Dataset Information

Reliability of genomic prediction for milk fatty acid composition by using a multi-population reference and incorporating GWAS results.

ABSTRACT:

Background

Large-scale phenotyping for detailed milk fatty acid (FA) composition is difficult due to expensive and time-consuming analytical techniques. Reliability of genomic prediction is often low for traits that are expensive/difficult to measure and for breeds with a small reference population size. An effective method to increase reference population size could be to combine datasets from different populations. Prediction models might also benefit from incorporation of information on the biological underpinnings of quantitative traits. Genome-wide association studies (GWAS) show that genomic regions on Bos taurus chromosomes (BTA) 14, 19 and 26 underlie substantial proportions of the genetic variation in milk FA traits. Genomic prediction models that incorporate such results could enable improved prediction accuracy in spite of limited reference population sizes. In this study, we combine gas chromatography quantified FA samples from the Chinese, Danish and Dutch Holstein populations and implement a genomic feature best linear unbiased prediction (GFBLUP) model that incorporates variants on BTA14, 19 and 26 as genomic features for which random genetic effects are estimated separately. Prediction reliabilities were compared to those estimated with traditional GBLUP models.

Results

Predictions using a multi-population reference and a traditional GBLUP model resulted in average gains in prediction reliability of 10% points in the Dutch, 8% points in the Danish and 1% point in the Chinese populations compared to predictions based on population-specific references. Compared to the traditional GBLUP, implementation of the GFBLUP model with a multi-population reference led to further increases in prediction reliability of up to 38% points in the Dutch, 23% points in the Danish and 13% points in the Chinese populations. Prediction reliabilities from the GFBLUP model were moderate to high across the FA traits analyzed.

Conclusions

Our study shows that it is possible to predict genetic merits for milk FA traits with reasonable accuracy by combining related populations of a breed and using models that incorporate GWAS results. Our findings indicate that international collaborations that facilitate access to multi-population datasets could be highly beneficial to the implementation of genomic selection for detailed milk composition traits.

SUBMITTER: Gebreyesus G

PROVIDER: S-EPMC6487064 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Reliability of genomic prediction for milk fatty acid composition by using a multi-population reference and incorporating GWAS results.

Gebreyesus Grum G Bovenhuis Henk H Lund Mogens S MS Poulsen Nina A NA Sun Dongxiao D Buitenhuis Bart B

Genetics, selection, evolution : GSE 20190427 1

<h4>Background</h4>Large-scale phenotyping for detailed milk fatty acid (FA) composition is difficult due to expensive and time-consuming analytical techniques. Reliability of genomic prediction is often low for traits that are expensive/difficult to measure and for breeds with a small reference population size. An effective method to increase reference population size could be to combine datasets from different populations. Prediction models might also benefit from incorporation of information ...[more]

PMID: 31029078

Similar Datasets

Project description:BackgroundGenome-wide association studies (GWAS) were performed at the sequence level to identify candidate mutations that affect the expression of six major milk proteins in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) dairy cattle. Whey protein (α-lactalbumin and β-lactoglobulin) and casein (αs1, αs2, β, and κ) contents were estimated by mid-infrared (MIR) spectrometry, with medium to high accuracy (0.59 ≤ R2 ≤ 0.92), for 848,068 test-day milk samples from 156,660 cows in the first three lactations. Milk composition was evaluated as average test-day measurements adjusted for environmental effects. Next, we genotyped a subset of 8080 cows (2967 MON, 2737 NOR, and 2306 HOL) with the BovineSNP50 Beadchip. For each breed, genotypes were first imputed to high-density (HD) using HD single nucleotide polymorphisms (SNPs) genotypes of 522 MON, 546 NOR, and 776 HOL bulls. The resulting HD SNP genotypes were subsequently imputed to the sequence level using 27 million high-quality sequence variants selected from Run4 of the 1000 Bull Genomes consortium (1147 bulls). Within-breed, multi-breed, and conditional GWAS were performed.ResultsThirty-four distinct genomic regions were identified. Three regions on chromosomes 6, 11, and 20 had very significant effects on milk composition and were shared across the three breeds. Other significant effects, which partially overlapped across breeds, were found on almost all the autosomes. Multi-breed analyses provided a larger number of significant genomic regions with smaller confidence intervals than within-breed analyses. Combinations of within-breed, multi-breed, and conditional analyses led to the identification of putative causative variants in several candidate genes that presented significant protein-protein interactions enrichment, including those with previously described effects on milk composition (SLC37A1, MGST1, ABCG2, CSN1S1, CSN2, CSN1S2, CSN3, PAEP, DGAT1, AGPAT6) and those with effects reported for the first time here (ALPL, ANKH, PICALM).ConclusionsGWAS applied to fine-scale phenotypes, multiple breeds, and whole-genome sequences seems to be effective to identify candidate gene variants. However, although we identified functional links between some candidate genes and milk phenotypes, the causality between candidate variants and milk protein composition remains to be demonstrated. Nevertheless, the identification of potential causative mutations that underlie milk protein composition may have immediate applications for improvements in cheese-making.

Project description:Today, genomic prediction (GP) is an established technology in plant and animal breeding programs. Current standard methods are purely based on statistical considerations but do not make use of the abundant biological knowledge, which is easily available from public databases. Major questions that have to be answered before biological prior information can be used routinely in GP approaches are which types of information can be used, and at which points they can be incorporated into prediction methods. In this study, we propose a novel strategy to incorporate gene annotation into GP of complex phenotypes by defining haploblocks according to gene positions. Haplotype effects are then modeled as categorical or as numerical allele dosage variables. The underlying concept of this approach is to build the statistical model on variables representing the biologically functional units. We evaluate the new methods with data from a heterogeneous stock mouse population, the Drosophila Genetic Reference Panel (DGRP), and a rice breeding population from the Rice Diversity Panel. Our results show that using gene annotation to define haploblocks often leads to a comparable, but for some traits to a higher, predictive ability compared to SNP-based models or to haplotype models that do not use gene annotation information. Modeling gene interaction effects can further improve predictive ability. We also illustrate that the additional use of markers that have not been mapped to any gene in a second separate relatedness matrix does in many cases not lead to a relevant additional increase in predictive ability when the first matrix is based on haploblocks defined with gene annotation data, suggesting that intergenic markers only provide redundant information on the considered data sets. Therefore, gene annotation information seems to be appropriate to perceive the importance of DNA segments. Finally, we discuss the effects of gene annotation quality, marker density, and linkage disequilibrium on the performance of the new methods. To our knowledge, this is the first work that incorporates epistatic interaction or gene annotation into haplotype-based prediction approaches.

Dataset Information

Reliability of genomic prediction for milk fatty acid composition by using a multi-population reference and incorporating GWAS results.

Background

Results

Conclusions

Publications

Reliability of genomic prediction for milk fatty acid composition by using a multi-population reference and incorporating GWAS results.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets