Section: Genomics
Topic: Genetics/Genomics, Plant biology

SNP discovery by exome capture and resequencing in a pea genetic resource collection

Aubert, Grégoire1  ; Kreplak, Jonathan1 ; Leveugle, Magalie2, 3; Duborjal, Hervé2, 3; Klein, Anthony1; Boucherot, Karen1; Vieille, Emilie1; Chabert-Martinello, Marianne1; Cruaud, Corinne4 ; Bourion, Virginie1 ; Lejeune-Hénaut, Isabelle5 ; Pilet-Nayel, Marie-Laure6 ; Bouchenak-Khelladi, Yanis1 ; Francillonne, Nicolas7, 8 ; Tayeh, Nadim1 ; Pichon, Jean-Philippe2, 3; Rivière, Nathalie2, 9; Burstin, Judith1 
1 Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
2 Biogemma, F-63720 Chappes, France
3 Present address: Limagrain F-63720 Chappes, France
4 Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France
5 BioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203, Estrées-Mons, France
6 IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
7 Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France
8 Université Paris-Saclay, INRAE, BioinfOmics, Plant bioinformatics facility, 78026, Versailles, France
9 Present address: HM-Clause 49800 Loire-Authion

Corresponding author(s): Aubert, Grégoire (Gregoire.Aubert@inrae.fr)

10.24072/pcjournal.332 - Peer Community Journal, Volume 3 (2023), article no. e100.

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Pea is a major pulse crop in temperate regions and a model plant in genetics. Large genetic marker resources are needed to assess the genetic diversity in the species genepool and to provide selection tools for breeders. In this study, we used second-generation sequencing to perform an exome-capture protocol using a diverse pea germplasm collection, and produced a resource of over 2 million Single Nucleotide Polymorphisms. This dataset was then used to characterize the genetic diversity present in the panel and compute phylogenetic and structure analyses. The development of this resource paves the way for Genome-wide association studies and the development of powerful genotyping tools.

Published online:
DOI: 10.24072/pcjournal.332
Type: Research article
Mots-clés : Pea; Single Nucleotide Polymorphism; Exome capture; diversity

Aubert, Grégoire 1; Kreplak, Jonathan 1; Leveugle, Magalie 2, 3; Duborjal, Hervé 2, 3; Klein, Anthony 1; Boucherot, Karen 1; Vieille, Emilie 1; Chabert-Martinello, Marianne 1; Cruaud, Corinne 4; Bourion, Virginie 1; Lejeune-Hénaut, Isabelle 5; Pilet-Nayel, Marie-Laure 6; Bouchenak-Khelladi, Yanis 1; Francillonne, Nicolas 7, 8; Tayeh, Nadim 1; Pichon, Jean-Philippe 2, 3; Rivière, Nathalie 2, 9; Burstin, Judith 1

1 Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
2 Biogemma, F-63720 Chappes, France
3 Present address: Limagrain F-63720 Chappes, France
4 Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France
5 BioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203, Estrées-Mons, France
6 IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
7 Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France
8 Université Paris-Saclay, INRAE, BioinfOmics, Plant bioinformatics facility, 78026, Versailles, France
9 Present address: HM-Clause 49800 Loire-Authion
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
@article{10_24072_pcjournal_332,
     author = {Aubert, Gr\'egoire and Kreplak, Jonathan and Leveugle, Magalie and Duborjal, Herv\'e and Klein, Anthony and Boucherot, Karen and Vieille, Emilie and Chabert-Martinello, Marianne and Cruaud, Corinne and Bourion, Virginie and Lejeune-H\'enaut, Isabelle and Pilet-Nayel, Marie-Laure and Bouchenak-Khelladi, Yanis and Francillonne, Nicolas and Tayeh, Nadim and Pichon, Jean-Philippe and Rivi\`ere, Nathalie and Burstin, Judith},
     title = {SNP discovery by exome capture and resequencing in a pea genetic resource collection},
     journal = {Peer Community Journal},
     eid = {e100},
     publisher = {Peer Community In},
     volume = {3},
     year = {2023},
     doi = {10.24072/pcjournal.332},
     language = {en},
     url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.332/}
}
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%A Lejeune-Hénaut, Isabelle
%A Pilet-Nayel, Marie-Laure
%A Bouchenak-Khelladi, Yanis
%A Francillonne, Nicolas
%A Tayeh, Nadim
%A Pichon, Jean-Philippe
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Aubert, Grégoire; Kreplak, Jonathan; Leveugle, Magalie; Duborjal, Hervé; Klein, Anthony; Boucherot, Karen; Vieille, Emilie; Chabert-Martinello, Marianne; Cruaud, Corinne; Bourion, Virginie; Lejeune-Hénaut, Isabelle; Pilet-Nayel, Marie-Laure; Bouchenak-Khelladi, Yanis; Francillonne, Nicolas; Tayeh, Nadim; Pichon, Jean-Philippe; Rivière, Nathalie; Burstin, Judith. SNP discovery by exome capture and resequencing in a pea genetic resource collection. Peer Community Journal, Volume 3 (2023), article  no. e100. doi : 10.24072/pcjournal.332. https://peercommunityjournal.org/articles/10.24072/pcjournal.332/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.genomics.100237

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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