Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts

Publication Overview
TitleDevelopment and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts
AuthorsHulse-Kemp AM, Ashrafi H, Zheng X, Wang F, Hoegenauer KA, Maeda AB, Yang SS, Stoffel K, Matvienko M, Clemons K, Udall JA, Van Deynze A, Jones DC, Stelly DM
TypeJournal Article
Journal NameBMC genomics
Volume15
Issue1
Year2014
Page(s)945
CitationHulse-Kemp AM, Ashrafi H, Zheng X, Wang F, Hoegenauer KA, Maeda AB, Yang SS, Stoffel K, Matvienko M, Clemons K, Udall JA, Van Deynze A, Jones DC, Stelly DM. Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts. BMC genomics. 2014 Oct 30; 15(1):945.

Abstract

BACKGROUND
Cotton (Gossypium spp.) is the largest producer of natural fibers for textile and is an important crop worldwide. Crop production is comprised primarily of G. hirsutum L., an allotetraploid. However, elite cultivars express very small amounts of variation due to the species monophyletic origin, domestication and further bottlenecks due to selection. Conversely, wild cotton species harbor extensive genetic diversity of prospective utility to improve many beneficial agronomic traits, fiber characteristics, and resistance to disease and drought. Introgression of traits from wild species can provide a natural way to incorporate advantageous traits through breeding to generate higher-producing cotton cultivars and more sustainable production systems. Interspecific introgression efforts by conventional methods are very time-consuming and costly, but can be expedited using marker-assisted selection.

RESULTS
Using transcriptome sequencing we have developed the first gene-associated single nucleotide polymorphism (SNP) markers for wild cotton species G. tomentosum, G. mustelinum, G. armourianum and G. longicalyx. Markers were also developed for a secondary cultivated species G. barbadense cv. 3-79. A total of 62,832 non-redundant SNP markers were developed from the five wild species which can be utilized for interspecific germplasm introgression into cultivated G. hirsutum and are directly associated with genes. Over 500 of the G. barbadense markers have been validated by whole-genome radiation hybrid mapping. Overall 1,060 SNPs from the five different species have been screened and shown to produce acceptable genotyping assays.

CONCLUSIONS
This large set of 62,832 SNPs relative to cultivated G. hirsutum will allow for the first high-density mapping of genes from five wild species that affect traits of interest, including beneficial agronomic and fiber characteristics. Upon mapping, the markers can be utilized for marker-assisted introgression of new germplasm into cultivated cotton and in subsequent breeding of agronomically adapted types, including cultivar development.

Features
This publication contains information about 118,443 features:
Feature NameUniquenameType
TAMU_Gb379_006399TAMU_Gb379_006399genetic_marker
TAMU_Gb379_006438TAMU_Gb379_006438genetic_marker
TAMU_Gb379_006442TAMU_Gb379_006442genetic_marker
TAMU_Gb379_006447TAMU_Gb379_006447genetic_marker
TAMU_Gb379_006460TAMU_Gb379_006460genetic_marker
TAMU_Gb379_006461TAMU_Gb379_006461genetic_marker
TAMU_Gb379_006462TAMU_Gb379_006462genetic_marker
TAMU_Gb379_006490TAMU_Gb379_006490genetic_marker
TAMU_Gb379_006491TAMU_Gb379_006491genetic_marker
TAMU_Gb379_006492TAMU_Gb379_006492genetic_marker
TAMU_Gb379_006493TAMU_Gb379_006493genetic_marker
TAMU_Gb379_006500TAMU_Gb379_006500genetic_marker
TAMU_Gb379_006524TAMU_Gb379_006524genetic_marker
TAMU_Gb379_006525TAMU_Gb379_006525genetic_marker
TAMU_Gb379_006526TAMU_Gb379_006526genetic_marker
TAMU_Gb379_006530TAMU_Gb379_006530genetic_marker
TAMU_Gb379_006577TAMU_Gb379_006577genetic_marker
TAMU_Gb379_006581TAMU_Gb379_006581genetic_marker
TAMU_Gb379_006588TAMU_Gb379_006588genetic_marker
TAMU_Gb379_006602TAMU_Gb379_006602genetic_marker
TAMU_Gb379_006642TAMU_Gb379_006642genetic_marker
TAMU_Gb379_006648TAMU_Gb379_006648genetic_marker
TAMU_Gb379_006666TAMU_Gb379_006666genetic_marker
TAMU_Gb379_006670TAMU_Gb379_006670genetic_marker
TAMU_Gb379_006714TAMU_Gb379_006714genetic_marker

Pages

Libraries
This publication contains information about 1 libraries:
Library NameUnique NameOrganism
TAMU_CottonSNP63KTAMU_CottonSNP63KGossypium spp.
Properties
Additional details for this publication include:
Property NameValue
Publication TypeJournal Article
eISSN1471-2164
ISSN1471-2164
Journal AbbreviationBMC Genomics
LanguageEnglish
Language AbbrENG
Publication Date2014 Oct 30
Publication ModelPrint-Electronic
URLhttp://www.biomedcentral.com/1471-2164/15/945