# Genomic selection programs for yield stability in pea

Anthony Klein, Vincent Richer, J.F. Herbommez, P. Declerck, M. Floriot, Jean-Philippe Pichon, H. Duborjal, M. Leveugle, Emilie Vieille, Karen Boucherot, et al.

► To cite this version:

Anthony Klein, Vincent Richer, J.F. Herbommez, P. Declerck, M. Floriot, et al. Genomic selection programs for yield stability in pea. 4. Annual Meeting PeaMUST, Nov 2016, Dijon, France. 1 p. hal-01603996

HAL Id: hal-01603996

https://hal.science/hal-01603996

Submitted on 5 Jun 2020

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PeaMUST

KLEIN A¹, RICHER V¹, HERBOMMEZ J-F², DECLERCK P³, FLORIOT M⁴, PICHON J-P⁵, DUBORJAL H⁵, LEVEUGLE M⁵, VIEILLE E¹, BOUCHEROT K¹, JACQUIN F¹, HOUTIN H¹, BLANC N⁶, VALDRINI J-M⁷, WALCZAK P⁸, BLERIOT O⁹, HANOCQ E⁹, CHASSIN A¹⁰, BATAILLON P¹¹, BURSTIN J¹*

1 INRA, UMR1347 AGROÉCOLOGIE, BP86510, 21065 DIJON CEDEX, FRANCE

2 KWS MOMONT, 7 RUE MARTINVAL, 59246 MONS EN PEVELE, FRANCE

3 RAGT 2N, ROUTE D'EPINCY, 28150 LOUVILLE LA CHENARD, FRANCE

4 AGRI OBTENTIONS, FERME DE GAUVILLIERS, 78660 ORSONVILLE, FRANCE

5 BIOGEMMA, ROUTE D'ENNEZAT, CS90126, 63720 CHAPPES, FRANCE

6 INRA, UE0115 DOMAINE EXPÉRIMENTAL D'ÉPOISSES, 21110 BRETENIERE, FRANCE

* Corresponding author: judith.burstin@inra.fr

7 INRA, UE0787 DOMAINE EXPÉRIMENTAL DE LA MOTTE AU VICOMTE, BP35327, 35653 LE RHEU CEDEX, FRANCE

8 INRA, UE1373 FOURRAGES ENVIRONNEMENT RUMINANTS LUSIGNAN, CS80006, 86600 LUSIGNAN, FRANCE

9 INRA, UE0972 GRANDES CULTURES INNOVATION ENVIRONNEMENT - PICARDIE, 2 CHAUSSÉE BRUNEHAUT - ESTRÉES-MONS, BP50136, 80203 PERONNE CEDEX, FRANCE

10 INRA, UE1375 PHÉNOTYPAGE AU CHAMP DES CÉRÉALES, 5 CHEMIN DE BEAULIEU, 63039 CLERMONT-FERRAND CEDEX, FRANCE

11 INRA, UE0802 DOMAINE EXPÉRIMENTAL D'AUZEVILLE, 24 CHEMIN DE BORDE-ROUGE, CS 52627, 31326 CASTANET-TOLOSAN CEDEX

Moment
LA FORCE FERTILE

RAGT
2n

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biogemma

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Genomic selection is a breeding method that uses increasingly abundant genomic information and statistical modelling to select superior genotypes based on genomic estimated breeding values (GEBV). The aims of the PeaMUST work-package 1 are : 1- to build a genomic selection prediction equation for yield stability in low-input cropping systems, 2- to implement a genomic selection program and, 3- to evaluate the genetic progress obtained after one and two genomic selection cycles. A classical GEBV breeding scheme was defined.

## Training population phenotyping

<figure><img src="image_5.png" /><figcaption>Yield dynamic stability of winter pea population in 2016</figcaption></figure>

A spring dry pea and a conventional winter pea population were phenotyped in multi-site field yield trial networks between 2013 and 2016. The DIAGVAR method was used to model G x E interactions and evaluate the impact of environmental covariates on yield stability.

## Exome capture resequencing

Training populations were genotyped using exome capture resequencing. 746k and 1.2 M SNPs were discovered in the spring and the conventional winter pea populations, respectively.

<figure><img src="image_6.png" /><figcaption>Genetic diversity in spring pea training population</figcaption></figure>

## GEBV prediction equation

The GBLUP statistical method was selected to develop the GEBV prediction equation. 9 traits were retained for prediction based on their prediction accuracies (Q²) and importance in the breeding scheme.

<figure><img src="image_7.png" /><figcaption>Prediction accuracies (Q²) in spring pea training population for 7 traits - 16 environments 2013-2014-2015 - 300 genotypes</figcaption></figure>

## GEBV prediction in breeding population

Genomic estimated breeding values have been computed for the 1262 individuals of the spring pea breeding population. 20 lines were selected based on GEBV as potential breeders for next generation in 2017.

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<table><thead><tr><th>Correlations</th><th>5kmk_GBLUP</th></tr></thead><tbody><tr><td>Seed weight observed vs predicted</td><td>0.46</td></tr><tr><td>Thousand Seed Weight observed vs predicted</td><td>0.31</td></tr><tr><td>Flowering date observed vs predicted</td><td>0.53</td></tr><tr><td>Duration of Flowering observed vs predicted</td><td>0.20</td></tr><tr><td>Height difference observed vs predicted</td><td>0.52</td></tr></tbody></table>

Genomic selection programs are currently developed in spring pea, conventional winter pea and photoperiodic winter pea. Implementation in spring pea has provided the first GEBV equation and a selection index built from 9 important traits. Based on the GEBV, the superior genotypes were selected as progenitors for the second generation of genomic selection. They will be evaluated under field conditions in 2017-18 to measure the genetic gain and the breeding method efficiency.

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