Comparative analysis of simple sequence repeats and synteny across ten Oryza species: Implications for stress response and genetic diversity

Abstract

Rice is a pivotal food source for most of the global population, necessitating a strategic focus on maximizing its production under diverse conditions through various methods. As molecular markers, simple sequence repeats (SSRs) emerge as instrumental tools in product enhancement and molecular research. This study employs in silico methods to predict the presence of molecular markers across distinct genomic and genic regions within ten Oryza species. Subsequently, we conducted a comprehensive comparison and synteny analysis of common molecular markers shared among most species, particularly those implicated in stress responses, utilizing McscanX. Beyond identifying common SSRs across the ten species under investigation, we delved into the functional analysis of these markers, specifically pinpointing those associated with stress. Additionally, our investigation illustrated the uniform distribution of SSRs along chromosomes and created a physical map showcasing their prevalence. Notably, chromosomes 1, 2, and 3 exhibited a higher density of molecular markers compared to their counterparts. Furthermore, our study highlighted that Oryza glumipatula, Oryza brachyantha, Oryza meridionalis, and Oryza longistaminata species manifested more pronounced differences in SSR markers compared to other Oryza species. The implications of these findings extend to applications in genetic diversity assessment, genetic mapping, and molecular marker-assisted selection breeding, providing valuable insights for future research and development in the field.