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Nearly 57,000 single-nucleotide polymorphisms (SNP) genotyped with the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA) were investigated to determine usefulness of the associated SNP for genomic prediction. Genotypes were obtained for 12,591 bulls and cows, and SNP were selected based on 5,503 bulls with genotypes from a larger set of SNP. The following SNP were deleted: 6,572 that were monomorphic, 3,213 with scoring problems (primarily because of poor definition of clusters and excess number of clusters), and 3,649 with a minor allele frequency of <2%. Number of SNP for each minor allele frequency class (≥2%) was fairly uniform (777 to 1,004). For 5 contiguous SNP assigned to chromosome 7, no bulls were heterozygous, which indicated that those SNP are actually on the nonpseudoautosomal portion of the X chromosome. Another 178 SNP that were not assigned to a chromosome but that had many fewer heterozygotes than expected were also assigned to the X chromosome. Existence of Hardy-Weinberg equilibrium was investigated by comparing observed with expected heterozygosity. For 11 SNP, the observed percentage of heterozygous individuals differed from the expected by >15%; therefore, those SNP were deleted. For 2,628 SNP, the genotype at another SNP was highly correlated (i.e., genotypes were identical for >99.5% of bulls), and those were deleted. After edits, 40,874 SNP remained. A parent- progeny conflict was declared when the genotypes were alternate homozygotes. Mean number of conflicts was 2.3 when pedigree was correct and 2,411 when it was incorrect. The sire was genotyped for >93% of animals. Maternal grandsire genotype was similarly checked; however, because alternate homozygotes could be valid, a conflict threshold of 16% was used to indicate a need for further investigation. Genotyping consistency was investigated for 21 bulls genotyped twice with differences primarily from SNP that were not scored in one of the genotypes. Concordance for readable SNP was extremely high (99.96-100%). Thousands of SNP that were polymorphic in Holsteins were monomorphic in Jerseys or Brown Swiss, which indicated that breedspecific SNP sets are required or that all breeds need to be considered in the SNP selection process. Genotypes from the Illumina BovineSNP50 BeadChip are of high accuracy and provide the basis for genomic evaluations in the United States and Canada. [ABSTRACT FROM AUTHOR]

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 effects on calving ease, several conformation traits, longevity, and total merit. Prediction accuracy was highest using a heavy-tailed prior assuming that each marker had an effect on each trait, rather than assuming a normal distribution of effects as in a linear model, or that only some loci have nonzero effects. A prior model combining heavy tails with finite alleles produced results that were intermediate compared with the individual models. Differences between models were small (1 to 2%) for traits with no major genes and larger for heavy tails with traits having known quantitative trait loci (QTL; 6 to 8%). Analysis of bull recessive codes suggested that marker effects from genomic selection may be used to identify regions of chromosomes to search in detail for candidate genes, but individual single nucleotide polymorphisms were not tracking causative mutations with the exception of diacylglycerol O-acyltransferase 1. Additive genetic merits were constructed for each chromosome, and the distribution of BTA14-specific estimated breeding value (EBV) showed that selection primarily for milk yield has not changed the distribution of EBV for fat percentage even in the presence of a known QTL. Such chromosomal EBV also may be useful for identifying complementary mates in breeding programs. The QTL affecting dystocia, conformation, and economic merit on BTA18 appear to be related to calf size or birth weight and may be the result of longer gestation lengths. Results validate quantitative genetic assumptions that most traits are due to the contributions of a large number of genes of small additive effect, rather than support the finite locus model. [ABSTRACT FROM AUTHOR]

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 BovineSNP50 BeadChip and DNA from semen contributed by US and Canadian artificial-insemination organizations to the Cooperative Dairy DNA Repository. Genomic predictions for 5 yield traits, 5 fitness traits, 16 conformation traits, and net merit were computed using a linear model with an assumed normal distribution for marker effects and also using a nonlinear model with a heavier tailed prior distribution to account for major genes. The official parent average from 2003 and a 2003 parent average computed from only the subset of genotyped ancestors were combined with genomic predictions using a selection index. Combined predictions were more accurate than official parent averages for all 27 traits. The coefficients of determination (R²) were 0.05 to 0.38 greater with nonlinear genomic predictions included compared with those from parent average alone. Linear genomic predictions had R² values similar to those from nonlinear predictions but averaged just 0.01 lower. The greatest benefits of genomic prediction were for fat percentage because of a known gene with a large effect. The R² values were converted to realized reliabilities by dividing by mean reliability of 2008 daughter deviations and then adding the difference between published and observed reliabilities of 2003 parent averages. When averaged across all traits, combined genomic predictions had realized reliabilities that were 23% greater than reliabilities of parent averages (50 vs. 27%), and gains in information were equivalent to 11 additional daughter records. Reliability increased more by doubling the number of bulls genotyped than the number of markers genotyped. Genomic prediction improves reliability by tracing the inheritance of genes even with small effects. [ABSTRACT FROM AUTHOR]

This study addresses the utility of 11 blood groups as selection aids in Holstein breeding schemes and considers issues inherent to the approach of resolving quantitative variation into components that are due to quantitative trait loci. The data consisted of predicted transmitting abilities of 22,614 bulls, first lactation information on 1,924,171 cows, and type scores on 447,800 cows. Linear models were fitted under male half-sib designs, female half-sib designs, and granddaughter designs as well as under the assumption of direct effects of the markers. The evolution of allele frequencies through time was determined, and previous research results were synthesized according to criteria of consistency of biological significance. The inconsistency of results across studies and analytical designs alludes to the importance of the intrinsic nonadditivity of genetic and biological phenomena to quantitative trait locus detection and marker-assisted selection. In our analyses, three associations met the criteria of consistency--a C blood group effect on rump angle, an L effect on milk yield and composition traits, and an S effect on milk fat yield. The M locus appears to be directly associated with effects on milk and protein yields. An enhanced understanding of the biochemical and physiological bases of quantitative genetics should be a long-term objective of this type of genetic analysis.

The potential of trait-based analysis to detect quantitative trait loci was investigated using blood group polymorphisms as the marker systems and milk and type traits in Holstein cattle as the quantitative traits. Within large half-sib families, animals were ranked on their predicted transmitted abilities or phenotypes, and blood group allele frequencies were compared between the upper and lower 5% tails of the distributions. Genotype frequencies within large families were also examined for evidence of selection. All of the major effects that had previously been detected using linear model analyses were identified by the trait-based analyses of a C blood group effect on rump angle, an L effect on milk yield and composition traits, an S effect on milk fat yield, and a direct effect of the M locus on milk and protein yields. These results provide additional support for the biological validity of these associations and also demonstrate the utility of trait-based analysis for the detection of quantitative trait loci within existing dairy breeding programs. However, just as in the linear model analyses, an analytical strategy should be utilized that allows the identification of the effects that are consistent across environments and genetic backgrounds.

Holstein sires (n = 340) with milk, milk fat, semen unit fertility, daughter stayability evaluations, and semen price for 1986 were studied. Effects of variation in sire fertility and daughter stayability on profitability of sire selection using the net present value criterion were estimated. The model estimated expected profit from a cow bred to pregnancy from future production and from cattle disposal and replacement after discounting costs and returns to the time of insemination. Effects of semen sexing and semen unit dilution on profitability to determine optimal breeding strategies for dairy herds were examined. Sire profitability increased with herd average conception rate and sire selection intensity. Daughter stayability had a greater impact on profitability than semen unit fertility when profit maximization was computed under the criterion of breeding a cow to pregnancy. Genetic progress for production was compromised when selecting to maximize profit. Dilution of semen units seems profitable only when semen availability is limited for high demand sires. The use of sexed female semen may only be appropriate when it can generate additional income from the sale of surplus heifers.

Result of insemination was verified for 329,314 artificial inseminations by 882 service sires to 97,245 Holstein cows in 1,075 herds between May 1970 and December 1983. Estimates of systematic environmental and genetic components of cow and service sire components of conception rate were obtained preliminary to development of a fertility monitoring system. Conception rate was 2.9% higher in stanchion than loose housed herds and 2.3% higher in grade than registered cows. Fall months were superior to winter months, the greatest difference being 6.1% between October and January. Conception rate increased with herd milk production, decreased with both increased cow age, and increased herd size in mature and old cows. Regions and inseminators within regions were highly variable. Conception may be influenced by semen price; however, week day of insemination and duration of semen storage had no effect. Conception rate decreased for semen by bulls 8 yr and older, was lowest for semen harvested in June, but no season of collection effect was detected. No genetic trends for cow and service sire conception rate were found; heritability and repeatability were .08 and .06, respectively. Genetic correlations between cow and service sire conception rate and these components with first lactation production and semen output measures were all near zero. Therefore, the relationship between sire fertility and daughter fertility is near zero.