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_022279TAMU_Gb379_022279genetic_marker
TAMU_Gb379_022289TAMU_Gb379_022289genetic_marker
TAMU_Gb379_022296TAMU_Gb379_022296genetic_marker
TAMU_Gb379_022305TAMU_Gb379_022305genetic_marker
TAMU_Gb379_022318TAMU_Gb379_022318genetic_marker
TAMU_Gb379_022326TAMU_Gb379_022326genetic_marker
TAMU_Gb379_022327TAMU_Gb379_022327genetic_marker
TAMU_Gb379_022334TAMU_Gb379_022334genetic_marker
TAMU_Gb379_022344TAMU_Gb379_022344genetic_marker
TAMU_Gb379_022348TAMU_Gb379_022348genetic_marker
TAMU_Gb379_022349TAMU_Gb379_022349genetic_marker
TAMU_Gb379_022352TAMU_Gb379_022352genetic_marker
TAMU_Gb379_022372TAMU_Gb379_022372genetic_marker
TAMU_Gb379_022385TAMU_Gb379_022385genetic_marker
TAMU_Gb379_022386TAMU_Gb379_022386genetic_marker
TAMU_Gb379_022398TAMU_Gb379_022398genetic_marker
TAMU_Gb379_022405TAMU_Gb379_022405genetic_marker
TAMU_Gb379_022421TAMU_Gb379_022421genetic_marker
TAMU_Gb379_022425TAMU_Gb379_022425genetic_marker
TAMU_Gb379_022429TAMU_Gb379_022429genetic_marker
TAMU_Gb379_022431TAMU_Gb379_022431genetic_marker
TAMU_Gb379_022440TAMU_Gb379_022440genetic_marker
TAMU_Gb379_022453TAMU_Gb379_022453genetic_marker
TAMU_Gb379_022470TAMU_Gb379_022470genetic_marker
TAMU_Gb379_022471TAMU_Gb379_022471genetic_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