The fate of deleterious variants in a barley genomic prediction population

Thomas J.Y. Kono, Chaochih Liu, Emily E. Vonderharr, Daniel Koenig, Justin C. Fay, Kevin P. Smith, Peter L. Morrell

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Targeted identification and purging of deleterious genetic variants has been proposed as a novel approach to animal and plant breeding. This strategy is motivated, in part, by the observation that demographic events and strong selection associated with cultivated species pose a “cost of domestication.” This includes an increase in the proportion of genetic variants that are likely to reduce fitness. Recent advances in DNA resequencing and sequence constraint-based approaches to predict the functional impact of a mutation permit the identification of putatively deleterious SNPs (dSNPs) on a genome-wide scale. Using exome capture resequencing of 21 barley lines, we identified 3855 dSNPs among 497,754 total SNPs. We generated whole-genome resequencing data of Hordeum murinum ssp. glaucum as a phylogenetic outgroup to polarize SNPs as ancestral vs. derived. We also observed a higher proportion of dSNPs per synonymous SNPs (sSNPs) in low-recombination regions of the genome. Using 5215 progeny from a genomic prediction experiment, we examined the fate of dSNPs over three breeding cycles. Adjusting for initial frequency, derived alleles at dSNPs reduced in frequency or were lost more often than other classes of SNPs. The highest-yielding lines in the experiment, as chosen by standard genomic prediction approaches, carried fewer homozygous dSNPs than randomly sampled lines from the same progeny cycle. In the final cycle of the experiment, progeny selected by genomic prediction had a mean of 5.6% fewer homozygous dSNPs relative to randomly chosen progeny from the same cycle.

Original languageEnglish (US)
Pages (from-to)1531-1544
Number of pages14
JournalGenetics
Volume213
Issue number4
DOIs
StatePublished - Dec 2019

Bibliographical note

Funding Information:
The authors thank Ana Poets and Tyler Tiede for sharing computer code used in data analysis; Maria Muñoz-Amatriaían and Timothy Close for providing SNP genotyping data from barley genetic mapping populations that included the variety Morex, used for the reference genome; Shiaoman Chao for providing raw genotyping data; Angelica Guercio for library preparation of the H. murinum sample that was used in this study; Sebastian Beier for physical positions for a portion of genotyped SNPs; and Li Lei, Yong Jiang, Jochen Reif, Albert Schulthess, Ruth Shaw, Robert Stupar, Peter Tiffin, and Yusheng Zhao for valuable comments on an earlier version of the text. This research was carried out with hardware and software support provided by the Minnesota Supercomputing Institute at the University of Minnesota. We acknowledge financial support from the National Science Foundation (grant IOS-1339393), the Minnesota Agricultural Experiment Station Variety Development fund, and a University of Minnesota Doctoral Dissertation Fellowship (in support of T.J.Y.K). The funders had no role in study design, data collection and analysis, the decision to publish, or preparation of the manuscript.

Funding Information:
The authors thank Ana Poets and Tyler Tiede for sharing computer code used in data analysis; Maria Mu?oz-Amatria?an and Timothy Close for providing SNP genotyping data from barley genetic mapping populations that included the variety Morex, used for the reference genome; Shiaoman Chao for providing raw genotyping data; Angelica Guercio for library preparation of the H. murinum sample that was used in this study; Sebastian Beier for physical positions for a portion of genotyped SNPs; and Li Lei, Yong Jiang, Jochen Reif, Albert Schulthess, Ruth Shaw, Robert Stupar, Peter Tiffin, and Yusheng Zhao for valuable comments on an earlier version of the text. This research was carried out with hardware and software support provided by the Minnesota Supercomputing Institute at the University of Minnesota. We acknowledge financial support from the National Science Foundation (grant IOS-1339393), the Minnesota Agricultural Experiment Station Variety Development fund, and a University of Minnesota Doctoral Dissertation Fellowship (in support of T.J.Y.K). The funders had no role in study design, data collection and analysis, the decision to publish, or preparation of the manuscript.

Publisher Copyright:
Copyright © 2019 by the Genetics Society of America

Keywords

  • Deleterious variants
  • Genomic prediction
  • Multiparent population

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