ArticleBioinformatics (Oxford, England)2024
MPH: fast REML for large-scale genome partitioning of quantitative genetic variation.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed.
- Pangenome-based structural variant imputation enables large-scale genotype-phenotype studies in dairy cattle.Nature communications · 2026Article
- Across-breed analyses of genome-wide association studies for stature and mammary gland morphology in cattle reveal pleiotropic effects of the Friesian POLLED haplotype.Genetics, selection, evolution : GSE · 2026Article
- Article
- Powerful one-dimensional scan to detect heterotic quantitative trait loci.Nature communications · 2025Article
- Fine-mapping methods for complex traits: essential adaptations for samples of related individuals.Briefings in bioinformatics · 2025Article
- Genetic parameters for image-based estimations of swine feet and leg conformation traits.Journal of animal science · 2025Article
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Abstract
motivationGenome partitioning of quantitative genetic variation is useful for dissecting the genetic architecture of complex traits. However, existing methods, such as Haseman-Elston regression and linkage disequilibrium score regression, often face limitations when handling extensive farm animal datasets, as demonstrated in this study.
resultsTo overcome this challenge, we present MPH, a novel software tool designed for efficient genome partitioning analyses using restricted maximum likelihood. The computational efficiency of MPH primarily stems from two key factors: the utilization of stochastic trace estimators and the comprehensive implementation of parallel computation. Evaluations with simulated and real datasets demonstrate that MPH achieves comparable accuracy and significantly enhances convergence, speed, and memory efficiency compared to widely used tools like GCTA and LDAK. These advancements facilitate large-scale, comprehensive analyses of complex genetic architectures in farm animals. AVAILABILITY AND IMPLEMENTATION: The MPH software is available at https://jiang18.github.io/mph/.
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