Abstract
AbstractGenomic imprinting causes alleles to influence the phenotype in a parent-of-origin-specific manner. In attempts to determine the effects of imprinted loci, gametic relationship matrices have widely been used in pedigree-based parent-of-origin analyses of population data. One drawback of this is the size of these matrices because they represent each individual by two gametic effects. Significantly fewer equations are needed if a previously published reduced imprinting model is used that relates observations from progeny without its own offspring to the transmitting abilities of their parents. This can be accomplished using a numerator relationship matrix, with only a single row and column per parent and ancestors. However, the reduced model is not applicable when the parents have records. To better handle the curse of dimensionality, we propose a combination of average gametic effects (transmitting abilities) for individuals without their own records and single gametic effects for others. The generalized gametic relationship matrix is the covariance of this mixture of genetic effects that allows for a significant reduction in the number of equations in gametic models depending on the trait, depth of pedigree, and population structure. It can also render the reduced model much more flexible by including observations from parents. Rules for setting-up its inverse from a pedigree are derived and implemented on an open-source program. The application of the same principles to phased marker data leads to a genomic version of the generalized gametic relationships. The implementation of generalized gametic models to the ASReml package is illustrated through worked examples.
Publisher
Cold Spring Harbor Laboratory
Reference24 articles.
1. Hot topic: A unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final score
2. Blunk, I. , und N. Reinsch , 2014: Genetic variance components when fluctuating imprinting patterns are present. Proceedings of the 10th World Congress Applied to Livestock Genetics, 17-22. August 2014, Vancouver, BC, Canada, pp. 17–22
3. Parsimonious model for analyzing parent-of-origin effects related to beef traits in dual-purpose Simmental;J. Anim. Sci,2017
4. A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse data;Animal,2017
5. Scanning the genomes of parents for imprinted loci acting in their un-genotyped progeny;Sci. Rep,2019