Technical Note: Use of Marker Based Relationships with MTDFREML

¹ Institute for Genetic Diversity, Cornell University, Ithaca, NY 14853, USA
² Department of Clinical Sciences, Cornell University, Ithaca, NY 14853, USA
³ Institute for Genetic Diversity, Cornell University, Ithaca, NY 14853, USA; USDA-ARS Cornell University, 159 Biotechnology Bldg, Ithaca, NY 14853, USA
⁴ USDA-ARS A218 Animal Sciences, University of Nebraska, Lincoln, NE 68583-0908, USA

^* To whom correspondence should be addressed. E-mail: lvanvleck{at}unlnotes.unl.edu.

	Abstract

The wide spread use of the set of MTDFREML 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 both obtainable and desirable. The addition of a new program to the set of MTDFREML programs is described which allows users the flexibility to calculate relationships using either standard pedigree files or an arbitrary relationship matrix based on genetic marker information. The strategy behind this modification and its design are described. An application is illustrated in a QTL association study for canine hip dysplasia.

Key Words: breeding value estimation, MTDFREML, QTL association study, variance component estimation