Short-Day Legume Crops Exhibit a Conserved Molecular-Genetic Basis for Early Flowering, Maturity and Adaptation to Long-Day Environments in High-Latitude Regions

Originating from low and middle latitudes, soybean, common bean, mung bean, and adzuki bean are typical short-day legumes. Through long-term natural evolution and artificial selection, numerous ultra-early maturing varieties adapted to long-day conditions have emerged in these four short-day legumes, becoming a crucial component of agricultural ecosystems in high-latitude regions. Therefore, investigations into the molecular mechanisms governing flowering time and exploration of adaptive mechanisms across diverse short-day legumes are critically essential. In this study, we identified the homologous of soybean key flowering-time genes including E1–E4, GmFT2a, and GmFT5a in common bean, mung bean, and adzuki bean through Blastp. Phylogenetic analysis revealed close genetic relationships, with soybean clustering with common bean, while mung bean and adzuki bean are more closely related. Through cloning of the coding sequences of E1–E4, FT2a, and FT5a homologs in both late and early maturing varieties of soybean, common bean, mung bean, and adzuki bean, natural variations and haplotypes were analyzed and identified. We found that frameshift/nonsynonymous mutations in E1–E4 homologs correlated with early maturity, whereas FT orthologs remained highly conserved in ultra-early maturing varieties of four short-day legumes. Distinct E‑genotype combinations emerged as ecological signatures—ultra-early soybean (e1e2e3e4), common bean (E1e2e3e4), and mung/adzuki beans (e1E2e3e4). Expression levels of E1–E4 in the ultra-early maturing varieties of four short-day legumes were generally lower than in the late maturing varieties, while FT2a/FT5a homologs exhibited the opposite trend. This study reveals the variation hotspots in major flowering genes of short-day legumes and establishes genotype combinations for varieties from different ecological types. These findings provide molecular targets for breeding short-day legume varieties adapted to high-latitude, long-day conditions and offer scientific guidance for expanding the cultivation areas of short-day legumes.