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_TBb080B03r293TAMU_GH_TBb080B03r293genetic_marker
TAMU_GH_TBb080C15r80TAMU_GH_TBb080C15r80genetic_marker
TAMU_GH_TBb080C22f494TAMU_GH_TBb080C22f494genetic_marker
TAMU_GH_TBb080D20f384TAMU_GH_TBb080D20f384genetic_marker
TAMU_GH_TBb080E07f153TAMU_GH_TBb080E07f153genetic_marker
TAMU_GH_TBb080F12f401TAMU_GH_TBb080F12f401genetic_marker
TAMU_GH_TBb080F23f289TAMU_GH_TBb080F23f289genetic_marker
TAMU_GH_TBb080F24f236TAMU_GH_TBb080F24f236genetic_marker
TAMU_GH_TBb080G21f170TAMU_GH_TBb080G21f170genetic_marker
TAMU_GH_TBb080H14r93TAMU_GH_TBb080H14r93genetic_marker
TAMU_GH_TBb080I11f207TAMU_GH_TBb080I11f207genetic_marker
TAMU_GH_TBb080J21r153TAMU_GH_TBb080J21r153genetic_marker
TAMU_GH_TBb080K01r255TAMU_GH_TBb080K01r255genetic_marker
TAMU_GH_TBb080K14r123TAMU_GH_TBb080K14r123genetic_marker
TAMU_GH_TBb080M20r419TAMU_GH_TBb080M20r419genetic_marker
TAMU_GH_TBb080O05r653TAMU_GH_TBb080O05r653genetic_marker
TAMU_GH_TBb080O08r566TAMU_GH_TBb080O08r566genetic_marker
TAMU_GH_TBb080O13r276TAMU_GH_TBb080O13r276genetic_marker
TAMU_GH_TBb080O16r311TAMU_GH_TBb080O16r311genetic_marker
TAMU_GH_TBb080P07f697TAMU_GH_TBb080P07f697genetic_marker
TAMU_GH_TBb081A04f376TAMU_GH_TBb081A04f376genetic_marker
TAMU_GH_TBb081B08f450TAMU_GH_TBb081B08f450genetic_marker
TAMU_GH_TBb081C24r297TAMU_GH_TBb081C24r297genetic_marker
TAMU_GH_TBb081F05r43TAMU_GH_TBb081F05r43genetic_marker
TAMU_GH_TBb081H01r322TAMU_GH_TBb081H01r322genetic_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