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_Arm_064665TAMU_Arm_064665genetic_marker
TAMU_Arm_064668TAMU_Arm_064668genetic_marker
TAMU_Arm_064691TAMU_Arm_064691genetic_marker
TAMU_Arm_064714TAMU_Arm_064714genetic_marker
TAMU_Arm_064716TAMU_Arm_064716genetic_marker
TAMU_Arm_064757TAMU_Arm_064757genetic_marker
TAMU_Arm_064771TAMU_Arm_064771genetic_marker
TAMU_Arm_064797TAMU_Arm_064797genetic_marker
TAMU_Arm_064808TAMU_Arm_064808genetic_marker
TAMU_Arm_064842TAMU_Arm_064842genetic_marker
TAMU_Arm_064855TAMU_Arm_064855genetic_marker
TAMU_Arm_064870TAMU_Arm_064870genetic_marker
TAMU_Arm_064935TAMU_Arm_064935genetic_marker
TAMU_Arm_064941TAMU_Arm_064941genetic_marker
TAMU_Arm_064953TAMU_Arm_064953genetic_marker
TAMU_Arm_064956TAMU_Arm_064956genetic_marker
TAMU_Arm_064959TAMU_Arm_064959genetic_marker
TAMU_Arm_064962TAMU_Arm_064962genetic_marker
TAMU_Arm_064986TAMU_Arm_064986genetic_marker
TAMU_Arm_065031TAMU_Arm_065031genetic_marker
TAMU_Arm_065034TAMU_Arm_065034genetic_marker
TAMU_Arm_065038TAMU_Arm_065038genetic_marker
TAMU_Arm_065048TAMU_Arm_065048genetic_marker
TAMU_Arm_065058TAMU_Arm_065058genetic_marker
TAMU_Arm_065074TAMU_Arm_065074genetic_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