title: Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high-density, high-resolution consensus genetic map.
abstract: Single nucleotide polymorphism (SNP) arrays represent important genotyping tools for innovative strategies in both basic research and applied breeding. Pea is an important food, feed and sustainable crop with a large (about 4.45 Gbp) but not yet available genome sequence. In the present study, 12 pea recombinant inbred line populations were genotyped using the newly developed GenoPea 13.2K SNP Array. Individual and consensus genetic maps were built providing insights into the structure and organization of the pea genome. Largely collinear genetic maps of 3918-8503 SNPs were obtained from all mapping populations, and only two of these exhibited putative chromosomal rearrangement signatures. Similar distortion patterns in different populations were noted. A total of 12 802 transcript-derived SNP markers placed on a 15 079-marker high-density, high-resolution consensus map allowed the identification of ohnologue-rich regions within the pea genome and the localization of local duplicates. Dense syntenic networks with sequenced legume genomes were further established, paving the way for the identification of the molecular bases of important agronomic traits segregating in the mapping populations. The information gained on the structure and organization of the genome from this research will undoubtedly contribute to the understanding of the evolution of the pea genome and to its assembly. The GenoPea 13.2K SNP Array and individual and consensus genetic maps are valuable genomic tools for plant scientists to strengthen pea as a model for genetics and physiology and enhance breeding.
authors.affiliation: INRA, UMR1347 Agroécologie, F-21065, Dijon, France.
authors.forename: Nadim
authors.initials: N
authors.lastname: Tayeh
authors.affiliation: INRA, US1279 Étude du Polymorphisme des Génomes Végétaux, CEA-IG/Centre National de Génotypage, F- 91057, Evry, France.
authors.forename: Christelle
authors.initials: C
authors.lastname: Aluome
authors.affiliation: INRA, UMR320/UMR8120 Génétique Quantitative et Évolution - Le Moulon, F-91190, Gif-sur-Yvette, France.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Falque
authors.affiliation: INRA, UMR1347 Agroécologie, F-21065, Dijon, France.
authors.forename: Françoise
authors.initials: F
authors.lastname: Jacquin
authors.affiliation: INRA, UMR1347 Agroécologie, F-21065, Dijon, France.
authors.forename: Anthony
authors.initials: A
authors.lastname: Klein
authors.affiliation: INRA, US1279 Étude du Polymorphisme des Génomes Végétaux, CEA-IG/Centre National de Génotypage, F- 91057, Evry, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Chauveau
authors.affiliation: INRA, US1279 Étude du Polymorphisme des Génomes Végétaux, CEA-IG/Centre National de Génotypage, F- 91057, Evry, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Bérard
authors.affiliation: INRA, UMR1347 Agroécologie, F-21065, Dijon, France.
authors.forename: Hervé
authors.initials: H
authors.lastname: Houtin
authors.affiliation: INRA, UMR1347 Agroécologie, F-21065, Dijon, France.
authors.forename: Céline
authors.initials: C
authors.lastname: Rond
authors.affiliation: INRA, UMR1347 Agroécologie, F-21065, Dijon, France.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Kreplak
authors.affiliation: INRA, UMR1347 Agroécologie, F-21065, Dijon, France.
authors.forename: Karen
authors.initials: K
authors.lastname: Boucherot
authors.affiliation: INRA, UMR1347 Agroécologie, F-21065, Dijon, France.
authors.forename: Chantal
authors.initials: C
authors.lastname: Martin
authors.affiliation: INRA, UMR1349 Institut de Génétique Environnement et Protection des Plantes, F-35653, Le Rheu, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Baranger
authors.affiliation: INRA, UMR1349 Institut de Génétique Environnement et Protection des Plantes, F-35653, Le Rheu, France.
authors.forename: Marie-Laure
authors.initials: ML
authors.lastname: Pilet-Nayel
authors.affiliation: Crop Development Centre, University of Saskatchewan, SK S7N 5A8, Saskatoon, Canada.
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Warkentin
authors.affiliation: INRA, US1279 Étude du Polymorphisme des Génomes Végétaux, CEA-IG/Centre National de Génotypage, F- 91057, Evry, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Brunel
authors.affiliation: INRA, UMR1347 Agroécologie, F-21065, Dijon, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Marget
authors.affiliation: INRA, US1279 Étude du Polymorphisme des Génomes Végétaux, CEA-IG/Centre National de Génotypage, F- 91057, Evry, France.
authors.forename: Marie-Christine
authors.initials: MC
authors.lastname: Le Paslier
authors.affiliation: INRA, UMR1347 Agroécologie, F-21065, Dijon, France.
authors.forename: Grégoire
authors.initials: G
authors.lastname: Aubert
authors.affiliation: INRA, UMR1347 Agroécologie, F-21065, Dijon, France.
authors.forename: Judith
authors.initials: J
authors.lastname: Burstin
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D023281:Genomics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D018532:Pisum sativum / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D018744:DNA, Plant
keywords: GenoPea 13.2K SNP Array; consensus genetic map; duplication; genome structure and organization; pea (Pisum sativum L.); recombinant inbred lines; single nucleotide polymorphism; synteny