Increased prediction accuracy using a genomic feature model including prior information on quantitative trait locus regions in purebred Danish Duroc pigs

BMC Genetics
Pernille SarupPeter Sørensen

Abstract

In animal breeding, genetic variance for complex traits is often estimated using linear mixed models that incorporate information from single nucleotide polymorphism (SNP) markers using a realized genomic relationship matrix. In such models, individual genetic markers are weighted equally and genomic variation is treated as a "black box." This approach is useful for selecting animals with high genetic potential, but it does not generate or utilise knowledge of the biological mechanisms underlying trait variation. Here we propose a linear mixed-model approach that can evaluate the collective effects of sets of SNPs and thereby open the "black box." The described genomic feature best linear unbiased prediction (GFBLUP) model has two components that are defined by genomic features. We analysed data on average daily gain, feed efficiency, and lean meat percentage from 3,085 Duroc boars, along with genotypes from a 60 K SNP chip. In addition information on known quantitative trait loci (QTL) from the animal QTL database was integrated in the GFBLUP as a genomic feature. Our results showed that the most significant QTL categories were indeed biologically meaningful. Additionally, for high heritability traits, prediction accuracy was ...Continue Reading

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Citations

Mar 10, 2018·G3 : Genes - Genomes - Genetics·Palle Duun RohdePernille Sarup
Feb 28, 2019·Epigenetics : Official Journal of the DNA Methylation Society·Lingzhao FangGeorge E Liu
Dec 29, 2019·Bioinformatics·Palle Duun RohdePeter Sørensen
Oct 7, 2017·Frontiers in Plant Science·Brigitte ManginNicolas B Langlade
Nov 11, 2017·Evolution; International Journal of Organic Evolution·Michael ØrstedTorsten Nygaard Kristensen
Aug 29, 2019·Genetics·Palle Duun RohdeTorsten Nygaard Kristensen
Sep 30, 2020·International Journal of Molecular Sciences·Osvin ArriagadaAndrés R Schwember
May 31, 2019·Genetics, Selection, Evolution : GSE·Bart BuitenhuisNina A Poulsen
Dec 8, 2020·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Margareth E BotelhoRenata Veroneze
Dec 10, 2020·Journal of Animal Science and Biotechnology·Shaopan YeZhe Zhang
Mar 29, 2021·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Hélène RoméJust Jensen
Oct 1, 2019·Genetics·Palle Duun RohdeTorsten Nygaard Kristensen

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Methods Mentioned

BETA
chip

Software Mentioned

GBLUP
GFBLUP
MASS
GFBULP

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