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.

Features
This publication contains information about 170 features:
Feature NameUniquenameType
TAMU_GH_TBb002K23f282TAMU_GH_TBb002K23f282genetic_marker
TAMU_GH_TBb004F08r214TAMU_GH_TBb004F08r214genetic_marker
TAMU_GH_TBb007K19f439TAMU_GH_TBb007K19f439genetic_marker
TAMU_GH_TBb007K19f685TAMU_GH_TBb007K19f685genetic_marker
TAMU_GH_TBb076O12f641TAMU_GH_TBb076O12f641genetic_marker
TAMU_GH_TBb076O12r258TAMU_GH_TBb076O12r258genetic_marker
TAMU_GH_TBb078C15f709TAMU_GH_TBb078C15f709genetic_marker
TAMU_GH_TBb083H08f198TAMU_GH_TBb083H08f198genetic_marker
TAMU_GH_TBh033B17f116TAMU_GH_TBh033B17f116genetic_marker
TAMU_GH_TBh035I01r479TAMU_GH_TBh035I01r479genetic_marker
TAMU_GH_TBh036E15r180TAMU_GH_TBh036E15r180genetic_marker
TAMU_GH_TBh037P04r277TAMU_GH_TBh037P04r277genetic_marker
TAMU_GH_TBb007K19r128TAMU_GH_TBb007K19r128genetic_marker
TAMU_GH_TBb007K19r318TAMU_GH_TBb007K19r318genetic_marker
TAMU_GH_TBb009K12r147TAMU_GH_TBb009K12r147genetic_marker
TAMU_GH_TBb009K12r639TAMU_GH_TBb009K12r639genetic_marker
TAMU_GH_TBb083H08f513TAMU_GH_TBb083H08f513genetic_marker
TAMU_GH_TBb083H08r322TAMU_GH_TBb083H08r322genetic_marker
TAMU_GH_TBb083H08r388TAMU_GH_TBb083H08r388genetic_marker
TAMU_GH_TBb092L11f286TAMU_GH_TBb092L11f286genetic_marker
TAMU_GH_TBh041C21f404TAMU_GH_TBh041C21f404genetic_marker
TAMU_GH_TBh041C21r310TAMU_GH_TBh041C21r310genetic_marker
TAMU_GH_TBh057E07f457TAMU_GH_TBh057E07f457genetic_marker
TAMU_GH_TBh074J09r413TAMU_GH_TBh074J09r413genetic_marker
TAMU_GH_TBb011K11f449TAMU_GH_TBb011K11f449genetic_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
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