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.

Buckwheat (Fagopyrum tataricum) is native to Yunnan, China, and as a miscellaneous grain crop with high nutritional value, it has received increased attention from farmers and enterprises in recent years. In June 2024, we observed severe anthracnose in the buckwheat cultivation area in Malu Township and Jiache Township, Huize County, Qujing City, Yunnan Province, China. In this study, six isolates (SM01–SM06) of anthracnose with similar morphology were obtained using the tissue isolation method, which was due to the fact that this disease is highly pathogenic to buckwheat. The strain SM02 was selected as a representative isolate for biological characterization and molecular phylogenetic analysis, and a phylogenetic tree was constructed based on the ACT, CHS, and ITS genes to determine its taxonomic status. The selected SM02 isolate was further identified as Colletotrichum kahawae. Biological characterization showed that the representative strain SM02 exhibited optimal growth for in vitro cultivation under a photoperiod, temperature, pH, carbon source, and nitrogen source of 12L:12D, 25 °C, pH 7.0, glucose, and beef extract, respectively. Host range testing demonstrated that C. kahawae might infect important field crops, including maize, wheat, oats, and potatoes. In conclusion, C. kahawae causes buckwheat anthracnose in China, which might hinder the production of buckwheat. This study provides insight into anthracnose disease in buckwheat and provides a basis for further investigations to assess and implement effective disease management strategies.

Stem architecture is a key determinant of lodging resistance, yield potential, and mechanical harvestability in Tartary buckwheat ( Fagopyrum tataricum ), yet the genetic basis of stem-related traits remains poorly understood. In this study, a diverse panel of 244 Tartary buckwheat accessions was evaluated for five stem architectural traits, including plant height (PH), stem diameter (SD), branch number on the main stem (BNMS), node number on the main stem (NNMS), and stem wall thickness (TST), across three field environments (Huize 2025, Songming 2024, and Songming 2025). Genome-wide association study (GWAS) was performed using 280,377 high-quality Single Nucleotide Polymorphisms (SNPs) to identify loci associated with stem architecture traits. Substantial phenotypic variation was observed for all traits, with broad-sense heritability varying among traits and environments, likely reflecting the high sensitivity of Tartary buckwheat to environmental conditions across the three contrasting field environments. Strong positive correlations were detected between PH and NNMS, while SD and TST showed weak correlations with other traits, indicating partially independent genetic control. GWAS identified a major significant association region on chromosome (Chr) 4 affecting both PH and NNMS (Chr4: 31011474–31099420), while BNMS, SD, and TST displayed more dispersed or polygenic genetic architectures. Candidate genes within associated regions were mainly annotated to functions related to cell-wall modification, developmental regulation, and metabolic processes, suggesting potential mechanisms underlying stem architecture variation. Cross-trait analysis revealed extensive shared genetic control between PH and NNMS but relatively independent genetic regulation of BNMS and stem mechanical traits. These findings provide novel insights into the genetic architecture of stem traits in Tartary buckwheat and identify candidate loci for marker-assisted breeding of optimized plant architecture. Because PH and NNMS on the one hand and BNMS, SD and TST on the other are under largely independent genetic control, the Chr4 block and the trait-specific loci identified here can be combined by marker-assisted pyramiding to develop lodging-resistant, mechanization-ready cultivars.