Deleterious variants in Asian Rice and the potential cost of domestication

Qingpo Liu, Yongfeng Zhou, Peter L. Morrell, Brandon S. Gaut, Song Ge

Research output: Contribution to journalArticlepeer-review

67 Scopus citations


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 (Oryza 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 with 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 system from outcrossing to predominantly selfing. Forward simulations suggest that this shift in mating system may have been the dominant factor in shaping both deleterious and neutral diversity in rice.

Original languageEnglish (US)
Pages (from-to)908-924
Number of pages17
JournalMolecular biology and evolution
Issue number4
StatePublished - Apr 1 2017

Bibliographical note

Funding Information:
We would like to thank three anonymous reviewers for contributing comments that greatly improved the article. We thank J. Aguirre, T. Kono, D. Seymour, L Li, and A. Poets for reading earlier versions of the article, and J. Aguirre for assistance with a figure. J. Ross-Ibarra also provided comments and a revised version of XP-CLR. QL is supported by the National Natural Science Foundation of China (grant no. 31471431) and the Training Program for Outstanding Young Talents of Zhejiang A&F University. YZ is supported by the International Postdoctoral Exchange Fellowship Program 2015 awarded by the Office of China Postdoctoral Council. PLM is supported by NSF Plant Genome Program (DBI-1339393). BSG is supported by NSF IOS-1542703 and the Albert and Elaine Borchard Foundation.

Publisher Copyright:
© The Author 2017.

Copyright 2017 Elsevier B.V., All rights reserved.


  • Bottleneck
  • Domestication
  • SNPs
  • Selective sweep


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