Development of a 63K SNP Array for Cotton and High-Density Mapping of Intra- and Inter-Specific Populations of Gossypium spp

Publication Overview
TitleDevelopment of a 63K SNP Array for Cotton and High-Density Mapping of Intra- and Inter-Specific Populations of Gossypium spp
AuthorsHulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Giband M, Hague S, Hinze LL, Kochan KJ, Riggs PK, Scheffler JA, Udall JA, Ulloa M, Wang SS, Zhu QH, Bag SK, Bhardwaj A, Burke JJ, Byers RL, Claverie M, Gore MA, Harker DB, Islam MS, Jenkins JN, Jones DC, Lacape JM, Llewellyn DJ, Percy RG, Pepper AE, Poland JA, Mohan Rai K, Sawant SV, Kumar Singh S, Spriggs A, Taylor JM, Wang F, Yourstone SM, Zheng X, Lawley CT, Ganal MW, Van Deynze A, Wilson IW, Stelly DM
TypeJournal Article
Journal NameG3 (Bethesda, Md.)
Year2015
CitationHulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Giband M, Hague S, Hinze LL, Kochan KJ, Riggs PK, Scheffler JA, Udall JA, Ulloa M, Wang SS, Zhu QH, Bag SK, Bhardwaj A, Burke JJ, Byers RL, Claverie M, Gore MA, Harker DB, Islam MS, Jenkins JN, Jones DC, Lacape JM, Llewellyn DJ, Percy RG, Pepper AE, Poland JA, Mohan Rai K, Sawant SV, Kumar Singh S, Spriggs A, Taylor JM, Wang F, Yourstone SM, Zheng X, Lawley CT, Ganal MW, Van Deynze A, Wilson IW, Stelly DM. Development of a 63K SNP Array for Cotton and High-Density Mapping of Intra- and Inter-Specific Populations of Gossypium spp. G3 (Bethesda, Md.). 2015 Apr 22.
Publication CodeG3-5-1187

Abstract

High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection and studying patterns of genomic diversity among cotton cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intra-specific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative inter-specific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array are developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal ex Seemann, G. mustelinum Miers x Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson & Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intra-specific and one inter-specific, 3,533 SNP markers were co-occurring in both maps. The produced intra-specific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The developed CottonSNP63K array and cluster file along with the marker sequences is a valuable new resource for the global cotton research community.

Germplasm
This publication contains information about 2 stocks:
Stock NameGRIN IDSpeciesType
3-79 x TM-1, F2Gossypium barbadense x hirsutumpopulation
Phytogen 72 x Stoneville 474, F2Gossypium hirsutumpopulation
Features
This publication contains information about 69,997 features:
Feature NameUniquenameType
TAMU_GH_TBb027F22f522TAMU_GH_TBb027F22f522genetic_marker
TAMU_GH_TBb027F24r459TAMU_GH_TBb027F24r459genetic_marker
TAMU_GH_TBb027G09r451TAMU_GH_TBb027G09r451genetic_marker
TAMU_GH_TBb027G16f351TAMU_GH_TBb027G16f351genetic_marker
TAMU_GH_TBb027H17r508TAMU_GH_TBb027H17r508genetic_marker
TAMU_GH_TBb027J23f560TAMU_GH_TBb027J23f560genetic_marker
TAMU_GH_TBb027K02f94TAMU_GH_TBb027K02f94genetic_marker
TAMU_GH_TBb027K02f545TAMU_GH_TBb027K02f545genetic_marker
TAMU_GH_TBb027K13f157TAMU_GH_TBb027K13f157genetic_marker
TAMU_GH_TBb027K16r239TAMU_GH_TBb027K16r239genetic_marker
TAMU_GH_TBb027L06r210TAMU_GH_TBb027L06r210genetic_marker
TAMU_GH_TBb027M17f112TAMU_GH_TBb027M17f112genetic_marker
TAMU_GH_TBb027N18r722TAMU_GH_TBb027N18r722genetic_marker
TAMU_GH_TBb027P12r169TAMU_GH_TBb027P12r169genetic_marker
TAMU_GH_TBb027P16f315TAMU_GH_TBb027P16f315genetic_marker
TAMU_GH_TBb027P16r314TAMU_GH_TBb027P16r314genetic_marker
TAMU_GH_TBb027P18f98TAMU_GH_TBb027P18f98genetic_marker
TAMU_GH_TBb027P24f115TAMU_GH_TBb027P24f115genetic_marker
TAMU_GH_TBb028B07f89TAMU_GH_TBb028B07f89genetic_marker
TAMU_GH_TBb028C02r362TAMU_GH_TBb028C02r362genetic_marker
TAMU_GH_TBb028C19r438TAMU_GH_TBb028C19r438genetic_marker
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TAMU_GH_TBb028G08f519TAMU_GH_TBb028G08f519genetic_marker
TAMU_GH_TBb028I01r724TAMU_GH_TBb028I01r724genetic_marker
TAMU_GH_TBb028I15r466TAMU_GH_TBb028I15r466genetic_marker

Pages

Featuremaps
This publication contains information about 2 maps:
Map Name
3-79 x TM-1, F2 (2015 SNP)
Phytogen 72 x Stoneville 474, F2 (2015 SNP)
Libraries
This publication contains information about 1 libraries:
Library NameUnique NameOrganism
TAMU_CottonSNP63KTAMU_CottonSNP63KGossypium spp.
Properties
Additional details for this publication include:
Property NameValue
Journal NameG3
Publication CodeG3-5-1187
Language AbbrENG
Publication TypeJournal Article
eISSN2160-1836
ISSN2160-1836
Publication Date2015 Apr 22
Publication ModelPrint-Electronic
Journal CodeG3
Elocation10.1534/g3.115.018416
Journal AbbreviationG3 (Bethesda)
CopyrightCopyright © 2015 Author et al.
LanguageEnglish