Exploring Allelic Variation between Rice Parental Lines via SSR-based Genotyping

Abstract

Rice productivity is increasingly threatened by climate change–induced water scarcity, necessitating the integration of molecular tools to improve breeding efficiency. The present study aimed to explore genome-wide allelic variation between two contrasting rice parental lines, HUR-917 and IR18A1145, through SSR-based genotyping to identify informative polymorphic markers for drought-related breeding applications. A total of 584 SSR markers distributed across the 12 rice chromosomes were screened using PCR amplification, and amplified products were resolved via agarose gel electrophoresis. Alleles were scored based on fragment size differences, and polymorphism percentage was calculated to assess genetic divergence between the parental lines. Out of the 584 markers screened, 158 exhibited clear polymorphisms, corresponding to a polymorphism rate of 25.68%. Chromosome 3 showed the highest number of polymorphic loci (18), while chromosome 8 exhibited the highest polymorphism frequency (32.65%). Dinucleotide repeat motifs predominated among the polymorphic markers, reflecting substantial allelic variability between the two parents. The moderate level of polymorphism indicates sufficient genetic divergence to enable effective parental differentiation and genomic tracking in downstream breeding programs. The identified polymorphic SSR markers provide a robust molecular resource for parental characterization and future marker-assisted breeding targeting drought-associated genomic regions, thereby supporting the development of resilient rice cultivars adapted to water-limited environments.