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_Mus_007429TAMU_Mus_007429genetic_marker
TAMU_Mus_007430TAMU_Mus_007430genetic_marker
TAMU_Mus_007501TAMU_Mus_007501genetic_marker
TAMU_Mus_007570TAMU_Mus_007570genetic_marker
TAMU_Mus_007608TAMU_Mus_007608genetic_marker
TAMU_Mus_007621TAMU_Mus_007621genetic_marker
TAMU_Mus_007727TAMU_Mus_007727genetic_marker
TAMU_Mus_007879TAMU_Mus_007879genetic_marker
TAMU_Mus_007989TAMU_Mus_007989genetic_marker
TAMU_Mus_008162TAMU_Mus_008162genetic_marker
TAMU_Mus_008182TAMU_Mus_008182genetic_marker
TAMU_Mus_008263TAMU_Mus_008263genetic_marker
TAMU_Mus_008382TAMU_Mus_008382genetic_marker
TAMU_Mus_008531TAMU_Mus_008531genetic_marker
TAMU_Mus_008569TAMU_Mus_008569genetic_marker
TAMU_Mus_008571TAMU_Mus_008571genetic_marker
TAMU_Mus_008702TAMU_Mus_008702genetic_marker
TAMU_Mus_008726TAMU_Mus_008726genetic_marker
TAMU_Mus_008732TAMU_Mus_008732genetic_marker
TAMU_Mus_008813TAMU_Mus_008813genetic_marker
TAMU_Mus_008814TAMU_Mus_008814genetic_marker
TAMU_Mus_008848TAMU_Mus_008848genetic_marker
TAMU_Mus_008929TAMU_Mus_008929genetic_marker
TAMU_Mus_009228TAMU_Mus_009228genetic_marker
TAMU_Mus_009261TAMU_Mus_009261genetic_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