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_TBb102M13r88TAMU_GH_TBb102M13r88genetic_marker
TAMU_GH_TBb102N10r408TAMU_GH_TBb102N10r408genetic_marker
TAMU_GH_TBb102O14f278TAMU_GH_TBb102O14f278genetic_marker
TAMU_GH_TBb102O19f453TAMU_GH_TBb102O19f453genetic_marker
TAMU_GH_TBb102P09f182TAMU_GH_TBb102P09f182genetic_marker
TAMU_GH_TBb102P22r162TAMU_GH_TBb102P22r162genetic_marker
TAMU_GH_TBb103A17r316TAMU_GH_TBb103A17r316genetic_marker
TAMU_GH_TBb103A19r141TAMU_GH_TBb103A19r141genetic_marker
TAMU_GH_TBb103D01r639TAMU_GH_TBb103D01r639genetic_marker
TAMU_GH_TBb103D10f840TAMU_GH_TBb103D10f840genetic_marker
TAMU_GH_TBb103D18r260TAMU_GH_TBb103D18r260genetic_marker
TAMU_GH_TBb103E20r92TAMU_GH_TBb103E20r92genetic_marker
TAMU_GH_TBb103F23f220TAMU_GH_TBb103F23f220genetic_marker
TAMU_GH_TBb103H07r384TAMU_GH_TBb103H07r384genetic_marker
TAMU_GH_TBb103H11r185TAMU_GH_TBb103H11r185genetic_marker
TAMU_GH_TBb103J19r337TAMU_GH_TBb103J19r337genetic_marker
TAMU_GH_TBb103J22r400TAMU_GH_TBb103J22r400genetic_marker
TAMU_GH_TBb103L15r661TAMU_GH_TBb103L15r661genetic_marker
TAMU_GH_TBb103M20f564TAMU_GH_TBb103M20f564genetic_marker
TAMU_GH_TBb103N05f321TAMU_GH_TBb103N05f321genetic_marker
TAMU_GH_TBb103O07f197TAMU_GH_TBb103O07f197genetic_marker
TAMU_GH_TBb103P05f582TAMU_GH_TBb103P05f582genetic_marker
TAMU_GH_TBb104A18r703TAMU_GH_TBb104A18r703genetic_marker
TAMU_GH_TBb104B06r695TAMU_GH_TBb104B06r695genetic_marker
TAMU_GH_TBb104B13f196TAMU_GH_TBb104B13f196genetic_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