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Calculation and Delivery of US Genomic Evaluations for Dairy Cattle
In April 2013, the responsibility for calculation and distribution of genomic evaluations for dairy cattle was transferred from the USDA to the US dairy industry’s Council on Dairy Cattle Breeding; the responsibility for development of evaluation methodology remained with the USDA. The Council on Dairy Cattle Breeding has implemented a fee schedule to provide operational funds as well as an incentive for continued submission of phenotypic data necessary for estimation of genomic effects. Since April 2013, substantial improvements have been made to the evaluation system. The number of SNP used for all evaluations has been increased to 61,013 from 45,195. The Jersey reference population has been increased by 1,186 Danish bull genotypes obtained through an exchange with Viking Genetics International (Skara, Sweden). Genomic evaluations for Ayrshires were released to the industry. Cutoff studies to assess the accuracy of data available 4 yr earlier for predicting current data showed the mean gain in reliability across traits for Holsteins was 0.5 percentage points from adding 15,818 SNP, 1.2 percentage points for adding the Jersey bulls, and 8.2 percentage points over parent average for Ayrshires. The weighting for cow evaluations used to estimate SNP effects has been reduced. Also, the deregression of the traditional PTA is jointly across animals instead of 1 animal at a time. Each animal gets credit for its own records and for records of its non-genotyped progeny. This prevents double counting of traditional information when parents and progeny are both genotyped. For yield traits, genotyped-daughter evaluations are not removed because the cow adjustment made them incompatible. Adjustment of cow weights improved the regression of genomic evaluation on future performance and reduced bias. Multitrait traditional evaluations for heifer and cow conception rates are used to estimate SNP effects for those traits. Imputed values are now provided for gene tests for bovine leucocyte adhesion deficiency, complex vertebral malformation, deficiency of uridine monophosphate synthase, syndactyly, Weaver Syndrome, spinal dismyelination, spinal muscular atrophy, red coat color, and polledness. Four tests for haplotypes that affect fertility or stillbirth rate were added (HH4 and HH5 for Holsteins, BH2 for Brown Swiss, and AH1 for Ayrshires). As of February 2014, over 538,000 genotypes are used in genomic evaluation with a mean of 18,000 added monthly. Genomic evaluations are released for animals from 36 countries, an indication of the global demand for them.
Keywords: Dairy Cattle, Genomic Evaluation, Holstein