Abstract
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. In order 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 >3000 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.
Highlights
Polyploidy, or whole genome duplication (WGD), has long been associated with crop domestication and diversity (Anderson, 1969; Lewis, 1980; Heiser, 1990; Hilu, 1993; Paterson, 2005; Udall & Wendel, 2006; Meyer et al, 2012; Renny-Byfield & Wendel, 2014)
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
We 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
Summary
Polyploidy, or whole genome duplication (WGD), has long been associated with crop domestication and diversity (Anderson, 1969; Lewis, 1980; Heiser, 1990; Hilu, 1993; Paterson, 2005; Udall & Wendel, 2006; Meyer et al, 2012; Renny-Byfield & Wendel, 2014). A recent phylogenetic analysis found that domesticated plants have experienced significantly more polyploidy than their wild relatives (Salman-Minkov et al, 2016). Polyploidy often precedes domestication and crops are nearly twice as likely to be domesticated in lineages with a relatively recent WGD compared to those without (Salman-Minkov et al, 2016). The niches of polyploid plants evolve faster than their diploid relatives (Baniaga et al, 2020). These features may collectively give polyploids unique advantages over diploids during domestication and the global spread of crops that occurred with human population expansion
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