Deleterious variants in Asian rice and the potential cost of domestication

BioRxiv : the Preprint Server for Biology
Qingpo LiuBrandon S Gaut


Many SNPs are predicted to encode deleterious amino acid variants. These slightly deleterious mutations can provide unique insights into population history, the dynamics of selection, and the genetic bases of phenotypes. This is especially true for domesticated species, where a history of bottlenecks and selection may affect the frequency of deleterious variants and signal a cost of domestication. Here we investigated the numbers and frequencies of deleterious variants in Asian rice (O. sativa), focusing on two varieties (japonica and indica) and their wild relative (O. rufipogon). We investigated three signals of a potential cost of domestication in Asian rice relative to O. rufipogon: an increase in the frequency of deleterious SNPs (dSNPs), an enrichment of dSNPs compared to synonymous SNPs (sSNPs), and an increased number of deleterious variants. We found evidence for all three signals, and domesticated individuals contained ~3-4% more deleterious alleles than wild individuals. Deleterious variants were enriched within low recombination regions of the genome and experienced frequency increases similar to sSNPs within regions of putative selective sweeps. A characteristic feature of rice domestication was a shift in mating s...Continue Reading

Related Concepts

Rice (Dietary)
Wild bird
Single Nucleotide Polymorphism
Oryza rufipogon

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