J. Anim Sci.
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J. Anim Sci. 2007. 85:881-885. doi:10.2527/jas.2006-656
© 2007 American Society of Animal Science
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ANIMAL GENETICS

Technical note: Use of marker-based relationships with multiple-trait derivative-free restricted maximal likelihood

Z. Zhang*, R. J. Todhunter{dagger}, E. S. Buckler*,{ddagger} and L. D. Van Vleck§,1

* Institute for Genetic Diversity, Cornell University, Ithaca, NY 14853; and {dagger} Department of Clinical Sciences, Cornell University, Ithaca, NY 14853; and {ddagger} USDA-ARS Cornell University, 159 Biotechnology Bldg, Ithaca, NY 14853; and and § USDA-ARS A218 Animal Sciences, University of Nebraska, Lincoln 68583-0908

1 Corresponding author: lvanvleck{at}unlnotes.unl.edu

The widespread use of the set of multiple-trait derivative-free REML programs for prediction of breeding values and estimation of variance components has led to significant improvement in traits of economic importance. The initial version of this software package, however, was generally limited to pedigree-based relationships. With continued advances in genomic research and the increased availability of genotyping, relationships based on molecular markers are obtainable and desirable. The addition of a new program to the set of multiple-trait derivative-free REML programs is described that allows users the flexibility to calculate relationships using standard pedigree files or an arbitrary relationship matrix based on genetic marker information. The strategy behind this modification and its design is described. An application is illustrated in a QTL association study for canine hip dysplasia.

Key Words: breeding value estimation • multiple-trait derivative-free restricted maximal likelihood • quantitative trait locus association study • variance component estimation






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