Pan-genomic open reading frames: A potential supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction

Zhengcao Li; Henner Simianer

doi:10.1371/journal.pgen.1008995

Pan-genomic open reading frames: A potential supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction

PLoS Genet. 2020 Aug 24;16(8):e1008995. doi: 10.1371/journal.pgen.1008995. eCollection 2020 Aug.

Authors

Zhengcao Li^{1

2}, Henner Simianer¹

Affiliations

¹ Animal Breeding and Genetics Group, Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.
² State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.

Abstract

Pan-genomic open reading frames (ORFs) potentially carry protein-coding gene or coding variant information in a population. In this study, we suggest that pan-genomic ORFs are promising to be utilized in estimation of heritability and genomic prediction. A Saccharomyces cerevisiae dataset with whole-genome SNPs, pan-genomic ORFs, and the copy numbers of those ORFs is used to test the effectiveness of ORF data as a predictor in three prediction models for 35 traits. Our results show that the ORF-based heritability can capture more genetic effects than SNP-based heritability for all traits. Compared to SNP-based genomic prediction (GBLUP), pan-genomic ORF-based genomic prediction (OBLUP) is distinctly more accurate for all traits, and the predictive abilities on average are more than doubled across all traits. For four traits, the copy number of ORF-based prediction(CBLUP) is more accurate than OBLUP. When using different numbers of isolates in training sets in ORF-based prediction, the predictive abilities for all traits increased as more isolates are added in the training sets, suggesting that with very large training sets the prediction accuracy will be in the range of the square root of the heritability. We conclude that pan-genomic ORFs have the potential to be a supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Breeding
Genome / genetics*
Genome-Wide Association Study
Genomics*
Genotype
Open Reading Frames / genetics*
Phenotype
Polymorphism, Single Nucleotide / genetics
Quantitative Trait Loci / genetics*

Grants and funding

ZCL thanks China Scholarship Council for financial support. We acknowledge support by the German Research Foundation and the Open Access Publication Funds of the Göttingen University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.