Novel biotic stress responsive candidate gene based SSR (cgSSR) markers from rice

Developing host resistance is an effective measure to minimize the yield losses caused by biotic stresses in crop plants. Generation of genomic resources greatly facilitates the development of resistant plants. Microsatellite markers speed up the selection procedure and introgression of resistant alleles in rice breeding programme. Candidate gene based SSR (cgSSR) markers are preferred over genomic SSR due to their tighter linkage with the trait governing loci. This study describes the identification and analysis of cgSSR markers from biotic stress responsive genes of rice. Among the selected 308 different biotic stress responsive genes of rice, 176 gene sequences were found to harbour a total of 364 SSR loci. Tri-nucleotide motif was found to be the most abundant (51.09%), followed by di- (45.05%) and tetra-nucleotide (3.84%). Intron and CDS are the two locations where most of the cgSSR loci were found, followed by 5UTR and 3UTR. In order to validate, polymorphism survey was done in 25 Oryza sativa genotypes using 35 cgSSR primer pairs. Among the 35 cgSSR, 27 cgSSR exhibited loci specific amplification with an average allele number of 5.66 per primer and mean PIC value of 0.226. Further, out of 27, 21 cgSSRs were found to be cross transferable to the wild species belonging to the Sativa complex; while 19 were found to be transferable to the species belonging to the Officinalis complex. The novel biotic stress-responsive cgSSR markers developed here could be used in marker-assisted introgression and pyramiding of resistant allele into elite rice cultivars from other rice germplasm as well as from wild relatives of rice.