Prediction of likelihood of conception in dairy cows using milk mid-infrared spectra collected before the first insemination and machine learning algorithms.

Accurate and ex-ante prediction of cows' likelihood of conception (LC) based on milk composition information could improve reproduction management on dairy farms. Milk composition is already routinely measured by mid-infrared (MIR) spectra, which are known to change with advancing stages of pregnancy. For lactating cows, MIR spectra may also be used for predicting the LC. Our objectives were to classify the LC at first insemination using milk MIR spectra data collected from calving to first insemination and to identify the spectral regions that contribute the most to the prediction of LC at first insemination. After quality control, 4,866 MIR spectra, milk production, and reproduction records from 3,451 Holstein cows were used. The classification accuracy and area under the curve (AUC) of 6 models comprising different predictors and 3 machine learning methods were estimated and compared. The results showed that partial least square discriminant analysis (PLS-DA) and random forest had higher prediction accuracies than logistic regression. The classification accuracy of good and poor LC cows and AUC in herd-by-herd validation of the best model were 76.35 ± 10.60% and 0.77 ± 0.11, respectively. All wavenumbers with values of variable importance in the projection higher than 1.00 in PLS-DA belonged to 3 spectral regions, namely from 1,003 to 1,189, 1,794 to 2,260, and 2,300 to 2,660 cm-1. In conclusion, the model can predict LC in dairy cows from a high productive TMR system before insemination with a relatively good accuracy, allowing farmers to intervene in advance or adjust the insemination schedule for cows with a poor predicted LC.

Predicting survival in dairy cattle by combining genomic breeding values and phenotypic information.

Advances in technology and improved data collection have increased the availability of genomic estimated breeding values (gEBV) and phenotypic information on dairy farms. This information could be used for the prediction of complex traits such as survival, which can in turn be used in replacement heifer management. In this study, we investigated which gEBV and phenotypic variables are of use in the prediction of survival. Survival was defined as survival to second lactation, plus 2 wk, a binary trait. A data set was obtained of 6,847 heifers that were all genotyped at birth. Each heifer had 50 gEBV and up to 62 phenotypic variables that became gradually available over time. Stepwise variable selection on 70% of the data was used to create multiple regression models to predict survival with data available at 5 decision moments: distinct points in the life of a heifer at which new phenotypic information becomes available. The remaining 30% of the data were kept apart to investigate predictive performance of the models on independent data. A combination of gEBV and phenotypic variables always resulted in the model with the highest Akaike information criterion value. The gEBV selected were longevity, feet and leg score, exterior score, udder score, and udder health score. Phenotypic variables on fertility, age at first calving, and milk quantity were important once available. It was impossible to predict individual survival accurately, but the mean predicted probability of survival of the surviving heifers was always higher than the mean predicted probability of the nonsurviving group (difference ranged from 0.014 to 0.028). The model obtained 2.0 to 3.0% more surviving heifers when the highest scoring 50% of heifers were selected compared with randomly selected heifers. Combining phenotypic information and gEBV always resulted in the highest scoring models for the prediction of survival, and especially improved early predictive performance. By selecting the heifers with the highest predicted probability of survival, increased survival could be realized at the population level in practice.

Genetic analysis of udder conformation traits derived from automatic milking system recording in dairy cows.

Cartesian teat coordinates measured by automatic milking systems (AMS) provide new opportunities to record udder conformation traits and to study changes in udder conformation genetically and phenotypically within and between parities. The objective of this study was to estimate heritabilities and repeatabilities of AMS-based udder conformation traits within parities, to estimate genetic correlations between parities for AMS-based udder conformation traits, and to estimate genetic correlations between AMS-based udder conformation traits and classifier-based udder conformation traits, longevity, and udder health. Data from 70 herds, including 12,663 first-parity cows, 10,206 second-parity cows, and 7,627 third-parity cows, were analyzed using univariate and bivariate mixed animal models. Heritabilities of the AMS udder conformation traits were large (0.37-0.67) and genetic correlations between the AMS udder conformation traits and classifier-based traits were strong (>0.91). Repeatabilities within parities were large as well (0.89-0.97), indicating that a single record on udder conformation per lactation reflects udder conformation well. Genetic correlations of AMS udder conformation traits between parities were strong (0.88-1.00) and were stronger than the permanent environmental correlations. This shows that udder conformation changes over parities, but this change is mostly due to nongenetic factors. Based on these results, the current herd classification system, where cows are scored on udder conformation once in first parity, is sufficient. The AMS udder conformation traits as defined in this study have limited value as replacement for classifier-based udder conformation traits because they have smaller genetic correlations with functional traits than classifier-based traits. In summary, udder conformation hardly changes genetically between parities and is highly repeatable within parities. Udder conformation traits based on AMS need fine-tuning before they can replace classifier-based traits, and AMS teat coordinates probably contain additional information about udder health that is yet to be explored.

Comparing regression, naive Bayes, and random forest methods in the prediction of individual survival to second lactation in Holstein cattle.

In this study, we compared multiple logistic regression, a linear method, to naive Bayes and random forest, 2 nonlinear machine-learning methods. We used all 3 methods to predict individual survival to second lactation in dairy heifers. The data set used for prediction contained 6,847 heifers born between January 2012 and June 2013, and had known survival outcomes. Each animal had 50 genomic estimated breeding values available at birth and up to 65 phenotypic variables that accumulated over time. Survival was predicted at 5 moments in life: at birth, at 18 mo, at first calving, at 6 wk after first calving, and at 200 d after first calving. The data sets were randomly split into 70% training and 30% testing sets to evaluate model performance for 20-fold validation. The methods were compared for accuracy, sensitivity, specificity, area under the curve (AUC) value, contrasts between groups for the prediction outcomes, and increase in surviving animals in a practical scenario. At birth and 18 mo, all methods had overlapping performance; no method significantly outperformed the other. At first calving, 6 wk after first calving, and 200 d after first calving, random forest and naive Bayes had overlapping performance, and both machine-learning methods outperformed multiple logistic regression. Overall, naive Bayes has the highest average AUC at all decision points up to 200 d after first calving. Random forest had the highest AUC at 200 d after first calving. All methods obtained similar increases in survival in the practical scenario. Despite this, the methods appeared to predict the survival of individual heifers differently. All methods improved over time, but the changes in mean model outcomes for surviving and non-surviving animals differed by method. Furthermore, the correlations of individual predictions between methods ranged from r = 0.417 to r = 0.700; the lowest correlations were at first calving for all methods. In short, all 3 methods were able to predict survival at a population level, because all methods improved survival in a practical scenario. However, depending on the method used, predictions for individual animals were quite different between methods.

Genetic correlations between dressage, show jumping and studbook-entry inspection traits in a process of specialization in Dutch Warmblood horses.

Sport performance in dressage and show jumping are two important traits in the breeding goals of many studbooks. To determine the optimum selection scheme for jumping and dressage, knowledge is needed on the genetic correlation between both disciplines and between traits measured early in life and performance in competition in each discipline. This study aimed to estimate genetic parameters to support decision-making on specialization of breeding horses for dressage and show jumping in Dutch warmblood horses. Genetic correlations between performance of horses in dressage and show jumping were estimated as well as the genetic correlation between traits recorded during studbook-entry inspections and performance in dressage and show jumping competitions. The information on competition comprised the performance of 82 694 horses in dressage and 62 072 horses in show jumping, recorded in the period 1993-2012. For 26 056 horses, information was available for both disciplines. The information on traits recorded at studbook-entry inspections comprised 62 628 horses, recorded in the period 1992-2013. Genetic parameters were estimated from the whole dataset and from a subset without horses recorded in both disciplines. Additionally, the genetic parameters were estimated in three different time periods defined by horses' birth year. The genetic correlation between dressage and show jumping in the whole dataset was -0.23, and it was -0.03 when it was estimated from horses recorded in only one discipline. The genetic correlation between dressage and show jumping was more negative in the most recent time period in all the cases. The more negative correlation between disciplines in more recent time periods was not reflected in changes in the correlations between competitions traits and the traits recorded in the studbook-first inspection. These results suggest that a breeding programme under specialization might be most effective defining two separate aggregate breeding goals for each of the disciplines.

Analysis of competition performance in dressage and show jumping of Dutch Warmblood horses.

Most Warmblood horse studbooks aim to improve the performance in dressage and show jumping. The Dutch Royal Warmblood Studbook (KWPN) includes the highest score achieved in competition by a horse to evaluate its genetic ability of performance. However, the records collected during competition are associated with some aspects that might affect the quality of the genetic evaluation based on these records. These aspects include the influence of rider, censoring and preselection of the data. The aim of this study was to quantify the impact of rider effect, censoring and preselection on the genetic analysis of competition data of dressage and show jumping of KWPN. Different models including rider effect were evaluated. To assess the impact of censoring, genetic parameters were estimated in data sets that differed in the degree of censoring. The effect of preselection on variance components was analysed by defining a binary trait (sport-status) depending on whether the horse has a competition record or not. This trait was included in a bivariate model with the competition trait and used all horses registered by KWPN since 1984. Results showed that performance in competition for dressage and show jumping is a heritable trait (h2 ~ 0.11-0.13) and that it is important to account for the effect of rider in the genetic analysis. Censoring had a small effect on the genetic parameter for highest performance achieved by the horse. A moderate heritability obtained for sport-status indicates that preselection has a genetic basis, but the effect on genetic parameters was relatively small.

Esophageal Dysfunction in Friesian Horses: Morphological Features.

Megaesophagus appears to be more common in Friesian horses than in other breeds. A prevalence of approximately 2% was observed among Friesian horses presented to the Wolvega Equine Clinic and the Utrecht University Equine Clinic. In this study, morphologic changes in the esophagi of Friesian horses with megaesophagus were compared with those of 6 control horses. Of 18 horses with clinically observed megaesophagus, only 12 animals had esophageal dilation at necropsy, usually involving the thoracic portion. Muscular hypertrophy of the distal esophagus was present in only one-third of the affected horses, indicating that this change is not the most relevant cause of megaesophagus in Friesians. Increased deposition of clumped and disorganized collagen was present in these clinically affected horses mainly in the non-dilated portion of the esophagus. At necropsy, a decrease in neural elements and elastin was present principally in horses with megaesophagus. Mild degeneration and necrosis of the tunica muscularis along the entire length of the esophagus were present in clinically affected horses and encountered only rarely in control animals. There were no significant differences among affected and control horses with respect to inflammation, mineralization, or the number of cells of Cajal. The increased occurrence of megaesophagus in the Friesian breed compared with other horse breeds, together with the presence of abnormal collagen in very young foals, supports the hypothesis that megaesophagus is hereditary in Friesians.

Phenotypic and genetic relationships of bovine natural antibodies binding keyhole limpet hemocyanin in plasma and milk.

To improve the health status (resilience) of dairy cows, levels of natural antibodies (NAb) might be useful. The objective of the present study was to compare levels and to estimate genetic parameters for NAb measured in milk and plasma samples. Titers of NAb IgM and IgG isotype-binding keyhole limpet hemocyanin of 2,919 cows, in both plasma and milk, were measured using ELISA. Analysis revealed that NAb levels in milk significantly increased with parity, whereas they remained constant in plasma. Moderate positive phenotypic correlations were found between NAb levels in milk and in plasma: 0.18 for IgG and 0.40 for IgM. This indicates that NAb from milk and plasma might reflect different aspects of dairy cow health status. However, high genetic correlations were found for NAb in milk and plasma: 0.81 for IgG and 0.79 for IgM. Heritabilities (SE in parentheses) for NAb measured in plasma [0.15 (0.05) for IgG and 0.25 (0.06) for IgM] were higher than heritabilities of NAb measured in milk [0.08 (0.03) for IgG and 0.23 (0.05) for IgM]. Our results indicate that NAb measured in milk and plasma are heritable and likely have a common genetic background, suggesting that NAb levels measured in milk might be useful for genetic improvement of disease resistance.

Effect of specialization on genetic parameters of studbook-entry inspection in Dutch Warmblood horses.

Recent studies on data from the Dutch Warmblood Studbook (KWPN) have shown that the ongoing specialization of horses for either dressage (DH) or show jumping (JH) has led to a decreasing genetic relationship between the two subpopulations. The aim of this study was to analyse the effect of the specialization process on the genetic parameters of traits measured in the studbook-entry inspection of KWPN during the last fifteen years. Data from 18,125 DH and 23,800 JH recorded from 1998 until 2013 were used to analyse 13 traits scored in both DH and JH. Analyses were performed in a Bayesian framework. Firstly, variance components were estimated based on the whole data set. Secondly, genetic correlations between traits measured in DH or JH were estimated using bivariate analyses. Thirdly, three time periods were defined and genetic correlations between subpopulations were estimated within each period. Heritability was moderate (0.17-0.39) for both DH and JH. Genetic correlations between traits measured in DH or JH were not different from one considering the posterior standard deviation of the estimation; however, in most of the traits, a clear trend in reduction of the genetic correlation for traits expressed in DH and JH and an increase in their posterior standard deviation for recent years was observed. These results suggest that specialization could lead to differences in traits measured in DH and JH in the recent years.

High natural antibody titers of indigenous chickens are related with increased hazard in confinement.

Natural antibody (NAb) levels and survival rates were evaluated in 4 breeds of laying hens in Ethiopia: indigenous, improved indigenous, exotic layer, and crossbred. Titers of NAb isotypes IgG and IgM binding keyhole limpet hemocyanin (KLH) in serum were measured at 20, 26, 35, and 45 wk age. Repeated-measure ANOVA showed that IgG and IgM levels vary with time within each breed (P < 0.05). Indigenous chickens had significantly (P < 0.05) higher NAb levels at all ages. The Cox proportional hazard analysis showed increased hazard with increased levels of NAbs in the exotic layers (P < 0.05). However, the reduced hazards with increased levels of NAbs were not significant in the improved indigenous and crossbred chickens. Indigenous chickens showed increased hazard with increasing levels of NAb (P > 0.05). We concluded that not only the NAb levels but also the effect of Nabs on survival vary between indigenous and improved breeds. The results indicate that NAb levels are associated with survival in elite (improved) breeds, but are associated with increased hazard in indigenous chickens.

Genome-wide association study of insect bite hypersensitivity in Dutch Shetland pony mares.

Insect bite hypersensitivity (IBH) is the most common allergic disease present in horses worldwide. It has been shown that IBH is under genetic control, but the knowledge of associated genes is limited. We conducted a genome-wide association study to identify and quantify genomic regions contributing to IBH in the Dutch Shetland pony population. A total of 97 cases and 91 controls were selected and matched on withers height, coat colour and pedigree to minimise the population stratification. A blood sample was collected from participating Shetland pony mares, their IBH phenotype was scored and the owner filled in a questionnaire. A total of 40 021 single-nucleotide polymorphisms (SNPs) were fitted in a univariable logistic model fitting an additive effect. Analysis revealed no effects of population stratification. Significant associations with IBH were detected for 24 SNPs on 12 chromosomes [-log(10) (P-value) > 2.5]. Odds ratios of allele substitution effects of the unfavourable allele were between 1.94 and 5.95. The most significant SNP was found on chromosome 27, with an odds ratio of 2.31 and with an allele frequency of the unfavourable allele of 0.72 in cases and 0.53 in controls. Genome-wide association studies on additional horse populations are desired to validate the identified associations, to identify the genes involved in IBH and to develop genomic tools to decrease IBH prevalence.

Genome-wide association study of osteochondrosis in the tarsocrural joint of Dutch Warmblood horses identifies susceptibility loci on chromosomes 3 and 10.

Equine osteochondrosis is a developmental joint disease that is a significant source of morbidity affecting multiple breeds of horse. The genetic variants underlying osteochondrosis susceptibility have not been established. Here, we describe the results of a genome-wide association study of osteochondrosis using 90 cases and 111 controls from a population of Dutch Warmblood horses. We report putative associations between osteochondrosis and loci on chromosome 3 (BIEC2-808543; P = 5.03 × 10(-7) ) and chromosome 10 (BIEC2-121323; P = 2.62 × 10(-7) ).

Genome-wide SNP association-based localization of a dwarfism gene in Friesian dwarf horses.

The recent completion of the horse genome and commercial availability of an equine SNP genotyping array has facilitated the mapping of disease genes. We report putative localization of the gene responsible for dwarfism, a trait in Friesian horses that is thought to have a recessive mode of inheritance, to a 2-MB region of chromosome 14 using just 10 affected animals and 10 controls. We successfully genotyped 34,429 SNPs that were tested for association with dwarfism using chi-square tests. The most significant SNP in our study, BIEC2-239376 (P(2df)=4.54 × 10(-5), P(rec)=7.74 × 10(-6)), is located close to a gene implicated in human dwarfism. Fine-mapping and resequencing analyses did not aid in further localization of the causative variant, and replication of our findings in independent sample sets will be necessary to confirm these results.

Multiphasic nonlinear mixed growth models for laying hens.

Appropriate evaluation of BW and gain during rearing is required for optimal extended laying performance in laying hens. The objective of this study was to compare monophasic, diphasic, and triphasic Gompertz and logistic models describing BW and gain in individually fed free-run laying hens and to study the variation between individuals in shape parameters. Fifteen Lohmann Brown Lite hens were fed ad libitum from week 0 to 43 with a precision feeding system, measuring feed intake and BW individually in a group housed setting. Random variables related to mature weight and timing of maximum gain during the pubertal growth phase were introduced into the multiphasic model for BW with the best fit. For both the weight-age and gain-age functions, the diphasic and triphasic Gompertz and logistic model models fitted the data better than the monophasic models. The Gompertz model was able to identify the ages at the highest gain at similar time points for both BW and gain, whereas the logistic models failed to do so. The derivative of the multiphasic Gompertz models for the gain-age relationship identified age at the highest gain at similar ages as compared with the logistic models for gain. The mixed models predicted that the individual mature BW ranged from 1.83 kg to 2.10 kg and the variability in the timing of the highest rate of gain during the pubertal growth spurt ranged from 15.26 wk to 19.79 wk. Including random terms associated with the mature BW and the second inflection point of the diphasic Gompertz growth model allowed for identification of variability in the growth curve shape between individuals, which can be a tool to study the relationship between the individual growth curve shape and performance parameters.

Heritability of foot conformation and its relationship to sports performance in a Dutch Warmblood horse population.

REASONS FOR PERFORMING STUDY: Warmblood horse studbooks aim to breed horses with a conformation that will enable elite future performance, but reduce the risk of injuries and lameness. Negative conformational traits, such as asymmetrical or 'uneven' forefeet would possibly diminish performance. OBJECTIVES: To assess the prevalence and heritability of uneven feet and its genetic relationship to other conformation traits as well as to sporting performance later in life in Warmblood riding horses. METHODS: The databases of the Royal Dutch Warmblood Studbook (KWPN, n = 44,840 horses) and Royal Dutch Equestrian Sports Federation (KNHS, n = 33,459 horses in dressage and n = 30,474 horses in showjumping) were linked through the unique number of each registered horse. Therefore, heritabilities and genetic and phenotypic correlations could be estimated from the scores of the jury at studbook admission and the sports performance of that population in dressage and jumping over the period 1990-2002. RESULTS: The prevalence of uneven feet was 53% on average, and increased from under 4.5% during the first 3 years of recording to over 8% in the years from 2000 onwards. Heritability estimates of foot conformation traits were moderate and ranged from 0.16 for heel height to 0.27 for hoof shape. The genetic correlation between the trait of uneven feet and performance in competition was negative but weak: -0.09 with dressage and -0.12 with showjumping. CONCLUSIONS: Predisposition to uneven feet can be reduced by selection. Because of weak genetic correlations, the increased prevalence is not directly associated with selection for better sports performance or higher conformation grade. If the trait 'uneven feet' arises from a disproportionate relationship between height at the withers and neck length, then selection on conformation grade might result in development of uneven feet. In general, limb conformation has a moderate genetic relationship to conformation grade and foot conformation traits have a genetic relationship to sporting performance. Reducing occurrence of uneven feet by selection is possible, without limiting progress in sport performance.

Influence of foot conformation on duration of competitive life in a Dutch Warmblood horse population.

REASONS FOR PERFORMING STUDY: Warmblood horse studbooks aim to breed horses with a conformation that will enable elite future sports performance, but reduce the risk of early retirement due to lameness. Negative conformational traits, such as asymmetrical or 'uneven' forefeet may possibly shorten the career of sporthorses. OBJECTIVES: To investigate the significance of foot conformation at young age to duration of the career of sporthorses. METHODS: Databases of the Royal Dutch Warmblood Studbook (KWPN) and of the Royal Dutch Equestrian Sports Federation (KNHS) were matched and resulted in a dataset comprising 23,116 records of horses for which their conformation scores and duration of their sports career were available. Survival analysis was used to determine which of the conformation traits had a significant effect on duration of sports career in dressage and jumping at basic and elite level. RESULTS: Duration of competitive life was shorter for jumping than for dressage. A different set of risk factors was found for each level and discipline. The trait 'uneven feet' tended to shorten the competitive life in dressage, but was a significant risk factor at the elite level of jumping. CONCLUSIONS: Limb conformation and, in particular, the conformation of the distal limb, are important for duration of competitive life. From the prevalence of uneven feet in sports disciplines, it may be concluded that this is an undesirable trait, particularly at the elite level of jumping, since uneven feet have a detrimental effect on the duration of competitive life in a sporthorse population. POTENTIAL RELEVANCE: This study provided evidence that the conformation trait uneven feet has a negative effect on Warmblood jumping performance and, therefore, breeders should be encouraged to avoid this phenomenon at foal age.

Prevalence of various radiographic manifestations of osteochondrosis and their correlations between and within joints in Dutch warmblood horses.

REASONS FOR PERFORMING STUDY: Osteochondrosis (OC) is the most important orthopaedic developmental disorder in horses and may manifest in several different forms. No detailed study on the prevalence and/or interrelation of these forms is available, even though these data are a prerequisite for conclusive genetic studies. OBJECTIVES: To assess the prevalence of the various manifestations of OC as detected radiographically and to evaluate possible relationships between their occurrence within the same joint and between different joints. METHODS: The FP (femoropatellar), TC (tarsocrural) and MCP/MTP (metacarpophalangeal/metatarsophalangeal) joints of 811 yearlings selected randomly, descending from 32 representative stallions, were radiographed and scored for the presence and grade of osteochondrotic lesions. Results were compared at the sire, animal, joint and predilection site levels. RESULTS: In the FP joint, the percentage of animals showing normal joint contours in all sites was 60.7%. For the TC joint and the combined MCP/MTP joints, these figures were 68.6 and 64.6%, respectively. For all joints combined, the percentage dropped to 30.5%. Sedation improved detection of OC lesions in the FP joint. There was a high correlation between the right and left joints. The correlation between flattened bone contours and fragments was considerably less. CONCLUSIONS: Scoring on a detailed scale is necessary to achieve good insight into the prevalence of OC. Observations on the right and left joints can be combined in further analyses, whereas flattened bone contours and fragments should be evaluated as statistically different disorders. POTENTIAL RELEVANCE: This study provides insight into the prevalences of various manifestations of OC and their relationships, within and between joints. These results form the basis for detailed quantitative and/or molecular genetic studies that should lead to the establishment of breeding indices and/or genetic marker sets for OC.

Identification of environmental factors affecting the prevalence of insect bite hypersensitivity in Shetland ponies and Friesian horses in The Netherlands.

REASONS FOR PERFORMING STUDY: It is expected that climate and habitat factors influence the prevalence of culicoides and, therefore, the prevalence of insect bite hypersensitivity (IBH), but very little is described in the literature to prove the association of these factors. Prevalence varies widely from 3% in certain areas of Great Britain to 60% in certain parts of Australia. OBJECTIVES: To describe the influence of environmental factors on the prevalence of IBH in Shetland ponies and Friesian horses in The Netherlands. METHODS: Data on 3284 Shetland and 2824 Friesian mares (n = 6108) were collected in The Netherlands, based on 90 regions, according to postal codes. The climate components, amount of rainfall, number of warm days, number of cold days, and habitat components of soil type and type of vegetation were collected for each region. RESULTS: Prevalence of IBH varied widely from 0-71.4% per region. The results showed that the environment with low IBH-prevalence had high rainfall, many cold days and few warm days per year. Habitats with a low IBH-prevalence were based along the coast line. Habitats with increasing prevalence of IBH had soils of clay with heather and woody vegetation. Friesian mares had a higher IBH prevalence than Shetland mares, which could indicate an effect of genetic background or an effect of year. CONCLUSIONS: There is an environmental effect on IBH prevalence within The Netherlands, which is caused by climate and habitat factors. POTENTIAL RELEVANCE: The results provide a more accurate description of environmental factors and their impact on development of IBH; and should help better to understand habitat and climate effects, and to distinguish these from other effects, such as animal factors (genetics, age or sex).

Optimization of dairy cattle breeding programs for different environments with genotype by environment interaction.

Dairy cattle breeding organizations tend to sell semen to breeders operating in different environments and genotype x environment interaction may play a role. The objective of this study was to investigate optimization of dairy cattle breeding programs for 2 environments with genotype x environment interaction. Breeding strategies differed in 1) including 1 or 2 environments in the breeding goal, 2) running either 1 or 2 breeding programs, and 3) progeny testing bulls in 1 or 2 environments. Breeding strategies were evaluated on average genetic gain of both environments, which was predicted by using a pseudo-BLUP selection index model. When both environments were equally important and the genetic correlation was higher than 0.61, the highest average genetic gain was achieved with a single breeding program with progeny-testing all bulls in both environments. When the genetic correlation was lower than 0.61, it was optimal to have 2 environment-specific breeding programs progeny-testing an equal number of bulls in their own environment only. Breeding strategies differed by 2 to 12% in average genetic gain, when the genetic correlation ranged between 0.50 and 1.00. Ranking of breeding strategies, based on the highest average genetic gain, was relatively insensitive to heritability, number of progeny per bull, and the relative importance of both environments, but was very sensitive to selection intensity. With more intense selection, running 2 environment-specific breeding programs was optimal for genetic correlations up to 0.70-0.80, but this strategy was less appropriate for situations where 1 of the 2 environments had a relative importance less than 10 to 20%. Results of this study can be used as guidelines to optimize breeding programs when breeding dairy cattle for different parts of the world.

Possible negative effects of inbreeding on semen quality in Shetland pony stallions.

Inbreeding is widely believed to negatively affect reproductive performance. Indeed, in some species, high levels of inbreeding are thought to be the major cause of poor semen quality. It is, however, not clear whether inbreeding affects fertility in horses. In this study, the relationship between inbreeding and semen quality was examined in 285 immature Shetland pony stallions submitted for breeding soundness examination in March-April of the years 1992-1997. The majority of stallions examined were 3 years old (85%) and their coefficients of inbreeding ranged from 0 to 25% (mean+/-S.D.: 3+/-4.6%). For the purpose of analysis, stallions were divided into six inbreeding classes (0-1, 1-2, 2-5, 5-8, 8-12 and >12%) containing 132, 40, 42, 27, 25 and 19 animals, respectively. The degree of inbreeding significantly affected many aspects of sperm production and quality, based on a standard examination of two ejaculates collected at a 1.5-3h interval. In particular, coefficients of inbreeding above 2% were associated with lower percentages of motile (p<0.01) and morphologically normal sperm (p<0.001). When the data set was used to estimate heritability of semen characteristics, the high values calculated for sperm progressive motility (0.46) and concentration (0.24) suggested that these traits could be improved by phenotypic selection. These findings support the hypothesis that inbreeding has a detrimental effect on semen quality in Shetland ponies, although examination of multiple ejaculates after repeated semen collection to bring the animals to daily sperm output is needed to confirm this conclusion. Nevertheless, the results support previous suggestions that inbreeding is an important cause of reduced semen quality.