Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa

Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication. To test the connection between domestication and polyploidy, we identified and examined candidate genes associated with the domestication of the diverse crops of Brassica rapa. Like all "diploid" flowering plants, B. rapa has a diploidized paleopolyploid genome and experienced many rounds of whole genome duplication (WGD). We analyzed transcriptome data of more than hundred cultivated B. rapa accessions. Using a combination of approaches, we identified more than 3,000 candidate genes associated with the domestication of four major B. rapa crops. Consistent with our expectation, we found that the candidate genes were significantly enriched with genes derived from the Brassiceae mesohexaploidy. We also observed that paleologs contained significantly more genetic diversity than non-paleologs, suggesting that elevated genetic variation may explain why paleologs are enriched among domestication candidate genes. Our analyses demonstrate the key role of polyploidy in the domestication of B. rapa and provide support for its importance in the success of modern agriculture.