Genic Microsatellite Markers Based Characterization in Relation to Aerobic Adaptation of Rice Genotypes

Abstract

This study aimed to evaluate the genetic variation among rice genotypes to identify the entries with superior adaptation under aerobic cultivation and to determine the candidate gene-derived SSR markers based differentiation and divergence in relation to aerobic adaptation. The current experiment was conducted in the Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa Samastipur, Bihar, during the two Kharif seasons (2023 and 2024). Adopting a Randomized Block Design with three replications, 36 rice genotypes were evaluated across two consecutive growing seasons for grain yield per plant under aerobic and normal conditions, and genetic variation among rice genotypes was assessed using candidate gene-derived SSR markers. Genotypic performance was further analyzed using best linear unbiased prediction (BLUP) and genotypic adaptation was assessed based on relative mean performance and percentage change. Analysis of variance revealed significant (p < 0.01) genetic variation and genotype × environment interaction for this trait. Based on the relative mean performance and percentage change, 17 genotypes were classified as highly adapted to aerobic condition. Molecular profiling based on ten candidate gene-targeted genes specific 16 newly developed microsatellite markers detected altogether 47 allelic variants with an average of 2.9 alleles per primer. Allelic richness was observed for OsSAUR45a, OsNAR2.1a and OsNBS-LRRa, which are functionally associated with root architecture, nitrate uptake and aerobic adaptation, respectively. Polymorphism information content values ranged from 0.415 to 0.742, with a mean of 0.555, indicating a moderate to high level of polymorphism, suitable for diversity analysis. Cluster analysis based on molecular data grouped the genotypes into four major clusters, with PCoA supporting the spatial distribution of genetic profiles. This highlighted substantial genetic differentiation and divergence within the panel of genotypes under evaluation. The polymorphic markers identified along with the aerobically adapted and genetically diverse genotypes, offer valuable tools for genetic improvement in breeding programs aimed at developing rice cultivars optimized for aerobic production systems.