, Belgium. June 16th-20th 2025. www.icar2025.com
Selected Publications
Schoenaers S, Lee HK, Gonneau M, Faucher E, Levasseur T, Akary E, Claeijs N, Moussu S, Broyart C,
Balcerowicz D, AbdElgawad H, Bassi A, Damineli DSC, Costa A, Feijó JA, Moreau C, Bonnin E, Cathala B,
Santiago J, Höfte H, Vissenberg K.”Rapid alkalinization factor 22 has a structural and signalling role in root
hair cell wall assembly.” Nat Plants. 2024 Mar;10(3):494-511. doi: 10.1038/s41477-024-01637-8.
This study reveals the dual role of the peptide RAF22 in controlling root tip growth by functioning asa structural component organizing cell wall architecture and as a feedback signalling molecule that regulates
this process depending on its interaction partners.
Morales-Herrera S, Jourquin J, Coppé F, Lopez-Galvis L, De Smet T, Safi A, Njo M, Griffiths CA, Sidda
JD, Mccullagh JSO, Xue X, Davis BG, Van der Eycken J, Paul MJ, Van Dijck P, Beeckman T. “Trehalose-6phosphate signaling regulates lateral root formation in Arabidopsis thaliana.” Proc Natl Acad Sci U S A. 2023
Oct 3;120(40):e2302996120. doi: 10.1073/pnas.2302996120.
This work uncovers a tissue-specific network during the early phase of LR formation that balances
energy status with auxin signaling using trehalose 6-phosphate as a signaling molecule.

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Safi A, Smagghe W, Gonçalves A, Wang Q, Xu K, Fernandez AI, Cappe B, Riquet FB, Mylle E, Eeckhout D,
De Winne N, Van De Slijke E, Persyn F, Persiau G, Van Damme D, Geelen D, De Jaeger G, Beeckman T,
Van Leene J, Vanneste S. “Phase separation-based visualization of protein-protein interactions and kinase
activities in plants.” Plant Cell. 2023 Sep 1;35(9):3280-3302. doi: 10.1093/plcell/koad188.
This article presents the SYnthetic Multivalency in PLants (SYMPL)-vector set as a tool to assay
protein–protein interactions and kinase activity in planta based on phase separation.
Wang Y, Perez-Sancho J, Platre MP, Callebaut B, Smokvarska M, Ferrer K, Luo Y, Nolan TM, Sato T, Busch W,
Benfey PN, Kvasnica M, Winne JM, Bayer EM, Vukašinović N, Russinova E. “Plasmodesmata mediate cellto-cell transport of brassinosteroid hormones.” Nat Chem Biol. 2023 Nov;19(11):1331-1341. doi: 10.1038/
s41589-023-01346-x.
This study demonstrates that plasmodesmata are responsible for short-distance transport ofbrassinosteroid phytohormones between neighboring cells, and that brassinosteroids can autoregulate theirown motility by modulating the permeability of plasmodesmata.
Nguyen TH, Thiers L, Van Moerkercke A, Bai Y, Fernández-Calvo P, Minne M, Depuydt T, Colinas M,
Verstaen K, Van Isterdael G, Nützmann HW, Osbourn A, Saeys Y, De Rybel B, Vandepoele K, Ritter A,
Goossens A.”A redundant transcription factor network steers spatiotemporal Arabidopsis triterpene
synthesis. Nat Plants. 2023 Jun;9(6):926-937. doi: 10.1038/s41477-023-01419-8.
This paper describes the gene regulatory network in Arabidopsis thaliana that regulates cell-specificbiosynthesis of triterpenes, a class of specialized metabolites that modulate developmental and ecological
functions and comprise many therapeutic and other high-value compounds
Major Funding Sources- Flanders Institute for Biotechnology (VIB; www.vib.be)- European Union Framework Programs (cordis.europa.eu/)- Belgian Federal Science Policy Office (www.belspo.be)- Research Foundation – Flanders (FWO; http://www.fwo. be/en/index.aspx)- Fonds de la Recherche Scientifique (FNRS; http://www.frs-fnrs.be)- European Research Council (http://erc.europa.eu/)

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BRAZIL
Prepared by
Wagner L. Araújo
Departamento de Biologia Vegetal Universidade Federal de Viçosa 36570-900
Viçosa, MG, Brazil wlaraujo@ufv.br
Adriano Nunes Nesi
Departamento de Biologia Vegetal Universidade Federal de Viçosa 36570-900 Viçosa, MG, Brazil nunesnesi@
ufv.brPlanned events for 2024 and 2025
XIX Brazilian Congress of Plant Physiology,
Viçosa, Minas Gerais, Brazil, from October 7 to 12, 2024.

Selected Publications
Romero JM, Serrano-Bueno G, Camacho-Fernández C, Vicente MH, Ruiz MT, Pérez-Castiñeira JR, PérezHormaeche J, Nogueira FTS, Valverde F. CONSTANS, a HUB for all seasons: How photoperiod pervades
plant physiology regulatory circuits. Plant Cell. 2024 May 29;36(6):2086-2102. doi: 10.1093/plcell/koae090.
PMID: 38513610; PMCID: PMC11132886.
This review is dedicated to the functions of the protein CONSTANS (CO) other than photoperiodic
flowering in different plant species, further providing relevant ideas about CO protein structure and function,and in the evolution of photoperiodic sensing. Finally, the authors also discuss recent advances in agriculturaland biotechnological applications of CONSTANS and its structural homologs, the CONSTANS-like (COL)
genes.
Kfoury B, Rodrigues WFC, Kim SJ, Brandizzi F, Del-Bem LE. Multiple horizontal gene transfer events haveshaped plant glycosyl hydrolase diversity and function. New Phytol. 2024 Apr;242(2):809-824. doi: 10.1111/
nph.19595. Epub 2024 Feb 28. PMID: 38417454
This work sheds light on the macroevolutionary processes that have shaped the glycosyl hydrolases(GHs) repertoire in plants, highlighting the acquisition of GH families through horizontal transfer and therole of GHs in plant adaptation and defense mechanisms.
Pougy KC, Sachetto-Martins G, Almeida FCL, Pinheiro AS. 1 H, 15 N, and 13 C backbone and side chain
resonance assignments of the cold shock domain of the Arabidopsis thaliana glycine-rich protein AtGRP2.
Biomol NMR Assign. 2023 Jun;17(1):143-149. doi: 10.1007/s12104-023-10133-7. Epub 2023 May 5. PMID:
37145295.
This study investigate the mechanisms by which AtGRP2 (Arabidopsis thaliana glycine-rich protein2), a 19-kDa RNA-binding glycine-rich protein that regulates key processes in A. thaliana, specifically binds
its RNA targets. The authors were able to report ere the sequence-specific resonance assignments of AtGRP2CSD as a first step toward its structural, dynamics, and RNA binding characterization by NMR.

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Souza PVL, Hou LY, Sun H, Poeker L, Lehman M, Bahadar H, Domingues-Junior AP, Dard A, Bariat L,
Reichheld JP, Silveira JAG, Fernie AR, Timm S, Geigenberger P, Daloso DM. Plant NADPH-dependentthioredoxin reductases are crucial for the metabolism of sink leaves and plant acclimation to elevated CO2.
Plant Cell Environ. 2023 Aug;46(8):2337-2357. doi: 10.1111/pce.14631. Epub 2023 Jun 2. PMID: 37267089.
This study revealed that a previously unknown role of the NADPH-thioredoxin reductases (NTR)
system in regulating sink leaf metabolism and plant acclimation to high CO2 conditions
Barros JAS, Cavalcanti JHF, Pimentel KG, Magen S, Soroka Y, Weiss S, Medeiros DB, Nunes-Nesi A, Fernie
AR, Avin-Wittenberg T, Araújo WL. The interplay between autophagy and chloroplast vesiculation pathways
under dark-induced senescence. Plant Cell Environ. 2023 Dec;46(12):3721-3736. doi: 10.1111/pce.14701.
Epub 2023 Aug 24. PMID: 37615309.
By using a combination of genetic and biochemical approaches, this study revealed the significance ofthe chloroplast vesiculation pathway on the metabolic responses to induced senescence

Major Funding Sources• Sources Instituto Serrapilheira (Serrapilheira is a private nonprofit institution which promotes science inBrazil.
• National Council for Scientific and Technological Development (CNPq-Brazil)• Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES-Brazil)• Foundation for Research Assistance of the Sao Paulo State (FAPESP-Brazil)• Foundation for Research Assistance of the Rio de Janeiro State (FAPERJ-Brazil)• Foundation for Research Assistance of the Rio Grande do Sul State (FAPERGS-Brazil)• Foundation for Research Assistance of the Minas Gerais State (FAPEMIG-Brazil)

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CHILE
Prepared byAdrian A. Moreno, adrian.moreno@unab.cl, Universidad Andres Bello

Planned events for 2024 and 2025
- XLVII Reunión Anual 2024 Sociedad de Bioquímica y Biología Molecular de Chile (SBBMCh). La Serena,
Chile, 30 sep – 4 Oct. 2024.
A meeting hosted by the Chilean Society of Biochemistry and Molecular Biology. It included talks,
symposiums, and poster presentations. This year the society celebrates 50th years.
Organizer: Chilean Society of Biochemistry and Molecular Biology (https://www.sbbmch.cl/annualmeeting-2024/)

Selected Publications
Shanks CM, Rothkegel K, Brooks MD, Cheng CY, Alvarez JM, Ruffel S, Krouk G, Gutiérrez RA, Coruzzi GM.
Nitrogen sensing and regulatory networks: it’s about time and space. Plant Cell. 2024 May 1;36(5):1482-1503.
doi: 10.1093/plcell/koae038. PMID: 38366121; PMCID: PMC11062454.
(https://academic.oup.com/plcell/article/36/5/1482/7608181)
Up to date review on N nutrition.
Ibeas MA, Salinas-Grenet H, Johnson NR, Pérez-Díaz J, Vidal EA, Alvarez JM, Estevez JM. Filling the gaps
on root hair development under salt stress and phosphate starvation using current evidence coupled witha meta-analysis approach. Plant Physiol. 2024 Jun 26:kiae346. doi: 10.1093/plphys/kiae346. Epub ahead ofprint. PMID: 38918899.
(https://academic.oup.com/plphys/advance-article/doi/10.1093/plphys/kiae346/7699132)
A meta-analysis on existing evidence related to plant response to multiple combined stresses using as
model Pi deficiency and salt stress.

Major Funding Sources
ANID (Agencia Nacional de Investigación y Desarrollo(https://www.anid.cl/)
Iniciativa Científica Milenio(http://www.iniciativamilenio.cl/)
CORFO - Corporación de Fomento de la Producción(https://www.corfo.cl/)

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CHINA
Prepared by
Yuling Jiao, yuling.jiao@pku.edu.cn, School of Life Sciences and Center for
Quantitative Biology, Peking University

Please describe any new or updated experimental resources and/or software tools
available to Arabidopsis researchers that have been initiated or funded in your country in2023 or early 2024.
- TBtools-II: a Toolkit for Biologists integrating various biological data handling tools, a stand-alone softwarewith a user-friendly interface https://github.com/CJ-Chen/TBtools-II- scPlant: A framework for single-cell transcriptomic data analysis in plants https://github.com/compbioNJU/
scPlant- RLKdb: A curated database of plant receptor-like kinase families https://biotec.njau.edu.cn/rlkdb/- iCREPCP: A deep learning-based web server for identifying cis-regulatory elements within plant core
promoters http://www.hzau-hulab.com/icrepcp/

Planned events for 2024 and 2025
- 2024 International Conference on Molecular Plant Sciences, August 8-12, 2024, Shanghai (http://www.
molplant.org.cn/icmps2024)- 2024 Annual Meeting of the Chinese Society for Plant Biology, August 25-29, 2024, Chengdu, Sichuan- 2024 National Congress of Plant Biology, November 16-19, 2023, Guangzhou, Guangdong (http://ncpb.
net/)

Selected Publications
Chen JY, Yu RB, Li N, Deng ZG, Zhang XX, Zhao YR, Qu CF, Yuan YF, Pan ZX, Zhou YY, Li KL, Wang JJ,
Chen ZR, Wang XY, Wang XL, He SN, Dong J, Deng XW, Chen HD (2023). Amyloplast sedimentation repolarizes LAZYs to achieve gravity sensing in plants. Cell 186, 4788-4802.
This study identifies a molecular mechanism for gravity sensing in plants involving LAZY protein
phosphorylation and interaction with chloroplast translocons, leading to asymmetrical auxin distribution
and root growth.
Huang F, Luo X, Ou Y, Gao ZX, Tang QM, Chu ZZ, Zhu XG, He YH (2023). Control of histone
demethylation by nuclear-localized α-ketoglutarate dehydrogenase. Science 381, eadf8822.
This study discovered that the mitochondrial enzyme KGDH, which normally participates in the
respiratory tricarboxylic acid cycle, can also inhibit histone demethylases in the nucleus, thereby affecting
gene expression by altering histone methylation.

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Lan ZJ, Song ZH, Wang ZJ, Li L, Liu YQ, Zhi SH, Wang RH, Wang JZ, Li QY, Bleckmann A, Zhang L,
Dresselhaus T, Dong J, Gu HY, Zhong S, Qu LJ (2023). Antagonistic RALF peptides control an inter-generichybridization barrier on Brassicaceae stigmas. Cell 186, 4773-4787.
This study reveals a “lock-and-key” system involving receptor-like kinases and cell wall proteinsinteracting with stigmatic peptides, which controls pollen tube penetration and can be manipulated tofacilitate broad hybridization in crops.
Meng JG, Xu YJ, Wang WQ, Yang F, Chen SY, Jia PF, Yang WC, Li HJ (2023). Central-cell-produced attractants control fertilization recovery. Cell 186, 3593-3605.
This study reveals a female gamete-attraction system involving the secretion of peptides SALVAGER1and SALVAGER2, which enhance fertilization recovery and reproductive assurance when initial pollen tube
attraction fails.
Yu YQ, Tang WX, Lin WW, Li W, Zhou X, Li Y, Chen R, Zheng R, Qin GC, Cao WH, Pérez-Henríquez P,
Huang RF, Ma J, Qiu QQ, Xu ZW, Zou AL, Lin JC, Jiang LW, Xu TD, Yang ZB (2023). ABLs and TMKs are
co-receptors for extracellular auxin. Cell 186, 5457-5471.
This study identifies ABL1 and ABL2 as new auxin-binding proteins that function as co-receptors
with TMKs and ABP1, providing a clearer understanding of extracellular auxin perception in plants.
Zhao Y, Shi H, Pan Y, Lyu MH, Yang ZX, Kou XX, Deng XW, Zhong SW (2023). Sensory circuitry controls
cytosolic calcium-mediated phytochrome B phototransduction. Cell 186, 1230-1243.
Red light induces a rapid increase in cytosolic Ca2+, which is crucial for the nuclear translocation ofphytochrome B, thereby facilitating the cotyledon opening and expansion of etiolated Arabidopsis seedlings
during the transition from darkness to light.

Major Funding Sources
National Natural Science Foundation (NSFC) (https://www.nsfc.gov.cn/english/site_1/index.html)

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CZECH REPUBLIC
Prepared by
Viktor Žárský viktor@natur.cuni.cz
Charles university, Fac. of Science, Dept. of Exp. Plant Biology and Inst. of Exp.
Botany, Czech Acad. Sci., Prague

Please describe any new or updated experimental resources and/or software tools
available to Arabidopsis researchers that have been initiated or funded in your country in2023 or early 2024.
Authors from the lab of Kamil Růžička (Inst. Of Exp. Bot., Czech Acad. Of Sci.) in this paper Timofeyenko K, Kanavalau D, Alexiou P, Kalyna M, Růžička K. 2023. Catsnap: a user-friendly algorithm fordetermining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative
splicing. New Phytologist 238(4):1722-1732. DOI: 10.1111/nph.18799
Describe a new tool they developed to search for the conservation of protein variants – CATSNAP at https://catsnap.cesnet.cz/ .

Planned events for 2024 and 2025-

SEB/Soc. Of Exp. Biol. Conference 2024 – Prague, 2 – 5 July, Czech Republic

EMBO workshop – Plant genome stability and change 2024 – Olomouc, 16 – 19 June, Czech republic(organizer Aleš Pečínka – Inst. Of Exp. Bot., Czech Acad. Of Sci.)
European Plant Cytoskeletal Club/EPCC meeting 2024 Prague, from 27–28 June 2024, Prague, Czech
Republic (organizer Kateřina Schwarzerová, Dept. of Exp. Bot. , Fac. Of Science, Charles university, Prague)-

Green for Good VIIth meeting 2025 – Olomouc, from 1- 4 September, Czech republic. Selected

Publications
Serre, N. B. C., Wernerová, D., Vittal, P., Dubey, S. M., Medvecká, E., Jelínková, A., Petrášek, J., Grossmann,G., & Fendrych, M. (2023). The AUX1-AFB1-CNGC14 module establishes a longitudinal root surface pH
profile. eLife, 12, e85193. https://doi.org/10.7554/eLife.85193
Using new probe details of pH profile dynamics related to root growth and gravitropic response isdescribed.
Crhak Khaitova, L., Mikulkova, P., Pecinkova, J., Kalidass, M., Heckmann, S., Lermontova, I., & Riha, K.
(2024). Heat stress impairs centromere structure and segregation of meiotic chromosomes in Arabidopsis.
eLife, 12, RP90253. https://doi.org/10.7554/eLife.90253
Meiotic centromeres in Arabidopsis are highly sensitive to heat stress, and suggest that centromeresand kinetochores may represent a critical bottleneck in plant adaptation to increasing temperatures.

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Martinek, J., Cifrová, P., Vosolsobě, S., García-González, J., Malínská, K., Mauerová, Z., Jelínková, B.,
Krtková, J., Sikorová, L., Leaves, I., Sparkes, I., & Schwarzerová, K. (2023). ARP2/3 complex associates withperoxisomes to participate in pexophagy in plants. Nature plants, 9(11), 1874–1889. https://doi.org/10.1038/
s41477-023-01542-6
Participation of ARP2/3 complex is uncovered.
Huebbers, J. W., Caldarescu, G. A., Kubátová, Z., Sabol, P., Levecque, S. C. J., Kuhn, H., Kulich, I., Reinstädler,
A., Büttgen, K., Manga-Robles, A., Mélida, H., Pauly, M., Panstruga, R., & Žárský, V. (2024). Interplay of
EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew.
The Plant cell, 36(4), 1007–1035. https://doi.org/10.1093/plcell/koad319
Functional interaction between exocyst complex and MLOs in plant exocytosis is uncovered.
Fulneček, J., Klimentová, E., Cairo, A., Bukovcakova, S. V., Alexiou, P., Prokop, Z., & Riha, K. (2023). The SAP
domain of Ku facilitates its efficient loading onto DNA ends. Nucleic acids research, 51(21), 11706–11716.
https://doi.org/10.1093/nar/gkad850
That speed of conserved DNA repair Ku is not the decisive factor in stabilizing telomere or doublestrand break DNA structures

Major Funding Sources
Both major funding agencies for basic research- Czech Science Foundation (GACR) and Ministry of Education of CR (MSMT CR) - support regularly
projects based on the use of Arabidopsis as a model plant.
1. Czech Science Foundation/GAČR, Prague (http://www.gacr.cz)
2. Ministry of Education, Youth and Sports of Czech Republic, Prague (http://www.msmt.cz/research-anddevelopment-1)
Both institutions support also bilateral projects with selected countries.
Targeted or applied research is since recently supported also by the Technology Agency of the Czech Republic(TACR) and Arabidopsis model is accepted as a driver for applications.
3. Technology Agency of the Czech Republic (http://www.tacr.cz/english/)
4. Ministry of Agriculture, National Agency for Agricultural Research (NAZV) might support projects using
Arabidopsis as a driver for the applied research (http://eagri.cz/public/web/mze/poradenstvi-a-vyzkum/
vyzkum-a-vyvoj/narodni-agentura-pro-zemedelsky-vyzkum/)

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ESTONIA
Prepared by
Hanna Hõrak, hanna.horak@ut.ee, Institute of Technology, University of Tartu,
Nooruse 1, 50411, Tartu, Estonia

Please describe any new or updated experimental resources and/or software tools
available to Arabidopsis researchers that have been initiated or funded in your country in2023 or early 2024.
University of Tartu has available custom-built gas-exchange analysis devices for measuring
Arabidopsis whole-rosette photosynthesis and stomatal conductance under controlled conditions with theoption to address real-time stomatal responses to changes in air CO2 concentration, air humidity, lightquantity, and application of hormones. Contact: Hannes Kollist (hannes.kollist@ut.ee)

Selected Publications
Yeh et al, 2023, MPK12 in stomatal CO2 signaling: function beyond its kinase activity, New Phytologist
The study shows that the function of MPK12, a key kinase involved in mediating stomatal CO2
signalling, does not depend on its kinase activity.
Koolmeister et al, 2024, Stomatal CO2 responses at sub- and above-ambient CO2 levels employ different
pathways in Arabidopsis, Plant Physiology
The study shows that different guard cell signalling components mediate stomatal CO2 responses
under sub- and above-ambient CO2 concentration ranges.
Tulva et al, 2023, Plants lacking OST1 show conditional stomatal closure and wildtype-like growth sensitivity
at high VPD, Physiologia Plantarum
The study shows that normally high VPD-insensitive plants that lack OST1, a key kinase involvedin stomatal VPD responses, acquire stomatal sensitivity to high VPD when grown under reduced soil watercontent.

Major Funding Sources
Estonian Research Council, www.etag.ee

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FINLAND
Prepared by
Ari Pekka Mähönen, AriPekka.Mahonen@helsinki.fi, University of Helsinki

Planned events for 2024 and 2025
Centre of Excellence in Tree Biology, located in University of Helsinki, is organizing a conference called
Plants in a Changing World, 25-27th September 2024
https://www.helsinki.fi/en/researchgroups/viikki-plant-science-centre/plants-in-a-changing-world-2024

Selected Publications
Ivanauskaite, A., Rantala, M., Laihonen, L., Konert, M., Schwenner N., Mühlenbeck, J., Finkemeier, I. and
Mulo, P. (2023) Loss of chloroplast GNAT acetyltransferases results in distinct metabolic phenotypes in
Arabidopsis. Plant and Cell Physiology 64, 549-563.
Chloroplast acetyltransferases have an impact on the accumulation of metabolites in plant leaves.
Laihonen, L., Ranasinghe, U.T., Rantala, M., Tyystjärvi, E. and Mulo, P. (2024) Transcriptomic and proteomic
analyses of distinct Arabidopsis organs reveal high PSI-NDH complex accumulation in stems. Physiologia
Plantarum 176:e14227.
The photosynthetic machinery of Arabidopsis stems differs from that of other green tissues, and each
Arabidopsis organ possesses unique transcript profile.
Waszczak C, Yarmolinsky D, Leal Gavarrón M, Vahisalu T, Sierla M, Zamora O, Carter R, Puukko T, Sipari
N, Lamminmäki A, Durner J, Ernst D, Winkler JB, Paulin L, Auvinen P, Fleming AJ, Andersson MX, Kollist
H, Kangasjärvi J. (2024) Synthesis and import of GDP-L-fucose into the Golgi affect plant–water relations.
New Phytologist 241:747–763
Blocking the synthesis of GDP-L-fucose, or its import into the Golgi apparatus, leads to uncontrolled
transpiration of water from leaf tissues.
Bourdon M, Lyczakowski JJ, Cresswell R, Amsbury S, Vilaplana F, Le Guen MJ, Follain N, Wightman R, Su C,
Alatorre-Cobos F, Ritter M, Liszka A, Terrett OM, Yadav SR, Vatén A, Nieminen K, Eswaran G, Alonso-SerraJ, Müller KH, Iuga D, Miskolczi PC, Kalmbach L, Otero S, Mähönen AP, Bhalerao R, Bulone V, Mansfield SD,
Hill S, Burgert I, Beaugrand J, Benitez-Alfonso Y, Dupree R, Dupree P, Helariutta Y. (2023) Ectopic callose
deposition into woody biomass modulates the nano-architecture of macrofibrils. Nat Plants. 9:1530-1546.
poplar.

Overproduction of callose in wood leads to altered wood composition both in Arabidopsis andMajor Funding Sources
Research Council of Finland: https://www.aka.fi/en/
Jane and Aatos Erkko Foundation: http://www.jaes.fi.
The Ella and Georg Ehrnrooth Foundation https://www.ellageorg.fi/en
The Finnish Cultural Foundation https://skr.fi/en

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FRANCE
Prepared by
Cécile BOUSQUET-ANTONELLI, insb.das5f@cnrs.fr, CNRS, IBMP - Strasbourg& CNRS, 3 rue Michel Ange, ParisLoïc LEPINIEC, loic.lepiniec@inrae.fr, Université Paris-Saclay, INRAE, AgroParisTech, IJPBPlease describe any new or updated experimental resources and/or software tools
available to Arabidopsis researchers that have been initiated or funded in your country in2023 or early 2024.
Arabidopsis stock center, https://publiclines.versailles.inrae.fr/
ATOMEdb: Arabidopsis thaliana ORFeome database, http://tools.ips2.u-psud.fr/ATOMEdb
https://cnrgv.toulouse.inra.fr/Library/Arabidopsis
PHENOPSIS, https://bioweb.supagro.inrae.fr/phenopsis/Accueil.php?lang=En and PHENOSCOPE(http:// www.ijpb.versailles.inra.fr/en/plateformes/ppa/index. html) are high-throughput automatedphenotyping platforms at Montpellier and Versailles
SPS tools for Functional Genomics https://eng-saclay-plant-sciences.hub.inrae.fr/infrastructures

Planned events for 2024 and 2025
- PLANT SCIENCES IN THE ANTHROPOCENE, from March 24 to April 04, 2025, at Université ParisSaclay, France -The objective of this workshop is to address key challenges for the international plant science
community, from basic sciences to socio-economic and environmental aspects including climate change.
https://www.institut-pascal.universite-paris-saclay.fr/en/scientific-programs/plant-sciences-anthropocene- PERSPECTIVES ON PROTEIN NETWORKS IN PLANTS, Ibmp-cnrs, Strasbourg, France, September 19 20, 2024. https://pnp2024.sciencesconf.org- Post-transcriptional Gene Regulations in Plants (PGRP), September 3-5, 2024, Banyuls/mer, France.
https://pgrp2024.sciencesconf.org- 13TH INTERNATIONAL PLANT COLD HARDINESS SEMINAR (IPCHS), Clermont-Ferrand, France,
August 26 - 30, 2024? https://ipchs13.seminaire.inrae.fr- EPIPLANT/SEB 2024 the conference will start Wednesday, 10th-12th of July 2024 at Clermont Ferrand,
France. https://www.sebiology.org/events/epiplant-seb-2024.html- 5TH EPICATCH MEETING Bordeaux university, France, July 10 - 12, 2024 https://epicatch5.sciencesconf.
org- 14th International Conference of the French Society of Plant Biology 12 to 14 of June 2024, Bordeaux.
https://sciences-environnement.u-bordeaux.fr/evenements/14th-international-conference-french-societyplant-biology- The 16th International Conference on Reactive Oxygen and Nitrogen Species in Plants will take place in
Antibes, France, on 29,-31 May 2024. https://www.alphavisa.com/pog/2024/index.php- IJPB SYMPOSIUM 2024 - PLANT MODELING: OPPORTUNITIES AND CHALLENGES, 13-15 may 2024
/ IJPB for Plant Sciences, Versailles-Saclay, https://ijpb-plant-sciences.symposium.inrae.fr/

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Selected Publications
Steven Moussu et al. Plant cell wall patterning and expansion mediated by protein-peptide polysaccharide
interaction. Science 382, 719-725 (2023). DOI:10.1126/science.adi4720
Huy Cuong Tran et al. An mTRAN-mRNA interaction mediates mitochondrial translation initiation inplants. Science, 381, eadg0995 (2023). DOI:10.1126/science.adg0995
Lian, Q., et al. A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure
throughout the global species range. Nat Genet 56, 982–991 (2024). Doi :10.1038/s41588-024-01715-9
Arrivé, M. et al. A tRNA-modifying enzyme facilitates RNase P activity in Arabidopsis nuclei. Nat. Plants 9,2031–2041 (2023). DOI : 10.1038/s41477-023-01564-0
Vrielynck, et al. SCEP1 and SCEP2 are two new components of the synaptonemal complex central element.
Nat. Plants 9, 2016–2030 (2023). DOI : 10.1038/s41477-023-01558-y

Major Funding Sources• Research organizations such as CNRS, INRAE, CEA or Universities provide recurrent funding to theirlaboratories in addition to payment of salaries of permanent researchers and technicians. Thematic calls canalso be opened by these research organizations for their research laboratories to support emerging or risky
projects or to facilitate the development of interdisciplinary projects.
• The French national research agency, ANR (http:// www. agence-nationale-recherche.fr/en/about-anr/
about- the- french-national-research-agency/), provides funding for project-based research
The French Priority Research and Equipment Programme (PEPR) “Advanced Plant Selection” was launchedin March 2024 (30 ME), aiming to adapt agricultural production systems to cope with climate change,
while at the same time reducing phytosanitary and nutrient inputs, by supporting the development of NBTapproaches.

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GREECE
Prepared by
Stamatis Rigas srigas@aua.gr Agricultural University of Athens

Selected Publications
Isaioglou I, Podia V, Velentzas AD, Kapolas G, Beri D, Karampelias M, Plitsi PK, Chatzopoulos D, Samakovli
D, Roussis A, Merzaban J, Milioni D, Stravopodis DJ, Haralampidis K. 2024. APRF1 interactome reveals
HSP90 as a new player in the complex that epigenetically regulates flowering time in Arabidopsis thaliana.
Int. J. Mol. Sci. 25, 1313.
The interactome of APRF1 includes proteins that are localized in several subcellular compartments
and are implicated in multiple biological processes.
Liu C, Mentzelopoulou A, Muhammad A, Volkov A, Weijers D, Gutierrez-Beltran E, Moschou PN. 2023.
An actin remodeling role for Arabidopsis processing bodies revealed by their proximity interactome. EMBO
Journal 42, e111885.
In this work, the authors describe the link between condensates with a plasma membrane-localized
complex. They used proximity biotinylation approaches to characterize a condensate. This approach enabled
to link condensates, previously called “membrane-less organelles”, with membranes.
Liu C, Mentzelopoulou A, Papagavriil F, Ramachandran P, Perraki A, Claus L, Barg S, Dormann P, Jaillais Y,
Johnen P, Russinova E, Gizeli E, Schaaf G, Moschou PN. 2023. SEC14-like condensate phase transitions at
plasma membranes regulate root growth in Arabidopsis. PLoS Biol 21, e3002305.
In this work, the authors identified a membrane-associated protein that forms condensates and canundergo phase transitions: from liquid to more solid states. This transition depends on a well-conserved
protease. They also identified these transitions as components of auxin signaling.
Liu C, Mentzelopoulou A, Hatzianestis IH, Tzagkarakis E, Skaltsogiannis V, Ma X, Michalopoulou VA,
Romero-Campero FJ, Romero-Losada AB, Sarris PF, Marhavy P, Bolter B, Kanterakis A, Gutierrez-Beltran E,
Moschou PN. 2024. A proxitome-RNA-capture approach reveals that processing bodies repress coregulated
hub genes. Plant Cell 36, 559-584.
In this work, the authors repurpose proximity biotinylation approaches to capture the RNAs that
localize in condensates. They surprisingly identify that RNAs can localize in condensates together with
their encoded proteins. They also identify the pathway of ethylene as a converging point of RNA-protein
interactions.

Major Funding Sources•
General Secretariat for Research and Innovation (G.S.R.I.)•
The Hellenic Foundation for Research and Innovation (H.F.R.I.)•
European Regional Development Fund of the European Union and Greek national funds throughthe Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH–
CREATE–INNOVATE•ERC Consolidator Grants (CoG) 2023•
Rural Development Program of Greece, Sub-Measure 16.1 ‘Cooperation’

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ITALY
Prepared by
Alice Pajoro Alice.pajo ro@cnr.it Institute of Molecular Biology and Pathology,
National Research Council c/o , Sapienza, Pl. Aldo Moro 5, 00185 Rome, Italy

Planned events for 2024 and 2025•
Workshop on Plant Biology 2024 21st-23rd February 2024 Bertinoro•“Fascination of Plants Day” FoPD 2024 (https://plantday18may.org) May 2024, all around Italy•
Workshop on Molecular Mechanisms Controlling Flowering 16th-20th June 2024, Palermo•
Congress of the Italian Society of Agricultural Genetics SIGA 10th-13th September 2024, Bologna•
International Plant Science Conference (IPSC) 11th-13th September 2024, Teramo•
XVII Edition of the Congress of the Italian Federation of Life Sciences (FISV), September 18th-20th,
2024. Padova•
SBI Summer School “New Genomic Techniques in plant science”, 24th-26th September 2024, Torino•
Practical Course “Seeds of innovation: Genomic sequencing and GWAS in Agriculture”, 24th-27th
September 2024•
Integration and Regulation of Plant Proteolytic Pathways Gordon Research Conference, January 19 24, 2025. Barga (Lucca)•
Congress of the Italian Society of Agricultural Genetics SIGA September 2025.
•
International Plant Science Conference (IPSC) September 2025•
Congress of the Italian Federation of Life Sciences (FISV), September 2025.

Selected Publications
Gradogna A, Lagostena L, Beltrami S, Tosato E, Picco C, Scholz-Starke J, Sparla F, Trost P, Carpaneto A.
(2023) Tonoplast cytochrome b561 is a transmembrane ascorbate-dependent monodehydroascorbate
reductase: functional characterization of electron currents in plant vacuoles. New Phytologist 238(5):19571971. doi: 10.1111/nph.18823.
Measuring electron currents in isolated Arabidopsis vacuoles is not an easy task. Here the technique
is successfully used to show that ascorbate-dependent currents in mesophyll vacuoles are entirely due tocytochrome b-561 isoform A.
Russo G, Capitanio S, Trasoletti M, Morabito C, Krukowski P, Visentin I, Genre A, Schubert A, Cardinale
F (2023) Strigolactones promote the localization of the ABA exporter ABCG25 at the plasma membrane inroot epidermal cells of Arabidopsis thaliana. Journal Experimental Botany 74(18):5881-5895
doi: 10.1093/jxb/erad298.
We propose a new mechanism for ABA homeostasis regulation in the context of osmotic stressacclimation: the fine-tuning by strigolactones of ABCG25 localization in root cells
Coculo D, Del Corpo D, Ozáez Martínez M, Vera P, Piro G, De Caroli M, Lionetti, V. (2023) Arabidopsis
subtilases promote defense-related pectin methylesterase activity and robust immune responses tobotrytis infection. Plant Physiology and Biochemistry, Volume 201,2023,107865, https://doi.org/10.1016/j.
plaphy.2023.107865
The manuscript highlights the role of subtilases (SBTs) SBT3.3 and SBT3.5 as modulators of PME
activity in Arabidopsis against Botrytis to promptly boost immunity limiting the growth-defense trade-off.

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Triozzi PM, Brunello L, Novi G, Ferri G, Cardarelli F, Loreti E, Perales M, and Perata P. (2024).
Spatiotemporal oxygen dynamics in young leaves reveal cyclic hypoxia in plants. Molecular Plant. 17, 377–
394 https://doi.org/10.1016/j.molp.2024.01.006

We demonstrate that cyclic fluctuations in internal oxygen levels occur in young emerging leaves of
Arabidopsis plants. Cyclic hypoxia in plants is based on a mechanism requiring the ETHYLENE RESPONSE
FACTORS type VII (ERFVII). The ERFVII-dependent mechanism allows precise adjustment of leaf growth
in response to carbon status and oxygen availability within plant cells.
Possenti M, Sessa G, Alfé A, Turchi L, Ruzza V, Sassi M, Morelli G, Ruberti I (2024). HD-Zip II transcription
factors control distal stem cell fate in Arabidopsis roots by linking auxin signaling to the FEZ/SOMBRERO
pathway. Development 151 (8): dev202586 https://doi.org/10.1242/dev.202586
This article shows that HD-Zip II transcription factors regulate root stem cells activity bycounteracting the auxin-induced columella differentiation downstream of the FEZ/SMB proliferative module.

Major Funding Sources•
Italian Ministry of Education, University and Research (MUR) (https://www.mur.gov.it/it)
Program PRIN2020, PRIN2022, PRIN2022-PNRR
Agritech National Research Center, European Union Next-Generation EU (PIANO NAZIONALE DI
RIPRESA E RESILIENZA (PNRR) – MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 – D.D. 1032
17/06/2022, CN00000022). https://agritechcenter.it/
National Biodiversity Future Center NBFC, European Union Next-Generation EU PIANONAZIONALE DI RIPRESA E RESILIENZA (PNRR), Missione 4 Componente 2, “Dalla ricerca all’impresa”,
Investimento 1.4, Project CN00000033.
Rome Technopole” https://www.rometechnopole.it/ European Union “NextGenerationEU” program
PhD training programme PON ricerca e Innovazione 2014-2020. Asse IV Istruzione e ricerca per ilrecupero-”React-EU”. Azione IV.5, Dottorati su tematiche Green
Sapienza University of Rome
University of Milan, Department of Biosciences
National Research Council Co-found International Exchange Program CNR-Royal Society

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JAPAN
Prepared byMotoaki Seki, motoaki.seki@riken.jp, RIKEN CSRS
Masatomo Kobayashi, masatomo.kobayashi@riken.jp, RIKEN BRC
Shinya Hagihara, hagi@riken.jp, RIKEN CSRS
Masanori Okamoto, okamo@riken.jp, RIKEN CSRS
Yuki Nakamura, yuki.nakamura.yf@riken.jp, RIKEN CSRS
Satoshi Iuchi, satoshi.iuchi@riken.jp, RIKEN BRC

Please describe any new or updated experimental resources and/or software tools
available to Arabidopsis researchers that have been initiated or funded in your country in2023 or early 2024.
RIKEN Center for Sustainable Resource Science (CSRS) (http://www.csrs.riken.jp/en/)•
Platform for RIKEN Metabolomics (http://prime.psc.riken.jp/)•
RIKEN Arabidopsis Genome Encyclopedia (http://rarge-v2.psc.riken.jp/)
RIKEN BioResource Research Center (BRC) (https://epd.brc.riken.jp/en/)•
We have added the information of 85 mutant and transgenic lines of Arabidopsis to the Exp-Plant
Catalog (https://plant.rtc.riken.jp/resource/psi/psi_list2.html). Now 524 mutant and transgenic lines
deposited from Japanese scientists are on the Catalog.
•
We have released three callus cell lines established from suspension cell lines of Arabidopsis andgrape, since original suspension cell lines are not suitable for overseas transport (https://epd.brc.riken.jp/en/
archives/5762).
Kazusa DNA Research Institute (http://www.kazusa.or.jp/e/)- MassBase: a plant metabolome database (http://bit.ly/1Rlf9Dd)- Plant GARDEN Plant Genome And Resource Database ENtry (https://plantgarden.jp)- Kusaki DB: a database to assess existence and completeness of orthogroups in plant species (http://
pgdbjsnp.kazusa.or.jp/app/kusakidb) (https://hub.docker.com/r/ghelfi/kusakidb)
National Institute for Basic Biology (http://www.nibb.ac.jp)= ChaetoBase (Gene annotation database for Chaetoceros gracilis)(https://chaetoceros.nibb.ac.jp/)

Planned events for 2024 and 2025
- Mar. 17-19, 2024: 65th Annual Meeting of Japanese Society of Plant Physiologists. Kobe International
Conference Center, Kobe, Japan (https://jspp.org/annualmeeting/65/e_greeting.php).
- Jul. 9-12, 2024: EMBO｜COB Workshop “Plant Tropisms”. National Institute for Basic Biology, Okazaki,
Japan (https://meetings.embo.org/event/24-plant-tropisms).
- Sep. 13-16, 2024: 88th Annual Meeting of the Botanical Society of Japan. Utsunomiya University,
Utsunomiya, Japan (https://bsj88.org/en/en-meeting/).

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Selected Publications
Ngou, B.P.M., Wyler, M., Schmid, M.W., Kadota, Y., Shirasu, K. Evolutionary Trajectory of Pattern
Recognition Receptors in Plants. Nature Communications. (2024) 15: 308. https://doi.org/10.1038/s41467023-44408-3.
This research has advanced our understanding of the origins and evolution of plant immunity and has
enabled the rapid and accurate prediction of genes that function as immune receptors.
Isono K, Nakamura K, Hanada K, Shirai K, Ueki M, Tanaka K, Tsuchimatsu T, Iuchi S, Kobayashi M, Yotsui
I, Sakata Y, Taji T. LHT1/MAC7 contributes to proper alternative splicing under long-term heat stress andmediates variation in the heat tolerance of Arabidopsis. PNAS Nexus. (2023) 2(11):pgad348.
doi: 10.1093/pnasnexus/pgad348. PMID: 38024403; PMCID: PMC10644991.
Authors identified Arabidopsis LHT1/MAC7 that encodes a putative RNA helicase involved inmRNA splicing as a responsible gene for the variation in long-term heat tolerance between Ms-0 and Col-0
accessions.

Major Funding Sources
RIKEN and National Institute of Basic Biology are supported by MEXT.
Kazusa projects are supported by Chiba-Prefecture.
Grants-in-Aid for Science from MEXT, (http://www.jsps.go.jp/english/e-grants/)
CREST of Japan Science and Technology Corporation (http://bit.ly/22I8avZ)
ERATO of Japan Science and Technology Corporation (https://www.jst.go.jp/erato/en/index.html)
MIRAI Program of Japan Science and Technology Corporation (http://www.jst.go.jp/mirai/jp/about/index.
html)
Strategic International Cooperative Program (SICORP), JST-NSF Joint Research Project. (http://www.jst.
go.jp/inter/english/sicorp/index.html)“Impulsing Paradigm Change through Disruptive Technologies” (ImPACT) (http://www.jst.go.jp/impact/en/
outline. html)
MEXT “Cross-ministerial Strategic Innovation Promotion Program” (SIP) in 2014. (http://www.mext.go.jp/
english/ topics/1345957.htm)
PRESTO of Japan Science and Technology Corporation (https://www.jst.go.jp/kisoken/presto/en/index.html)
Moonshot Research and Development Program(https://www8.cao.go.jp/cstp/english/moonshot/top.html)
JST ACT-X(https://www.jst.go.jp/kisoken/act-x/index.html)
JST ASPIRE(https://www.jst.go.jp/aspire/en/)
JSY GteX(https://www.jst.go.jp/gtex/en/)

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NEW ZEALAND
Prepared by
Rowan Herridge, University of Otago (rowan.herridge@otago.ac.nz)

Planned events for 2024 and 2025
- Queenstown Research Week, 31st August-5 September 2024 (https://www.queenstownresearchweek.org/)- NZSPB Hybrid Hub Conference, Lincoln/Auckland/Palmerston North, 28-29th November, 2024 (contact
nick.albert@plantandfood.co.nz)

Selected Publications
Dong, Y.; Gupta, S.; Wargent, J.J.; Putterill, J.; Macknight, R.C.; Gechev, T.S.; Mueller-Roeber, B.; Dijkwel,
P.P. Comparative Transcriptomics of Multi-Stress Responses in Pachycladon cheesemanii and Arabidopsis
thaliana. Int. J. Mol. Sci. 2023, 24, 11323. https://doi.org/10.3390/ijms241411323
This article led by researchers at Massey University, with contributions from Otago and Aucklandshows how Arabidopsis can respond to stress and contrasts this with the stress-tolerant species P.
cheesemanii.
Kim, H., Kim, J., Choi, D. S., Kim, M. S., Deslandes, L., Jayaraman, J., & Sohn, K. H. (2024). Molecular basis
for the interference of the Arabidopsis WRKY54‐mediated immune response by two sequence‐unrelated
bacterial effectors. The Plant Journal, 118(3), 839-855.
This article led by researchers from Seoul National University and Plant and Food Research in New
Zealand identifies WRKY54 as a target of two bacterial effectors AvrRp4 and PopP2.

Major Funding Sources
Marsden Fund, Royal Society Te Aparangi (https://www.royalsociety.org.nz/what-we-do/funds-andopportunities/marsden)
MBIE Endeavor Fund (https://www.mbie.govt.nz/science-and-technology/science-and-innovation/fundinginformation-and-opportunities/investment-funds/endeavour-fund)

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NORWAY
Prepared byThorsten Hamann, Thorsten.hamann@ntnu.no, Norwegian University of Scienceand Technology

Please describe any new or updated experimental resources and/or software tools
available to Arabidopsis researchers that have been initiated or funded in your country in2023 or early 2024.
The national graduate school in Plant Biology (Photosyntech https://photosyntech.no/ ) is now fully active
and bringing together all stakeholders from across the plant science community.

Planned events for 2024 and 2025
- Norwegian Plant Biology conference organized in association with the National Norwegian PhD school in
Plant Biology, 20-22.3.2024 Oslo
- Fascination of Plants day 2024 and 2025 https://plantday18may.org organized by the
Norwegian University of Life Sciences.

Selected Publications
Structural evidence for MADS-box type I family expansion seen in new assemblies of Arabidopsis arenosa
and A. lyrata. Bramsiepe J, Krabberød AK, Bjerkan KN, Alling RM, Johannessen IM, Hornslien KS, Miller
JR, Brysting AK, Grini PE. Plant J. 2023; 116(3):942-961. doi: 10.1111/tpj.16401.
A multifaceted kinase axis regulates plant organ abscission through conserved signaling mechanisms.
Galindo-Trigo S, Khandare V, Roosjen M, Adams J, Wangler AM, Bayer M, Borst JW, Smakowska-Luzan E,
Butenko MA. Curr Biol. 2024; 34(13):3020-3030.e7. doi: 10.1016/j.cub.2024.05.057.
Adaptive protein evolution through length variation of short tandem repeats in Arabidopsis. Reinar WB,
Greulich A, Stø IM, Knutsen JB, Reitan T, Tørresen OK, Jentoft S, Butenko MA, Jakobsen KS. Sci Adv. 2023;
9(12):eadd6960. doi: 10.1126/sciadv.add6960.
Responsiveness to long days for flowering is reduced in Arabidopsis by yearly variation in
growing season temperatures. Kinmonth-Schultz H, Sønstebø JH, Croneberger AJ, Johnsen SS, Leder E,
Lewandowska-Sabat A, Imaizumi T, Rognli OA, Vinje H, Ward JK, Fjellheim S. Plant Cell Environ. 2023;
46(11):3337-3352. doi: 10.1111/pce.14632.

Major Funding Sources
Norwegian Research Council, forskningsradet.no
ERC, erc.eu

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POLAND
Prepared byRobert Malinowski, rmal@igr.poznan.pl, Institute of Plant Genetics Polish Academyof Sciences, Poznan, Poland

Selected Publications
Dluzewska, J., Dziegielewski, W., Szymanska-Lejman, M., Gazecka, M., Henderson, I.R., Higgins, J.D. and
Ziolkowski, P.A. (2023) MSH2 stimulates interfering and inhibits non-interfering crossovers in response to
genetic polymorphism. Nat Commun, 14, 6716.
Work provides the data that confirms central role of the MSH2 in a regulator of meiotic DSB repair in
Arabidopsis
Ochoa, J.C., Mukhopadhyay, S., Bieluszewski, T., Jędryczka, M., Malinowski, R. and Truman, W. (2023)
Natural variation in Arabidopsis responses to Plasmodiophora brassicae reveals an essential role for
Resistance to Plasmodiophora brasssicae 1 (RPB1). The Plant Journal, 116, 1421-1440.
The discovery of a single dominating resistance gene to clubroot disease in Arabidopsis thaliana.
Sarnowska, E., Kubala, S., Cwiek, P., Sacharowski, S., Oksinska, P., Steciuk, J., Zaborowska, M., Szurmak, J.M.,
Dubianski, R., Maassen, A., Stachowiak, M., Huettel, B., Ciesla, M., Nowicka, K., Rolicka, A.T., Alseekh, S.,
Bucior, E., Franzen, R., Skoneczna, A., Domagalska, M.A., Amar, S., Hajirezaei, M.-R., Siedlecki, J.A., Fernie,
A.R., Davis, S.J. and Sarnowski, T.J. (2023) A non-canonical function of Arabidopsis ERECTA proteins and arole of the SWI3B subunit of the SWI/SNF chromatin remodeling complex in gibberellin signaling. The Plant
Journal, 115, 788-802.
This work describes the role of SWI3B-containing SWI/SNF CRCs in gibberellin signaling

Major Funding Sources
National Science Centre Poland [https://www.ncn.gov.pl/en]

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PORTUGAL
Prepared by
Sílvia Vieira de Almeida Coimbra scoimbra@fc.up.pt University of Porto

Planned events for 2024 and 2025••

Iberian Plant Biology 2023. Braga Portugal 9-12 July
Youth Research Meeting (IJUP) 2023, in Porto, Portugal

Selected Publications
Figueiredo, R, Costa, M, Moreira, D, Moreira, M, Noble, J, Pereira, LG, Melo, P, Palanivelu, R, Coimbra,
S, Pereira, AM. 2024. JAGGER localization and function is dependent on GPI anchor addition. Plant
Reproduction DOI: 10.1007/s00497-024-00495-w
Different JAGGER proteins with deletions in predicted ω-site regions and GAS (GPI attachment
signal) domain, expected to compromise the addition of the GPI anchor, led to disruption of JAGGER
localization in the cell periphery. All JAGGER proteins with disrupted localization were also not able torescue the polytubey phenotype, pointing to the importance of GPI-anchor addition to in vivo function of
the JAGGER protein.
Moreira, D, Kaur, D, Pereira, AM, Held, MA, Showalter, AM, Coimbra, S. 2023. Type II arabinogalactans
initiated by hydroxyproline O-galactosyltransferases play important roles in pollen–pistil interactions. The
Plant Journal. DOI: 10.1111/tpj.16141
The present work demonstrates the functional importance of the carbohydrate moieties of AGPs inovule development and pollen–pistil interactions.
Figueiredo, R, Lopes, AL, Pereira, AM, Moreira, D, Silva, J, Ferreira, MJ, Pereira, LG, Coimbra, S. 2023.
The biology of arabinogalactan proteins in plant abiotic stress and reproduction. In: Geitmann A (ed)Plant Cell Walls – Research Milestones and Conceptual Insights. CRC Press, Taylor & Francis Group. DOI:
10.1201/9781003178309-16
In this review, we present an overview of the accumulated knowledge on AGP involvement in abiotic
stress tolerance and in plant reproduction, as these two physiological processes are essential for plant growthand seed yield, and consequently for sustainable food security.
Ferreira, MJ, Silva, J, Pinto, SC, Coimbra, S. 2023. I Choose you: Selecting accurate reference genes for
qPCR expression analysis in reproductive tissues in Arabidopsis thaliana. Biomolecules. DOI: 10.3390/
biom13030463
Our results showed that RCE1, SAC52 and TUA2 had the most stable expression in different flower
developmental stages while YLS8, HIS3.3 and ACT7 were the top-ranking reference genes for normalisationin mutant studies. Furthermore, we validated our results by analysing the expression pattern of genes
involved in reproduction and examining the expression of these genes in published mutant backgrounds.
Overall, we provided a pool of appropriate reference genes for expression studies in reproductive tissues of A.
thaliana.

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Lopes, AL, Moreira, D, Pereira, AM, Ferraz, R, Mendes, S, Pereira, LG, Colombo, L, Coimbra, S. 2023. AGPs
as molecular determinants of reproductive development. Annals of Botany. DOI: 10.1093/aob/mcad046
These findings reveal distinct AGP distribution patterns in different developmental mutants related
to the female reproductive unit in Arabidopsis. The value of the immunofluorescence labelling technique
is highlighted in this study as an invaluable tool to dissect the remodelling nature of the cell wall indevelopmental processes.

Major Funding Sources•
Fundação para a Ciência e Tecnologia (FCT) - https://www.fct.pt/•
Fundação “La Caixa” - https://fundacaolacaixa.pt/•
European funding – Marie Curie actions - https://marie-sklodowska-curie-actions.ec.europa.eu/•
Research Organizations such as LAQV Requimte (https://laqv.requimte.pt/), GreenUP (https://www.
fc.up.pt/GreenUPorto/pt/), CIBIO(https://cibio.up.pt/en/), GULBENKIAN (https://gulbenkian.pt/fundacao/
apresentacao/), ITQB (https://www.itqb.unl.pt/)

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SPAIN
Prepared byCristina Ferrandiz cferrandiz@ibmcp.upv.es Instituto de Biologia Molecular y
Celular de Plantas, CSIC-UPV www.ibmcp.upv.es/FerrandizLab

Planned events for 2024 and 2025•
6th International Symposium on Plant Apoplastic Diffusion Barriers (PADiBa) Girona, 02-05
September 2024•
EMBO Workshop “Cell death: friend or foe in animal and plant immunity” Sant Feliu de Guixols, 1115 November, 2024•
PlantAct Workshop, Madrid, April 2025. www.plant-act.org/es/blog•
Workshop “Plants under environmental stress: overcoming current climate changes. Baeza, 5-7
Noviembre, 2024.

Selected Publications
Sánchez-Vicente I, Albertos P, Sanz C, Wybouw B, De Rybel B, Begara-Morales JC, Chaki M, Mata-Pérez
C, Barroso JB, Lorenzo O. Reversible S-nitrosylation of bZIP67 by peroxiredoxin IIE activity and nitro-fatty
acids regulates the plant lipid profile. Cell Rep. 2024; 43(4):114091.
This work uncovers a new role of nitric oxide in controling seed lipid storage and the importance of
post-translational modification of transcription factors influenced by NO signaling.
Tremblay BJM, Santini CP, Cheng Y, Zhang X, Rosa S, Qüesta JI. Interplay between coding and non-coding
regulation drives the Arabidopsis seed-to-seedling transition. Nat Commun. 2024;15(1):1724.
A comprehensive study of different levels of regulation oftranscriptional events at the seed-to-seedling transition. Exciting resultscomposing a broad view of germination.
Martínez-Pérez M, Aparicio F, Arribas-Hernández L, Tankmar MD,
Rennie S, von Bülow S, Lindorff-Larsen K, Brodersen P, Pallas V. Plant
YTHDF proteins are direct effectors of antiviral immunity against an N6methyladenosine-containing RNA virus. EMBO J. 2023 42(18):e113378.
This elegant study provides new insights on the mechanism ofplant basal antiviral immunity based on demethylation of viral RNA.
•
Parra-Nunez P, Fernández-Jiménez N, Pachon-Penalba M,
Sanchez-Moran E, Pradillo M, Santos JL. Synthetically induced
Arabidopsis thaliana autotetraploids provide insights into the analysisof meiotic mutants with altered crossover frequency. New Phytol. 2024
241(1):197-208.
A clever strategy provides exciting new results to better
understand the meiosis and chromosome recombination in polyploids
made in Arabidopsis.

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63Perez-Garcia P, Pucciariello O, Sanchez-Corrionero A, Cabrera J, Del Barrio C, Del Pozo JC, Perales
M, Wabnik K, Moreno-Risueno MA. The cold-induced factor CBF3 mediates root stem cell activity,
regeneration, and developmental responses to cold. Plant Commun. 2023 Nov 13;4(6):100737.
A close view on the impact of environmental factors in stem cell behavior and responses made in
Arabidopsis roots exposed to cold.

Major Funding Sources
In Spain, Arabidopsis research is mainly funded by the State Research Agency (AEI) in competitive
calls launched every year (https://www.aei.gob.es/en/). In 2023, around 80 projects to individual laboratories
were granted, which is in line with previous years. Additional national calls and regional funding also support
other initiatives.
European funding for basic plant research is usually scarce, but several MSCA actions (IF, RISE,
or DN) have been awarded to Spanish fellows to work in Arabidopsis. In addition, ERC funding is alsofinancing grants in different schemes, i.e. AdG to Crisanto Gutiérrez (CBM), CoG to Clara SánchezRodriguez (CBGP), StG to Ivan Reyna-Llorens (CRAG) and Ainhoa Martínez-Medina (CSIC) or PoCG to
Ana Caño-Delgado (CRAG).

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SWEDEN
Prepared by
Maria E. Eriksson, maria.eriksson@umu.se, UPSC, Umeå University

Planned events for 2024 and 2025
- 30th Scandinavian Plant Physiology Society (SPPS) Conference, August 27-29, 2024, Copenhagen,Denmark
Plant Energy Management, Molecular Mechanisms and Signalling-August 26-30, 2024, Umeå, Sweden
14th Conference of the European Foundation for Plant Pathology
2nd -5thJune, 2025, Uppsala, Sweden

Selected Publications
Tran, H.C. et al. (2023) An mTRAN-mRNA interaction mediates mitochondrial translation initiation inplants. Science, 381 (6661) https://doi.1126/science.adg0995
Using Arabidopsis as a model system and characterization of mTRAN1 and mTRAN2, exclusively
found inside mitochondria and found essential for development/ growth. This work provides novel details
on translation initiation in specifically mitochondrial translation mechanisms that evolved from a common
bacterial ancestor.
Saarenpää, S. et al. (2023) Spatial metatranscriptomics resolves host-bacteria-fungi interactomes. Nature
Biotechnology, https://doi.org/10.1038/s41587-023-01979-2
This work offers advancement on understanding of multiple species interactions’ as they occur
using spatial metatranscriptomics of leaves from Arabidopsis grown outdoors. It shows tissue hotspots forinteractions of bacteria, fungi and Arabidopsis in in leaf tissues.
Hoffmann, G. et al. (2023) Cauliflower mosaic virus disease spectrum uncovers novel susceptibility factor
NCED9 in Arabidopsis thaliana. Journal of Experimental Botany 74 (15), https://doi.org/10.1093/jxb/erad204
Abscisic acid (ABA) is an important stress evoked plant hormone. This genome-wide association
study pinpoints variability in the 9-CIS-EPOXYCARTENOID DIOXYGENASE 9 (NCED9) locus as animportant susceptibility factor for Cauliflower mosaic virus (CaMV), as infection is nearly abolished in the
nced9 mutant. The importance of ABA homeostasis during CaMV infection was further underlined by theirfindings.
Derba-Maceluch, M. et al. (2023) Xylan glucuronic acid side chains fix suberin-like aliphatic compounds towood cell walls. New Phytologist 238 (1) https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.18712
By expressing fungus enzyme in wood as an enzymatic tool of wood composition, this work casts alight on hemicellulose composition and structure using Arabidopsis and Populus sp. tree cell walls as model
systems. They focus on xylan glucuronosylation, which affects the plant secondary cell wall properties, andprocessibility of wood going further.

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Zou, Y. et al., (2024) Thermoprotection by a cell membrane–localized metacaspase in a green alga Plant Cell
36 (3) https://doi.org/10.1093/plcell/koad289
The role of metacaspases (MCAs) in plants and algae are still not fully understood. This work adds
knowledge about their functions, important for future studies and applications in adaptation of plants tovariable temperatures.

Major Funding Sources
More general such as Human Frontiers https://www.hfsp.org/funding/hfsp-funding/research-grants,
EMBO https://www.embo.org/funding/,
ERC https://erc.europa.eu/,
EU https://www.mariecuriealumni.eu/news/european-funding-opportunities-10-websites-you-need-know
Nordic sources like Novo Nordisk Foundation https://novonordiskfonden.dk/en/grants/,
Nordforsk https://www.nordforsk.org/
Swedish governmental agencies and foundations such as;• The Swedish Research Council (VR); http://www.vr.se
VR supports researcher-initiated, basic research• The Swedish Foundation for Strategic Research; http://www.stratresearch.se
Supports strategic research in natural science, engineering and medicine• The Swedish Agency for Innovation Systems (VINNOVA); http://www.vinnova.se
Promotes sustainable growth by funding needs-driven research and the development of effective innovation
systems• The Swedish Research Council Formas; http://www.formas.se
Supports research (rather applied) and need-driven research in the areas Environment, Agricultural Sciences
and Spatial Planning• The Swedish Foundation for International Cooperation in Research and Higher Education (STINT) https://www.stint.se/en/our-programmes/
Supports research and teaching exchanges with a rather broad scope. For instance, it supports postdoctoral
stays outside the EU/EFTA (incl. the United Kingdom).

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SWITZERLAND
Prepared by
Reiko Akiyama, reiko.akiyama@ieu.uzh.ch, University of Zurich
Manuela Dahinden mdahinden@ethz.ch, Zurich-Basel Plant Science Center
Kentaro Shimizu, kentaro.shimizu@uzh.ch, University of Zurich

Please describe any new or updated experimental resources and/or software tools
available to Arabidopsis researchers that have been initiated or funded in your country in2023 or early 2024.
PlantServation, a method incorporating robust image-acquisition hardware and deep learning-based
software that extracts leaf color by detecting plant individuals automatically.
Akiyama R, Goto T, Tameshige T, Sugisaka J, Kuroki K, Sun J, Akita J, Hatakeyama M, Kudoh H, Kenta T,
Tonouchi A, Shimahara Y, Sese J, Kutsuna N, Shimizu-Inatsugi R, Shimizu KK (2023) Seasonal pigment
fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method
PlantServation. Nature Communications 14: 5792. https://doi.org/10.1038/s41467-023-41260-3
PlantServation_demo_set.zip https://zenodo.org/records/7321725
Planned events for 2024 and 2026 Conferences, symposiums• PSC Symposium 2024, 5 December, 2024 “Response to society and policy needs through plant, food andenergy sciences”, ETH Zürich
• SwissPLANT symposium 2025, 15 - 17 January 2025, Les Diablerets• Biology 25, early 2025, Zurich
Outreach activities• Outreach in general: https://www.plantsciences.uzh.ch/en/Outreach.html
Upcoming events
https://www.plantsciences.uzh.ch/en/rssnews.html

Selected Publications
Yew CL, Tsuchimatsu T, Shimizu-Inatsugi R, Yasuda S, Hatakeyama M, Kakui H, Ohta T, Suwabe K,
Watanabe M, Takayama S, Shimizu KK. (2023) Dominance in self-compatibility between subgenomesof allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility. Nature
Communications: 14: 7618. https://doi.org/10.1038/s41467-023-43275-2
Using the transgenic plants of the model polyploid species Arabidopsis kamchatica, the authors
showed the importance of dominance of self-incompatibility between two subgenomes in allopolyploidevolution.

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Yang H, Kim X, Sklenar J, Aubourg S, Sancho-Andrés G, Stahl E, Guillou MC, Gigli-Bisceglia N, Tran Van
Canh L, Bender KW, Stintzi A, Reymond P, Sanchez-Rodriguez C, Testerink C, Renou JP, Menke FLH,
Schaller A. Rhodes J and Zipfel C (2023) Subtilase-mediated biogenesis of the expanded family of SERINERICH ENDOGENOUS PEPTIDES. Nature Plants 9: 2085–2094. https://doi.org/10.1038/s41477-023-01583-x
In this paper, the authors defined the large divergent family of SCOOP secreted signaling peptides,
and characterized by cleavage by related subtilases.
Nawkar GM, Legris M, Goyal A, Schmid-Siegert E, Fleury J, Mucciolo A, De Bellis D, Trevisan M,
Schueler A, and Fankhauser C (2023). Air channels create a directional light signal to regulate hypocotyl
phototropism. Science 382, 935–940.
https://www.science.org/doi/10.1126/science.adh9384
This study reveals the importance of inter-cellular air channels for the establishment of light gradients
across a photosensitive tissue and a robust phototropic response.
Simonini S, Bencivenga S, Grossniklaus U (2024) A paternal signal induces endosperm proliferation upon
fertilization in Arabidopsis. Science 383 (6683): 646–653.
https://doi.org/10.1126/science.adj4996
This paper show that a sperm-derived signal induces the proliferation of a female gamete, the central
cell, precisely upon fertilization.
Moussu S, Lee HK, Haas KT, Broyart C, Rathgeb U, De Bellis D, Levasseur T, Schoenaers S, Fernandez GS,
Grossniklaus U, Bonnin E, Hosy E, Vissenberg K, Geldner N, Cathala B, Höfte H, Santiago J (2023) Plant cellwall patterning and expansion mediated by protein-peptide-polysaccharide interaction. Science 382: 719–
725. https://doi: 10.1126/science.adi4720
This paper reports a dual structural and signaling role for the complex of RAPID ALKALINIZATIONFACTOR 4 (RALF4) in pollen tube growth and in the assembly of complex extracellular polymers.
Highly cited researchers 2023 (members of the Plant Science Center):
Klaus Schläppi, Cross-field
Marcel van der Heijden, Microbiology
Cyril Zipfel, Plant and Animal Science

Major Funding Sources
Swiss National Science Foundation (SNSF) http://www.snf.ch/en/Pages/default.aspx• European Research Council (ERC), https://erc.europa.eu/• University Research Priority Program of Evolution in Action: From Genomes to Ecosystems (directors: Ueli
Grossniklaus, Kentaro K. Shimizu, University of Zurich), http://www.evolution.uzh.ch/en.html• University Research Priority Program of Global Change and Biodiversity (directors: Norman Backhaus,
Owen Petchey, Maria J. Santos, University of Zurich), https://www.gcb.uzh.ch/en.html

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UNITED KINGDOM
Prepared by
Geraint Parry, Arabidopsis Events UK arabidopsiseventsuk@gmail.com
Please describe any new or updated experimental resources and/or software tools
available to Arabidopsis researchers that have been initiated or funded in your country in2023 or early 2024.
Tuning Plant Promoters
Cai YM, Witham S, Patron NJ. Tuning Plant Promoters Using a Simple Split Luciferase Method to Assess
Transcription Factor-DNA Interactions. ACS Synth Biol. 2023 Nov 17;12(11):3482-3486. doi: 10.1021/
acssynbio.3c00094.
https://pubs.acs.org/doi/10.1021/acssynbio.3c00094?goto=supporting-info
Program for analysis of genomic repeats
Wlodzimierz P, Hong M, Henderson IR. TRASH: Tandem Repeat Annotation and Structural Hierarchy.
Bioinformatics. 2023 May 4;39(5):btad308. doi: 10.1093/bioinformatics/btad308.
Molecular cartography: a high-throughput quantitative in situ hybridization
Perico C, Zaidem M, Sedelnikova O, Bhattacharya S, Korfhage C, Langdale JA. Multiplexed in situ
hybridization reveals distinct lineage identities for major and minor vein initiation during maize leaf
development. Proc Natl Acad Sci U S A. 2024 Jul 9;121(28):e2402514121. doi: 10.1073/pnas.2402514121.

Planned events for 2024 and 2025
Empowering Research for Community Impact - OED Symposium 2024
10-11 September 2024, London, UK
https://www.sebiology.org/events/oed-symposium-2024.html
BSPP Plant Pathology Meeting
10-13 September 2024, Oxford, UK
https://bspp.bookingmanager.website/conference/ppath2024/
Advances in Nematology
5th December 2024, London UK
https://www.aab.org.uk/events/
Plant Biology Education: Creating a Vision for the Future
7-8 January 2025, Lancaster University, UK
https://cvent.me/LB9K1D
Genetics Society: Seed Plant SIG
8-9 April 2025, Durham, UK
https://genetics.org.uk/events/seed-plant/

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Selected Publications
Antoniou-Kourounioti RL, Meschichi A, Reeck
S, Berry S, Menon G, Zhao Y, Fozard J, Holmes
T, Zhao L, Wang H, Hartley M, Dean C, Rosa S,
Howard M. Integrating analog and digital modesof gene expression at Arabidopsis FLC. Elife. 2023
Jul 19;12:e79743. doi: 10.7554/eLife.79743.
Using quantitative fluorescent imagingof FLC mRNA and protein, together withmathematical modeling, we find that FLC
expression before cold is regulated by both
analog and digital modes. We observe a temporalseparation between the two modes, with analog
preceding digital. The analog mode can maintainintermediate expression levels at individual
FLC gene copies, before subsequent digitalsilencing, consistent with the copies switching
OFF stochastically and heritably without cold. This switch leads to a slow reduction in FLC expression at
the cell population level. These data present a new paradigm for gradual repression, elucidating how analog
transcriptional and digital epigenetic memory pathways can be integrated.
Brazel AJ, Fattorini R, McCarthy J, Franzen R, Rümpler F, Coupland G, Ó’Maoiléidigh DS. AGAMOUS
mediates timing of guard cell formation during gynoecium development. PLoS Genet. 2023 Oct
11;19(10):e1011000. doi: 10.1371/journal.pgen.1011000.
Here, we show that the MADS domain transcription factor AGAMOUS (AG) represses stomataldevelopment on the gynoecial valves, so that maturation of stomatal complexes coincides with fertilization.
We present evidence that this regulation by AG is mediated by direct transcriptional repression of a master
regulator of the stomatal lineage, MUTE, and show data that suggests this interaction is conserved among
several members of the Brassicaceae. This work extends our understanding of the mechanisms underlying
floral organ formation and provides a framework to decipher the mechanisms that control floral organ
photosynthesis.
Perrella G, Fasano C, Donald NA, Daddiego L, Fang W, Martignago D, Carr C, Conti L, Herzyk P,
Amtmann A. Histone Deacetylase Complex 1 and histone 1 epigenetically moderate stress responsiveness of
Arabidopsis thaliana seedlings. New Phytol. 2024 Jan;241(1):166-179. doi: 10.1111/nph.19165.
The combined findings of this study reveals a dual brake function of HDC1 via regulating both active
and repressive epigenetic marks on stress-inducible genes. This natural ‘anti-panic’ device offers a molecularleaver to tune stress responsiveness in plants.
Robson JK, Tidy AC, Thomas SG, Wilson ZA. Environmental regulation of male fertility is mediated throughArabidopsis transcription factors bHLH89, 91, and 10. J Exp Bot. 2024 doi: 10.1093/jxb/erad480.
bHLH89 and bHLH91 are shown to play a role in regulating fertility in response to light,
suggesting that they function in mitigating environmental variation to ensure fertility is maintained underenvironmental stress.

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Tavares H, Readshaw A, Kania U, de Jong M, Pasam RK, McCulloch H, Ward S, Shenhav L, Forsyth E, Leyser
O. Artificial selection reveals complex genetic architecture of shoot branching and its response to nitrate
supply in Arabidopsis. PLoS Genet. 2023 Aug 24;19(8):e1010863. doi: 10.1371/journal.pgen.1010863.
We use artificial selection under contrasting nitrate supplies to dissect the genetic architecture ofthis complex trait, where loci identified by association mapping failed to explain heritability estimates. We
found a consistent response to selection for high branching, with correlated responses in other traits suchas plasticity and flowering time. Genome-wide scans for selection and simulations suggest that at least tensof loci control this trait, with a distinct genetic architecture between low and high nitrate treatments. Whilesignals of selection could be detected in the populations selected for high branching on low nitrate, there
was very little overlap in the regions selected in three independent populations. Thus the regulatory network
controlling shoot branching can be tuned in different ways to give similar phenotypes.

Major Funding Sources
Biotechnology and Biological Sciences Research Council (BBSRC) http://www.bbsrc.ac.uk/
The Gatsby Charitable Foundation http://www.gatsby.org.uk/
European Research Council http://ec.europa.eu/research/era/index_en.htm
Natural Environment Research Council http://www.nerc.ac.uk
The Gates Foundation http://www.gatesfoundation.org/
The Leverhulme Trust: https://www.leverhulme.ac.uk/
The Newton Fund https://www.newtonfund.ac.uk/

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UNITED STATES and NORTH AMERICAN
ARABIDOPSIS STEERING COMMITTEE(NAASC)
Prepared by
Joanna Friesner arabidopsisconference@gmail.com, NAASC
Additional NAASC members contributing to this report:- Federica Brandizzi, Michigan State University, USA- Anna Stepanova, NC State University, USA- Keith Slotkin, Donald Danforth Plant Science Center & University of Missouri-Columbia, USA- Cris Argueso, Colorado State University, USA- Adrienne Roeder, Cornell University, USA- Dior Kelley, Iowa State University, USA- Gloria Muday, Wake Forest University, USA- Mentewab Ayalew, Spelman College, USA- Liang Song, University of British Columbia, CANADA- Mary Gehring, Whitehead Institute for Biomedical Research, MIT, USA- Sharon Kessler, Purdue University, USA-Zachary Nimchuk, University of North Carolina, Chapel Hill, USA
NAASC Early Career Scholars (term: Oct. 2023-Oct 2024)- Xiaohui Li, Purdue University, (Sept 2024- California Institute of Technology) , USA- Mingyuan Zhu, Duke University, USA- Adesola Tola, CANADA

Please describe any new or updated experimental resources and/or software tools
available to Arabidopsis researchers that have been initiated or funded in your country in2023 or early 2024.
Plant Membrane on a Chip: A new technique for creating supported lipid bilayers from plant
protoplast membranes has been published. This technique allows for the assay of transmembrane proteins
and other membrane constituents in a single lipid bilayer largely composed of the lipids from the plasma
membrane of the plant cell, on a slide so it is accessible for microscopy and experimentation.
Stuebler, M. Manzer, Z.A., Liu, H.-Y., Miller, J., Richter, A., Krishnan, S., Selivanovitch, E., Banuna, B.,
Jander, G., Reimhult, E., Zipfel, W.R., Roeder, A.H.K., Piñeros, M.A., and Daniel, S. (2024). Plant membraneon-a-chip: A platform for studying plant membrane proteins and lipids. ACS Applied Materials & Interfaces
16, 20092–20104. DOI: 10.1021/acsami.3c18562
PHYTOMap (plant hybridization-based targeted observation of gene expression map) is amultiplexed fluorescence in situ hybridization method that enables single-cell and spatial analysis of gene
expression in whole-mount plant tissue.
Nobori T, Oliva M, Lister R, Ecker JR. (2023). Multiplexed single-cell 3D spatial gene expression analysis inplant tissue using PHYTOMap. Nature Plants 9, 1026-1033. doi: 10.1038/s41477-023-01439-4.

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Single-cell proteomics on root cells.
Single-cell proteomics differentiates Arabidopsis root cell types
Montes C, Zhang J, Nolan TM, Walley JW (2024) Single-cell proteomics differentiates Arabidopsis root cell
types. New Phytologist DOI: 10.1111/nph.19923 PMID: 38923440
EXPOSE: Expansion microscopy in plant PrOtoplast SystEms (ExPOSE) increases the imaging
resolution of protoplasts by physical expansion of the fixed cells.
ExPOSE: A comprehensive toolkit to perform expansion microscopy in plant protoplast systems.
Cox Jr. K.L., Pardi S.A., O’Connor L., Klebanovych A., Huss D., Nusinow D.A., Meyers B.C., Czymmek K.J.
bioRxiv, DOI: 10.1101/2024.07.12.603300

Planned events for 2024 and 2025:
ICAR 2024
NAASC organized the 34th International Conference on Arabidopsis Research (ICAR2024) in San
Diego, California July 15-19, 2024. Attendance was 538 in person and 45 virtual participants. 249 of thein-person participants were early career (18 undergraduate students, 127 graduate students, 104 postdocs)
and 289 later career (83 pre-tenure or non-tenure track, 144 post-tenure faculty, and 62 others). NAASC
awarded 128 full conference registration fee waivers and/or travel grants, including 86 registration waivers
for students, postdoctoral scholars, and participants from non-US countries with severe financial barriers;
33 registration waivers and/or travel funds for invited plenary and keynote speaker, and 9 full-funding ISP(Inclusivity Scholar Program) awards for members of under-represented groups in US STEM.
The NAASC Early Career Scholars Subcommittee (ECSS) hosted an in-person workshop of “Career
Opportunities in Academia and Industry”, with seven panelists from academia, industry, and non-profit
sectors. There were more than 120 in-person attendees. The NAASC Inclusivity Scholars Subcommittee (ISS)
led by Cris Argueso, Ment Ayalew and Joanna Friesner again organized the ISP Cohort Program to support
members of under-represented groups in US STEM. These activities have been continuously supported by
the US National Science Foundation (NSF) since 2004. The goal of the ISP program is to develop a cohort ofawardees that may form lifelong supportive networks throughout their careers. ISP awardees met over Zoom
prior to ICAR and engaged in informal and social activities during ICAR organized by ISS leaders including
shared meals and career development and networking activities. New for ISP this year: NAASC invited 9
awardees funded by other groups to join several ISP activities, including two from Black in Plant Science UK
and seven from ROOT and SHOOT LEAPs RCN. The program was successful, and we hope that the crossprogram collaborations continue and expand in the future.
The conference kicked off with a touching Philip N. Benfey Memorial Symposium, which is available
on YouTube (https://www.youtube.com/watch?v=QCx1rPPg-Pw). The conference had a total of 47 sessions
including 10 plenary sessions with 37 talks: 4 keynote presentations (Dr. Keiko Sugimoto, Dr. Dolf Weijers,
Dr. Seung Yon (Sue) Rhee and Dr. José Dinneny) and 33 additional talks including the inaugural NAASC
Community Awards talks for “Excellence in Supporting Diversity, Equity, Inclusion & Belonging in the
Arabidopsis Community” and “Dissemination of Arabidopsis Knowledge”. The final NAASC community
award presentations were the “Philip N. Benfey Arabidopsis Community Lifetime Achievement Awards”(PACLA); awardee names are listed in the “Arabidopsis Community Awards” section below. Notably, ICAR
2024 featured ~300 additional talks in community organized sessions (9 workshops and 28 minisymposia)
which highlighted cutting edge science, career development, and translation from Arabidopsis to crops
and beyond. The community-organized minisymposia brought the most cutting-edge novel topics to theconference and highly diversified the speaker list. In addition, there were ~275 excellent posters presented ineach of two poster sessions.

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ICAR 2024 featured the 1st ICAR Science Art Show organized by NAASC member Cris Argueso with
about 15 beautiful and creative entries. The conference dinner was hosted at the Salk Institute with iconic
sunset views looking over the ocean. The Salk Institute provided sponsorship to lower ticket costs for the~325 attendees. The 5th Weed Stampede 5K Fun Run/Walk had about 50 participants. NAASC organized thefirst Weed Stampede during ICAR 2011-Madison, USA.
In 2024, the top 2 finishers (pictured) were ->#1 Isabella Burda, USA, time ~20:50#2 Jim Fouracre UK, time ~21:30
Notably, Isabella and Jim took a slight wrong turn and completed~5.3K vs the intended 5K!
The conference concluded with the Philip Benfey Arabidopsis
Community Lifetime Achievement (PACLA) Awards panel. Threeawardees joined in person (Dr. Joanne Chory, Dr. Joe Ecker, and Dr.
Chris Somerville) and two by Zoom (Dr. Jeff Dangl and Dr. Elliot
Meyerowitz). The awardees told stories of how they started working
with Arabidopsis, some of their biggest achievements, and theirideas for the future. The video is available on YouTube (https://www.
youtube.com/watch?v=mJLtihNI2M0).
Additional North American Arabidopsis Steering Committee activities• Professional development workshops & “My Plant Biology Story”• Arabidopsis Community website and Reddit group• Community awards• ISP (Inclusivity Scholars Program) cohort mentoring & other DEIB initiatives• Special issue of The Plant Cell focused on translational research from Arabidopsis to crops and otherorganisms• ICAR-focused research topic in Frontiers in Plant Science• Special Cell Biology Issue of Journal of Experimental Botany

Arabidopsis Community
The Arabidopsis Community has 444 members including 5 lifetime members and 35 membersthat were granted a membership waiver by request. Please join and become a member (https://www.
arabidopsiscommunity.org/join-ac). Membership is open to all Arabidopsis aficionados from all geographic
locations. The benefits of membership are:
• Early access to/discounts for NAASC-organized workshops and events• Ability to nominate/be nominated for Arabidopsis community awards• Access to the NAASC Arabidopsis Community (AC) Reddit board for sharing protocols, best practices,
gear & reagent advice, resources, solutions to common problems, conversations, & discussions.
• Free job postings and listings• 5% of member fees go to our Equity Fund to support of minoritized members & others with financial need
• Support of fundamental plant biology and DEIB initiatives in plant biology• Opportunities to contribute to community initiatives• (North American members only) Nomination, voting, and service eligibility for NAASC Board of Directors
and Early Career Scholar members

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Arabidopsis Community Awards
2024 marked the inaugural year of Arabidopsis Community awards.
Philip N. Benfey Arabidopsis Community Lifetime Achievement Awards (PACLA) for excellence inArabidopsis research, impactful and positive mentoring, and community service. This award has been named
after Philip Benfey who exhibited all these qualities. The inaugural PACLA awardees are:
Dr. Joanne Chory, Salk Institute for Biological Studies
Dr. Jeff Dangl, University of North Carolina, Chapel Hill
Dr. Joe Ecker, Salk Institute for Biological Studies
Dr. Elliot Meyerowitz, California Institute of Technology
Dr. Chris Somerville, University of California, Berkeley (emeritus) and Open Philanthropy LLC
NAASC Excellence in Supporting Diversity, Equity, Inclusion & Belonging in the Arabidopsis Community
Awards for excellence in mentoring, supporting, training, and/or advocating for others that are members ofunder-represented communities. The inaugural awardees are:Dr. Terri Long, North Carolina State University (NCSU)
Dr. Beronda Montgomery, Grinnell College
Dr. Román Ramos Báez, University of Chicago
Dr. Imani Madison, North Carolina State University (NCSU)
NAASC Dissemination of Arabidopsis Knowledge Awards for innovative teaching, outreach activities/
initiatives, and/or communication for Arabidopsis & plant biology. The inaugural awardees are:
Dr. Alison Crowe, University of Washington
Dr. Molly Edwards, Science in Real Life
George Redei Seed Stock Award for the researcher that donates the most seeds to the Arabidopsis Biological
Resource Center. The second annual awardee is:
Dr. Diana Wolf, University of Alaska, Fairbanks for donating 92 Arabidopsis kamchatica accessions in 2023.
Plant Method Exchange (PMEX) platform
The NAASC Early Career Scholars Subcommittee (ECSS) is working to build the Plant Method Exchange(PMEX) platform. The ECSS aims to build a platform in connection with the plant biology researchcommunity to efficiently share their protocols and easily discuss potential optimizations. We also expect sucha platform to promote the standardization of the common experimental set-up. We hope the future successof this platform, powered by NAASC, will be of a strong testimonial for the broader impacts of NAASC andincrease the inclusiveness of plant biology research. The PMEX website was created (https://plant-methods.
owlstown.net/). We are calling for submissions for more protocols and recruiting volunteers for review. We
hope to build a comprehensive, curated, and free open-access protocol sharing platform in five years.

Selected Publications:
NAASC HIGHLIGHT: Yaschenko, A.E., Alonso, J.M., and Stepanova, A.N. (2024). Arabidopsis as a modelfor translational research. Plant Cell, koae065. https://doi.org/10.1093/plcell/koae065.
A comprehensive review summarizing the multitude of ways findings in Arabidopsis have beentranslated to crop plants and beyond.

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Liu, P., Panda, K., Edwards, S.A., Swanson, R., Yi, H., Pandesha, P., Hung, Y.-H., Klaas, G., Ye, X., Collins,
M.V., et al. (2024). Transposase-assisted target-site integration for efficient plant genome engineering. Nature
631, 593–600. https://doi.org/10.1038/s41586-024-07613-8.
The Slotkin lab has engineered a transposable element into a toolkit for sequence-specific insertion of
DNA into plant genomes.
Olatunji D., Clark N.M., Kelley D.R. (2023) The class VIII myosin ATM1 is required for root apical meristem
function. Development 150, dev201762. doi: 10.1242/dev.201762.PMID: 37306290
This paper demonstrates that plant-specific myosins can control cell division, which ultimately
impacts organ size and stem cell proliferation.
Cao M., Platre M.P., Tsai H.H., Zhang L., Nobori T., Armengot L., Chen Y., He W., Brent L., Coll N.S.,
Ecker J.R., Geldner N., Busch W. (2024) Spatial IMA1 regulation restricts root iron acquisition on MAMP
perception. Nature. 625, 750-759. doi: 10.1038/s41586-023-06891-y.
This paper reveals a mechanism through which the plant navigates the tradeoff between making ironbioavailable for itself and also for pathogenic bacteria.
Nolan, T.M., Vukašinović, N., Hsu, C.-W., Zhang, J., Vanhoutte, I., Shahan, R., Taylor, I.W., Greenstreet, L.,
Heitz, M., Afanassiev, A., et al. (2023). Brassinosteroid gene regulatory networks at cellular resolution in the
Arabidopsis root. Science 379, eadf4721. https://doi.org/10.1126/science.adf4721.
Nolan used time-series single cell RNA-seq to show that the brassinosteroid signaling network
regulates the transition from proliferation to elongation in the Arabidopsis root cortex.

Major Funding Sources- US Arabidopsis Research is primarily supported by funding through the Federal Government via the
National Science Foundation (NSF): http://www.nsf.gov/- Additional support from:- US Department of Agriculture (USDA): http://www.usda.gov/- US Department of Energy (DOE): http://energy.gov/- National Institutes of Health (NIH): http://www.nih.gov/- National Aeronautics and Space Administration (NASA): http://www.nasa.gov/

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International Conferenceon Arabidopsis Research
ICAR2025
Ghent, Belgium
June 16th-20th 2025

http://www.icar2025.com/
Hosted at De Bijloke

6 Plenary Sessions
20+ Concurrents/Workshops
2x Poster Sessions
Social at Viernulvier Concertzall

Keynote Speakers
Paula Casati
Jiri Friml
Jane Parker#ICAR2025