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PubMed1999

Interaction between milk yield of Holstein cows in Mexico and the United States.

Genotype by environment interaction for milk yield was investigated by analyzing 55,162 mature equivalent, first lactation records of daughters from 1339 Holstein sires in Mexico and 499,401 daughters from 663 Holstein sires in the northeastern US. There were 474 US sires in common. Herd-year standard deviation was used to define non-overlapping high (> or = 1600 kg) and low (< or = 1300 kg) Mexican environments and a low (< or = 1025 kg) US environment. Variance components across Mexican environments were about 40% less than those of the US environment. Genetic correlation coefficients between milk yield in various Mexican environments and all US environments ranged from 0.60 to 0.71 and were different from unity (P < 0.001). Genetic correlation coefficients with low environment in the US ranged between 0.69 and 0.93; the largest correlation was between the low US and high Mexico environments. Both reductions in the size of genetic variance in Mexican environments relative to the US and genetic correlation coefficients less than unity were indicative of genotype by environment interaction. A significant rank change in estimated breeding values (EBV) of sires in Mexican environments relative to the US was another indicator of genotype of EBV of a sire estimated from daughters performances in low and high environments in Mexico were 0.46 and 0.62 against EBV of sires estimated from all data in the US. Against EBV estimated from the low environment in the US they were 0.57 and 0.83. The US low environment was a better predictor of performance in Mexican environments.

Animals↗

PubMed2003

Repeatability estimates for milk coagulation traits and non-coagulation of milk in Finnish Ayrshire cows.

Effects of systematic environmental factors and milk production and quality traits on milk coagulation properties (MCP), and on repeatability of those traits were estimated from 979 milk samples collected once a month over a period of 2 years from 83 Finnish Ayrshire cows. Estimation was based on a multitrait animal model and REML methodology. In addition, persistence of non-coagulation of milk in individual cows, and factors associated with it were established from a sub sample of 24 cows producing non-coagulating (NC) milk at least once. MCP were at their best during the first lactation, at the beginning and at the end of lactation, and during grazing seasons. Variation in MCP with systematic environmental factors was partly due to variation in composition and quality of milk, especially in pH and ln (somatic cell count, SCC). Coefficients of repeatability for milk coagulation time and curd firmness were 0.65 and 0.68. These estimates were of the same magnitude as those for protein content, but were higher than those for daily milk yield, fat content, pH, and SCC. Based on the repeatability estimates for the milk coagulation traits and effects of the environmental factors, cows should be sampled at least three times during a lactation to estimate reliably breeding values for the milk coagulation traits. A total of 10% of the milk samples did not coagulate in 30 min after addition of rennet. Cows that produced NC milk at least once (30% of the cows) could be classified into those that produced NC milk only a few times during a lactation and those that produced NC milk at almost every sampling. Based on logistic regression analyses, peak and mid-lactation, high milk yield, low protein and fat content and high pH increased the risk of non-coagulation of milk.

Animals↗

PubMed1997

Genetics of canine hip dysplasia.

OBJECTIVE: To document genetic progress in improving hip quality of dogs maintained in a closed breeding colony to produce dogs for training as guides for blind people. DESIGN: Prospective analysis of hip quality records from a breeding trial that encompassed 3 full generations and included some dogs born into the fourth and fifth generations. ANIMALS: Hip quality was assessed for 2,037 German Shepherd Dogs and 1,821 Labrador Retrievers from 1980 to 1996. PROCEDURE: A subjective hip score assigned by 1 radiologist was used to assess hip quality during the study period. In the past 8 years, the distraction index was also used. Genetic change was produced by selecting a small percentage of dogs to be parents of the next generation. Dogs were selected to become parents of the next generation on the basis of estimated breeding values. These were calculated by combining observed values of individual dogs with known relationships in the population pedigrees to predict which dogs were the best candidates for selection as parents. RESULTS: In < 5 generations of selection, the percentage of German Shepherd Dogs with canine hip dysplasia at 12 to 16 months of age decreased from 55 to 24%. Among Labrador Retrievers, the percentage decreased from 30 to 10%. CLINICAL IMPLICATIONS: This report gives practitioners documented proof that genetic selection will work to improve hip quality. Dog breeders must be advised to be patient, however, to allow enough generations to elapse to make meaningful genetic change.

Animals↗

PubMed1985

Variance-covariance components associated with trimester yields of milk and fat and multiple trait sire evaluation for trimester yields.

Genotypic and phenotypic variances and covariances for milk and fat yields of three equally-spaced intervals in first lactation, days 1 to 90, 91 to 180, and 181 to 270, were estimated from 26,523 records of initial progeny-test daughters of 2,086 Holstein sires. Henderson's method 3 was used with a model that included fixed herd-years, fixed age-month of freshening, and random sire and residual effects. Heritabilities for milk yields were .21, .21, and .13 for the first, second, and third 90 days in lactation and for fat yields were .19, .16, and .10. Heritabilities for milk and fat yields over the entire 270 days postpartum were .22 and .22. Genetic correlations among partial yields were high and ranged from .74 to .99 for milk and .86 to .99 for fat. Genotypic and phenotypic variances were used to predict breeding values for trimester milk yield by multiple trait, mixed model procedures for 3,797 Holstein artificial insemination sires from 283,900 first-lactation milk records of their daughters during the first 90, second 90, and third 90 days in lactation. Correlations among proofs for the three trimesters ranged from .85 to .94. Correlation between the sum of three trimester multiple trait proofs and proof for milk yield for 270 days of lactation from single trait analysis was .99. Correlations among proofs indicate sires may rank differently for milk yield in the three periods.

Animals↗

PubMed1999

Supply of genetic information--amount, format, and frequency.

The volume and complexity of genetic information is increasing because of new traits and better models. New traits may include reproduction, health, and carcass. More comprehensive models include the test day model in dairy cattle or a growth model in beef cattle. More complex models, which may include nonadditive effects such as inbreeding and dominance, also provide additional information. The amount of information per animal may increase drastically if DNA marker typing becomes routine and quantitative trait loci information is utilized. In many industries, evaluations are run more frequently. They result in faster genetic progress and improved management and marketing opportunities but also in extra costs and information overload. Adopting new technology and making some organizational changes can help realize all the added benefits of the improvements to the genetic evaluation systems at an acceptable cost. Continuous genetic evaluation, in which new records are accepted and breeding values are updated continuously, will relieve time pressures. An online mating system with access to both genetic and marketing information can result in mating recommendations customized for each user. Such a system could utilize inbreeding and dominance information that cannot efficiently be accommodated in the current sire summaries or off-line mating programs. The new systems will require a new organizational approach in which the task of scientists and technicians will not be simply running the evaluations but also providing the research, design, supervision, and maintenance required in the entire system of evaluation, decision making, and distribution.

Animals↗

PubMed1997

Antibody response to Actinobacillus pleuropneumoniae antigens after vaccination of pigs bred for high and low immune response.

To enhance inherent general resistance to infectious diseases an indirect strategy of selective breeding for multiple immune response traits representing both antibody and cell-mediated immune response has been pursued over several generations in pigs. High and low response lines differ significantly not only in response to antigens included in the estimated breeding values upon which the selection was based, but also to other antigens. To test whether or not the lines also differed in antibody response to vaccination, high and low response pigs were given a commercial Actinobacillus pleuropneumoniae vaccine, and their serum antibody to three constituent antigens, carbohydrates (CHO) 1 and 5 and lipopolysaccharide (LPS) 1 was measured by enzyme immunoassay. The high line had significantly (P < or = 0.05) more antibody to all antigens except at day 28 to CHO antigen 5. The frequency of non-response to vaccination was also less in the high response pigs to CHO antigen 1 (P < or = 0.01) and to the LPS antigen (P < or = 0.06) but not to the CHO antigen 5. Based upon these observation it is concluded that the high immune response pigs are more responsive to the commercial vaccine than are the low response pigs and that the strategy of altering population immune response by multi-trait selective breeding may be useful in facilitating vaccine-based health management programs for livestock.

Actinobacillus pleuropneumoniae↗

PubMed2005

Prediction of accuracy of estimated Mendelian sampling terms.

This study describes a general framework for predicting the accuracy of Mendelian sampling terms when truncation selection is applied on best linear unbiased prediction (BLUP) estimated breeding values. A selection index approach is followed. The pseudo-BLUP index is extended to include terms related to the Mendelian sampling term. Predicted accuracies are compared with those obtained through stochastic computer simulation. Good predictions for the accuracy of the Mendelian sampling term were obtained both at selection time and at convergence of long-term contributions of selected candidates for a range of heritabilities and population structures. The prediction approach developed provides a key tool for obtaining predictions of genetic response from quadratic optimization that maximizes the rate of genetic progress while restricting the rate of inbreeding.

Breeding↗

PubMed1990

Alternative methods of selection for litter size in mice: I. Characterization of base population and development of methods.

Studies on a base population of mice were used to establish an index of components of litter size and a physiological model for measuring uterine capacity to be used subsequently in a selection experiment evaluating alternative methods for practicing selection to increase litter size. Heritability estimates of litter size, ovulation rate and ova success (fraction of ova resulting in fully formed pups) were .18, .33 and .15, respectively. No significant genetic or phenotypic correlation was found between overall ovulation rate and ova success. Phenotypic means and genetic variances were higher for characteristics measured on the right than on the left side of the reproductive tract. Linear and quadratic selection indexes, derived for a quadratic definition of breeding value, were compared. The linear index was predicted to be .99 as efficient as the quadratic one. Due to simplicity, the linear index (I = 1.21 x ovulation rate + 9.05 x ova success), scaled to have variance the same as litter size, was chosen for use. Ovulation rate in unilaterally ovariectomized females was .95 of that in females with both ovaries. No hypertrophy of the ipsilateral uterine horn in unilaterally ovariectomized females was found before implantation of embryos. Thus, unilateral ovariectomy appears to provide a physiological state to measure uterine capacity (as litter size) in the mouse.

Animals↗

PubMed2026

Transition from Conventional to Genomic Selection (ssGBLUP) led to improve in accuracy gains and selection decisions in Sahiwal Cattle.

By using genome-wide markers to predict an individual's genetic potential, the introduction of Genomic Selection (GS) has transformed animal breeding. This greatly accelerated selection for complex traits by lowering reliance on drawn-out field trials, allowing for faster genetic gains in livestock. However, there is little research on the effects of genomic selection on Sahiwal cattle in India, and comparing it to the current culling or selection process is even more uncommon, particularly in nations with fewer genotyped animals. This study is an initial effort to address the aforementioned gaps in knowledge. Genomic selection was implemented in Sahiwal cattle for the 305 days milk yield using univariate animal model and the single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) method. The Effective Population size (Ne) of the Sahiwal herd was calculated using genomic data and was reported for the previous generation to be 71.927. The heritability of 305 days milk yield was estimated as 0.177 ± 0.068. Genomic estimated breeding values (GEBVs) were predicted for each individual using ssGBLUP, yielding a mean prediction accuracy of 43.11%, compared with 40.88% obtained using conventional pedigree-based BLUP. Cross-validation further demonstrated superior predictive performance of ssGBLUP, with accuracies of 76.82% and 70.50% for ssGBLUP and PBLUP, respectively. To further check the effectiveness of the genomic selection methodology, we also compared the GEBVs obtained and compared it with the Expected Progeny Difference (EPD) which is being applied in our farm for culling decisions. It was seen that GEBVs obtained from ssGBLUP methodology were also in line with the conventionally used method of EPD. The use of genomic selection enables genetic studies with limited pedigree information. Additionally, the ssGBLUP methodology allows to check for pedigree errors, where family relationships are incorrectly recorded. The EPD and GEBVs were consistent with one another, indicating that genomic selection may also be utilised to support culling and selection decisions in a farm. Thus, in a conventional animal breeding program with constraint resources and an incomplete pedigree, we recommend employing the ssGBLUP model for regular genomic assessment and identification of suitable candidates to effectively carry out a genomic selection program.

Animals↗

PubMed1991

Threshold models applied to Holstein conformation traits.

Threshold animal models were applied to five conformation traits of Canadian Holsteins. The estimated breeding values for sires from the threshold model allowed the calculation of predicted percentages of daughters in the desirable categories. Results were compared with those from a linear animal model in terms of their ability to predict future percentages of daughters in the desirable categories using an independent set of data. There was no advantage in a threshold model compared with a conventional linear animal model in its ability to predict future daughter performance. This was likely due to the 18 categories used in the classification of major type traits in Canada and the nearly normal distribution of observations across categories.

Animals↗

PubMed2002

Genetic parameters and responses of linear type, yield traits, and somatic cell scores to divergent selection for predicted transmitting ability for type in Holsteins.

The objective was to examine the direct and correlated responses of linear type, yield traits, and somatic cell scores (SCS) to divergent selection for predicted transmitting ability for type (PTAT) in Holsteins, while maintaining selection for yield traits across lines. For four generations, one-half of the University of Nebraska research Holstein herd was bred to Holstein sires with PTAT > 1.50 and the other half to sires with PTAT < 1.25, with nearly equal predicted transmitting abilities for yield traits for both groups. Estimates of genetic and residual correlations and heritabilities were obtained from REML estimates of (co)variance components. Model for type traits included fixed effect of date cows were classified, effects of age in days at freshening, and stage of lactation at classification. Year-season when cows freshened was fixed effect in model for yield and SCS. Animal genetic and residual effects were random. Final score, milk, fat, and protein yields, and SCS had heritability estimates of 0.38, 0.13,0.22, 0.09, and 0.38, respectively. Heritability estimates for type traits ranged from 0.04 to 0.52. Estimates of genetic correlations of final score with SCS and milk, fat, and protein yields were -0.64, 0.01, -0.18, and 0.06, respectively. Estimates of genetic correlations among linear type traits ranged from -0.77 to 1.00. Means of estimated breeding values for final score, stature, strength, body depth, fore udder attachment, rear udder height and width, udder cleft, udder depth, and front teat placement were significantly different between lines in the third generation. Milk, fat, and protein yields were not significantly different between lines in third generation, whereas SCS was significantly different. Estimate of genetic correlation between final score and SCS suggest that selection on PTAT would result in a change for SCS. In this study, divergent selection on PTAT of sires had a significant effect on udder and body traits, but little or no effect on feet and leg traits.

Animals↗

PubMed2006

Association of a melanocortin 4 receptor (MC4R) polymorphism with performance traits in Lithuanian White pigs.

The melanocortin 4 receptor is expressed in virtually all brain regions of mammals and plays an important role in energy homeostasis. Polymorphisms in this gene may thus be related to growth and obesity. In pigs, a non-synonymous polymorphic site was described (Asp298Asn) and demonstrated to affect cAMP production and to alter adenylyl cyclase signalling. Association studies revealed significant linkage of this mutation with production trait in pigs. In this study, 207 Lithuanian White pigs were genotyped at the MC4R locus and analysed on relationships between genotype and breeding values for several performance traits. The observed allele and genotype frequencies did not deviate significantly from Hardy-Weinberg equilibrium (wildtype allele 0.59; mutant allele 0.41) and are comparable with those described in other Large White populations. The mutant Asn298 allele of the MC4R gene was significantly associated with increased test daily gain, higher lean meat percentage and lower backfat thickness. There was a trend towards an improved feed conversion ratio (p = 0.065) in animals with the mutant allele whereas no significant effect was found on lifetime daily gain. These results indicate that the MC4R polymorphism should be integrated in selection programmes in the Lithuanian White to improve carcass composition.

Adenylyl Cyclases↗

PubMed1999

Prediction of daily milk yields from a limited number of test days using test day models.

A data set of weekly milk yield records was used to compare different test day models for their ability to interpolate and extrapolate missing milk yields. The criteria to compare the models were 1) the (co)variance structure modeled compared with the observed (co)variance structure in the data and 2) mean square error of predictions of missing observations (MSEP), which compared the predicted value of a missing record to the known value of the record. The test day models used were LEG(m), which are Legendre polynomials with an order of fit of m, and EXP, which is an exponential lactation function. When fitting the LEG(m) models, criteria 1) and 2) generally improved with an increasing order of fit as expected. The model EXP, which contains three random regression coefficients, was between LEG(1) and LEG(2), which contain two and three coefficients, respectively. The improvement of the criteria with m in LEG(m) became negligible after LEG(5). Thus, a 5th order Legendre polynomial yields a good fit with a minimum number of parameters. Also, the correlation structure of milk yields among days in milk modeled by LEG(5) resembled the correlation structure that was observed in the data. However, the modeled variances at the end of lactation were larger than those observed in the data except when LEG(0) was used. Legendre polynomials with a fit less than five yielded correlation structures that clearly deviated from the observed correlations, especially in the case of LEG(0). Overall, LEG(5) is preferred to develop a genetic TDM for breeding value estimation.

Analysis of Variance↗

PubMedDate not supplied

Divergent selection on 63-day body weight in the rabbit: response on growth, carcass and muscle traits.

The effects of selection for growth rate on weights and qualitative carcass and muscle traits were assessed by comparing two lines selected for live body weight at 63 days of age and a cryopreserved control population raised contemporaneously with generation 5 selected rabbits. The animals were divergently selected for five generations for either a high (H line) or a low (L line) body weight, based on their BLUP breeding value. Heritability (h2) was 0.22 for 63-d body weight (N = 4754). Growth performance and quantitative carcass traits in the C group were intermediate between the H and L lines (N = 390). Perirenal fat proportion (h2 = 0.64) and dressing out percentage (h2 = 0.55) ranked in the order L < H = C (from high to low). The weight and cross-sectional area of the Semitendinosus muscle, and the mean diameter of the constitutive myofibres were reduced in the L line only (N = 140). In the Longissimus muscle (N = 180), the ultimate pH (h2 = 0.16) and the maximum shear force reached in the Warner-Braztler test (h2 = 0.57) were slightly modified by selection.

Age Factors↗

PubMed2001

Predicting rates of inbreeding for livestock improvement schemes.

This article presents a deterministic method to predict rates of inbreeding (deltaF) for typical livestock improvement schemes. The method is based on a recently developed general theory to predict rates of inbreeding, which uses the concept of long-term genetic contributions. A typical livestock breeding population was modeled, with overlapping generations, BLUP selection, and progeny testing of male selection candidates. Two types of selection were practiced: animals were either selected by truncation on estimated breeding values (EBV) across age classes, or the number of parents selected from each age class was set to a fixed value and truncation selection was practiced within age classes. Bulmer's equilibrium genetic parameters were obtained by iterating on a pseudo-BLUP selection index and deltaF was predicted for the equilibrium situation. Predictions were substantially more accurate than predictions from other available methods, which ignore the effect of selection on deltaF. Predictions were accurate for schemes with up to 20 sires. Predicted deltaF was somewhat too low for schemes with more than 20 sires, which was due to the use of simple linear models to predict genetic contributions. The present method provides a computationally feasible (i.e., deterministic) tool to consider both the rate of inbreeding and the rate of genetic gain when optimizing livestock improvement schemes.

Animals↗

PubMed2006

Feasibility of a linear scoring method of udder morphology for the selection scheme of Sardinian sheep.

Breeders are increasingly interested in improving the machine milkability of Sardinian dairy sheep by selection for udder morphology. Nine-point linear scales were developed to appraise teat placement, degree of suspension of the udder, udder depth, and degree of separation of the 2 halves. Repeatabilities within and across lactation were estimated on an experimental flock. Ewes were scored at least 3 times a year from 1999 to 2003. Within-lactation repeatabilities were greater than 0.70 for all linear traits, whereas across-lactation repeatabilities ranged from 0.59 to 0.66. The first linear combination of basic traits, obtained by principal component analysis, was highly correlated with teat placement, degree of suspension of the udder, and udder depth and showed an across-lactation repeatability of 0.76. These results indicate that an accurate evaluation of animals is possible by a single, early lifetime score. Genetic parameters of linear udder traits were estimated using a REML method applied to a sire model. Data were selected from 76,984 scores of Sardinian yearling ewes collected by 31 classifiers from 1999 to 2004. Two models were compared, one fitting the contemporary group effect as fixed and the other as random. Heritabilities of udder traits ranged from 0.19 to 0.31. The model with the random contemporary group effect produced slightly higher heritabilities and higher correlations between the sires' estimated breeding values and the daughters' average scores. As a whole, the genetic correlations between udder traits were favorable, indicating that selection for one trait will produce a positive evolution of the overall udder conformation. In particular, the degree of suspension of the udder was highly correlated with udder depth (0.82). Genetic correlations with milk yield were unfavorable but generally low, with the exception of udder depth (-0.48). Genetic trends were estimated using an animal model. Only udder depth showed a negative constant genetic trend. Overall results indicated that genetic improvement of the udder morphology of Sardinian ewes is feasible, with major emphasis on teat placement and degree of udder suspension, traits showing the highest heritabilities and low unfavorable genetic correlations with milk yield.

Animals↗

PubMed2002

Purebred-crossbred performance and genetic evaluation of postweaning growth and carcass traits in Bos indicus x Bos taurus crosses in Australia.

Growth and carcass data on 7,154 cattle from a purebred project and 1,241 cattle from a crossbred project, comprising 916 first-crosses and 325 purebred Brahman controls, were analyzed to estimate genetic parameters, including the genetic correlations between purebred and crossbred performance (rpc). The data also allowed the estimation of sire breed means for various growth and carcass traits. Crossbred calves were produced using 9 Angus, 8 Hereford, 7 Shorthorn, 14 Belmont Red, and 8 Santa Gertrudis sires bred to Brahman dams. These same sires produced 1,568 progeny in a separate purebreeding project. Cattle in both projects were managed under two finishing regimens (pasture and feedlot) to representative market live weights of 400 (domestic), 520 (Korean), and 600 kg (Japanese). The traits studied included live weight at around 400 d of age (400W), hot carcass weight (CWT), retail beef yield percentage (RBY), intramuscular fat percentage (IMF), rump fat depth (P8), and preslaughter ultrasound scanned eye muscle area (SEMA). Estimated breeding values (EBV) of sires from their BREEDPLAN genetic evaluations were used to assess their value in predicting crossbred performance. Regressions of actual crossbred calf performance on sire EBV for each of the traits differed little from their expectation of 0.5. Angus sires produced crossbred carcasses with the highest P8 and lowest RBY but highest IMF. In contrast, crossbred progeny from Belmont Red sires had the lightest 400W and CWT, lowest P8, and highest RBY. Estimates of rpc were 0.48, 0.48, 0.83, 0.95, 1.00, and 0.78 for 400W, CWT, RBY, IMF, P8, and SEMA, respectively. Commercial breeders selecting sires for crossbreeding programs with Brahman females, based on EBV computed from purebred data, might encounter some reranking of sire's performance for weight-related traits, with little expected change in carcass traits.

Adipose Tissue↗

PubMed2006

Technical note: Use of marker-based relationships with multiple-trait derivative-free restricted maximal likelihood.

The widespread use of the set of multiple-trait derivative-free REML programs for prediction of breeding values and estimation of variance components has led to significant improvement in traits of economic importance. The initial version of this software package, however, was generally limited to pedigree-based relationships. With continued advances in genomic research and the increased availability of genotyping, relationships based on molecular markers are obtainable and desirable. The addition of a new program to the set of multiple-trait derivative-free REML programs is described that allows users the flexibility to calculate relationships using standard pedigree files or an arbitrary relationship matrix based on genetic marker information. The strategy behind this modification and its design is described. An application is illustrated in a QTL association study for canine hip dysplasia.

Animals↗