Genome-wide analysis of the gene families of resistance gene analogues in cotton and their response to Verticillium wilt

Publication Overview
TitleGenome-wide analysis of the gene families of resistance gene analogues in cotton and their response to Verticillium wilt
AuthorsChen JY, Huang JQ, Li NY, Ma XF, Wang JL, Liu C, Liu YF, Liang Y, Bao YM, Dai XF
TypeJournal Article
Journal NameBMC plant biology
Volume15
Issue1
Year2015
Page(s)148
CitationChen JY, Huang JQ, Li NY, Ma XF, Wang JL, Liu C, Liu YF, Liang Y, Bao YM, Dai XF. Genome-wide analysis of the gene families of resistance gene analogues in cotton and their response to Verticillium wilt. BMC plant biology. 2015; 15(1):148.

Abstract

BACKGROUND
Gossypium raimondii is a Verticillium wilt-resistant cotton species whose genome encodes numerous disease resistance genes that play important roles in the defence against pathogens. However, the characteristics of resistance gene analogues (RGAs) and Verticillium dahliae response loci (VdRLs) have not been investigated on a global scale. In this study, the characteristics of RGA genes were systematically analysed using bioinformatics-driven methods. Moreover, the potential VdRLs involved in the defence response to Verticillium wilt were identified by RNA-seq and correlations with known resistance QTLs.

RESULTS
The G. raimondii genome encodes 1004 RGA genes, and most of these genes cluster in homology groups based on high levels of similarity. Interestingly, nearly half of the RGA genes occurred in 26 RGA-gene-rich clusters (Rgrcs). The homology analysis showed that sequence exchanges and tandem duplications frequently occurred within Rgrcs, and segmental duplications took place among the different Rgrcs. An RNA-seq analysis showed that the RGA genes play roles in cotton defence responses, forming 26 VdRLs inside in the Rgrcs after being inoculated with V. dahliae. A correlation analysis found that 12 VdRLs were adjacent to the known Verticillium wilt resistance QTLs, and that 5 were rich in NB-ARC domain-containing disease resistance genes.

CONCLUSIONS
The cotton genome contains numerous RGA genes, and nearly half of them are located in clusters, which evolved by sequence exchanges, tandem duplications and segmental duplications. In the Rgrcs, 26 loci were induced by the V. dahliae inoculation, and 12 are in the vicinity of known Verticillium wilt resistance QTLs.

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Additional details for this publication include:
Property NameValue
URLhttp://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-015-0508-3
eISSN1471-2229
ISSN1471-2229
Journal AbbreviationBMC Plant Biol.
LanguageEnglish
Language AbbrENG
Publication Date2015
Publication ModelElectronic
Publication TypeJournal Article
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PMID: PubMedPMID:26084488