Mining, genetic mapping and expression analysis of EST-derived resistance gene homologs (RGHs) in cotton

Background: Cotton is the dominant textile crop and also serves as an important oil crop. An estimated 15% economic loss associated with cotton production in China has been caused by diseases, and no resistance genes have been cloned in this crop. Molecular markers developed from resistance gene homologues (RGHs) might be tightly linked with target genes and could be used for marker-assisted selection (MAS) or gene cloning. Results: To genetically map expressed RGHs, 100 potential pathogenesis-related proteins (PRPs) and 215 resistance gene analogs (RGAs) were identified in the cotton expressed sequence tag database, and 347 specific primers were developed. Meanwhile, 61 cotton genome-derived RGA markers and 24 resistance gene analog polymorphism (RGAP) markers from published papers were included to view their genomic distribution. As a result, 38 EST-derived and 17 genome-derived RGH markers were added to our interspecific genetic map. These 55 markers were distributed on 18 of the 26 cotton chromosomes, with 34 markers on 6 chromosomes (Chr03, Chr04, Chr11, Chr17, Chr19 and Chr26). Homologous RGHs tended to be clustered; RGH clusters appeared on 9 chromosomes, with larger clusters on Chr03, Chr04 and Chr19, which suggests that RGH clusters are widely distributed in the cotton genome. Expression analysis showed that 19 RGHs were significantly altered after inoculation with the V991 stain of Verticillium dahliae. Comparative mapping showed that four RGH markers were linked with mapped loci for Verticillium wilt resistance. Conclusions: The genetic mapping of RGHs confirmed their clustering in cotton genome. Expression analysis and comparative mapping suggest that EST-derived RGHs participate in cotton resistance. RGH markers are seemed to be useful tools to detected resistance loci and identify candidate resistance genes in cotton.