BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences and Perspectives for Genetic Mapping

Publication Overview
TitleBAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences and Perspectives for Genetic Mapping
AuthorsHulse-Kemp AM, Ashrafi H, Stoffel K, Zheng X, Saski C, Scheffler BE, Fang DD, Chen ZJ, Van Deynze A, Stelly DM
TypeJournal Article
Journal NameG3 (Bethesda, Md.)
Year2015
CitationHulse-Kemp AM, Ashrafi H, Stoffel K, Zheng X, Saski C, Scheffler BE, Fang DD, Chen ZJ, Van Deynze A, Stelly DM. BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences and Perspectives for Genetic Mapping. G3 (Bethesda, Md.). 2015 Apr 9.

Abstract

A bacterial artificial chromosome library and BAC-end sequences for cultivated cotton (Gossypium hirsutum L.) have recently been developed. This report presents on genome-wide single nucleotide polymorphism mining utilizing resequencing data with BAC-end sequences as a reference by alignment of twelve G. hirsutum L. lines, one G. barbadense L. line, and one G. longicalyx Hutch & Lee line. A total of 132,262 intraspecific SNPs have been developed for G. hirsutum, while 223,138 and 470,631 interspecific SNPs have been developed for G. barbadense and G. longicalyx, respectively. Using a set of interspecific SNPs, 11 randomly selected, and 77 SNPs that are putatively associated with the homeologous chromosome pair 12 and 26, we mapped 77 SNPs into two linkage groups representing these chromosomes, spanning a total of 236.2 cM in an interspecific F2 population (G. hirsutum TM-1 x G. barbadense 3-79). The mapping results validated the approach for reliably producing large numbers of both intraspecific and interspecific SNPs aligned to BAC-ends. This will allow for future construction of high-density integrated physical and genetic maps for cotton and other complex polyploid genomes. The methods developed will allow for future Gossypium resequencing data to be automatically genotyped for identified SNPs along the BAC-end sequence reference for anchoring sequence assemblies and comparative studies.

Libraries
This publication contains information about 1 libraries:
Library NameUnique NameOrganism
TAMU_CottonSNP63KTAMU_CottonSNP63KGossypium spp.
Properties
Additional details for this publication include:
Property NameValue
CopyrightCopyright © 2015 Author et al.
eISSN2160-1836
Elocation10.1534/g3.115.017749
ISSN2160-1836
Journal AbbreviationG3 (Bethesda)
LanguageEnglish
Language AbbrENG
Publication Date2015 Apr 9
Publication ModelPrint-Electronic
Publication TypeJournal Article
URLhttp://www.g3journal.org/content/5/6/1095.short
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DatabaseAccession
PMID: PubMedPMID:25858960