PT  - JOURNAL ARTICLE
AU  - Xinshuai Qi
AU  - Hong An
AU  - Tara E. Hall
AU  - Chenlu Di
AU  - Paul D. Blischak
AU  - Michael T. W. McKibben
AU  - Yue Hao
AU  - Gavin C. Conant
AU  - J. Chris Pires
AU  - Michael S. Barker
TI  - Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in <em>Brassica rapa</em>
AID  - 10.1101/842351
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 842351
4099  - http://biorxiv.org/content/early/2020/10/15/842351.short
4100  - http://biorxiv.org/content/early/2020/10/15/842351.full
AB  - 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 crop varieties 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 100 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 crop varieties. 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 were significantly more diverse than non-paleologs.Our analyses find evidence for that genetic diversity derived from ancient polyploidy played a key role in the domestication of B. rapa and provide support for its importance in the success of modern agriculture.Competing Interest StatementThe authors have declared no competing interest.