DEVELOPMENT OF STATISTICAL METHODS FOR THE ANALYSIS OF GENETIC (CO)VARIANCE MATRICES CALCULATED USING SINGLE NUCLEOTIDE POLYMORPHISMS
Animal Improvement Programs
Project Number: 1245-31000-101-03
Nonfunded Cooperative Agreement
Start Date: Dec 01, 2010
End Date: Nov 30, 2012
ARS Project Plan 1265-31000-096-00D has two objectives that directly relate to this agreement. The first is to develop methods to incorporate high-density genomic data in predictions of genetic merit, and the second is to investigate correlations among traits to efficiently combine evaluations to select for healthy dairy animals capable of producing quality milk at a low cost in many environments. The Cooperator has the expertise and infrastructure to develop statistical methods for the analysis of genome- and chromosome-wide (co)variance matrices calculated from genetic marker effects. Such methods may be useful for understanding the biology of economically important traits in dairy cattle, as well as identifying important nodes in gene networks.
Single nucleotide polymorphism (SNP) effects estimated independently in the Italian and U.S. Brown Swiss cattle populations by the 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 the Cooperator will jointly develop the statistical methods using a shared set of simulated data. The methods will be applied by AIPL to U.S. data and by the Cooperator to Italian data. Results will be used to compare the two populations.