Elucidating the genetic diversity and population structure of African rice (Oryza glaberrima) germplasm using microsatellite markers

Abstract

The enhancement of genetic traits in any crop variety significantly relies on the existing diversity within the population, enabling the creation of resilient plants to ensure a consistent food supply. As Oryza glaberrima species still persist as an unexplored source of genetic and allelic variants of potential value, the current study was conducted in order to assess the morpho-molecular diversity among 31 accessions of O. glaberrima and a mega-check variety. The findings revealed a considerable genetic base in the rice germplasm, characterized by 44 polymorphic SSRs producing 136 alleles. The allele frequency varied from 0.4375 to 0.9688, with Polymorphic Information Content (PIC) values between 0.0587 and 0.6136 and an average gene diversity of 0.3318. Markers RM22171, RM25310, SSR12-4.8, SSR-8.6, SSR9-15.7 and SSR9-9.5 excelled due to their higher allele number, gene diversity and PIC, attributing their utility in identifying diverse genotypes. Marker-trait association (MTA) studies revealed RM190, SSR-8.6, and RM6748 with potential applicability in marker-assisted breeding programs due to their association with spikelets per panicle. Moreover, the grouping of the accessions based on molecular phylogeny is concurrent with the population structure and principal coordinate analysis pattern in the present study. However, on examining the clusters formed through agro-morphological and molecular data, only a few common accessions were observed to be grouped, emphasizing the necessity of integrating both approaches for a comprehensive understanding of genetic variability. Altogether, EC861804 and EC861818 stand out as the diverse accessions that could be utilized as potential genetic resources in rice improvement programs with the utilization of the gene-linked markers unearthed from the current study.