Assessment of seventy-three rice germplasm by using simple sequence repeats markers

Abstract

Genetic information of germplasm is the initial requirement for crop breeding programs. Rice is one of the oldest domesticated crop species endowed with rich genetic diversity which accounts for over 100,000 landraces and improved cultivars. The aim of the present study was to evaluate the genetic assessment of rice germplasm originating from India, the Philippines, China, and Malaysia through simple sequence repeat (SSR) markers. About 64 alleles were produced over 24 SSR primer amplifications over the whole genome of rice. The number of alleles ranged from 1 to 4 with an average of 2.67. Out of 64 amplified bands, 58 bands were polymorphic and 6 were monomorphic bands. Most of the primers showed high polymorphic information content (PIC). The PIC value ranged from 0.53 to 0.87. The cluster analysis indicates that the 73 varieties originating from India, the Philippines, China, and Malaysia were grouped separately and made two major clusters (seven groups). Among the two major clusters, one cluster had 18 genotypes which originated from the Phillipines, and China with 29% similarity with other varieties originating from India and Malaysia. Further, it was divided into two subgroups which had eight genotypes and the other had 10 genotypes with 41% similarity among themselves. All 10 genotypes were international varieties suitable for cultivation in medium land ecosystems. The second major cluster had 55 varieties including commercial rice varieties originating from India and Malaysia. The genotype ‘Swarna’ and ‘Manaswini’ had 76% similarity with each other and 69% similarity with the ‘Bhanja’ & ‘Ghanteswari’ which might be the genome association. The second major cluster had 55 genotypes divided into two minor groups. The first group had one genotype, i.e. ‘IR 63141-B-18-B’ with 34% similarity with the other 54 genotypes. The second minor group (54 genotypes) again was divided into two groups; one group had five genotypes with 51% similarity. Another group had 49 genotypes divided into two sub-minor groups. Based on this study, the larger range of similarity values using SSR markers provides greater confidence for the assessment of genetic relationships among the varieties. These genotypes are suitable for cultivation in upland ecosystems. The information obtained from the SSR profile helps to identify the variety diagnostic markers in 73 rice germplasm accessions. The intra- and inter-variation might be useful for breeders to improve the rice varieties through selective breeding and cross breeding programs.