Affiliation:
1. Department of Animal Science, North Carolina State University , Raleigh, NC 27695, United States
Abstract
Abstract
Motivation
Genome 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.
Results
To 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/.
Funder
USDA National Institute of Food and Agriculture
Publisher
Oxford University Press (OUP)