Genetic and Environmental Determinants Underlying the Dynamics of Soybean Flowering Time

Flowering time, determined by genetic loci and environmental cues, is crucial for soybeans' geographic distribution and regional adaptability. This study aimed to generate a workflow of genetic and environmental analysis for determinants of soybean flowering time. By investigating flowering time in both natural populations and recombinant inbred lines (RIL) across eight environments spanning from 18°15'10″ N to 43°49'02″ N across two years, we found that photothermal ratio (PTR) strongly correlated with early- and mid-pre-flowering stages (16-23 days after planting). We detected 298 Quantitative Trait Locus (QTLs) in the natural population and 20 QTLs in the RIL for trait mean and 6 plasticity indicators, with 6 QTLs and 58 QTLs overlapping. Notably, seven quantitative trait nucleotide (QTNs) and eight QTN by environment interactions were colocalised with the above plasticity QTLs. By integrating 82 main-effect, plasticity and genotype-by-environment (G×E) interaction loci and environmental index PTR_16-23, we proposed a simplified and stable prediction model with an average 4.40% and 2.42% increase in accuracy for flowering time in a single environment and across environments over that of 1726 genome-wide flowering time loci, respectively. This study propels the field of adapting diverse genotypes to dynamic environments and addressing the challenges posed by climate change.