Microsatellite marker based characterization and divergence analysis among rice varieties

Abstract

The simple sequence repeat (SSR) marker analysis was carried out to determine the diversity among 18 rice varieties grown in Bihar. In total, 223 alleles were detected at the 30 SSR loci, of which all were polymorphic. The number of alleles generated by each marker ranged from 3 to 12 with an average 7.43 alleles per locus. The size of alleles ranged from 66 (RM 161) to 607 bp (RM 128). Polymorphism information content (PIC) values ranged 0.059 (RM 161) to 0.929 (RM 429) with an average of 0.665 per marker. A dendrogram based on SSR polymorphism grouped all the 18 rice varieties into three major clusters, effectively differentiating the long, medium and short period of maturity varieties, except Richharia that has short maturity period but placed with medium maturity period varieties. It could be concluded that SSR markers are powerful tools to assess the genetic diversity of the varieties. The knowledge about genetic diversity will be helpful to select parental plant for hybridization according to the changing climate.