Genome-wide association study and candidate gene prioritization for stem architectural traits in Tartary buckwheat

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.