Molecular Diversity and Population Structure Analysis of Oat (Avena sativa L.) Using Multi-Marker Profiling

Abstract

Modern genomics-assisted approaches enable high-resolution dissection of allelic variation within oat germplasm, paving the way for trait-based selection. Ensuring food and nutritional security begins with harnessing the full genetic potential of crop germplasm. In this study, the untapped genetic variability of oat (Avena sativa L.) germplasm was explored using a robust multi-marker system approach. A total of 62 oat accessions were molecularly characterized using three complementary marker systems - CAAT box-derived polymorphism (CBDP), sequence characterized amplified region (SCAR), and simple sequence repeats (SSR) - to uncover genetic diversity and structure within the population. Among 80 primers, 29 revealed clear polymorphisms, generating 128 alleles with an average of 4.41 alleles per primer. Notably, marker CBDP-10 produced the highest number of bands (10), underscoring its effectiveness in capturing genetic variation. Unique, genotype-specific bands were observed, demonstrating the precision of the markers in distinguishing diverse oat lines. SCAR markers proved particularly valuable in identifying traits linked to important quality attributes, such as β-glucan content and protein quality. Multivariate analysis, including Principal Component Analysis and Unweighted Pair Group Method with Arithmetic Mean-based clustering, revealed consistent genotype groupings, supported by STRUCTURE analysis, which partitioned the accessions into two distinct genetic subpopulations. A low but statistically significant correlation (Mantel test) between molecular and phenotypic/quality data matrices highlighted the reliability of molecular profiling in reflecting underlying trait diversity. This comprehensive molecular investigation offers key insights into the genetic landscape of oat germplasm and identifies promising markers for future breeding applications. By validating genetic distances, our findings provide insights into molecular diversity and identify genetically divergent accessions that may serve as potential parental resources for future oat improvement programs.