Genetic diversity of farmers' varieties of rice of central India using microsatellite and blast linked markers

The genetic diversity of 45 farmers' varieties collected from agro-climatic zones of central India were characterized using 26 simple sequence repeats (SSRs) and ten blast-linked markers. A total of 58 alleles representing 26 SSR loci were detected with frequency ranging from 2 to 4 (mean 2.23) alleles per locus. The polymorphism information content values for SSR markers varied from 0.50 to 0.88 for the primers RM449 and RM279, respectively. Further, the average marker index and effective multiplex ratio of 3.31 and 4.48 per primer, respectively could be observed. A dendrogram based on UPGMA exhibited clear-cut discrimination of the farmers' varieties into two major clusters representing their geographical origin. Out of ten blast resistance genes screened, only Pik-h was widely distributed with 97.8% frequency and farmers' variety Dihula Safed showed amplification for maximum of seven blast resistance genes. Inclusively, all the 45, indigenous farmers' varieties represented a wide range of genetic variability and SSR markers proved to be a powerful tool in revealing genetic diversity and relationships. The presence of different blast resistance genes in farmers' varieties with diverse traits can be utilized further in the future breeding programme.

Automated summary

This study characterized the genetic diversity of farmers' varieties in central India using SSR markers and blast-linked markers. The results showed clear geographical discrimination among the varieties and the presence of multiple blast resistance genes, which could be utilized in future breeding programs.