Abstract #40

# 40
Practical implications for genetic modeling in the genomics era for the dairy industry.
Paul M. VanRaden*1, 1Animal Genomics and Improvement Lab, Agriculture Research Service, USDA, Beltsville, MD.

Genetic models convert data into estimated breeding values and other information useful to breeders. The goal is to provide accurate and timely predictions of the future performance for each animal (or embryo). Modeling involves defining traits, editing raw data, removing environmental effects, including genetic-by-environmental interactions and correlations among traits, and accounting for nonadditive inheritance or nonnormal distributions. Data included phenotypes and pedigrees during the last century and genotypes within the last decade. Genomic data can include markers, haplotypes, and causative effects such as insertions, deletions, or point mutations; most models also include polygenic effects because the markers do not track causative variants perfectly. Total numbers of known variants have increased rapidly from thousands to hundreds of thousands to millions. Nonlinear models add precision for traits influenced by major genes, but linear models work well for traits with more normally distributed genomic effects. Numbers of genotyped animals in US dairy evaluations increased rapidly from a few thousand in 2009 to about 1 million in 2015. Most are young females that will contribute to estimating allele effects in the future, but only about 100,000 have phenotypes so far. Traditional animal models may become biased by genomic preselection because Mendelian sampling of phenotyped progeny and mates is no longer expected to average 0. Single-step models that combine pedigree and genomic relationships can account for such selection, but approximations and new algorithms are needed to avoid excessive computation. Traditional animal models may include all breeds and crossbreds, but most genomic evaluations are still computed within breed. Inclusion of inbreeding, heterosis, dominance, and interactions can improve precision. Multitrait genomic models may be preferred for traits with many missing records or when foreign records are included as pseudo-observations, but most countries use multitrait traditional evaluations followed by single-trait genomic evaluations. A final goal is to explain how the models work so that breeders can more confidently apply the predictions in their selection programs.

Key Words: genetic evaluation, genomic selection, mixed models

Speaker Bio
Paul VanRaden is a research geneticist with the U.S. Department of Agriculture in Beltsville, Maryland. Paul joined USDA in 1988 after a PhD in animal breeding at Iowa State University and postdoc at the University of Wisconsin. Paul became interested in genetics while by employed by the Dairy Herd Improvement Association, collecting milk samples in Illinois while in high school after growing up on a dairy farm. At USDA, his research introduced the net merit index in 1994 and genetic evaluations for productive life, somatic cell score, and fertility. He introduced adjustments for inbreeding and crossbreeding in U.S. evaluations and statistical methods to include data from a wider variety of DHI testing programs. Recent research has focused on computing genomic evaluations from national and international datasets. Paul developed new imputation methods to combine data from low, medium, and high-density chips and from whole genome DNA sequences. Rapidly expanding genomic datasets keep Paul VanRaden and many other researchers in this field busy developing new tools for breeders.