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PubMed1997

Benefit of multiple trait selection to increase reproductive traits: experimental evidence from golden hamsters.

Fifteen generations of selection were conducted to study responses for litter size at birth (LSB), weight at weaning of standardized litter (LWW), and individual body weight at 8 wk of age (BW8) using golden hamsters as an experimental model for pigs. The experiment involved three lines: selection on an aggregate breeding value of LSB, LWW, and BW8 (line W); selection on an aggregate breeding value of LSB and LWW (line R); and a randomly selected control (line C). Selection in W and R was based on breeding values from a multiple trait animal model. Restricted maximum likelihood with an animal model was used to estimate genetic parameters and genetic trends. Heritability estimates for LSB, LWW, and BW8 were .10, .47, and .52, respectively, and genetic correlations between traits were all positive. The mean estimated breeding value (EBV) for LSB in generation 15 was +2.2 pups in W and R. The mean EBV for LWW in generation 15 was +318 g for W and +174 g for R, and for BW8 means were +64 g and +24 g, respectively. Average inbreeding at generation 16 was 13.4, 19.5, and 8.0% for W, R, and C, respectively. Including BW8 in the selection criterion reduced inbreeding and had a beneficial effect on selection responses in LSB, LWW, and BW8.

Animals↗

PubMed2006

Short communication: genetic evaluation of the interval from first to last insemination with survival analysis and linear models.

Sire breeding values for the interval between the first and last insemination were predicted using 4 proportional hazards models (survival analyses) and 2 linear mixed models to determine which would result in a more accurate genetic evaluation. A stochastic simulation describing the reproductive cycle of first-parity cows was conducted, in which true breeding values for conception rate were created. The model included the effects of sire and herd. The highest correlations between true breeding values for conception rate and breeding values for the interval between first and last insemination predicted by the survival analysis model and the linear model were 0.803 and 0.744, respectively. The results showed that when pregnancy status was known, survival models were more accurate than linear models to predict breeding values for conception rate when using observations on the interval between first and last insemination.

Animals↗

PubMed1999

Progeny testing sires selected by independent culling levels for below-average birth weight and high yearling weight or by mass selection for high yearling weight.

Breeding values of sires resulting from selection either for reduced birth weight and increased yearling weight (YB, n = 8) or for increased yearling weight alone (YW, n = 9) were compared with each other and with sires representative of the population before selection began (BS, n = 12) using progeny testing. Reference sires (n = 6) connected these Line 1 sires with the Hereford international genetic evaluation. Thirty-five sires produced 525 progeny that were evaluated through weaning. After weaning, 225 steer progeny were individually fed, slaughtered, and carcass data collected. Data were analyzed using restricted maximum likelihood procedures for multiple traits to estimate breeding values for traits measured on the top-cross progeny while simultaneously accounting for selection of the sires. Results of the progeny test substantiate within-line results for traits upon which sires were selected. Breeding values for gestation length were greater in YB sires than in YW sires and were unchanged relative to BS sires. Breeding values for growth rate and feed intake for the YB and YW sires were greater than for BS sires. Predicted breeding values for indicators of fat deposition tended to be greater in YB sires and less in YW sires relative to BS sires, although YB and YW sires had similar breeding values for marbling score. Selection based on easily and routinely measured growth traits, although achieving the intended direct responses, may not favorably affect all components of production efficiency. Further, divergence of selection lines may not be easily anticipated from preexisting parameter estimates, particularly when selection is based on more than one trait.

Animals↗

PubMed2002

Using conformation traits to improve reliability of genetic evaluation for herd life based on survival analysis.

Genetic evaluation for herd life based on survival analysis utilizes information available on all animals, dead (uncensored) and alive (censored), but the reliability of bulls' breeding values depends only on the number of uncensored daughters. Therefore, information on correlated conformation traits scored on daughters during their first lactation may be essential for the evaluation of young bulls with mostly censored daughters. Currently available programs for genetic evaluation based on survival analysis cannot combine indirect information on conformation traits with direct information on herd life, nor can they estimate genetic covariances between herd life and conformation traits. In this study, an alternative approach has been developed and tested using data on Swiss Simmental and Red & White cattle. Genetic covariances were approximated using breeding values for herd life from a survival analysis and BLUP breeding values for 26 linear conformation traits from a separate multivariate analysis. An index combining direct breeding values for herd life and indirect breeding values obtained from conformation traits was constructed. The relative weighting of both information sources varied depending on the amount of available information. The maximum reliability based only on conformation traits was 0.64. Except for old bulls with >100 uncensored daughters, the combined reliability was always higher than the direct reliability from survival analysis.

Animals↗

PubMed2004

General and specific combining ability from partial diallels of radiata pine: implications for utility of SCA in breeding and deployment populations.

Variances for general combining ability (GCA) and specific combining ability (SCA) and the relationship between mid-parental GCA and SCA effects were estimated for tree diameter (DBH) from a series of 20 sets of 6x6 half-diallel mating experiments in radiata pine, planted at ten sites across Australia. Significant SCA variance for DBH was almost equal to GCA variance for the combined analysis of all ten sites. The importance of SCA variance varied among sites, from non-significant to SCA variance accounting for all genetic variation among full-sib families. Significant SCA x site interaction was detected among the ten sites. A significant and positive correlation between mid-parental breeding values and best linear unbiased predictions of the SCA effects was observed. About a quarter of extra genetic gain is achievable through use of SCA variance if selection is based on the best breeding values. To fully exploit genetic gain from SCA variance in a deployment population, positive assortative matings are required for the best parents. It is estimated that the additional deployment gain of 46.0% for ten sites combined, or 52.9% for four sites combined that had significant GCA as well as SCA effects, were achievable relative to gain from GCA only, if all SCA variance within this breeding population was exploited. For a breeding population, selection for breeding values may be sufficient due to positive correlations between breeding values and SCA values. For a deployment population to capture more SCA genetic gain, it is preferable to make more pair-wise mating for parents with higher breeding values.

Australia↗

PubMed1991

Genetic and environmental trends for litter size in swine.

Best linear unbiased predictors (BLUP) of breeding values for additive direct and additive maternal genetic effects were estimated from 3,944 purebred Yorkshire and Landrace first-parity litters recorded on the Quebec Record of Performance Sow Productivity Program and born between 1977 and 1987. Breeding values for gilts, dams, and sires were estimated using an individual animal model for measures of litter size of total number born (NOBN), number born alive (NOBA), and number weaned (NOWN). Environmental trends were estimated from average herd-year solutions, and genetic trends were estimated by regression of estimated breeding value on year of birth. Environmental trends were positive for all traits in both breeds but were significant only for NOWN in Landrace (.051 +/- .021 pigs/yr). Genetic trends were very small but were mainly negative for direct breeding value and combined direct and maternal breeding value. Significant estimates of genetic trends (P less than .05) were observed only within the Yorkshire breed, and these ranged from -.012 +/- .004 to .004 +/- .002 pigs/yr.

Age Factors↗

PubMed2005

Milk urea nitrogen concentration: heritability and genetic correlations with reproductive performance and disease.

The objectives of this study were to estimate the heritability of milk urea nitrogen (MUN) concentration and describe the genetic relationship between MUN and reproductive performance and between MUN and diseases in Holsteins. Dairy Records Management Systems (Raleigh, NC) provided lactation data. The Danish Agricultural Advisory Center provided breeding value estimates for diseases. Infrared (IR) and wet chemistry (WC) data were analyzed separately. Heritabilities and genetic correlations for 2 different measures of MUN and reproductive performance were estimated with an animal model using ASREML. Heritabilities for MUN were estimated using all lactations combined (lactations 1 through 5) and separately for first lactation and second lactation. Genetic correlations with reproduction and health were estimated separately for parities 1 and 2. Herd-test-day or herd-year-season along with age at calving and days in milk were included as fixed effects in all models. Heritability estimates for all lactations combined were 0.15 for WC MUN and 0.22 for IR MUN. Genetic correlations between WC MUN and 2 measures of reproductive performance, days to first service, and first service conception were not different from zero. In contrast, the genetic correlation between WC MUN and days open of 0.21 in first lactation and 0.41 in second lactation indicated that higher WC MUN values were associated with increased days open. Correlations among estimated breeding values for MUN and estimated breeding values for Danish diseases identified no significant relationships. Although the results of this study indicate that heritable variation for MUN exists, the inability to identify significant genetic relationships with several measures of disease or reproductive performance appears to limit the value of MUN in selection for disease resistance and improved reproduction.

Animals↗

PubMed1997

Commercial approaches to genetic selection for growth and feed conversion in domestic poultry.

Tremendous genetic progress has been observed historically for growth and feed conversion through the efforts of the primary breeding companies. However, significant between-strain variation still exists due to differences in selection emphasis and selection techniques practiced by these organizations. This paper provides an overview of methods currently employed in commercial poultry breeding with reference to factors complicating program design and future challenges facing the industry. Mass selection for body weight has resulted in a significant reduction in the number of days required to grow bird to market weight with indirect improvements in feed conversion. Direct selection for feed conversion is accomplished through part record testing of males that have been preselected for body weight, conformation, and defect traits. Data are commonly subjected to complex statistical analysis both to correct feed conversion for variation in body weight and to improve the accuracy of breeding value estimates. Feed conversion breeding values of male sibs are sometimes used for the selection of female candidates as well. Selection for growth rate and efficiency has resulted in negative complications, such as ascites, reduced reproductive performance, skeletal abnormalities, and increased carcass fatness. Some of these factors may be partially ameliorated through modified selection practices. If not addressed by the breeding industry, the disruption of physiological homeostasis might ultimately represent economic and genetic barriers to further progress in improving growth and efficiency. Modern techniques in molecular genetics, utilized in conjunction with traditional quantitative genetic approaches, will provide additional opportunities to circumvent these physiological complications associated with genetic selection for growth and feed efficiency.

Animals↗

PubMed2000

A multiple-trait herd cluster model for international dairy sire evaluation.

International dairy sire evaluations have traditionally been calculated using a two-step process. Lactation records within each country are used to predict national estimated breeding values, then these national breeding values are transformed to the genetic base, scale, and units of measurement of other countries by using conversion formulae or the multiple-trait, across-country evaluation method. A major limitation of this approach is the need to define environments (traits) according to country borders. Herds located in small, neighboring countries may be much more similar in management, climate, and genetic background than herds located far apart within a single large country. In the present study, international genetic evaluation with herd clusters is proposed. Data consisted of 4.6 million lactation records from 46,000 herds in Austria, Belgium, Czech Republic, Denmark, Estonia, Finland, Israel, Switzerland, and five regions of the US (Midwest, Northeast, Northwest, Southeast, and Southwest). Herds were grouped into clusters based on data of 13 descriptive variables: herd size, calving interval, milking frequency, age at first calving, milk yield, month of calving, predicted transmitting ability of sire for milk, percentage North American genes of sire, latitude, altitude, temperature, rainfall, and percentage of arable land used for pasture. Five clusters were formed; each cluster contained herds from 5 to 11 countries or regions. Genetic correlations between herd clusters ranged from 0.81 to 0.97. The herd cluster model is intuitively appealing, because genetic merit of an animal is predicted for each unique environment or management system, regardless of country borders. This model is parsimonious (the number of traits was reduced from 13 to 5) and is computationally feasible for large data sets.

Animals↗

PubMed2001

Analysis of survival in dairy cows with supplementary data on type scores and housing systems from a region of northwest Germany.

In survival analysis, type traits can be included as covariates to evaluate their use as predictors for survival. One problem in such an analysis is the availability of suitable data. Whereas data on the length of productive life (LPL) of individual cows can be retrieved from milk recording data, for type traits, all cows in the population must be scored for type at least once. In the present analysis, a dataset from the Osnabruck region in northwestern Germany, which fulfilled this requirement in recent years, was used. Data consisted of 169,733 cows with information on LPL for calving years 1980 to 1996 (dataset I) and of 39,233 cows with information on LPL and type for calving years 1990 to 1996 (dataset II). A further dataset (III) contained 43,116 cows from calving years 1987 to 1996 and included information on the housing system for each herd. The basic model included stage of lactation, relative production within herd, change of herd size, and year-season as time dependent effects; age at calving as a time-independent effect; and herd-year-season and sire as random effects. Other effects (information on type, housing system) were included additionally. For data-set II, the scores for 15 linear type traits were also included as corrected phenotypic values, estimated breeding values, and residuals from a previous BLUP analysis. The package Survival Kit 3.0 was used for all analyses. The results indicate a moderate heritability of 0.17 and 0.18 for true and functional LPL (dataset I). Almost all type traits analyzed (dataset II) exceeded a 0.001 level of significance in their effect on survival. The strongest relationships between survival and type were found for udder depth, fore udder attachment, and front teat placement. The main result from the comparison of housing systems (dataset III) was that bedding has a positive effect on survival.

Age Factors↗

PubMed2001

Non-additive genetic effects in animal selection.

Genetic evaluation of purebred farm animals has been carried out for about half a century, employing additive approximation to describe the genetic background. An evaluated animal has been attributed a single breeding value for each trait of the breeding goal. The predicted additive genetic value of an animal equals the average breeding value of its parents. Although the selection based on the additive approach has proved successful, there still is a possibility of increasing the reliability of the breeding value estimation by accounting for non-additive genetic effects of dominance and epistasis, disregarded in the additive model. In the non-additive model, the expected quality of the progeny equals the average of the parents plus an effect resulting from the interaction between the parents. In this case, the evaluated animal may have as many breeding values as there are possible candidates to mate to, for each trait. The dominance and epistatic effects have already been accounted for in selecting animals or populations for some crossbreeding plans (combining ability, heterosis, and recombination loss). Also, using crossbreds for the sake of the breeding value estimation of purebred animals requires removing the non-additive effects from the crossbred performance and distributing the additive component between the purebreds. Combining ability is more and more discussed as a factor for matings within breed to produce terminal progeny.

Journal Article↗

PubMed2000

Genetic parameters and trends of milk, fat, days open, and body weight after calving in North Carolina experimental herds.

The main objective of this study was to estimate genetic trends for 3.7% FCM, fat yield, days open, and predicted body weight after calving in six experimental dairy herds owned by the State Farm Division of the North Carolina Department of Agriculture. Body weights were predicted from heart girths measured at or before the first test day after calving. Data analyzed were 23,052 records from 8575 cows, daughters of 681 bulls. Heritabilities and breeding values were estimated using the multiple-trait, derivative-free REML programs and a single-trait repeatability model. Breeding values of cows were averaged by and regressed on birth year to estimate genetic trends. Genetic correlations between traits were estimated by correlating breeding values. Estimates of heritability were 0.25 for 3.7% FCM, 0.28 for fat yield, 0.03 for days open, and 0.17 for predicted body weight. Unfavorable genetic relationships were found between yields and days open and between yields and body weight. Genetically, cows that were heavier after calving produced less milk and fat but conceived earlier than smaller cows. Genetic changes in yields and days open were greater for cows born after 1970, but the greatest genetic changes were after 1980 (FCM, 94.7 kg/yr; fat yield, 3.46 kg/yr; days open, 1.1 d/yr). Breeding values for body weight increased for cows born from 1950 to 1970, decreased until 1980, and increased for later parities. The results of our study suggest that AI organizations may need to include fertility traits in progeny testing and relax the emphasis on increased body weight.

Animals↗

PubMed2003

A comparison of hydrogen ion concentration and pH genetic predictions and fixed effect estimations when assessing pork quality.

An evaluation of ultimate pH (pH) and hydrogen ion concentration (H+) was conducted to determine if the mathematical conversion of H+ to pH could affect 1. fixed and random effect inferences and 2. prediction of genetic merit of animals when either pH or H+ is used as an indicator in the assessment of pork quality. Data from 4,262 purebred animals and 577 sires having complete three-generation pedigrees from the 1991 to 2001 National Barrow Show Progeny Tests were utilized in this study. Existing loin muscle pH data were converted to their original H+. Numerical changes in values occurred across all fixed effects and in the case of breed and test, changes in differences among subclasses occurred. These changes may result in differing inferences that can be made depending on whether pH or H+ is used as the dependent variable. Heritability estimates for pH and H+ were 0.52 +/- 0.074 and 0.62 +/- 0.078, respectively. The Pearson correlation between pH and H+ breeding values was -0.92. Spearman Rank correlation of -0.91 between pH and H+ breeding values was calculated and indicates that sires do not rank the same when ordered by breeding values for each trait. When pH is the selection objective, the selection differential reduction in H+ from these data ranges from 3.8 to 9.1%. Additionally, only 77.7% of the estimated genetic progress per generation in H+ is realized when selection (5% selected) is based on pH. The genetic correlation between pH and H+ was -0.96. Changes in the absolute values of the genetic correlations between various pork quality indicator traits and pH or H+ concentration were 0.04 or less. Differences in pH and H+ results could impact decisions made by swine breeders and meat processors who are concerned about pork quality. This, combined with the greater heritability and biochemical reality for H+, indicates that H+ rather than pH is the more appropriate trait breeders and processors should focus on when attempting to improve pork quality.

Animals↗

PubMed2006

Genetic evaluation of mastitis in dairy cattle using linear models, threshold models, and survival analysis: a simulation study.

The objective was to study, by simulation, whether survival analysis results in a more precise genetic evaluation for mastitis in dairy cattle than cross-sectional linear models and threshold models by using observation periods for mastitis of 2 lengths (the first 150 d of lactation, and the full lactation, respectively). True breeding values for mastitis liability on the underlying scale were simulated for daughters of 400 sires (average daughter group size, 60 or 150), and the possible event of a mastitis case within lactation for each cow was created. For the linear models and the threshold models, mastitis was defined as a binary trait within either the first 150 d of lactation or the full lactation. For the survival analysis, mastitis was defined as the number of days from calving to either the first case of mastitis (uncensored record) or to the day of censoring (i.e., day of culling, lactation d 150 or day of next calving; censored record). Cows could be culled early in lactation (within 10 d after calving) for calving-related reasons or later on because of infertility. The correlation between sire true breeding values for mastitis liability and sire predicted breeding values was greater when using the full lactation data (0.76) than when using data from the first 150 d (0.70) with an average of 150 daughters per sire. The corresponding results were 0.60 and 0.53, respectively, with an average of 60 daughters per sire. Under these simulated conditions, the method used had no effect on accuracy. The higher accuracy of sire breeding values can be translated into a greater genetic gain, unless counteracted by a longer generation interval.

Animals↗

PubMed2005

Genetic evaluation of dairy cattle with test-day models with autoregressive covariance structures and with a 305-d model.

This study compared genetic evaluations from 3 test-day (TD) models with different assumptions about the environmental covariance structure for TD records and genetic evaluations from 305-d lactation records for dairy cows. Estimates of genetic values of 12,071 first-lactation Holstein cows were obtained with the 3 TD models using 106,472 TD records. The compound symmetry (CS) model was a simple test-day repeatability animal model with compound symmetry covariance structure for TD environmental effects. The ARs and ARe models also used TD records but with a first-order autoregressive covariance structure among short-term environmental effects or residuals, respectively. Estimates of genetic values with the TD models were also compared with those from a model using 305-d lactation records. Animals were genetically evaluated for milk, fat, and protein yields, and somatic cell score (SCS). The largest average estimates of accuracy of predicted breeding values were obtained with the ARs model and the smallest were with the 305-d model. The 305-d model resulted in smaller estimates of correlations between average predicted breeding values of the parents and lactation records of their daughters for milk and protein yields and SCS than did the CS and ARe models. Predicted breeding values with the 3 TD models were highly correlated (0.98 to 1.00). Predicted breeding values with 305-d lactation records were moderately correlated with those with TD models (0.71 to 0.87 for sires and 0.80 to 0.87 for cows). More genetic improvement can be achieved by using TD models to select for animals for higher milk, fat, and protein yields, and lower SCS than by using models with 305-d lactation records.

Analysis of Variance↗

PubMed2006

Analysis of litter size and days to lambing in the Ripollesa ewe. II. Estimation of variance components and response to phenotypic selection on litter size.

A performance data set from 376 Ripollesa purebred ewes of the experimental flock of the Universitat Autònoma of Barcelona was analyzed using a bivariate Bayesian threshold-linear model. The data set contained 1,598 litter size records and 1,699 days-to-lambing records. The model included the additive genetic effect of each animal and 3 nongenetic sources of variation: ewe age, year of lambing, and the permanent environmental effect characterized by the ewe. The flock was phenotypically selected for litter size since 1986, and replacement ewes and rams were selected from the progeny of the more prolific ewes, which had at least 3 deliveries recorded. The phenotypic trend for litter size was positive, whereas days to lambing followed an unclear pattern. Both traits had low heritabilities; 0.13 for litter size and 0.11 for days to lambing. Response to selection was evaluated through (a) the average breeding value of the ewe lambs chosen annually, and (b) the average breeding value of the overall flock. The first measurement suggested a positive trend for litter size, although it showed important oscillations. On the other hand, the average breeding value for the overall flock showed a stable positive tendency after yr 4 of selection, with estimates clearly different from zero after yr 11 of selection. A significant increase in the incidence of multiple births was observed, with a mode of approximately 10%. The correlated response in days to lambing did not show a significant trend. The effect of year of lambing also positively influenced both litter size and days to lambing, although important oscillations were observed between years. Results indicated that litter size in sheep can be effectively improved through phenotypic selection, even in small flocks; moreover, days to lambing could also be genetically improved, given the estimate obtained for its heritability.

Animals↗

PubMed1991

Evaluation of performance-tested boars using a single-trait animal model.

Data structure designs for breeding value estimation of performance-tested boars using mixed-model methodology were compared. Computer models were based on estimates of parameters from the literature and from results of a survey of test station managers. Results were compared using accuracy (the correlation of true and estimated breeding values) and prediction error variance (PEV). The single-trait animal model included a fixed effect due to station-season, a random effect due to breeding value for ADG or backfat, and a random error term. Family size, number of families per test, and relationships among animals within and across tests were varied. Prediction error variance decreased faster for small families than for large ones as number of families increased, but increasing numbers of animals per pen was most important, especially if test size was optimized. With no other genetic ties, full-sibs were much more accurately evaluated than half-sibs. Designs that included sire ties among families within a station-season resulted in increased PEV. Increasing the number of full-sibs and(or) increasing the number of families per test would help to optimize PEV and correct this problem. Tying station-seasons with the relationship matrix improved the average accuracy of predicted breeding values. Placing full-sibs in different stations resulted in the greatest accuracy of evaluation, but a large number of half-sib (sire) ties resulted in comparable accuracies. Half-cousin ties did not improve accuracy of evaluation but could result in significant genetic progress by increasing the selection differential.

Adipose Tissue↗

PubMed2001

Implementation of a routine genetic evaluation for longevity based on survival analysis techniques in dairy cattle populations in Switzerland.

Genetic evaluation of sires for functional longevity of their daughters based on survival analysis has been implemented in the populations of Braunvieh, Simmental, and Holstein cattle in Switzerland. A Weibull mixed sire-maternal grandsire survival model was used to estimate breeding values of sires with data on cows that calved since April 1, 1980. Data on Braunvieh and Simmental cows included about 1.1 million records, data on Holstein cows comprised about 220,000 records. Data contained approximately 20 to 24% right-censored records and 6 to 9% left-truncated records. Besides the random sire and maternal grandsire effects, the model included effects of herd-year-season, age at first calving, parity, stage of lactation, alpine pasturing (Braunvieh and Simmental), and relative milk yield and relative fat and protein percentage within herd to account for culling for production. Heritability of functional longevity, estimated on a subset of data including approximately 150,000 animals, were 0.181, 0.198, and 0.184 for Braunvieh, Simmental, and Holstein, respectively. Breeding values were estimated for all sires with at least six daughters or three granddaughters in the data. Breeding values of sires are expressed in months of functional productive life and published in sire catalogs along with breeding values for production traits.

Animals↗