Genetic Diversity and Population Structure of Mozambican Lowland Rainfed Rice (Oryza sativa L.) Using DArTseq SNP Markers

Rice (Oryza sativa L.) is an important staple crop in Mozambique, and understanding its genetic diversity is essential for crop improvement, genetic resources management and conservation. However, molecular characterization of Mozambican rice germplasm remains limited. This study assessed genetic diversity and population structure of 40 lowland rainfed rice genotypes using 3473 high-quality single nucleotide polymorphism (SNP) markers generated through DArTseq™ genotyping-by-sequencing platform. Results revealed moderate genetic diversity with a mean polymorphism information content of 0.25, indicating moderate marker informativeness. Unbiased expected heterozygosity (uHe = 0.314) was higher than observed heterozygosity (Ho = 0.125), reflecting the inbreeding nature of rice (FIS = 0.357). Model-based admixture analysis identified four subpopulations, with 20% of genotypes classified as admixed. Substantial genetic differentiation was observed among these subpopulations (FST = 0.267), which was broadly consistent with the principal coordinate analysis and the neighbor-joining tree. Furthermore, a high mean Manhattan dissimilarity index (0.70), indicated strong genetic divergence across the panel. Analysis of molecular variance revealed significant variation among subpopulations (32.90%) and within subpopulations (67.10%). These findings provide foundational genetic insights to guide Mozambican rice breeding programs and support the long-term conservation of local germplasm.