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_017932TAMU_Gb379_017932genetic_marker
TAMU_Gb379_017939TAMU_Gb379_017939genetic_marker
TAMU_Gb379_017948TAMU_Gb379_017948genetic_marker
TAMU_Gb379_017949TAMU_Gb379_017949genetic_marker
TAMU_Gb379_017951TAMU_Gb379_017951genetic_marker
TAMU_Gb379_017955TAMU_Gb379_017955genetic_marker
TAMU_Gb379_017960TAMU_Gb379_017960genetic_marker
TAMU_Gb379_017964TAMU_Gb379_017964genetic_marker
TAMU_Gb379_017966TAMU_Gb379_017966genetic_marker
TAMU_Gb379_017967TAMU_Gb379_017967genetic_marker
TAMU_Gb379_017976TAMU_Gb379_017976genetic_marker
TAMU_Gb379_017977TAMU_Gb379_017977genetic_marker
TAMU_Gb379_017978TAMU_Gb379_017978genetic_marker
TAMU_Gb379_017979TAMU_Gb379_017979genetic_marker
TAMU_Gb379_017990TAMU_Gb379_017990genetic_marker
TAMU_Gb379_017991TAMU_Gb379_017991genetic_marker
TAMU_Gb379_017992TAMU_Gb379_017992genetic_marker
TAMU_Gb379_018013TAMU_Gb379_018013genetic_marker
TAMU_Gb379_018030TAMU_Gb379_018030genetic_marker
TAMU_Gb379_018033TAMU_Gb379_018033genetic_marker
TAMU_Gb379_018034TAMU_Gb379_018034genetic_marker
TAMU_Gb379_018035TAMU_Gb379_018035genetic_marker
TAMU_Gb379_018055TAMU_Gb379_018055genetic_marker
TAMU_Gb379_018078TAMU_Gb379_018078genetic_marker
TAMU_Gb379_018096TAMU_Gb379_018096genetic_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