Included in recombination theme

Research area: evolutionary_biology

Deleterious variants in Asian rice and the potential cost of domestication

Created on 5th June 2016

Qingpo Liu; Yongfeng Zhou; Peter L. Morrell; Brandon S. Gaut;

SNPs that are predicted to encode deleterious amino acid variants provide unique insights into population history, the dynamics of selection, and the genetic bases of phenotypes. This may be especially true for domesticated species, where a history of bottlenecks and selection can contribute to the accumulation of deleterious SNPs (dSNPs). Here we investigate the numbers and frequencies of deleterious variants in Asian rice (O. sativa), focusing on two separate varieties (japonica and indica) that may have been domesticated independently. Comparative analyses in two population datasets each for japonica and indica rice -- using SNPs identified in separate variant calling pipelines and applying two distinct tools for the prediction of deleterious variants -- were consistent in indicating that the transition to domesticated rice has shifted site frequency spectra for all derived variants but particularly for dSNPs. This potential “cost of domestication” is higher in genomic regions of low recombination and within regions of putative selective sweeps. A characteristic feature of rice domestication was a shift in mating system from outcrossing to predominantly selfing. Using forward simulations, we show that this shift in mating system likely ameliorates the cost of domestication through purging of deleterious variants.

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