SNP discovery by exome capture and resequencing in a pea genetic resource collection
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...
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| Language: | English |
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2023-10-01
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| Online Access: | https://peercommunityjournal.org/articles/10.24072/pcjournal.332/ |
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| author | 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 |
| author_facet | 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 |
| author_sort | Aubert, Grégoire |
| collection | DOAJ |
| description | 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.
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| format | Article |
| id | doaj-art-cbb3852c110847b39112e73ccd9dd79a |
| institution | Kabale University |
| issn | 2804-3871 |
| language | English |
| publishDate | 2023-10-01 |
| publisher | Peer Community In |
| record_format | Article |
| series | Peer Community Journal |
| spelling | doaj-art-cbb3852c110847b39112e73ccd9dd79a2025-02-07T10:16:48ZengPeer Community InPeer Community Journal2804-38712023-10-01310.24072/pcjournal.33210.24072/pcjournal.332SNP discovery by exome capture and resequencing in a pea genetic resource collection Aubert, Grégoire0https://orcid.org/0000-0002-1867-5730Kreplak, Jonathan1https://orcid.org/0000-0001-5563-1932Leveugle, Magalie2Duborjal, Hervé3Klein, Anthony4Boucherot, Karen5Vieille, Emilie6Chabert-Martinello, Marianne7Cruaud, Corinne8https://orcid.org/0000-0002-4752-7278Bourion, Virginie9https://orcid.org/0009-0007-7236-5489Lejeune-Hénaut, Isabelle10https://orcid.org/0000-0002-2630-2387Pilet-Nayel, Marie-Laure11https://orcid.org/0000-0002-4505-1907Bouchenak-Khelladi, Yanis12https://orcid.org/0000-0002-6412-864XFrancillonne, Nicolas13https://orcid.org/0000-0002-0665-4350Tayeh, Nadim14https://orcid.org/0000-0003-0098-8322Pichon, Jean-Philippe15Rivière, Nathalie16Burstin, Judith17https://orcid.org/0000-0002-4125-3499Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, FranceAgroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, FranceBiogemma, F-63720 Chappes, France; Present address: Limagrain F-63720 Chappes, FranceBiogemma, F-63720 Chappes, France; Present address: Limagrain F-63720 Chappes, FranceAgroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, FranceAgroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, FranceAgroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, FranceAgroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, FranceGenoscope, Institut François Jacob, CEA, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, FranceAgroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, FranceBioEcoAgro, INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, 2, Chaussée Brunehaut, F-80203, Estrées-Mons, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceAgroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, FranceUniversité Paris-Saclay, INRAE, URGI, 78026, Versailles, France; Université Paris-Saclay, INRAE, BioinfOmics, Plant bioinformatics facility, 78026, Versailles, FranceAgroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, FranceBiogemma, F-63720 Chappes, France; Present address: Limagrain F-63720 Chappes, FranceBiogemma, F-63720 Chappes, France; Present address: HM-Clause 49800 Loire-AuthionAgroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, FrancePea 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. https://peercommunityjournal.org/articles/10.24072/pcjournal.332/Pea; Single Nucleotide Polymorphism; Exome capture; diversity |
| spellingShingle | 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 Pea; Single Nucleotide Polymorphism; Exome capture; diversity |
| title | SNP discovery by exome capture and resequencing in a pea genetic resource collection
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| title_full | SNP discovery by exome capture and resequencing in a pea genetic resource collection
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| title_fullStr | SNP discovery by exome capture and resequencing in a pea genetic resource collection
|
| title_full_unstemmed | SNP discovery by exome capture and resequencing in a pea genetic resource collection
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| title_short | SNP discovery by exome capture and resequencing in a pea genetic resource collection
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| title_sort | snp discovery by exome capture and resequencing in a pea genetic resource collection |
| topic | Pea; Single Nucleotide Polymorphism; Exome capture; diversity |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.332/ |
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