Population structure and ecotype‐associated genomic differentiation in Bangladeshi rice germplasm ( Oryza sativa L.)

In Bangladeshi rice (Oryza sativa L.) germplasm, cultivars or landraces are traditionally classified into four principal ecotypes based on seasonal moisture regimes: Boro, Aman, Aus, and Jhum. The relationships among ecotype differentiation, genomic ancestry, and population structure remain poorly understood. We investigated the genetic diversity and population structure of 333 Bangladeshi rice accessions with respect to their ecotype classification. We identified a total of 25,994 single nucleotide polymorphism (SNP) markers across the whole genome of this panel. From the SNP data and discriminant analysis of principal components, STRUCTURE analysis, genetic diversity analysis, and neighbor-joining analyses, we identified three groups, corresponding to Aromatic, Indica, and Aus. They differed in both genetic ancestry and degree of ecotype-associated differentiation. Aus consisted of all four ecotypes and showed clear ecotype-associated differentiation, suggesting adaptation to distinct ecological environments. Aromatic accessions shared a common genetic background and maintained partial ecotype-associated differentiation between Aman and Boro. Indica showed reduced genetic diversity and weak ecotype differentiation, reflecting intensive crop improvement and ecotype admixture. The genomic population structure of Bangladeshi rice germplasm was therefore shaped by both ecological adaptation and human-mediated selection across distinct ancestry groups. Our findings provide deeper insights into the genetic and ecological foundations of this germplasm, supporting its future use in genome-wide association studies and genomic prediction and its exploitation for rice improvement in Bangladesh and beyond.