Journal
JOURNAL OF HEREDITY
Volume 107, Issue 4, Pages 372-379Publisher
OXFORD UNIV PRESS INC
DOI: 10.1093/jhered/esw020
Keywords
complex traits; G-BLUP analysis; genome-wide marker data; P-BLUP analysis; software
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Funding
- School of Forest Resources and Conservation at the University of Florida
- Institute of Food and Agricultural Science at the University of Florida
- Specialty Crop Block Grant from the Florida Department of Agriculture and Consumer Services
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Genomic and pedigree-based best linear unbiased prediction methodologies (G-BLUP and P-BLUP) have proven themselves efficient for partitioning the phenotypic variance of complex traits into its components, estimating the individuals' genetic merits, and predicting unobserved (or yet-to-be observed) phenotypes in many species and fields of study. The GenoMatrix software, presented here, is a user-friendly package to facilitate the process of using genome-wide marker data and parentage information for G-BLUP and P-BLUP analyses on complex traits. It provides users with a collection of applications which help them on a set of tasks from performing quality control on data to constructing and manipulating the genomic and pedigree-based relationship matrices and obtaining their inverses. Such matrices will be then used in downstream analyses by other statistical packages. The package also enables users to obtain predicted values for unobserved individuals based on the genetic values of observed related individuals. GenoMatrix is available to the research community as a Windows 64bit executable and can be downloaded free of charge at: http://compbio.ufl.edu/software/genomatrix/.
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