ArticleGenetics, selection, evolution : GSE2013
The effect of using genealogy-based haplotypes for genomic prediction.
Article in Genetics, selection, evolution : GSE, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Integrating Significant SNPs Identified by GWAS for Genomic Prediction of the Number of Ribs and Carcass Length in Suhuai Pigs.Animals : an open access journal from MDPI · 2025Article
- Genomic prediction with haplotype blocks in wheat.Frontiers in plant science · 2023Article
- Genomic Prediction Using LD-Based Haplotypes in Combined Pig Populations.Frontiers in genetics · 2022Article
- Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing.International journal of molecular sciences · 2021Review
- Genomic Prediction Accuracy Using Haplotypes Defined by Size and Hierarchical Clustering Based on Linkage Disequilibrium.Frontiers in genetics · 2020Article
- A Study of Genomic Prediction of 12 Important Traits in the Domesticated Yak (Animals : an open access journal from MDPI · 2019Article
- SNP and Haplotype-Based Genomic Selection of Quantitative Traits inPlants (Basel, Switzerland) · 2019Article
- Haplotype-based genotyping-by-sequencing in oat genome research.Plant biotechnology journal · 2018Article
- Including α s1 casein gene information in genomic evaluations of French dairy goats.Genetics, selection, evolution : GSE · 2016Article
- On the distance of genetic relationships and the accuracy of genomic prediction in pig breeding.Genetics, selection, evolution : GSE · 2014Article
- The impact of population structure on genomic prediction in stratified populations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
- Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations.Journal of animal science and biotechnology · 2013Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundGenomic prediction uses two sources of information: linkage disequilibrium between markers and quantitative trait loci, and additive genetic relationships between individuals. One way to increase the accuracy of genomic prediction is to capture more linkage disequilibrium by regression on haplotypes instead of regression on individual markers. The aim of this study was to investigate the accuracy of genomic prediction using haplotypes based on local genealogy information.
methodsA total of 4429 Danish Holstein bulls were genotyped with the 50K SNP chip. Haplotypes were constructed using local genealogical trees. Effects of haplotype covariates were estimated with two types of prediction models: (1) assuming that effects had the same distribution for all haplotype covariates, i.e. the GBLUP method and (2) assuming that a large proportion (π) of the haplotype covariates had zero effect, i.e. a Bayesian mixture method.
resultsAbout 7.5 times more covariate effects were estimated when fitting haplotypes based on local genealogical trees compared to fitting individuals markers. Genealogy-based haplotype clustering slightly increased the accuracy of genomic prediction and, in some cases, decreased the bias of prediction. With the Bayesian method, accuracy of prediction was less sensitive to parameter π when fitting haplotypes compared to fitting markers.
conclusionsUse of haplotypes based on genealogy can slightly increase the accuracy of genomic prediction. Improved methods to cluster the haplotypes constructed from local genealogy could lead to additional gains in accuracy.
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