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Loss of pod dehiscence is a key step during soybean [Glycine max (L.) Merr.]domestication. Genome-wide association analysis for soybean shatteringidentified loci harboring Pdh1, NST1A and SHAT1-5. Pairwise epistaticinteractions were observed, and the dehiscent Pdh1 overcomes the resistanceconferred by NST1A or SHAT1-5 locus, indicating that Pdh1 predominates poddehiscence expression. Further candidate gene association analysis identified anonsense mutation in NST1A associated with pod dehiscence. Allele compositionand population differential analyses unraveled that Pdh1 and NST1A, but notSHAT1-5, underwent domestication and modern breeding selections. Geographicanalysis showed that in Northeast China (NEC), indehiscence at both Pdh1 andNST1A were required by cultivated soybean; while indehiscent Pdh1 alone iscapable of coping shattering in Huang-Huai-Hai (HHH) valleys where itoriginated; and no specific indehiscence was required in Southern China (SC).Geo-climatic investigation revealed strong correlation between relativehumidity and frequency of indehiscent Pdh1 across China. This studydemonstrates that the epistatic interaction between Pdh1 and NST1A fulfills apivotal role in determining the level of resistance against pod dehiscence.Humidity shapes the distribution of indehiscent alleles. Our results alsosuggest that HHH valleys, not NEC, was at least one of the origin centers ofcultivated soybean.

Genetic control and geo-climate adaptation of pod dehiscence provide novel insights into the soybean domestication and expansion