# Genetic architecture of leaf specialized metabolites in sessile oak (Quercus petraea)

Domitille Coq-Etchegaray, Stéphane Bernillon, Grégoire Le Provost, Antoine Kremer, Alexis Ducousso, Benjamin Brachi, Céline Lalanne, Fabrice Bonne, Annick Moing, Christophe Plomion

► To cite this version:

Domitille Coq-Etchegaray, Stéphane Bernillon, Grégoire Le Provost, Antoine Kremer, Alexis Ducousso, et al.. Genetic architecture of leaf specialized metabolites in sessile oak (Quercus petraea). Congress of the European Society for Evolutionary Biology (ESEB), Lukáš Kratochvíl, Aug 2019, Prague (Czech Republic), Czech Republic. **hal-04144342**

HAL Id: hal-04144342

https://hal.inrae.fr/hal-04144342

Submitted on 28 Jun 2023

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# Genetic architecture of leaf specialized metabolites in sessile oak (Quercus petraea)

Domitille Coq--Etchegaray, Stéphane Bernillon, Grégoire Le-Provost, Antoine Kremer, Alexis Ducousso, Céline Lalanne, Fabrice Bonne, Annick Moing, Christophe Plomion, Benjamin Brachi

<figure><img src="image_2.png" /></figure>

domitille.coq-etchegaray@inrae.fr

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@dcoqetchegaray

01/09/2022
# Sessile oak (Quercus petraea) and specialized metabolites

* Dominant tree species in Europe

* 15% of French forests

* Foundation species & associated with a rich insect community

* Influenced by specialized metabolites produced by oaks?

<figure><img src="image_4.png" /></figure>
# Sessile oak (Quercus petraea) and specialized metabolites

* Dominant tree species in Europe

* 15% of French forests

* Foundation species & associated with a rich insect community

* Influenced by specialized metabolites produced by oaks?

<figure><img src="image_5.png" /></figure>
* Dominant tree species in Europe

* 15% of French forests

* Foundation species & associated with a rich insect community

* Influenced by specialized metabolites produced by oaks?

* Leaf metabolites in oaks:

* Impact leaf herbivory (ex: Bertić et al. 2021)

* Resistance to abiotic stresses (ex: Aranda et al. 2020)

<figure><img src="image_6.png" /></figure>

Source: Valdés Correcher, E. (2020). Drivers of insect herbivory in Pedunculate oak (Quercus robur) from tree to biogeographical scale. 201.

<figure><img src="image_7.png" /></figure>
# Genetic basis of leaf specialized metabolites within sessile oaks

1

Is there variation for specialized metabolites among and/or within oak populations?

2

What proportion of the variation in leaf specialized metabolites is explained by genetic variation?

3

Is the variation of specialized metabolites locally adaptive? In what proportion?
# Oak leaves sampling, metabolomics & genomics dataset

9 provenances in a
common garden

<figure><img src="image_8.png" /></figure>

225 trees (25x9)

<figure><img src="image_9.png" /></figure>

<figure><img src="image_10.png" /></figure>

<figure><img src="image_11.png" /></figure>

0

5

10

Longitude

56

Edinburgh

52

United Kingdom

48

44

Latitude
# Oak leaves sampling, metabolomics & genomics dataset

<figure><img src="image_12.png" /></figure>

9 provenances in a
common garden

<figure><img src="image_13.png" /></figure>

225 trees (25x9)

<figure><img src="image_14.png" /></figure>

**Whole genome low depth sequencing (~10X)**
~1,400,000 SNPs

Illumina Paired-end
150 bp

<figure><img src="image_15.png" /></figure>
# Oak leaves sampling, metabolomics & genomics dataset

9 provenances in a
common garden

<figure><img src="image_16.png" /></figure>

225 trees (25x9)

<figure><img src="image_17.png" /></figure>

**Whole genome low depth sequencing (~10X)**
~1,400,000 SNPs

Illumina Paired-end
150 bp

**High throughput untargeted LC-MS**
219 molecules

10 min gradient
(QTOF)

<figure><img src="image_18.png" /></figure>

<figure><img src="image_19.png" /></figure>
350K SNPs capture weak population structure

<figure><img src="image_20.png" /></figure>

Average pairwise FST: 0.008
Leaf specialized metabolites profile depends on branch height

<figure><img src="image_21.png" /></figure>

Variation within individuals, likely influenced
by exposition to sunlight.
Nearly no phenotypic differentiation between provenances

<figure><img src="image_22.png" /></figure>

No differentiation between provenances at
the leaf metabolome scale
Nearly no phenotypic differentiation between provenances

<figure><img src="image_23.png" /></figure>

No differentiation between provenances at
the leaf metabolome scale

<figure><img src="image_24.png" /></figure>

Variation within provenances at the
molecule scale for the majority of molecules
Nearly no phenotypic differentiation between provenances

<figure><img src="image_25.png" /></figure>

No differentiation between provenances at
the leaf metabolome scale

<figure><img src="image_26.png" /></figure>

Variation within provenances at the
molecule scale for the majority of molecules
Nearly no phenotypic differentiation between provenances

<figure><img src="image_27.png" /></figure>

No differentiation between provenances at
the leaf metabolome scale

<figure><img src="image_28.png" /></figure>

Variation within provenances at the
molecule scale for the majority of molecules
Specialized metabolites variation is largely genetically determined

<figure><img src="image_29.png" /></figure>

Genome-wide efficient mixed-model association

Univariate Linear Mixed Model

(GEMMA)

Proportion of specialized metabolites variance
explained by the genetic similarity among trees

(kinship matrix)

50% of molecules have more than 70% of
their variation explained by the genetic
variation
# Genome wide association of specialized metabolites

<figure><img src="image_30.png" /></figure>

One major locus associated with the variation of the molecule

serine carboxypeptidase-like clade I

Chromosomes
# Genome wide association of specialized metabolites

23 molecule variations associated with one or two loci

<figure><img src="image_31.png" /></figure>
<figure><img src="image_32.png" /></figure>

The genotypes for genetic markers associated with molecule variations are in the 9 provenances
Associated markers are not differentiated among provenances

<figure><img src="image_33.png" /></figure>

The genotypes for genetic markers
associated with molecule variations are in
the 9 provenances

<figure><img src="image_34.png" /></figure>

Molecules with heritable variation have low
F<sub>ST</sub> values
Conclusion-No evidence of local adaptation for measured molecules

Weak phenotypic differentiation
among provenances

Intra-individual variation of
specialized metabolites

Most of the variation within
oak provenances

Specialized metabolites variation
is heritable

Oligogenic architecture of
the variation

Polymorphisms within the
9 provenances

Most molecules measured are not locally adaptive

**Hypothesis:** Maintenance of variation within oak provenances
(balanced selection)
Genetic marker development at loci associated with specialized metabolites
~screening natural oak populations

Is the variation of specialized metabolites correlated with tree growth ?
(fitness)

<figure><img src="image_35.png" /></figure>

<figure><img src="image_36.png" /></figure>

<figure><img src="image_37.png" /></figure>
**Supervisors**

Benjamin Brachi
Christophe Plomion

<figure><img src="image_38.png" /></figure>

Stéphane Bernillon,
Grégoire Le-Provost,
Antoine Kremer,
Alexis Ducousso,
Céline Lalanne,
Fabrice Bonne,
Annick Moing

**Hypothesis:** Maintenance of variation within oak provenances
(balanced selection)

<figure><img src="image_39.png" /></figure>

INRAE

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biogeco

<figure><img src="image_41.png" /></figure>

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clermont

auvergne

métropole

Université

de BORDEAUX

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<figure><img src="image_44.png" /></figure>

METABOHUB

AgreenSkills

Pathways for inventive researchers

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BORDEAUX
METABOLOME