Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in US Holsteins. 2011

S Tsuruta, and I Misztal, and I Aguilar, and T J Lawlor
Animal and Dairy Science Department, University of Georgia, Athens, Georgia 30602, USA. shogo@uga.edu

Currently, the USDA uses a single-trait (ST) model with several intermediate steps to obtain genomic evaluations for US Holsteins. In this study, genomic evaluations for 18 linear type traits were obtained with a multiple-trait (MT) model using a unified single-step procedure. The phenotypic type data on up to 18 traits were available for 4,813,726 Holsteins, and single nucleotide polymorphism markers from the Illumina BovineSNP50 genotyping Beadchip (Illumina Inc., San Diego, CA) were available on 17,293 bulls. Genomic predictions were computed with several genomic relationship matrices (G) that assumed different allele frequencies: equal, base, current, and current scaled. Computations were carried out with ST and MT models. Procedures were compared by coefficients of determination (R(2)) and regression of 2004 prediction of bulls with no daughters in 2004 on daughter deviations of those bulls in 2009. Predictions for 2004 also included parent averages without the use of genomic information. The R(2) for parent averages ranged from 10 to 34% for ST models and from 12 to 35% for MT models. The average R(2) for all G were 34 and 37% for ST and MT models, respectively. All of the regression coefficients were <1.0, indicating that estimated breeding values in 2009 of 1,307 genotyped young bulls' parents tended to be biased. The average regression coefficients ranged from 0.74 to 0.79 and from 0.75 to 0.80 for ST and MT models, respectively. When the weight for the inverse of the numerator relationship matrix (A(-1)) for genotyped animals was reduced from 1 to 0.7, R(2) remained almost identical while the regression coefficients increased by 0.11-0.26 and 0.12-0.23 for ST and MT models, respectively. The ST models required about 5s per iteration, whereas MT models required 3 (6) min per iteration for the regular (genomic) model. The MT single-step approach is feasible for 18 linear type traits in US Holstein cattle. Accuracy for genomic evaluation increases when switching ST models to MT models. Inflation of genomic evaluations for young bulls could be reduced by choosing a small weight for the A(-1) for genotyped bulls.

UI MeSH Term Description Entries
D008957 Models, Genetic Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment. Genetic Models,Genetic Model,Model, Genetic
D010641 Phenotype The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. Phenotypes
D001947 Breeding The production of offspring by selective mating or HYBRIDIZATION, GENETIC in animals or plants. Breedings
D002417 Cattle Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor. Beef Cow,Bos grunniens,Bos indicus,Bos indicus Cattle,Bos taurus,Cow,Cow, Domestic,Dairy Cow,Holstein Cow,Indicine Cattle,Taurine Cattle,Taurus Cattle,Yak,Zebu,Beef Cows,Bos indicus Cattles,Cattle, Bos indicus,Cattle, Indicine,Cattle, Taurine,Cattle, Taurus,Cattles, Bos indicus,Cattles, Indicine,Cattles, Taurine,Cattles, Taurus,Cow, Beef,Cow, Dairy,Cow, Holstein,Cows,Dairy Cows,Domestic Cow,Domestic Cows,Indicine Cattles,Taurine Cattles,Taurus Cattles,Yaks,Zebus
D005838 Genotype The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS. Genogroup,Genogroups,Genotypes
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D014481 United States A country in NORTH AMERICA between CANADA and MEXICO.
D014644 Genetic Variation Genotypic differences observed among individuals in a population. Genetic Diversity,Variation, Genetic,Diversity, Genetic,Diversities, Genetic,Genetic Diversities,Genetic Variations,Variations, Genetic
D016678 Genome The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA. Genomes
D056726 Genetic Association Studies The analysis of a sequence such as a region of a chromosome, a haplotype, a gene, or an allele for its involvement in controlling the phenotype of a specific trait, metabolic pathway, or disease. Candidate Gene Identification,Candidate Gene Analysis,Candidate Gene Association Studies,Candidate Gene Association Study,Gene Discovery,Genotype-Phenotype Association,Genotype-Phenotype Associations,Genotype-Phenotype Correlation,Genotype-Phenotype Correlations,Analyses, Candidate Gene,Analysis, Candidate Gene,Association Studies, Genetic,Association Study, Genetic,Association, Genotype-Phenotype,Associations, Genotype-Phenotype,Candidate Gene Analyses,Correlation, Genotype-Phenotype,Correlations, Genotype-Phenotype,Discovery, Gene,Gene Analyses, Candidate,Gene Analysis, Candidate,Gene Identification, Candidate,Genetic Association Study,Genotype Phenotype Association,Genotype Phenotype Associations,Genotype Phenotype Correlation,Genotype Phenotype Correlations,Identification, Candidate Gene,Studies, Genetic Association,Study, Genetic Association

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