Balancing selection contributed to domestication of autopolyploid sugarcane (Saccharum officinarum L.)

Sugarcane was domesticated in New Guinea about 10,000 years ago, and the domesticated species Saccharum officinarum is autooctoploid. For diploid domesticated crops, genetic diversity is reduced for those genes controlling favorable traits. However, the domestication traits in sugarcane such as sugar content and biomass yield are controlled by multiple genes with multiple alleles. A genomics approach to identify genes involved in the transition from wild to domesticated may provide useful insight into complex polyploid traits such as sucrose accumulation. Fifteen accessions each of domesticated S. officinarum and the wild species S. robustum and eighteen accessions of S. spontaneum were used for sequencing of leaf and stalk transcriptomes. We found high allelic diversity among genes expressed in the stalk tissues where the domesticated S. officinarum (Fis = 0.69) surprisingly has higher allele diversity than its wild relative S. spontaneum (Fis = 0.41). However, there were no SNP loci with extremely high FST values despite the observed higher average FST among the three species, indicative of the action of balancing selection. This is corroborated by nucleotide diversity and site frequency spectrum (SFS) patterns that show that majority of expressed genes in S. officinarum have comparable per-site heterozygosity to the wild species. These candidate domestication genes, bearing signatures of balancing selection and excess singleton SNPs in S. officinarum, perturbs pathways involved in sucrose and starch metabolism.