DOI: 10.5061/dryad.3bk3j9krn
title: QTL mapping for seedling and adult plant resistance to stripe and leaf rust in two winter wheat populations

description: The two recombinant inbred lines (RIL) populations developed by crossing
 Almaly × Avocet S (206 RILs) and Almaly × Anza (162 RILs) were used to
 detect the novel genomic regions associated with adult plant resistance
 (APR) and seedling or all-stage resistance (ASR) to yellow rust (YR) and
 leaf rust (LR). Both the populations were evaluated for YR APR in two
 environments (2018 and 2019) and LR APR in three environments (2018, 2019,
 and 2020) in the Anza population and two environments (2018 and 2019) in
 the Avocet population; both the populations were phenotyped for one
 environment during 2020 for LR and YR ASR and genotyped using high
 throughput DArTseq technology. A set of 51 QTLs including 22 for YR APR,
 nine for LR APR, nine for YR ASR, and 11 for LR ASR were identified. Also,
 a set of 13 stable QTLs including nine QTLs (QYR-APR-2A.1, QYR-APR-2A.2,
 QYR-APR-4D.2, QYR-APR-1B, QYR-APR-2B.1, QYR-APR-2B.2, QYR-APR-3D,
 QYR-APR-4D.1, and QYR-APR-4D.2) for YR APR and four QTLs (QLR-APR-4A,
 QLR-APR-2B, QLR-APR-3B, and QLR-APR-5A.2) for LR APR were identified. In
 silico analysis revealed that the key putative candidate genes such as
 Cytochrome P450, Protein kinase-like domain superfamily, Zinc-binding
 ribosomal protein, SANT/Myb domain, WRKY transcription factor,
 Nucleotide-sugar transporter, and NAC domain superfamily were in
 the QTL regions and involved in the regulation of host response towards
 the pathogen infection. The stable QTLs identified in this study are
 useful for developing rust-resistant varieties through marker-assisted
 selection (MAS).
description: Phenotypic
 dataset Seedling resistance in
 greenhouse The<em> P. striiformis</em> races
 were differentiated in 2020  using a set of 12 wheat lines developed in
 the Avocet wheat background and on nine supplemental wheat differentials
 using a method developed by Johnson et al. 1972. Determination of the type
 of plant reaction was carried out twice within 14–20 days after infection
 according to the Gassner and Straib accounting scale (Gassner and Straib,
 1932). At the same time, reactions of 0, 1, and 2 points were assigned to
 the resistant type R (Resistant), and 3 and 4 points were assigned to the
 susceptible type S (Susceptible). The <em>P. triticina</em>
 races were also differentiated during 2020 using 20 near-isogenic lines
 (NILs) developed in Thatcher background each carrying one of the
 LR-resistant genes. (Kolmer et al., 2014; Schachtel et al., 2012; Kolmer
 and Ordonez, 2007). The virulence of the phenotypes was determined on
 these 20 differential lines and encoded with 0 and 1 for avirulence and
 virulence, respectively (Kolmer and Ordonez, 2007; Long and Kolmer, 1989).
 The Virulence Analysis Tools (Schachtel et al., 2012) was used for the
 nomenclature of<em> P. triticina</em> races. The type of
 response to leaf rust was determined twice within 14-20 days after
 infection according to the scale of Mains and Jackson (1926). Reactions of
 0, 1, and 2 points were assigned to the resistant type R (Resistant), and
 3 and 4 points were assigned to the susceptible type S
 (Susceptible). The seedlings of the RIL population from Almaly
 × Avocet S cross along with the parents were inoculated with two races
 of<em> P. striiformis</em> i.e., 108E187 (Pst_1) and 110E191
 (Pst_2) and two races of <em>P. triticina</em> i.e., MLTTH and
 TLTTR to determine the race-specific resistance. Similarly, the RIL
 population from Almaly × Anza cross along with parents were inoculated
 with two races of <em>P. striiformis </em>i.e., 108E187
 (Pst_1) and 101E191 (Pst_3) and four races of <em>P.
 triticina</em> i.e., THTTQ, TCTTR, TCPTQ, and THTTR. The plants were
 infected with spores at 3-leaf stage and humid chamber was created for 24
 hours. The seedling infection type of RIL was scored using the same
 approach as for rases differentiation. 
 Phenotyping for Adult Plant
 Resistance in Field  The field phenotyping for YR and LR APR was done
 during 2018 and 2019 for both the populations and an additional year
 during 2020 for LR APR for the Anza population at Kazakh Research
 Institute of Agriculture and Crop Production (KazNIIZiR), Almalybak.
 Pathogen racial mixtures from the local population were used to inoculate
 the mapping populations. The method of Roelfs et al. (1992) was followed
 for spore sampling, storage, and propagation. The pathogen was propagated
 in a greenhouse on the susceptible wheat variety, Morocco. The
 experimental wheat material was inoculated with a mixture of spores and
 talc in the ratio of 1:100 by spraying with an aqueous suspension of
 spores with 0.001% Tween-80 at a stem elongation stages (Z21-32). After
 infection, the plots were wrapped with plastic cover for 16-18 hours to
 create high humidity. After the manifestation of diseases on
 susceptible control varieties, an assessment (2–3 times) of rust
 resistance was carried out. Leaf and yellow rust resistance of wheat
 accessions was evaluated using the modified Cobb
 scale (Peterson et al., 1948; McIntosh et al., 1995). 
  The scoring was based both on disease severity
 (proportion of leaf area infected) and on the plant response to infection
 (reaction type). Plant responses were recorded as resistant (R),
 moderately resistant (MR), moderately susceptible (MS), and susceptible
 (S) reactions. Genotypic dataset
 The genomic DNA was extracted from parents and each RIL from both
 populations following the modified CTAB
 (cetyltrimethylammonium bromide) method (Dreisigacker et al., 2012). The DArTseq technology was used for
 genotyping of both the RILs in Genetic
 Analysis and Service for Agriculture (SAGA) lab based in Mexico (Edet et al., 2018).
 Briefly, the sequencing of
 mapping populations was carried out at
 192-plexing on Illumina HiSeq2500 with 1 × 77-bp reads.
 Allele calls for
 SNPs were generated through proprietary analytical pipeline developed by
 DArT P/L (Sansaloni et
 al., 2011). Further, genetic locations of the SNPs were
 identified by using 100K consensus map
 given by SAGA (Sansaloni
 et al. unpublished).   The markers
 were filtered and removed the monomorphic markers, markers with
 &gt;30% missing data, high heterozygosity percentage (&gt;30%),
 low allele frequency (&lt;5%) using MS Excel. The BIN functionality in
 IciMapping 4.2 QTL software was used to remove redundant markers. A
 filtered set of 1293 and 1127 high-quality SNPs were finally used for QTL
 analysis in Anza and Avocet
 populations.
description: This README file was generated on 2023-11-10 by Nagenahalli Dharmegowda
 Rathan. GENERAL INFORMATION 1\. Title of Dataset: QTL mapping for seedling
 and adult plant resistance to stripe and leaf rust in two winter wheat
 populations 2\. Author Information A. Principal Investigator Contact
 Information Name: Alma Kokhmetova Institution: Institute of Plant Biology
 and Biotechnology, Kazakhstan Email: gen\_kalma@mail.ru B. Other
 Corresponding authors Name: Nagenahalli Dharmegowda Rathan Institution:
 Coverta Agriscience, Hyderabad, Telangana, India Email:
 rathanndnagl27@gmailcom Name: Deepmala Sehgal Institution: Syngenta,
 Jealott’s Hill International Research Centre, Bracknell, United Kingdom
 Email: deepmala.sehgal@syngenta.com Name: Gopalareddy Krishnappa
 Institution: ICAR-Sugarcane Breeding Institute, Coimbatore, India Email:
 gopalgpb@gmail.com 3\. Date of data collection \(single date\, range\,
 approximate date\): 2018\-2020 4\. Geographic location of data collection:
 Kazakh Research Institute of Agriculture and Crop Production
 \(KazNIIZiR\)\, Almalybak \(43°13′09″N and 76°36′17″E\) and All\-Russian
 Institute of Plant Protection \(ARIPP\)\, St Petersburg\, Russia
 \(59°73′73″N\, 30°42′47″E\) 5\. Information about funding sources that
 supported the collection of the data: Science Committee of the Ministry of
 Science and Higher Education of the Republic of Kazakhstan \(grant no\.
 AP09258991 and grant no\. BR18574099\, the task 02\)\. SHARING/ACCESS
 INFORMATION 1\. Licenses/restrictions placed on the data: n/a 2\. Links to
 publications that cite or use the data: Kokhmetova A, Rathan ND, Sehgal D,
 Malysheva A, Kumarbayeva M, Nurzhuma M, Bolatbekova A, Krishnappa G,
 Gultyaeva E, Kokhmetova A, Keishilov Z and Bakhytuly K (2023), QTL mapping
 for seedling and adult plant resistance to stripe and leaf rust in two
 winter wheat populations. Front. Genet. 14:1265859. doi:
 10.3389/fgene.2023.1265859 3\. Links to other publicly accessible
 locations of the data: None 4\. Links/relationships to ancillary data
 sets: None 5\. Was data derived from another source? No A. If yes, list
 source(s): NA 6\. Recommended citation for this dataset: Kokhmetova A,
 Rathan ND, Sehgal D, Malysheva A, Kumarbayeva M, Nurzhuma M, Bolatbekova
 A, Krishnappa G, Gultyaeva E, Kokhmetova A, Keishilov Z and Bakhytuly K
 (2023. Data from: QTL mapping for seedling and adult plant resistance to
 stripe and leaf rust in two winter wheat populations. Dryad Digital
 Repository. https://doi.org/10.5061/dryad.3bk3j9krn. DATA & FILE
 OVERVIEW 1\. File List: A) Phenotypic\_data B) Genotypic\_data 2\.
 Relationship between files\, if important: The same RILs were phenotyped
 for wheat rusts and also genotyped with DARTSeq technology to use in QTL
 mapping\. 3\. Additional related data collected that was not included in
 the current data package: None 4\. Are there multiple versions of the
 dataset? No A. If yes, name of file(s) that was updated: NA i. Why was the
 file updated? NA ii. When was the file updated? NA
 #########################################################################
 DATA-SPECIFIC INFORMATION FOR: Phenotypic\_data 1\. Number of variables:
 11 for Anza population and 8 for Avocet population 2\. Number of
 cases/rows: 164 for Anza population and 208 for Avocet population 3\.
 Variable List: * Rust races evaluated: * Anza Population (11 variables):
 Leaf Rust seedling resistance (Races: THTTQ, TCTTR, TCPTQ, THTTR), Leaf
 Rust adult plant resistance (Year: 2018, 2019, 2020), Yellow Rust seedling
 resistance (Races: Pst1, Pst3), Yellow Rust adult plant resistance (Year:
 2018, 2019) * Avocet Population (8 variables): Leaf Rust seedling
 resistance (Races: MLTTH, TLTTR), Leaf Rust adult plant resistance (Year:
 2018, 2019), Yellow Rust seedling resistance (Races: Pst1, Pst2), Yellow
 Rust adult plant resistance (Year: 2018, 2019) * Number of Recombinant
 Inbred Lines (RILs): 164 in Anza poulation and 208 from Avocet population
 * Geographic location of data collection: * Yellow and Leaf Rust adult
 plant resistance: Kazakh Research Institute of Agriculture and Crop
 Production (KazNIIZiR), Almalybak (43°13′09″N and 76°36′17″E) * Yellow and
 Leaf Rust seedling resistance: All-Russian Institute of Plant Protection
 (ARIPP), St Petersburg, Russia (59°73′73″N, 30°42′47″E) 4\. Missing data
 codes: None 5\. Specialized formats or other abbreviations used: None
 #########################################################################
 DATA-SPECIFIC INFORMATION FOR: Genotypic\_data 1\. Number of variables:
 168 for Anza population and 212 for Avocet population 2\. Number of
 cases/rows: 1293 for Anza population and 1127 for Avocet population 3\.
 Variable List: * rs#: Marker name * alleles: Allele calls for each marker
 * Sequence: Sequence information of each marker *
 Chrom\_Wheat\_ConsensusMap\_version\_4: Chromosome location of each marker
 from Chrom\\\_Wheat\\\_ConsensusMap\\\_version\\\_4 * Rest of the
 variables: First two are parents and the rest are RILs. 4\. Missing data
 codes: NN 5\. Specialized formats or other abbreviations used:
 A\-Adinine\, T\-Thymine\, G\-Guanine\, C\-Cytosine
 #########################################################################