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Genetic diversity study of indigenous rice accessions from northern mountainous areas of Pakistan using microsatellite/SSR markers

A total of 96 indigenous rice accessions from Northern areas of Pakistan were used as research material, while IR6, JP5, Nipponbare, and Super-basmati were included as check for comparison. Total genomic DNA was isolated from dehusked dry seeds and young seedlings of all the lines using standard protocols utilizing 36 SSR primers distributed over 12 chromosomes of rice. The major objective of the present study was to estimate the genetic diversity within and among the subpopulation of indigenous rice accessions and secondly to examine the extent of population structure of indigenous rice germplasm from northern Pakistan. A total of 127 different scorable and reproducible alleles were scored. The total number of alleles per loci amplified by each SSR primer ranged from 2-7 with an average of 3.5 alleles per locus. The PIC values ranged widely among loci from 0.39 (RM240 on chromosome 2) to 0.80 (RM119 on chromosome 4) with an average of 0.638 per locus. UPGMA (unweighted pair group method) analysis clustered rice accessions into eight major groups, I to VIII effectively differentiating most of the japonica and other short and long non-aromatic accessions. Microsatellites showed sufficient variation to distinguish between indica and japonica type. A number of SSR markers obtained could be used to generate indica and japonica specific markers, and to differentiate rice grown at high altitudes of Northern Pakistan into two different groups.