Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between gossypium hirsutum and G. barbadense.

Publication Overview
TitleGenome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between gossypium hirsutum and G. barbadense.
AuthorsYu Y; Yuan D; Liang S; Li X; Wang X; Lin Z; Zhang X
TypeJournal Article
Journal NameBMC Genomics
Volume12
Year2011
Page(s)15
CitationYu Y, Yuan D, Liang S, Li X, Wang X, Lin Z, Zhang X. Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between gossypium hirsutum and G. barbadense. BMC genomics. 2011; 12:15
Publication CodeBMCGN-12-15

Abstract

Background: Cotton, with a large genome, is an important crop throughout the world. A high-density genetic linkage map is the prerequisite for cotton genetics and breeding. A genetic map based on simple polymerase chain reaction markers will be efficient for marker-assisted breeding in cotton, and markers from transcribed sequences have more chance to target genes related to traits. To construct a genome-wide, functional markerbased genetic linkage map in cotton, we isolated and mapped expressed sequence tag-simple sequence repeats (EST-SSRs) from cotton ESTs derived from the A1, D5, (AD)1, and (AD)2 genome. Results: A total of 3177 new EST-SSRs developed in our laboratory and other newly released SSRs were used to enrich our interspecific BC1 genetic linkage map. A total of 547 loci and 911 loci were obtained from our EST-SSRs and the newly released SSRs, respectively. The 1458 loci together with our previously published data were used to construct an updated genetic linkage map. The final map included 2316 loci on the 26 cotton chromosomes, 4418.9 cM in total length and 1.91 cM in average distance between adjacent markers. To our knowledge, this map is one of the three most dense linkage maps in cotton. Twenty-one segregation distortion regions (SDRs) were found in this map; three segregation distorted chromosomes, Chr02, Chr16, and Chr18, were identified with 99.9% of distorted markers segregating toward the heterozygous allele. Functional analysis of SSR sequences showed that 1633 loci of this map (70.6%) were transcribed loci and 1332 loci (57.5%) were translated loci. Conclusions: This map lays groundwork for further genetic analyses of important quantitative traits, markerassisted selection, and genome organization architecture in cotton as well as for comparative genomics between cotton and other species. The segregation distorted chromosomes can be a guide to identify segregation distortion loci in cotton. The annotation of SSR sequences identified frequent and rare gene ontology items on each chromosome, which is helpful to discover functions of cotton chromosomes.
Features
This publication contains information about 3,177 features:
Feature NameUniquenameType
HAU1281HAU1281genetic_marker
HAU1282HAU1282genetic_marker
HAU1283HAU1283genetic_marker
HAU1284HAU1284genetic_marker
HAU1285HAU1285genetic_marker
HAU1286HAU1286genetic_marker
HAU1287HAU1287genetic_marker
HAU1288HAU1288genetic_marker
HAU1289HAU1289genetic_marker
HAU1290HAU1290genetic_marker
HAU1291HAU1291genetic_marker
HAU1292HAU1292genetic_marker
HAU1293HAU1293genetic_marker
HAU1294HAU1294genetic_marker
HAU1295HAU1295genetic_marker
HAU1296HAU1296genetic_marker
HAU1297HAU1297genetic_marker
HAU1298HAU1298genetic_marker
HAU1299HAU1299genetic_marker
HAU1300HAU1300genetic_marker
HAU1301HAU1301genetic_marker
HAU1302HAU1302genetic_marker
HAU1303HAU1303genetic_marker
HAU1304HAU1304genetic_marker
HAU1305HAU1305genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
Emian-22 x 3-79, BC1 (2011)
Properties
Additional details for this publication include:
Property NameValue
Journal AbbreviationBMC Genomics
DOI10.1186/1471-2164-12-15
Elocation10.1186/1471-2164-12-15
Publication ModelElectronic
ISSN1471-2164
Publication Date2011
Publication TypeResearch Support, Non-U.S. Gov't
Language Abbreng
Publication TypeJournal Article
Journal CountryEngland
eISSN1471-2164
Journal CodeBMCGN
LanguageEnglish
Publication CodeBMCGN-12-15
Published LocationEngland