Development of Statistical Methods for the Analysis of Genetic (Co)variance Matrices Calculated Using Single Nucleotide Polymorphisms
Animal Genomics and Improvement Laboratory
Project Number: 1245-31000-101-06
Nonfunded Cooperative Agreement
Start Date: Dec 31, 2012
End Date: Dec 30, 2014
The objective of this agreement is to develop statistical methods for the analysis of the eigenstructure (and eigenvalues resulting from decomposition of a matrix) of genetic (co)variance matrices constructed using high-density DNA marker data. At present, the effect of different (co)variance structures on matrix decompositions is not well understood, which hinders interpretation of those values. Knowledge of relationships among marker effects estimates, specific genetic (co)variance structures, and the eigenstructures of those matrices will improve the understanding of the biology of economically important traits in dairy cattle. Such tools may also facilitate the automated discovery of interesting features in high-dimensional data sets.
Single nucleotide polymorphism (SNP) effects estimated independently in the Italian and U.S. Brown Swiss cattle populations by Cooperator and ARS, respectively, will be used to develop methods for comparing genetic (co)variance matrices for various traits of economic importance in those breeds. Methods developed will be reported in the scientific literature. ARS and Cooperator will jointly develop the statistical methods using a shared set of simulated data. The methods will be applied by ARS to U.S. data and by the Cooperator to Italian data. Results will be used to compare the two populations.