Tartary buckwheat cotyledon size varieties undergo distinct transcriptional reprogramming of phytohormone signaling under cold and UV stresses

Fagopyrum tataricum (TB) is a characteristic high-altitude crop in China. The cotyledon, as a key photosynthetic and nutrient storage organ at the seedling stage, plays critical roles in early growth and stress tolerance, but the molecular linkage between cotyledon size and abiotic stress resistance remains unclear. In this study, 279 TB accessions were phenotyped for cotyledon area, height, and width across three ecological regions over two consecutive years, and were classified into large, medium, and small cotyledon types via phenotypic clustering analysis. Two representative accessions, Ft104 (large cotyledon) and Ft32 (small cotyledon), were selected for further experiments. Cytological observations showed that cotyledon size was associated with differences in epidermal cell size and density, with small-cotyledon accessions exhibiting a higher number of cells per unit area. Physiological assays at the germination stage demonstrated that small-cotyledon accessions exhibited faster water absorption, stronger seedling emergence capacity, and more stable degradation of storage substances. Under low-temperature and UV-B stress, small-cotyledon accessions accumulated less malondialdehyde (MDA) and displayed significantly higher activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT), indicating enhanced stress tolerance. Transcriptomic analysis and WGCNA identified 18 co-expression modules, of which MEcoral4 was associated with cotyledon morphology and stress-related physiological traits and was enriched in plant hormone signal transduction. Three candidate genes, FtAUX22D, FtARG7, and FtPYL4, were further examined by qRT-PCR across multiple accessions. Heterologous expression in yeast provided preliminary evidence that FtPYL4 enhances cold-stress tolerance. Targeted LC-MS/MS profiling further revealed genotype-dependent changes in endogenous phytohormones and auxin-related metabolites, with Ft32 showing higher accumulation of several indole-related metabolites and SA under stress, whereas Ft104 exhibited a pronounced JA response to UV-B. Together, these results indicate an association between cotyledon-size phenotype and abiotic-stress responses involving phytohormone-related transcriptional and metabolic reprogramming in Tartary buckwheat.