Effect of synchronization and semen sorting on artificial insemination bull fertility.

Field data were collected over a period of 2 yr by artificial insemination technicians for the purpose of evaluating differences among bulls in their fertility when synchronization and semen sorting were involved. First, main effects of synchronization and semen sorting were found to reduce bull fertility by 1.5 and 12.7%, respectively. Second, the interaction of both factors with bull fertility significantly enhanced the evaluation models. Differences between 2 sets of adjusted conception rates for synchronized and nonsynchronized services ranged from 0.5 to 2.9%, whereas differences between 2 sets of adjusted conception rates for sorted and conventional semen ranged from -1.8 to 15.2%. This implies that using conventional fertility models that ignore these effects may not be sufficiently accurate in situations where synchronization or semen sorting are involved. Accounting for synchronization and especially for semen sorting to evaluate bulls on their fertility and the production of separate sets of conception rates under each situation are essential.

Genetic impacts of using female-sorted semen in commercial and nucleus herds.

This study was designed to investigate the genetic effects of using sorted semen in a dairy cattle population. Progress was monitored in elite and commercial animals over 20 yr of selection. To study the genetic impact of using sorted semen in commercial herds, a scenario was evaluated in which female-sorted semen was available to commercial herds. Second, to study the genetic impact of using sorted semen in nucleus herds, scenarios were simulated in which female-sorted semen was used only in a centralized nucleus herd, in which multiple ovulation and embryo transfer (MOET) took place. Because of the additional advantage of marker-assisted selection when sorted semen was used in nucleus herds, a second scenario was simulated in which both sorted semen and marker-assisted selection were implemented. In the scenario in which female-sorted semen was used in commercial herds, a large genetic advantage was observed early in commercial cows. The average superiority in first-lactation cows exceeded 30% in yr 11, relative to a base scheme with regular semen, but continued to decrease until it reached 9% in yr 20. The increased selection intensity in commercial cows contributed to the genetic merit of future cows (cow-to-cow contribution), but the contribution of the nucleus grew over time and gradually marginalized the cow-to-cow contribution. The genetic advantage of gender control in MOET schemes was minimal except when marker-assisted selection was also available. Two factors that affected the contribution of marker-assisted selection were studied: 1) within- vs. across-family selection of donors, and 2) the number of loci in the quantitative trait locus component. Schemes that selected donors regardless of their family structure were superior, and the quantitative trait locus component with more loci increased the effectiveness of sorted semen. Finally, we studied a reduced MOET scheme in which the number of harvested females was reduced from 42 to 25/yr. The reduced scheme in combination with female-sorted semen was not found to be genetically inferior to the large scheme in combination with regular semen.

Effect of semen thaw method on conception rate in four large commercial dairy heifer herds.

Semen processed with procedures intended to permit a flexible thaw method is used to breed millions of cows yearly. One method of thawing straws, the "pocket thaw" is used extensively with semen prepared with these procedures. Published field data is lacking for thaw method comparisons with semen processed to permit flexible-thawing. The objective of the present study was to measure the effect of semen thaw method (warm-water or pocket thaw) over all seasons and its interaction with herds, inseminators, straw package size, and sperm number on conception rate in commercial dairy heifer herds using semen processed with procedures historically optimized for success with flexible-thawing. Professional inseminators performed 11,215 services over a 16-month period in four large herds, achieving a 67.6% conception rate. Thaw method was alternated weekly. Thaw effect on conception status, determined by 70 days non-return rate, was estimated by a generalized linear mixed model. Neither thaw method nor number of sperm per straw significantly affected probability of conception (P=0.658 and 0.769, respectively). No interactions of thaw method with herd, sperm number, season, straw size, and straw size by season were detected (P=0.297, 0.526, 0.365, 0.723, and 0.824, respectively). Bull, herd, inseminator within herd, year, season, and straw size affected conception rate (P=0.002, 0.000, 0.000, 0.000, 0.000, and 0.014, respectively). In conclusion, for semen processed with procedures that permit flexible-thawing, thaw method (pocket thaw versus warm-water thaw) did not affect conception rate under commercial conditions and with routine semen handling methods.

Genetic basis and risk factors for infectious and noninfectious diseases in US Holsteins. I. Estimation of genetic parameters for single diseases and general health.

Health data collected from 1996 to 1999 from 177 herds in Minnesota and Wisconsin were analyzed to establish genetic basis for infectious and noninfectious diseases. Three types of health traits were targeted. First, available infectious conditions were used to identify animals that are superior in their general immunity (including innate immunity) for infectious diseases. Generalized immunity may be thought of as a combination of immune responses to a variety of immune system challenges. Second, single infectious and noninfectious diseases were analyzed separately. Third, infectious reproductive diseases as one category of related conditions, and cystic ovary disease as one category of 3 related noninfectious ovary disorders were studied. Data were analyzed using a threshold model that included herd, calving year, season of calving, and parity as cross-classified fixed factors; and sire and cow within sires as random effects. Days at risk and days in milk at the beginning of a record were included by fitting the days as continuous covariates in the model. A heritability value of 0.202 +/- 0.083 was estimated for generalized immunity. Heritability values of 0.141 and 0.161 were estimated for uterine infection and mastitis, respectively. Heritability of single noninfectious disorders ranged from 0.087 to 0.349. The amount of additive genetic variance recovered in the underlying scale of noninfectious disorders tended to zero when combining multiple conditions. The study supports combining infectious diseases into categories of interest but we do not recommend the same approach for noninfectious disorders.

Correlations among body condition scores from various sources, dairy form, and cow health from the United States and Denmark.

The objectives of this study were to estimate genetic correlations among body condition scores (BCS) from various sources, dairy form, and measures of cow health. Body condition score and dairy form evaluated during routine type appraisal was obtained from the Holstein Association USA, Inc. A second set of BCS was obtained from Dairy Records Managements Systems (DRMS) and was recorded by producers that use PCDART dairy management software. Disease observations were obtained from recorded veterinarian treatments in several dairy herds in the United States. Estimated breeding values for diseases in Denmark were also obtained. Genetic correlations among BCS, dairy form, and cow health traits in the United States were generated with sire models. Models included fixed effects for age, DIM, and contemporary group. Random effects included sire, permanent environment, herd-year season for health traits, and error. Predicted transmitting abilities (PTA) for BCS and dairy form were correlated with estimated breeding values for disease in Denmark. The genetic correlation estimate between BCS from DRMS and BCS from the Holstein Association USA, Inc., was 0.85. The genetic correlation estimate between BCS and a composite of all diseases in the United States was -0.79, and PTA for BCS was favorably correlated with an index of resistance to disease other than mastitis in Denmark (0.27). Dairy form was positively correlated with a composite of all diseases in the United States (0.85) and was unfavorably correlated with an index for resistance to disease other than mastitis in Denmark (-0.29). Adjustment for protein yield PTA had a minimal affect on correlations between PTA for BCS or dairy form and disease in Denmark. Selection for higher body condition or lower dairy form with continued selection for yield may slow deterioration in cow health as a correlated response to selection for increased yield.

Superiority of QTL-assisted selection in dairy cattle breeding schemes.

The superiority of selection schemes employing information about a known quantitative trait locus (QTL) over conventional schemes is examined for dairy cattle breeding schemes. Stochastic simulation of a dairy cattle population with selection practices, structures, and parameters similar to the US Holstein population was implemented. Additive genetic effects were estimated by an animal model. Two schemes were compared: a QTL-assisted selection scheme in which the genotype of a known QTL was accounted for in the animal model as a fixed factor, and a QTL-free selection scheme in which the QTL was simulated but was not fit separately in the animal model. Under the QTL-assisted selection scheme, all animals in the mixed model were assumed to be genotyped for the QTL. The effect of using QTL information on the genetic response, the frequency of the favorable QTL allele, and the accuracy of evaluation were examined. Moreover, the effect was studied in four distinct paths of selection: active sires, proven young bulls, bull dams, and first-lactation cows. Average superiority values of 4.6, 7.6, 11.7, and 1.1% for genetic response were observed over 16 yr of selection for active sires, young bulls, bull dams, and first-lactation cows, respectively. Frequency of the favorable QTL allele changed faster in bull dams than males, and was the slowest in first-lactation cows. Finally, accuracy of evaluation under the QTL-assisted selection scheme was higher than under the QTL-free selection scheme. Young bulls ofthe QTL-assisted selection scheme on average had 0.049 higher accuracy, and first-lactation cows had on average 0.185 higher accuracy than corresponding animals of the QTL-free selection scheme.

A rapid method for computing the inverse of the gametic covariance matrix between relatives for a marked quantitative trait locus.

The inverse of the gametic covariance matrix between relatives, G(-1), for a marked quantitative trait locus (QTL) is required in best linear unbiased prediction (BLUP) of breeding values if marker data are available on a QTL. A rapid method for computing the inverse of a gametic relationship matrix for a marked QTL without building G itself is presented. The algorithm is particularly useful due to the approach taken in computing inbreeding coefficients by having to compute only few elements of G. Numerical techniques for determining, storing, and computing the required elements of G and the nonzero elements of the inverse are discussed. We show that the subset of G required for computing the inbreeding coefficients and hence the inverse is a tiny proportion of the whole matrix and can be easily stored in computer memory using sparse matrix storage techniques. We also introduce an algorithm to determine the maximum set of nonzero elements that can be found in G(-1) and a strategy to efficiently store and access them. Finally, we demonstrate that the inverse can be efficiently built using the present techniques for very large and inbred populations.

Properties of threshold model predictions.

Estimation of genetic parameters and accuracy of threshold model genetic predictions were investigated. Data were simulated for different population structures by using Monte Carlo techniques. Variance components were estimated by using threshold models and linear sire models applied to untransformed data, logarithmically transformed data, and transformation to Snell scores. Effects of number of categories (2, 5, and 10), incidence of categories (extreme, moderate, and normal), heritability in the underlying scale (.04, .20, and .50), and data structure (unbalanced and balanced) on accuracy of genetic prediction were investigated. The real importance of using a threshold model was to estimate genetic parameters. An expected heritability of .20 was estimated to be .22 and .10 by a threshold model and a linear model, respectively. Accuracy increased significantly with a larger number of categories, a more normal distribution of incidences, increased heritability, and more balanced data. Even threshold models were shown to be more efficient with more than two categories (e.g., binomial). Transformation of scale did not accomplish the purpose intended.