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Efficient methods for processing genomic data were developed to increase reliability of estimated breeding values and to estimate thousands of marker effects simultaneously. Algorithms were derived and computer programs tested with simulated data for 2,967 bulls and 50,000 markers distributed randomly across 30 chromosomes. Estimation of genomic inbreeding(More)
Genetic progress will increase when breeders examine genotypes in addition to pedigrees and phenotypes. Genotypes for 38,416 markers and August 2003 genetic evaluations for 3,576 Holstein bulls born before 1999 were used to predict January 2008 daughter deviations for 1,759 bulls born from 1999 through 2002. Genotypes were generated using the Illumina(More)
Copy number variation (CNV) represents another important source of genetic variation complementary to single nucleotide polymorphism (SNP). High-density SNP array data have been routinely used to detect human CNVs, many of which have significant functional effects on gene expression and human diseases. In the dairy industry, a large quantity of SNP(More)
New terms and definitions were developed to explain national USDA genetic evaluations computed by an animal model. An animal's PTA combines information from its own records and records of all its relatives through a weighted average of 1) average of parents' evaluations, 2) half of its yield deviation, and 3) average across progeny of twice progeny(More)
We report putative quantitative trait loci affecting female fertility and milk production traits using the merged data from two research groups that conducted independent genome scans in Dairy Bull DNA Repository grandsire families to identify quantitative trait loci (QTL) affecting economically important traits. Six families used by both groups had been(More)
Genetic effects for many dairy traits and for total economic merit are evenly distributed across all chromosomes. A high-density scan using 38,416 single nucleotide polymorphism markers for 5,285 bulls confirmed 2 previously known major genes on Bos taurus autosomes (BTA) 6 and 14 but revealed few other large effects. Markers on BTA18 had the largest(More)
A genome scan was conducted in the North American Holstein-Friesian population for quantitative trait loci (QTL) affecting production and health traits using the granddaughter design. Resource families consisted of 1,068 sons of eight elite sires. Genome coverage was estimated to be 2,551 cM (85%) for 174 genotyped markers. Each marker was tested for(More)
Five new recessive defects were discovered in Holsteins, Jerseys, and Brown Swiss by examining haplotypes that had a high population frequency but were never homozygous. The method required genotypes only from apparently normal individuals and not from affected embryos. Genotypes from the BovineSNP50 BeadChip (Illumina, San Diego, CA) were examined for(More)
A national fertility evaluation was developed based on pregnancy rate, which measures the percentage of nonpregnant cows becoming pregnant within each 21-d opportunity period. Data for evaluation are days open, which are calculated as date pregnant minus previous calving date. Date pregnant is determined from last reported breeding or from subsequent(More)
Genetic and environmental factors that might affect gestation length (GL) were investigated. Data included information from >11 million parturitions from 1999 through 2006 for 7 US dairy breeds. Effects examined were year, herd-year, month, and age within parity of conception; parturition code (sex and multiple-birth status); lactation length and(More)