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_TBh104K24r574TAMU_GH_TBh104K24r574genetic_marker
TAMU_GH_TBh104L04f485TAMU_GH_TBh104L04f485genetic_marker
TAMU_GH_TBh104L04r511TAMU_GH_TBh104L04r511genetic_marker
TAMU_GH_TBh104L09f327TAMU_GH_TBh104L09f327genetic_marker
TAMU_GH_TBh104L11r167TAMU_GH_TBh104L11r167genetic_marker
TAMU_GH_TBh104L16f154TAMU_GH_TBh104L16f154genetic_marker
TAMU_GH_TBh104L20f108TAMU_GH_TBh104L20f108genetic_marker
TAMU_GH_TBh104L20r367TAMU_GH_TBh104L20r367genetic_marker
TAMU_GH_TBh104L23r651TAMU_GH_TBh104L23r651genetic_marker
TAMU_GH_TBh104M04r381TAMU_GH_TBh104M04r381genetic_marker
TAMU_GH_TBh104M11r168TAMU_GH_TBh104M11r168genetic_marker
TAMU_GH_TBh104M12r292TAMU_GH_TBh104M12r292genetic_marker
TAMU_GH_TBh104M15r365TAMU_GH_TBh104M15r365genetic_marker
TAMU_GH_TBh104M20f73TAMU_GH_TBh104M20f73genetic_marker
TAMU_GH_TBh104M21r525TAMU_GH_TBh104M21r525genetic_marker
TAMU_GH_TBh104N05f35TAMU_GH_TBh104N05f35genetic_marker
TAMU_GH_TBh104N15f152TAMU_GH_TBh104N15f152genetic_marker
TAMU_GH_TBh104N16r616TAMU_GH_TBh104N16r616genetic_marker
TAMU_GH_TBh104N22f137TAMU_GH_TBh104N22f137genetic_marker
TAMU_GH_TBh104O06r225TAMU_GH_TBh104O06r225genetic_marker
TAMU_GH_TBh104O07f660TAMU_GH_TBh104O07f660genetic_marker
TAMU_GH_TBh104O09f319TAMU_GH_TBh104O09f319genetic_marker
TAMU_GH_TBh104O11f467TAMU_GH_TBh104O11f467genetic_marker
TAMU_GH_TBh104O19r585TAMU_GH_TBh104O19r585genetic_marker
TAMU_GH_TBh104O22r228TAMU_GH_TBh104O22r228genetic_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