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_TBh087E19r322TAMU_GH_TBh087E19r322genetic_marker
TAMU_GH_TBh087E22f129TAMU_GH_TBh087E22f129genetic_marker
TAMU_GH_TBh087F04r57TAMU_GH_TBh087F04r57genetic_marker
TAMU_GH_TBh087F05f105TAMU_GH_TBh087F05f105genetic_marker
TAMU_GH_TBh087F09f56TAMU_GH_TBh087F09f56genetic_marker
TAMU_GH_TBh087F09r401TAMU_GH_TBh087F09r401genetic_marker
TAMU_GH_TBh087F12f620TAMU_GH_TBh087F12f620genetic_marker
TAMU_GH_TBh087F17f294TAMU_GH_TBh087F17f294genetic_marker
TAMU_GH_TBh087F21f331TAMU_GH_TBh087F21f331genetic_marker
TAMU_GH_TBh087F23r577TAMU_GH_TBh087F23r577genetic_marker
TAMU_GH_TBh087G03r155TAMU_GH_TBh087G03r155genetic_marker
TAMU_GH_TBh087G04f534TAMU_GH_TBh087G04f534genetic_marker
TAMU_GH_TBh087G05r18TAMU_GH_TBh087G05r18genetic_marker
TAMU_GH_TBh087G09f137TAMU_GH_TBh087G09f137genetic_marker
TAMU_GH_TBh087G09r201TAMU_GH_TBh087G09r201genetic_marker
TAMU_GH_TBh087G16f456TAMU_GH_TBh087G16f456genetic_marker
TAMU_GH_TBh087G17r655TAMU_GH_TBh087G17r655genetic_marker
TAMU_GH_TBh087G19r440TAMU_GH_TBh087G19r440genetic_marker
TAMU_GH_TBh087G22f401TAMU_GH_TBh087G22f401genetic_marker
TAMU_GH_TBh087G24f379TAMU_GH_TBh087G24f379genetic_marker
TAMU_GH_TBh087G24r148TAMU_GH_TBh087G24r148genetic_marker
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TAMU_GH_TBh087H10f88TAMU_GH_TBh087H10f88genetic_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