Genetic Control and Eco-Geographic Adaption of Pod Dehiscence during Soybean Domestication.

Loss of pod shattering (indehiscence) is a key step during soybean [Glycine max (L.) Merr.] domestication. We report that a single nucleotide substitution leading to a truncated NST1A is associated with pod indehiscence in soybean. However, the pod indehiscence conferred by NST1A can be overcome by the dehiscence at Pdh1 that promotes the torsion force of the pod walls. Alleles distribution analysis of the soybean landraces in China indicated that the level of pod indehiscence increases from South to North. In Southern China (SC), the indehiscence at NST1A alone is able to cope with pod shattering, whereas the indehiscence at Pdh1 is essential for soybean domestication in Northern China. In Northeast China (NEC), however, the indehiscence of both loci is required. Further geo-climatic investigation revealed strong but negative correlation (r = -0.75, P < 10^-5) between the regional composition of indehiscent Pdh1 and the relative humidity. Based on the origin of indehiscent allele and the constitution of the indehiscent alleles at each region, this study suggests that Huang-Huai-Hai valleys and SC, but not NEC, are the centers of origin of cultivated soybean. This study demonstrated that soybean domestications have strong topographic signatures as part of the genome adaptation to the environmental conditions. It also provides insights into the soybean expansion and rapid domestication of wild legume species.