Genetic diversity and population structure analysis of aromatic rice germplasm using SSR markers

Genetic diversity and structure in aromatic rice

Abstract

Aromatic rice landraces represent a unique and valuable genetic resource due to their traditional, nutritional, and commercial significance. In the present study, 48 aromatic rice germplasm were evaluated for population structure and genetic diversity using 23 polymorphic simple sequence repeat (SSR) markers. The SSR markers revealed high levels of polymorphism, with polymorphic information content (PIC) values ranging from 0.47 to 0.88 (mean = 0.72) and gene diversity values ranging from 0.52 to 0.89 (mean = 0.75). Major allele frequencies ranged from 0.21 to 0.65. Population structure analysis grouped the germplasms into three distinct subpopulations (SP1, SP2, SP3), with five germplasms identified as admixtures. Cluster analysis using the UPGMA method further classified the germplasms into two major clusters and four subclusters. A clear geographic pattern was observed in the clustering: all eight germplasms from Punjab grouped closely within a single major cluster, while most germplasms from Chhattisgarh, Odisha, and Assam clustered together along with several Southeast Asian germplasm. Analysis of molecular variance showed that 84% of the total genetic variation existed among individuals within populations, while 16% was due to variation among populations. These results confirm the presence of substantial genetic diversity within aromatic rice germplasm and demonstrate the effectiveness of SSR markers in characterizing population structure. The findings provide a valuable genetic foundation for the selection of diverse parental lines, and conservation strategies aimed at improving and utilizing aromatic rice in crop improvement programs.