Genome-wide association study identifies candidate genes contributing to flowering time variation in Lotus japonicus in Japan

Flowering time is an important factor in plant fitness and local adaptation. Genome-wide association (GWA) studies have allowed the identification of candidate genes in certain plant species for various traits, including flowering time. Lotus japonicus is widely found throughout the Japanese archipelago. To obtain flowering time data with more prominent difference as more suitable indicator of environmental adaptation, flowering time data were collected for 132 wild accessions originating from various points across this region under shorter day length conditions than in previous studies. The results showed latitudinal variations in flowering time, with southern accessions flowering earlier. Comparing data from four flowering times with varying conditions revealed greater differences under a shorter day length. It is likely that day length significantly affects flowering time in this species. GWA analyses were conducted on flowering time variation measured in this study and the ratios between flowering time under different conditions. Candidate genes different from previous study were detected, including orthologues of known flowering time genes in each analysis. Correlation tests between flowering time and strongly detected single-nucleotide polymorphisms (SNPs) in the GWA analysis suggested that approximately 60% of flowering time variation can be explained by the two main SNPs. This result suggests that the majority of the variation could be explained by a small number of genetic factors. Considering the strong association with flowering time variation, these candidates may be responsible for these differences and therefore can be related to local adaptation in this species.