Exploring the genetic architecture and improving genomic prediction accuracy for mastitis and milk production traits in dairy cattle by mapping variants to hepatic transcriptomic regions responsive to intra-mammary infection

Genetics, Selection, Evolution : GSE
Lingzhao FangPeter Sørensen

Abstract

A better understanding of the genetic architecture of complex traits can contribute to improve genomic prediction. We hypothesized that genomic variants associated with mastitis and milk production traits in dairy cattle are enriched in hepatic transcriptomic regions that are responsive to intra-mammary infection (IMI). Genomic markers [e.g. single nucleotide polymorphisms (SNPs)] from those regions, if included, may improve the predictive ability of a genomic model. We applied a genomic feature best linear unbiased prediction model (GFBLUP) to implement the above strategy by considering the hepatic transcriptomic regions responsive to IMI as genomic features. GFBLUP, an extension of GBLUP, includes a separate genomic effect of SNPs within a genomic feature, and allows differential weighting of the individual marker relationships in the prediction equation. Since GFBLUP is computationally intensive, we investigated whether a SNP set test could be a computationally fast way to preselect predictive genomic features. The SNP set test assesses the association between a genomic feature and a trait based on single-SNP genome-wide association studies. We applied these two approaches to mastitis and milk production traits (milk, fat an...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
Aug 29, 2019·Genetics·Palle Duun RohdeTorsten Nygaard Kristensen
Sep 26, 2020·Animals : an Open Access Journal From MDPI·Guoyu HuYounes Miar
Oct 18, 2020·G3 : Genes - Genomes - Genetics·Mariem NsibiJean-Luc Regnard
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
Oct 1, 2019·Genetics·Palle Duun RohdeTorsten Nygaard Kristensen
Apr 28, 2021·G3 : Genes - Genomes - Genetics·Viktor MilkevychMogens Sandø Lund
Sep 22, 2017·Journal of Proteome Research·Andreas TholeyEmøke Bendixen
Nov 10, 2021·G3 : Genes - Genomes - Genetics·Evan M LongKelly R Robbins

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Methods Mentioned

BETA
biopsies
RNA-Seq
chip

Software Mentioned

BayesR
Bioconductor
EMMAX
GFBLUP
BayesRC
Rsubread
edgeR
R
GBLUP

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