Balancing selection contributed to domestication of autopolyploid sugarcane (Saccharum officinarum L.)
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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.
KeywordsDomestication Polyploid Population genetics Selection scan Sugarcane
This project was supported by grants from the International Consortium for Sugarcane Biotechnology, EBI BP2012OO2J17, the Texas Governor’s Office Emerging Technology Funds, Bioenergy, and US DOE DE-SC0010686.
RM conceived the study; RM, JS and CN designed the study; JA and JWP conducted the lab work; CMW, RV and YBP contributed to the analyses and manuscript revisions; JA analyzed the data and wrote the manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare no conflict of interest.
Informed consent was obtained from all individual participants included in the study.
- Aitken K, McNeil M, Henry R, Kole C (2010) Diversity analysis. In: Henry R, Kole C (eds) Genet. Genomics Breed. Sugarcane. Science Publishers, Inc, Enfield, N.H., pp 19–42Google Scholar
- Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Babraham Bioinforma 1. doi: citeulike-article-id:11583827Google Scholar
- Cordeiro G, Amouyal O, Eliott F, Henry R (2007) Sugarcane. In: Kole C (ed) Genome Mapp Mol. Breed. Spring, Heidelberg, pp 175–203Google Scholar
- Da Silva JAG, Sorrells ME (1996) Linkage Analysis in Polyploids using Molecular Markers. In: Jauhar P (ed) Methods of Genome Analysis in Plants. CRC Press, Boca Raton, FL, pp 211–228Google Scholar
- Garcia AAF, Kido EA, Meza AN, Souza HMB, Pinto LR, Pastina MM, Leite CS, da Silva JAG, Ulian EC, Figueira A, Souza AP (2006) Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases. Theor Appl Genet 112:298–314CrossRefPubMedGoogle Scholar
- Wysoker A, Tibbetts K, Fennell T (2013) Picard tools version 1.90. http://picard.sourceforge.net