Using Sequence Variants in Linkage Disequilibrium with Causative Mutations to Improve Across-Breed Prediction in Dairy Cattle: A Simulation Study

Sequence data are expected to increase the reliability of genomic prediction by containing causative mutations directly, especially in cases where low linkage disequilibrium between markers and causative mutations limits prediction reliability, such as across-breed prediction in dairy cattle. In practice, the causative mutations are unknown, and prediction with only variants in perfect linkage disequilibrium with the causative mutations is not realistic, leading to a reduced reliability compared to knowing the causative variants. Our objective was to use sequence data to investigate the potential benefits of sequence data for the prediction of genomic relationships, and consequently reliability of genomic breeding values. We used sequence data from five dairy cattle breeds, and a larger number of imputed sequences for two of the five breeds. We focused on the influence of linkage disequilibrium between markers and causative mutations, and assumed that a fraction of the causative mutations was shared across breeds and had the same effect across breeds. By comparing the loss in reliability of different scenarios, varying the distance between markers and causative mutations, using either all genome wide markers from commercial SNP chips, or only the markers closest to the causative mutations, we demonstrate the importance of using only variants very close to the causative mutations, especially for across-breed prediction. Rare variants improved prediction only if they were very close to rare causative mutations, and all causative mutations were rare. Our results show that sequence data can potentially improve genomic prediction, but careful selection of markers is essential.

• Publication year

  2016

• Venue

  G3: Genes, Genomes, Genetics

• Publication date

  2016-06-13

• Fields of study

  Agricultural and Food Sciences, Medicine, Biology

• Identifiers
  DOI 10.1534/g3.116.027730PMID 27317779PMCID 4978908
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction.

  2015cited by this paper
• Genomic correlation: harnessing the benefit of combining two unrelated populations for genomic selection

  2015influential reference
• Accounting for Genetic Architecture Improves Sequence Based Genomic Prediction for a Drosophila Fitness Trait

  2015cited by this paper
• Sequence- vs. chip-assisted genomic selection: accurate biological information is advised

  2015cited by this paper
• Multibreed genome wide association can improve precision of mapping causative variants underlying milk production in dairy cattle

  2014cited by this paper
• Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle

  2014cited by this paper
• Genomic evaluation of cattle in a multi-breed context ☆

  2014cited by this paper
• Efficiency of multi-breed genomic selection for dairy cattle breeds with different sizes of reference population.

  2014cited by this paper
• Validation of associations for female fertility traits in Nordic Holstein, Nordic Red and Jersey dairy cattle

  2014cited by this paper
• Genome-wide association study using high-density single nucleotide polymorphism arrays and whole-genome sequences for clinical mastitis traits in dairy cattle.

  2014cited by this paper
• The Effects of Demography and Long-Term Selection on the Accuracy of Genomic Prediction with Sequence Data

  2014cited by this paper
• Prediction of Complex Human Traits Using the Genomic Best Linear Unbiased Predictor

  2013influential reference
• Toward genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions

  2013cited by this paper
• Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels.

  2012cited by this paper
• Fast and accurate genotype imputation in genome-wide association studies through pre-phasing

  2012influential reference
• Mutations in the bovineABCG2 and the ovineMSTN gene added to the few quantitative trait nucleotides identified in farm animals: a mini-review

  2011cited by this paper
• Extension of the bayesian alphabet for genomic selection

  2011cited by this paper
• Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows

  2011cited by this paper
• A framework for variation discovery and genotyping using next-generation DNA sequencing data

  2011cited by this paper
• Reliabilities of genomic prediction using combined reference data of the Nordic Red dairy cattle populations.

  2011cited by this paper
• Genomic selection in French dairy cattle

  2011influential reference
• Mapping genes for complex traits in domestic animals and their use in breeding programmes

  2009cited by this paper
• Accuracy of genomic breeding values in multi-breed dairy cattle populations

  2009cited by this paper
• Development and Characterization of a High Density SNP Genotyping Assay for Cattle

  2009cited by this paper
• Efficient methods to compute genomic predictions.

  2008influential reference
• A genome scan to detect quantitative trait loci for economically important traits in Holstein cattle using two methods and a dense single nucleotide polymorphism map.

  2008cited by this paper
• Linkage Disequilibrium and Persistence of Phase in Holstein–Friesian, Jersey and Angus Cattle

  2008cited by this paper
• Genomic selection.

  2007cited by this paper
• Genetic and functional confirmation of the causality of the DGAT1 K232A quantitative trait nucleotide in affecting milk yield and composition.

  2004cited by this paper
• Quantitative trait loci mapping in dairy cattle: review and meta-analysis

  2004cited by this paper
• Residual maximum likelihood estimation of (co)variance components in multivariate mixed linear models using average information

  1997influential reference
• Quantitative Trait Loci

  1995influential reference

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• QTL detection in multi-breed cattle populations including crossbred animals: a simulation study.

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• Genomic selection in plant breeding: key factors shaping two decades of progress.

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• Bioinformatic approach to identifying causative missense polymorphisms in animal genomes

  2024cites this paper
• Accuracy of Genomic Predictions Cross Populations with Different Linkage Disequilibrium Patterns

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• Using expression data to fine map QTL associated with fertility in dairy cattle

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• Genomic prediction based on preselected single‐nucleotide polymorphisms from genome‐wide association study and imputed whole‐genome sequence data annotation for growth traits in Duroc pigs

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• Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population

  2023cites this paper
• Using pre-selected variants from large-scale whole-genome sequence data for single-step genomic predictions in pigs

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• Importance of genetic architecture in marker selection decisions for genomic prediction

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• Utilizing Variants Identified with Multiple Genome-Wide Association Study Methods Optimizes Genomic Selection for Growth Traits in Pigs

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• Genomic prediction with whole-genome sequence data in intensely selected pig lines

  2022influential citation
• 287. Effect of informative polymorphism on accuracy of genomic prediction and heritability

  2022cites this paper
• 274. Improving accuracy of genomic prediction in distant populations by collecting sequence data over generations

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• Using large-scale whole-genome sequence data for single-step genomic predictions in maternal and terminal pig lines

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• High-precision early warning system for rice cadmium accumulation risk assessment.

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• Utility of multi-omics data to inform genomic prediction of heifer fertility traits.

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• Evaluation of Whole-Genome Sequence Imputation Strategies in Korean Hanwoo Cattle

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• Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize

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• Progress and opportunities through use of genomics in animal production.

  2022cites this paper
• Genomic prediction in Nordic Red dairy cattle considering breed origin of alleles.

  2022cites this paper
• Reducing greenhouse gas emissions through genetic selection in the Australian dairy industry.

  2022cites this paper
• GWAS and genomic prediction of milk urea nitrogen in Australian and New Zealand dairy cattle

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• Functionally prioritised whole-genome sequence variants improve the accuracy of genomic prediction for heat tolerance

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• Genome-wide association study with imputed whole-genome sequence variants including large deletions for female fertility in 3 Nordic dairy cattle breeds.

  2021cites this paper
• GMStool: GWAS-based marker selection tool for genomic prediction from genomic data

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  2020cites this paper
• Accuracy of genomic evaluation using imputed high-density genotypes for carcass traits in commercial Hanwoo population

  2020cites this paper
• Optimizing genomic prediction model given causal genes in a dairy cattle population.

  2020cites this paper
• Meta-analysis for milk fat and protein percentage using imputed sequence variant genotypes in 94,321 cattle from eight cattle breeds

  2020cites this paper
• Imputation for sequencing variants preselected to a customized low-density chip

  2020cites this paper
• Optimizing genomic prediction for Australian Red dairy cattle.

  2020cites this paper
• The evolving role of Fourier-transform mid-infrared spectroscopy in genetic improvement of dairy cattle

  2020cites this paper
• Improvement of genomic prediction by integrating additional single nucleotide polymorphisms selected from imputed whole genome sequencing data

  2019cites this paper
• Identification of causal factors for recessive lethals in dairy cattle with special focus on large chromosomal deletions

  2019cites this paper
• Lost pigs and broken genes: the search for causes of embryonic loss in the pig and the assembly of a more contiguous reference genome

  2019cites this paper
• Genomic predictions in purebreds with a multi-breed genomic relationship matrix.

  2019cites this paper
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  2019cites this paper
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  2019cites this paper
• Genomic prediction for numerically small breeds, using models with pre-selected and differentially weighted markers

  2018cites this paper
• Candidate mutations used to aid the prediction of genetic merit for female reproductive traits in tropical beef cattle

  2018cites this paper
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• Genome-wide association study using the Bayes C method for important traits in dairy yield in Colombian Holstein Cattle

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• Multibreed genomic prediction using multitrait genomic residual maximum likelihood and multitask Bayesian variable selection.

  2018cites this paper
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  2018cites this paper
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  2018cites this paper
• Multi-breed genomic prediction using Bayes R with sequence data and dropping variants with a small effect

  2017cites this paper
• Association analysis for udder index and milking speed with imputed whole-genome sequence variants in Nordic Holstein cattle.

  2017cites this paper
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  2017cites this paper
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  2016cites this paper
• Genomic prediction using preselected DNA variants from a GWAS with whole-genome sequence data in Holstein–Friesian cattle

  2016cites this paper
• Genomic selection in domestic animals: Principles, applications and perspectives.

  2016cites this paper
• Evaluating Sequence-Based Genomic Prediction with an Efficient New Simulator

  2016cites this paper