Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high-density, high-resolution consensus genetic map

Publication Overview
TitleDevelopment of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high-density, high-resolution consensus genetic map
AuthorsTayeh N, Aluome C, Falque M, Jacquin F, Klein A, Chauveau A, Berard A, Houtin H, Rond C, Kreplak J, Boucherot K, Martin C, Baranger A, Pilet-Nayel ML, Warkentin TD, Brunel D, Marget P, Le Paslier MC, Aubert G, Burstin J
TypeJournal Article
Journal NameThe Plant Journal
Volume84
Issue6
Year2015
Page(s)1257-1273
CitationTayeh N, Aluome C, Falque M, Jacquin F, Klein A, Chauveau A, Berard A, Houtin H, Rond C, Kreplak J, Boucherot K, Martin C, Baranger A, Pilet-Nayel ML, Warkentin TD, Brunel D, Marget P, Le Paslier MC, Aubert G, Burstin J. Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high-density, high-resolution consensus genetic map. 2015; 84(6):1257-1273.

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.
Features
This publication contains information about 15,000 features:
Feature NameUniquenameType
PsCam031628_18529_71PsCam031628_18529_71genetic_marker
PsCam031644_18537_503PsCam031644_18537_503genetic_marker
PsCam031706_18563_181PsCam031706_18563_181genetic_marker
PsCam031714_18566_286PsCam031714_18566_286genetic_marker
PsCam031743_18578_437PsCam031743_18578_437genetic_marker
PsCam031845_18606_377PsCam031845_18606_377genetic_marker
PsCam032831_18897_70PsCam032831_18897_70genetic_marker
PsCam032871_18907_254PsCam032871_18907_254genetic_marker
PsCam033220_19002_3674PsCam033220_19002_3674genetic_marker
PsCam033280_19017_359PsCam033280_19017_359genetic_marker
PsCam033309_19031_3180PsCam033309_19031_3180genetic_marker
PsCam033317_19036_2778PsCam033317_19036_2778genetic_marker
PsCam033332_19047_109PsCam033332_19047_109genetic_marker
PsCam033335_19049_466PsCam033335_19049_466genetic_marker
PsCam033351_19057_1319PsCam033351_19057_1319genetic_marker
PsCam033375_19072_938PsCam033375_19072_938genetic_marker
PsCam033413_19091_2260PsCam033413_19091_2260genetic_marker
PsCam033456_19113_1488PsCam033456_19113_1488genetic_marker
PsCam033484_19127_263PsCam033484_19127_263genetic_marker
PsCam033501_19135_29PsCam033501_19135_29genetic_marker
PsCam033502_19136_484PsCam033502_19136_484genetic_marker
PsCam033506_19139_965PsCam033506_19139_965genetic_marker
PsCam033580_19176_290PsCam033580_19176_290genetic_marker
PsCam033730_19276_1861PsCam033730_19276_1861genetic_marker
PsCam033734_19279_1939PsCam033734_19279_1939genetic_marker

Pages

Libraries
This publication contains information about 1 libraries:
Library NameUnique NameOrganism
GenoPea_13.2KGenoPea_13.2KN/A N/A
Stocks
This publication contains information about 16 stocks:
Stock NameUniquenameType
KazarKazaraccession
MelroseMelroseaccession
SommetteSommetteaccession
CeriseCeriseaccession
Baccara_x_PI180693-RILBaccara_x_PI180693-RILpopulation
JI296_x_DP-RILJI296_x_DP-RILpopulation
Champagne_x_Terese-RILChampagne_x_Terese-RILpopulation
VavD265_x_Cameor-RILVavD265_x_Cameor-RILpopulation
Ballet_x_Cameor-RILBallet_x_Cameor-RILpopulation
VavD265_x_Ballet-RILVavD265_x_Ballet-RILpopulation
Cameor_x_Melrose-RILCameor_x_Melrose-RILpopulation
Kazar_x_Cameor-RILKazar_x_Cameor-RILpopulation
Kazar_x_Melrose-RILKazar_x_Melrose-RILpopulation
China_x_Cameor-RILChina_x_Cameor-RILpopulation
Sommette_x_Cameor-RILSommette_x_Cameor-RILpopulation
Cerise_x_Cameor-F3Cerise_x_Cameor-F3population
Properties
Additional details for this publication include:
Property NameValue
URLhttp://onlinelibrary.wiley.com/doi/10.1111/tpj.13070/full