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_TBh011O21r590TAMU_GH_TBh011O21r590genetic_marker
TAMU_GH_TBh011P03f134TAMU_GH_TBh011P03f134genetic_marker
TAMU_GH_TBh011P03f464TAMU_GH_TBh011P03f464genetic_marker
TAMU_GH_TBh012A01f311TAMU_GH_TBh012A01f311genetic_marker
TAMU_GH_TBh012A02f18TAMU_GH_TBh012A02f18genetic_marker
TAMU_GH_TBh012A05f194TAMU_GH_TBh012A05f194genetic_marker
TAMU_GH_TBh012A09f371TAMU_GH_TBh012A09f371genetic_marker
TAMU_GH_TBh012A15f116TAMU_GH_TBh012A15f116genetic_marker
TAMU_GH_TBh012A15r103TAMU_GH_TBh012A15r103genetic_marker
TAMU_GH_TBh012A16f492TAMU_GH_TBh012A16f492genetic_marker
TAMU_GH_TBh012A17f523TAMU_GH_TBh012A17f523genetic_marker
TAMU_GH_TBh012A20f548TAMU_GH_TBh012A20f548genetic_marker
TAMU_GH_TBh012B01f518TAMU_GH_TBh012B01f518genetic_marker
TAMU_GH_TBh012B04r486TAMU_GH_TBh012B04r486genetic_marker
TAMU_GH_TBh012B06f359TAMU_GH_TBh012B06f359genetic_marker
TAMU_GH_TBh012B06r218TAMU_GH_TBh012B06r218genetic_marker
TAMU_GH_TBh012B10f39TAMU_GH_TBh012B10f39genetic_marker
TAMU_GH_TBh012B17r183TAMU_GH_TBh012B17r183genetic_marker
TAMU_GH_TBh012C04r501TAMU_GH_TBh012C04r501genetic_marker
TAMU_GH_TBh012C06f394TAMU_GH_TBh012C06f394genetic_marker
TAMU_GH_TBh012C09f235TAMU_GH_TBh012C09f235genetic_marker
TAMU_GH_TBh012C16r308TAMU_GH_TBh012C16r308genetic_marker
TAMU_GH_TBh012C16r430TAMU_GH_TBh012C16r430genetic_marker
TAMU_GH_TBh012C17f650TAMU_GH_TBh012C17f650genetic_marker
TAMU_GH_TBh012C19f351TAMU_GH_TBh012C19f351genetic_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