Signatures of soft sweeps across the Dt1 locus underlying determinate growth habit in soybean [Glycine max (L.) Merr.]

Determinate growth habit is an agronomically important trait associated with domestication in soybean. Previous studies have demonstrated that the emergence of determinacy is correlated with artificial selection on four non-synonymous mutations in the Dt1 gene. To better understand the signatures of the soft sweeps across the Dt1 locus and track the origins of the determinate alleles, we examined patterns of nucleotide variation in Dt1 and the surrounding genomic region of approximately 800 kb. Four local, asymmetrical hard sweeps on four determinate alleles, sized approximately 660, 120, 220 and 150 kb were identified, which constitute the soft sweeps for the adaptation. These variable-sized sweeps substantially reflected the strength and timing of selection, and indicated that the selection on the alleles had been completed rapidly within half a century. Statistics of EHH, iHS, H12 and H2/H1 based on haplotype data had the power to detect the soft sweeps, revealing distinct signatures...