Genotyping, distribution and structure of Benin’s rice germplasm using Infinium 7k SNP array

Abstract Rice ( Oryza spp.) cultivation has expanded considerably in West Africa over the past two decades, becoming a major staple crop, particularly in Benin. This expansion has been driven by the introduction of improved interspecific varieties such as NERICA and IR841, which are well adapted to local agroecological conditions. However, the coexistence of Asian rice and African rice in traditional farming systems promotes seed exchange and natural hybridization, leading to morphologically similar phenotypes that complicate varietal identification and management. This study combines molecular and socioeconomic approaches to investigate the genetic diversity and structure of rice germplasm, assess interspecific introgression, and relate genetic patterns to farmers’ selection criteria. A total of 79 rice accessions, including 7 reference varieties (TOG5681, TO5307, CG14, Azucena, Moroberekan, IR64 and IR841), were genotyped using a 7K SNP array. After quality filtering, 5,526 SNPs were retained for downstream analysis. The genetic diversity indexes showed that there was moderate variability, with an average PIC of 0.27 and a low heterozygosity (He = 0.06). Multivariate, phylogenetic, and structure analyses consistently revealed a strong population structure, with four main genetic groups. Most accessions clustered within the indica group, while others were assigned to aus, tropical japonica, or O. glaberrima , with evidence of admixture and introgression. Farmers’ preference analysis identified productivity, vegetative cycle, and disease resistance as the most important selection criteria. These findings provide insights into the structure and evolution of rice germplasm in Benin and support the development of breeding strategies that integrate both genetic diversity and farmers’ needs.