Fig. 4: Analyses of genetic diversity in the Sh1 and Pdh1 region and allele distribution in soybean populations.

a Genetic diversity (π) of G. soja (black), landrace with sh1 allele (brown) and landraces with pdh1 allele (blue) at the Sh1 and Pdh1 region on chromosome 16 (Zhonghuang 13 version 2) using 2,898 re-sequenced soybean accessions, including 103 G. soja, 1,048 landraces and 1,747 improved cultivars. 100-kb sliding windows with 10-kb steps were used. The selective sweep surrounding Sh1 (b) and Pdh1 (c). Individual vertical bars indicate 100-kb sliding windows with 10-kb steps. The selective sweep was identified by nucleotide diversity ratios of landrace with sh1 or pdh1 over the G. soja populations. d The frequencies of the causal mutations at sh1 and pdh1 positions in G. soja, landraces and cultivars. ‘G’ and ‘A’ indicate shattering susceptible and resistant alleles at Sh1, respectively. ‘T’ and ‘A’ indicated shattering susceptible and resistant alleles at Pdh1, respectively. e Co-selection of sh1 and pdh1 during domestication and improvements.