Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing

Publication Overview
TitleEnrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing
AuthorsWang H, Jin X, Zhang B, Shen C, Lin Z
TypeJournal Article
Journal NameDNA research : an international journal for rapid publication of reports on genes and genomes
Year2015
CitationWang H, Jin X, Zhang B, Shen C, Lin Z. Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing. DNA research : an international journal for rapid publication of reports on genes and genomes. 2015 Feb 5.

Abstract

RAD sequencing was performed using DH962 and Jimian5 as upland cotton mapping parents. Sequencing data for DH962 and Jimian5 were assembled into the genome sequences of ≈55.27 and ≈57.06 Mb, respectively. Analysing genome sequences of the two parents, 1,323 SSR, 3,838 insertions/deletion (InDel), and 9,366 single-nucleotide polymorphism (SNP) primer pairs were developed. All of the SSRs, 121 InDels, 441 SNPs, and other 6,747 primer pairs were screened in the two parents, and a total of 535 new polymorphic loci were identified. A genetic map including 1,013 loci was constructed using these results and 506 loci previously published for this population. Twenty-seven new QTLs for yield and fibre quality were identified, indicating that the efficiency of QTL detection was greatly improved by the increase in map density. Comparative genomics showed there to be considerable homology and collinearity between the AT and A2 genomes and between the DT and D5 genomes, although there were a few exchanges and introgressions among the chromosomes of the A2 genome. Here, the development of markers using parental RAD sequencing was effective, and a high-density intraspecific genetic map was constructed. This map can be used for molecular marker-assisted selection in cotton.

Germplasm
This publication contains information about 1 stocks:
Stock NameGRIN IDSpeciesType
DH962 X Ji Mian 5, F2Gossypium hirsutumpopulation
Features
This publication contains information about 1,955 features:
Feature NameUniquenameType
HAU-DJ-S257HAU-DJ-S257genetic_marker
HAU-DJ-S258HAU-DJ-S258genetic_marker
HAU-DJ-S259HAU-DJ-S259genetic_marker
HAU-DJ-S260HAU-DJ-S260genetic_marker
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HAU-DJ-S281HAU-DJ-S281genetic_marker

Pages

Projects
This publication contains information about 1 projects:
Project NameDescription
DJiM-F2-2015
Featuremaps
This publication contains information about 1 maps:
Map Name
DH962 X Ji Mian 5, F2 (2015)
Properties
Additional details for this publication include:
Property NameValue
ISSN1756-1663
Language AbbrENG
Elocationdsu047
Publication TypeJournal Article
eISSN1756-1663
URLhttps://academic.oup.com/dnaresearch/article/22/2/147/332826
Publication Date2015 Feb 5
Publication ModelPrint-Electronic
LanguageEnglish
Journal AbbreviationDNA Res.
Copyright© The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.