Insights into the genetic basis of natural selection and domestication from Sorghum

Analysis of gene sequences showing signatures of selection can provide insights into the evolution and domestication of an organism and can suggest ways to accelerate crop improvement. Using whole-genome resequencing and RNA-seq-derived SNP data from 69 diverse sorghum accessions, we characterized genetic variation and identified genes showing evidence of potentially important roles in sorghum domestication and adaptation. Sorghum genes showing evidence of recent selection based on fixation index (Fst) include Sb02g037735, a protease inhibitor functioning in seed storage; and Sb02g029450, with a double-stranded RNA binding motif. Ten genes showing evidence of selective sweeps include 4 ion transporters that all are located in likelihood intervals for QTLs related to drought resilience of sorghum. Of 15 genes containing 16 deleterious SNPs fixed for different alleles between domesticated and wild sorghums, significantly low Tajima's D indicates recent selection in two apoptotic ATPase-containing NB-ARC domain genes, signaling proteins involved in disease resistance and regulation of cell death. A group of 22 genes show evidence of convergent selection in sorghum, maize and rice. Integration of selection signatures, large-effect mutations, gene functional annotations, and positional (QTL) information suggests a small number of strong candidate genes involved in sorghum domestication and adaptation, while also identifying a broader set of plausible candidates. Comparison of genes under selection in sorghum, rice, and maize supports both convergent and divergent selection patterns during cereal evolution and domestication.