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_TBh004E19r358TAMU_GH_TBh004E19r358genetic_marker
TAMU_GH_TBh004E23r803TAMU_GH_TBh004E23r803genetic_marker
TAMU_GH_TBh004F01f240TAMU_GH_TBh004F01f240genetic_marker
TAMU_GH_TBh004F01r408TAMU_GH_TBh004F01r408genetic_marker
TAMU_GH_TBh004F12f257TAMU_GH_TBh004F12f257genetic_marker
TAMU_GH_TBh004F12r413TAMU_GH_TBh004F12r413genetic_marker
TAMU_GH_TBh004F14r44TAMU_GH_TBh004F14r44genetic_marker
TAMU_GH_TBh004F15f425TAMU_GH_TBh004F15f425genetic_marker
TAMU_GH_TBh004F19r50TAMU_GH_TBh004F19r50genetic_marker
TAMU_GH_TBh004F21r366TAMU_GH_TBh004F21r366genetic_marker
TAMU_GH_TBh004G10f142TAMU_GH_TBh004G10f142genetic_marker
TAMU_GH_TBh004G10r212TAMU_GH_TBh004G10r212genetic_marker
TAMU_GH_TBh004G13r26TAMU_GH_TBh004G13r26genetic_marker
TAMU_GH_TBh004H03r536TAMU_GH_TBh004H03r536genetic_marker
TAMU_GH_TBh004H07r426TAMU_GH_TBh004H07r426genetic_marker
TAMU_GH_TBh004H12f103TAMU_GH_TBh004H12f103genetic_marker
TAMU_GH_TBh004I01r753TAMU_GH_TBh004I01r753genetic_marker
TAMU_GH_TBh004I08f60TAMU_GH_TBh004I08f60genetic_marker
TAMU_GH_TBh004I12r475TAMU_GH_TBh004I12r475genetic_marker
TAMU_GH_TBh004I16f175TAMU_GH_TBh004I16f175genetic_marker
TAMU_GH_TBh004I16r384TAMU_GH_TBh004I16r384genetic_marker
TAMU_GH_TBh004J01r287TAMU_GH_TBh004J01r287genetic_marker
TAMU_GH_TBh004J08f129TAMU_GH_TBh004J08f129genetic_marker
TAMU_GH_TBh004J12f4TAMU_GH_TBh004J12f4genetic_marker
TAMU_GH_TBh004J12r235TAMU_GH_TBh004J12r235genetic_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