Genomic footprints of sorghum domestication and breeding selection for multiple end uses

Domestication and diversification have had profound effects on crop genomes. Originating in Africa and subsequently spreading to different continents, sorghum (Sorghum bicolor) has experienced multiple onsets of domestication and intensive breeding selection for various end uses. However, how these processes have shaped sorghum genomes is not fully understood. In the present study, population genomics analyses were performed on a worldwide collection of 445 sorghum accessions, covering wild sorghum and four end-use subpopulations with diverse agronomic traits. Frequent genetic exchanges were found among various subpopulations, and strong selective sweeps affected 14.68% (∼107.5 Mb) of the sorghum genome, including 3649, 4287, and 3888 genes during sorghum domestication, improvement of grain sorghum, and improvement of sweet sorghum, respectively. Eight different models of haplotype changes in domestication genes from wild sorghum to landraces and improved sorghum were observed, and Sh1- and SbTB1-type genes were representative of two prominent models, one of soft selection or multiple origins and one of hard selection or an early single domestication event. We also demonstrated that the Dry gene, which regulates stem juiciness, was unconsciously selected during the improvement of grain sorghum. Taken together, these findings provide new genomic insights into sorghum domestication and breeding selection, and will facilitate further dissection of the domestication and molecular breeding of sorghum.