Molecular diversity comparison in local rice accessions originated from Kalimantan and other islands of Indonesia

Indonesian local rice accessions are well cultivated, including in Kalimantan Island, along with diverse ecogeography and agricultural practices. The diversity existed in the local varieties constitutes valuable genetic resources for sustainable conservation and utilization. This study aimed to investigate the genetic diversity of local rice accessions predominantly from Kalimantan in comparison with other local origins’ accessions using simple sequence repeats (SSR) markers. A total of 48 local rice accessions of which 29 accessions originating from Kalimantan and the remaining 19 accessions from other regions in Indonesia were subjected to molecular diversity using 15 SSR markers. The SSR polymorphism revealed that 193 alleles with an average major allele frequency of 0.2 were observed. Considerable high genetic diversity was detected in these Indonesian local accessions as reflected by the average Polymorphic Information Content value and gene diversity index of 0.86 and 0.87, respectively. The dendrogram based on UPGMA and Nei’s genetic distance classified the 48 rice accessions into five clusters. The local varieties from Kalimantan dominated two clusters out of four clusters belonging with, indicating their close genetic relationship. These SSR markers demonstrated differentiation among local rice from Kalimantan according to the individual genetic properties rather than their geographical origins. Four out of the 29 Kalimantan’s rice accessions having most far distance with others derived from different islands, could be used as crossing parents after further evaluation of their phenotypic traits.