Genetic Diversity and Core Germplasm Development in Yunnan Tartary Buckwheat Based on Phenotypic and SNP Data

Southwest China harbors the world’s richest germplasm resources of Tartary buckwheat (Fagopyrum tataricum). However, their effective utilization is severely constrained by poor management and narrow genetic diversity. Developing a core collection is a key strategy for overcoming these bottlenecks and facilitates the efficient conservation and utilization of germplasm resources. Therefore, we aimed to assess the genetic diversity and population structure of a Tartary buckwheat germplasm collection from Yunnan Province and adjacent regions to establish a core collection. Whole-genome resequencing and phenotyping of four key agronomic traits were performed on 313 Tartary buckwheat accessions. Population genetic structure, differentiation, and diversity parameters were analyzed using single-nucleotide polymorphism (SNP) data. We obtained 3,433,676 high-quality SNP markers. The 313 accessions were classified into four ancestral populations and three phylogenetic groups, which revealed the complex patterns of genetic differentiation and gene flow. Phenotypic traits exhibited high genetic diversity, with wide variation ranges in key agronomic traits such as plant height, stem diameter, and branching characteristics, highlighting the richness of the germplasm resources. By integrating the phenotypic and SNP data, we constructed a core collection (Core-Merge) comprising 105 accessions (33.55% of the original collection). Core-Merge showed no significant differences in phenotypic traits compared to the original collection, exhibited a similar distribution in principal coordinate analysis, and demonstrated low kinship among individuals. The collection established in this study, Core-Merge, captures the maximum phenotypic and genotypic variability present in the original germplasm. The core germplasm collection provides a valuable foundation for the efficient conservation of, genetic research on, and molecular breeding of Tartary buckwheat.