Overcoming the genetic compensation response of soybean florigens to improve adaptation and yield at low latitudes

The classical soybean (Glycine max) trait long juvenile (LJ) is essentially a reduction in sensitivity to short-day (SD) conditions for induction and completion of flowering, and has been introduced into soybean cultivars to improve yield in tropical environments. However, only one locus, J, is known to confer LJ in low-latitude varieties. Here, we defined two quantitative trait loci contributing to the LJ trait, LJ16.1 and LJ16.2, and identified them as the florigen (FT) homologs FT2a and FT5a, respectively. The two selected florigen variations both delay flowering time under SD conditions by repressing the floral meristem identity gene GmAPETALA1. Single mutants have a relatively subtle effect on flowering time and displayed a substantial genetic compensation response, but this was absent in ft2a ft5a double mutants, which showed an enhanced LJ phenotype that translated to higher yields under SD conditions. A survey of sequence diversity suggests that FT2a and FT5a variants have diverse origins and have played distinct roles as soybean spread to lower latitudes. Our results show that integration of variants in the florigen genes offers a strategy for customizing flowering time to adjust adaptation and improve crop productivity in tropical regions. [Display omitted] •Natural variants of FT2a and FT5a confer the long-juvenile (LJ) trait in soybean•Selected FT variants repress AP1 and interact to enhance late maturity and yield•Single-ft mutants display genetic compensation, which is absent in double mutants•FT allelic diversification played distinct roles as soybean spread to the tropics Little is known about the genetics of soybean varieties adapted to low latitudes. Li et al. show variation in two florigen genes contributes to local adaptation and improved soybean yield. By exploiting combinations of alleles to overcome the genetic compensation response, this study offers a strategy to improve adaptation and crop productivity in tropical regions.