ArticleG3 (Bethesda, Md.)2018
Haplotype-Based Genome-Wide Prediction Models Exploit Local Epistatic Interactions Among Markers.
Article in G3 (Bethesda, Md.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- From family trials to genomic mate allocation: statistical and genomic strategies to accelerate sugarcane genetic improvement.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Efficiency under epistasis of haplotype-based genomic selection for pure line breeding.Heredity · 2026Article
- SNPs with High Linkage Disequilibrium Increase the Explained Genetic Variance and the Reliability of Genomic Predictions.Animals : an open access journal from MDPI · 2026Article
- Haplotype applications in genomic selection.Genome biology · 2026Review
- Integrative haplotype and SNP-based GWAS supports the identification of stable genomic loci controlling yield-related traits in soybean.Frontiers in plant science · 2026Article
- Haplotype-based autoencoders can reduce the dataset dimension and estimate haplotype block effects in different crop species.BMC bioinformatics · 2025Article
- Breaking down data silos across companies to train genome-wide predictions: A feasibility study in wheat.Plant biotechnology journal · 2025Article
- Assessment of the potential for genomic selection to improve resistance to fusarium stalk rot in maize.Frontiers in plant science · 2025Article
- Identification of transcription factor BnHDG4-A08 as a novel candidate associated with the accumulation of oleic, linoleic, linolenic, and erucic acid in Brassica napus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Genomic prediction within and across maize landrace derived populations using haplotypes.Frontiers in plant science · 2024Article
- Investigating the impact of non-additive genetic effects in the estimation of variance components and genomic predictions for heat tolerance and performance traits in crossbred and purebred pig populations.BMC genomic data · 2023Article
- Salinity stress tolerance prediction for biomass-related traits in maize (Zea mays L.) using genome-wide markers.The plant genome · 2023Article
- Genome-Wide Association Study Reveals Novel Loci Associated with Body Conformation Traits in Qinchuan Cattle.Animals : an open access journal from MDPI · 2023Article
- Sparse Phenotyping and Haplotype-Based Models for Genomic Prediction in Rice.Rice (New York, N.Y.) · 2023Article
- SNP- and haplotype-based single-step genomic predictions for body weight, wool, and reproductive traits in North American Rambouillet sheep.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2023Article
- Haplotype blocks for genomic prediction: a comparative evaluation in multiple crop datasets.Frontiers in plant science · 2023Article
- Genomic prediction with haplotype blocks in wheat.Frontiers in plant science · 2023Article
- Genomic prediction using information across years with epistatic models and dimension reduction via haplotype blocks.PloS one · 2023Article
- Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps.GigaScience · 2022Article
- Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations.Communications biology · 2022Article
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Abstract
Genome-wide prediction approaches represent versatile tools for the analysis and prediction of complex traits. Mostly they rely on marker-based information, but scenarios have been reported in which models capitalizing on closely-linked markers that were combined into haplotypes outperformed marker-based models. Detailed comparisons were undertaken to reveal under which circumstances haplotype-based genome-wide prediction models are superior to marker-based models. Specifically, it was of interest to analyze whether and how haplotype-based models may take local epistatic effects between markers into account. Assuming that populations consisted of fully homozygous individuals, a marker-based model in which local epistatic effects inside haplotype blocks were exploited (LEGBLUP) was linearly transformable into a haplotype-based model (HGBLUP). This theoretical derivation formally revealed that haplotype-based genome-wide prediction models capitalize on local epistatic effects among markers. Simulation studies corroborated this finding. Due to its computational efficiency the HGBLUP model promises to be an interesting tool for studies in which ultra-high-density SNP data sets are studied. Applying the HGBLUP model to empirical data sets revealed higher prediction accuracies than for marker-based models for both traits studied using a mouse panel. In contrast, only a small subset of the traits analyzed in crop populations showed such a benefit. Cases in which higher prediction accuracies are observed for HGBLUP than for marker-based models are expected to be of immediate relevance for breeders, due to the tight linkage a beneficial haplotype will be preserved for many generations. In this respect the inheritance of local epistatic effects very much resembles the one of additive effects.
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