SEARCH · PubMed Health

Results for “Breeding value”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 307 records · Page 17Linked to original sources

PubMed2004

Derivation and calculation of approximate reliabilities and daughter yield-deviations of a random regression test-day model for genetic evaluation of dairy cattle.

Test-day milk, fat, protein yield, and somatic cell score (SCS) were analyzed separately using data from the first 3 lactations and a random regression model. Data used in the model were from Austria, Germany, and Luxembourg and from Holstein, Red, and Jersey dairy cattle. For reliability approximation, a multiple-trait effective daughter contribution (MTEDC) method was developed under general multiple trait models, including random regression test-day models, by extending the single-trait daughter equivalents concept. The MTEDC was applied to the very large dairy population, with about 15.5 million animals. The calculation of reliabilities required less computer memory than the corresponding iteration program and a significantly lower computing time equivalent to 24 rounds of iteration. A formula for daughter-yield deviations was derived for bulls under multiple-trait models. Reliability associated with daughter-yield deviations was approximated using the MTEDC method. Both the daughter-yield deviation formula and associated reliability method were verified in a simulation study using the random regression test-day model. Correlations of lactation daughter-yield deviations with estimated breeding values calculated from a routine genetic evaluation were 0.996 for all bulls and 0.95 for young bulls having only daughters with short lactations.

Analysis of Variance↗

PubMed1997

Genetic evaluation by BLUP in two-breed terminal crossbreeding systems under dominance.

To obtain estimates of breeding values by BLUP using Henderson's mixed-model equations, it is necessary to invert the covariance matrix for each random effect in the model. In a model in which the genotypic value is included as a random effect (genotypic model), it is necessary to invert the genotypic covariance matrix. Under additive inheritance, the inverse of the genotypic covariance matrix can be computed efficiently. Under dominance inheritance, however, an efficient method to invert the genotypic covariance matrix has not yet been developed, especially for crossbred populations. Thus, the use of a genotypic model for BLUP is not suitable for genetic evaluation in large, crossbred populations. We present an equivalent model in which the genotypic effect is partitioned into additive and dominance effects. With this equivalent model, methods used for within-breed genetic evaluation by BLUP can be used for a two-breed terminal cross under dominance.

Alleles↗

PubMedDate not supplied

A method to optimize selection on multiple identified quantitative trait loci.

A mathematical approach was developed to model and optimize selection on multiple known quantitative trait loci (QTL) and polygenic estimated breeding values in order to maximize a weighted sum of responses to selection over multiple generations. The model allows for linkage between QTL with multiple alleles and arbitrary genetic effects, including dominance, epistasis, and gametic imprinting. Gametic phase disequilibrium between the QTL and between the QTL and polygenes is modeled but polygenic variance is assumed constant. Breeding programs with discrete generations, differential selection of males and females and random mating of selected parents are modeled. Polygenic EBV obtained from best linear unbiased prediction models can be accommodated. The problem was formulated as a multiple-stage optimal control problem and an iterative approach was developed for its solution. The method can be used to develop and evaluate optimal strategies for selection on multiple QTL for a wide range of situations and genetic models.

Animals↗

PubMed2004

Genetic associations of prolificacy with performance, carcass, meat quality, and leg conformation traits in the Finnish Landrace and Large White pig populations.

The objective of this study was to estimate genetic associations of prolificacy traits with other traits under selection in the Finnish Landrace and Large White populations. The prolificacy traits evaluated were total number of piglets born, number of stillborn piglets, piglet mortality during suckling, age at first farrowing, and first farrowing interval. Genetic correlations were estimated with two performance traits (ADG and feed:gain ratio), with two carcass traits (lean percent and fat percent), with four meat quality traits (pH and L* values in longissimus dorsi and semimembranosus muscles), and with two leg conformation traits (overall leg action and buck-kneed forelegs). The data contained prolificacy information on 12,525 and 10,511 sows in the Finnish litter recording scheme and station testing records on 10,372 and 9,838 pigs in Landrace and Large White breeds, respectively. The genetic correlations were estimated by the restricted maximum likelihood method. The most substantial correlations were found between age at first farrowing and lean percent (0.19 in Landrace and 0.27 in Large White), and fat percent (-0.26 in Landrace and -0.18 in Large White), and between number of stillborn piglets and ADG (-0.38 in Landrace and -0.25 in Large White) and feed:gain (0.27 in Landrace and 0.12 in Large White). The correlations are indicative of the benefits of superior growth for piglets already at birth. Similarly, the correlations indicate that age at first farrowing is increasing owing to selection for carcass lean content. There was also clear favorable correlation between performance traits and piglet mortality from birth to weaning in Large White (r(g) was -0.43 between piglet mortality and ADG, and 0.42 between piglet mortality and feed:gain), but not in Landrace (corresponding correlations were 0.26 and -0.22). There was a general tendency that prolificacy traits were favorably correlated with performance traits, and unfavorably with carcass lean and fat percents, whereas there were no clear associations between prolificacy and meat quality or leg conformation. In conclusion, accuracy of estimated breeding values may be improved by accounting for genetic associations between prolificacy, carcass, and performance traits in a multitrait analysis.

Adipose Tissue↗

PubMed1988

Relationships among growth hormone and prolactin secretory parameter estimates in Holstein bulls and their predicted differences for lactational traits.

Selection of dairy sires is based on the production records of their female ancestors, half-sibs and daughters. No trait expressed by the sire is used. Concentrations of growth hormone (GH) and prolactin (PRL), hormones produced in both males and females that are fundamental in lactation, may be correlated with production. A study was conducted to determine whether measures of these hormones in the sire would be useful predictors of lactational ability of daughters. Blood samples were collected at 15-min intervals for 8 h from 26 Holstein bulls (5.5 yr of age) that had one progeny summary available. Plasma concentrations of GH and PRL were quantified and the mean and baseline concentrations and the frequency and mean amplitude of the secretory peaks were determined for each bull. Concentrations among these values and bulls' predicted differences (PD) were determined. Significant negative correlations were detected for frequency of GH peaks and PD for yield of milk, fat and protein; correlations were positive for PRL baseline concentrations and PD for fat and protein (P less than .10), and correlations were negative for frequency of PRL peaks and PD for milk, fat and protein (P less than .10). Addition of estimates of bull hormone secretory parameters to breeding values based on performance of relatives considerably improved the accuracy (R2) for predicting progeny performance from sire information. Certain characteristics of the patterns of GH and PRL secretion may be heritable and aid in identification of superior dairy animals.

Animals↗

PubMed2003

Heritability of body length and measures of body density and their relationship to backfat thickness and loin muscle area in swine.

The objective of this study was to estimate heritability for body length (LEN) at the end of performance testing and to estimate genetic correlations with backfat (BF) thickness and loin muscle area (LMA) in Landrace, Yorkshire, Duroc, and Hampshire breeds of swine. Also examined were two measures of body density involving body length and weight and their relationships to backfat and loin muscle area. Data consisted of performance test records collected in a commercial swine operation from 1992 to 1999. Boars from 60% of the litters were culled at weaning based on a maternal breeding value of the dam. Remaining boars and all females were grown to 100 d of age (15,594, 55,497, 12,267, and 9,782 Landrace, Yorkshire, Duroc, and Hampshire pigs, respectively). At this time, all pigs were weighed (WT100) and selected for performance testing based on a combination of maternal and performance indexes, which differed by breed. All pigs were weighed at the end of the 77 d performance test (WT177) when BF, LMA, and LEN were measured. Two measures of body density involving length were calculated: Body mass index (BMI) = WT177/LEN2 and body density (DENSITY) = WT177/LEN. For each breed, genetic parameters were estimated using an animal model with random litter effects and multiple-trait REML procedures. A series of three-trait models including WT100 and combinations of two other traits in each analysis was conducted. Fixed effects included contemporary group and age as a covariate. Average estimates of heritability were 0.16 to 0.32 for LEN (unadjusted for WT177), 0.12 to 0.26 for LEN (adjusted for WT177), 0.23 to 0.33 for DENSITY, and 0.16 to 0.25 for BMI. Genetic correlations between LEN and LMA were low. Genetic correlations between LEN (unadjusted for WT177) and BF were 0.10 to 0.41. Adjusting LEN for WT177 gave correlations of 0.11 for Landrace and Hampshire and negative correlations (-0.06 and -0.19, respectively) for Yorkshire and Duroc. Genetic correlations between LMA and DENSITY and between LMA and BMI were comparable and ranged from 0.44 to 0.54. Genetic correlations between BF and DENSITY were slightly higher (0.53 to 0.68) than those between BF and BMI (0.37 to 0.67). In these data, not much relationship between BF and body length at a constant weight and age was found. There was a negative relationship between LMA and LEN at a constant weight and age, implying that longer pigs had smaller LMA.

Adipose Tissue↗

PubMedDate not supplied

Analysis of microsatellites and parentage testing in saltwater crocodiles.

Fifteen microsatellite loci were evaluated in farmed saltwater crocodiles for use in parentage testing. One marker (C391) could not be amplied. For the remaining 14, the number of alleles per locus ranged from two to 16, and the observed heterozygosities ranged from 0.219 to 0.875. The cumulative exclusion probability for all 14 loci was .9988. the 11 loci that showed the greatest level of polymorphism were used for parentage testing, with an exclusion probability of .9980. With these 11 markers on 107 juveniles from 16 known breeding pairs, a 5.6% pedigree error rate was detected. This level of pedigree error, if consistent, could have an impact on the accuracy of gentic parameter and breeding value estimation. The usefulness of these markers was also evaluated for assigning parentage in situations where maternity, paternity, or both may not be known. In these situations, a 2% error in parentage assignment was predicted. It is therefore recommended that more micro-satellite markers be used in these situations. The use of these microsatellite markers will broaden the scope of a breeding program, allowing progeny to be tested from adults maintained in large breeding lagoons for selection as future breeding animals.

Alligators and Crocodiles↗

PubMed1993

Selection for litter size, body weight, and pelt quality in mink (Mustela vison): experimental design and direct response of each trait.

In a five-generation selection experiment, separate lines of mink (Mustela vison) were subjected to selection for improved litter size at 3 wk (F line), BW in September (BS line), and underfur density (P line), and combined selection for litter size and BW (I line). Underfur density was subjectively judged on live animals. One unselected line served as a control (C line). Significant changes were achieved in each trait: litter size in the last generation was 5.3 in the F line vs 3.7 in the C line; September weight in males was 2,254 g in the BS line vs 1,979 g in the C line, and the underfur density score, graded using a 5-point scale, was 4.1 in the P line vs 2.9 in the C line. In the combined line (I line) litter size was only slightly improved, whereas BW was substantially increased (male mean = 2,194 g). A univariate animal model was used to predict genetic values and to estimate variance components with a REML procedure. Heritability estimates were .14 +/- .09 for litter size, .39 +/- .06 for September weight, and .21 +/- .06 for underfur density. It was confirmed that the reproductive performance of heavy of fat animals was poor. Responses were higher than predicted when selecting for September weight and underfur density. In the last generation the average breeding values, relative to the base generation, were +.8 kits for litter size (F line), +365 g for male September weight (BS line), and +1 point for underfur density (P line). The study suggests that negative maternal effects on litter size may exist in mink.

Animals↗

PubMed1991

C. R. Henderson: contributions to the dairy industry.

Through C. R. Henderson's position and the application of his knowledge, he had a major influence on genetic improvement in dairy cattle beginning in the 1950s. He developed herdmate comparisons in the United States. The first extensive program using pedigree selection and progeny testing of sires for use in AI was because of his suggestion. This program established the direction of dairy cattle improvement that still continues. He developed BLUP and discovered how to write the inverse of an additive genetic relationship matrix, A-1, without inverting the matrix. These accomplishments had a major impact on evaluation methods of dairy cattle and other livestock species. Use of BLUP and A-1 are standards for evaluation of breeding values all over the world. His pioneering work in estimation of components of variance and analyses of unbalanced data were also of primary importance for animal evaluation and many other applications. Henderson made a major contribution to mankind.

Animals↗

PubMed1991

C. R. Henderson: the unfinished legacy.

Ideas and methods developed by Henderson have been applied widely to BLUP of additive genetic merit of animals and estimation of components of variance. However, a number of other contributions of Henderson to theory and application of animal breeding and statistics have not been as fully examined and exploited. Some of these contributions are complete in their own right and others lay the groundwork to help resolve remaining problems. Henderson had insight and made contributions to the areas of analysis of line and breed cross data, hypothesis testing under mixed linear models, prediction of breeding values with unknown variances, and selection models. The general flexibility of Henderson's mixed model methods to quantify a large variety of biological effects is also illustrated and discussed in light of new technologies in genetics and biology.

Animals↗

PubMed2005

Correlated responses to divergent selection for phytate phosphorus bioavailability in a randombred chicken population.

The current study was undertaken to evaluate the correlated responses to 3 generations of divergent selection for phytate phosphorus bioavailability (PBA) in the Athens-Canadian randombred chicken population. The traits studied were BW at 4 wk of age, BW gain (BWG), feed consumption (FC), and feed conversion ratio (FCR) during a period of 3 d. The first evaluation criterion was the cumulated divergent correlated response (CR(C)), which was calculated as the line difference of the least square means of phenotypic values for each trait at a given generation after adjustment for sex and hatch effects. The results showed a consistent correlated response in BW across generations. The CR(C) at generation G3 was 26.8 g (P < 0.01). The chickens in the low PBA line (L line) had higher BW than the high PBA line (H line). The CR(C) for BWG, FC, and FCR were significant (P < 0.05) only at G3. The second evaluation criterion was the average best linear unbiased prediction estimated breeding value (EBV). The results showed asymmetric genetic trends in BW, BWG, and FC, and the correlated responses were mainly due to the genetic changes that occurred in H line because little genetic change occurred in L line across generations. At G3, the line differences of EBV were close to the CR(C) values for all the traits except FCR. This suggested that CR(C) and EBV criteria would tend to be consistent with the increase across generations. However, at G1 and G2, the line differences of the EBV actually deviated from the CR(C) values for BWG and FC. The inconsistency could be attributed to experimental errors and genetic drift that were not accounted by the fixed model for obtaining CR(C).

Animals↗

PubMed2006

Success at first insemination in Australian Angus cattle: analysis of uncertain binary responses.

Field data from Australian Angus herds were used to investigate 2 methods of analyzing uncertain binary responses for success or failure at first insemination. A linear mixed model that included herd, year, and month of mating as fixed effects; unrelated service sire, additive animal, and residual as random effects; and linear and quadratic effects of age at mating as covariates was used to analyze binary data. An average gestation length (GL) derived from artificial insemination data was used to assign an insemination date to females mated to natural service sires. Females that deviated from this average GL led to uncertain binary responses. Two analyses were carried out: 1) a threshold model fitted to uncertain binary data, ignoring uncertainty (M1); and 2) a threshold model fitted to uncertain binary data, accounting for uncertainty via fuzzy logic classification (M2). There was practically no difference between point estimates obtained from M1 and M2 for service sire and herd variance; however, when uncertain binary data were analyzed ignoring uncertainty (M1), additive variance and heritability estimates were greater than with M2. Pearson correlations indicated that no major reranking would be expected for service sire effects and animal breeding values using M1 and M2. Given the results of the current study, a threshold model contemplating uncertainty is suggested for noisy binary data to avoid bias when estimating genetic parameters.

Animals↗

PubMed2005

Evaluation of expected response to selection for orthopedic health and performance traits in Hanoverian Warmblood horses.

OBJECTIVE: To determine whether selection schemes accounting for orthopedic health traits were compatible with breeding progress in performance parameters in Hanoverian Warmblood horses. ANIMALS: 5,928 horses. PROCEDURE: Relative breeding values (RBVs) were predicted for osseous fragments in fetlock (metacarpo- and metatarsophalangeal) and tarsal joints, deforming arthropathy in tarsal joints, and pathologic changes in distal sesamoid bones. Selection schemes were developed on the basis of total indices for radiographic findings (TIR), dressage (TID), and jumping (TIJ). Response to selection was traced over 2 generations of horses for dressage and jumping ability and all-purpose breeding. Development of mean RBVs and mean total indices in sires and prevalences of orthopedic health traits in their offspring were used to assess response to selection. RESULTS: Giving equal weight toTIR andTID, TIJ, or a combined index of 60% TID and 40% TIJ, 43% to 53% of paternal grandsires and 70% to 82% of descending sires passed selection. In each case, RBVs and total indices increased by as much as 9% in selected sires, when compared with all sires, and prevalences of orthopedic health traits in offspring of selected sires decreased relatively by as much as 16%. When selection was exclusively based on TID, TIJ, or TID and TIJ, percentages of selected sires were 44% to 66% in the first and 73% to 84% in the second generation and TID and TIJ increased by 9% to 10% and 19% to 23%, respectively. CONCLUSIONS AND CLINICAL RELEVANCE: Compared with exclusively performance-based selection, percentages of selected sires changed slightly and breeding progress in TID, TIJ, or TID and TIJ was only slightly decreased; however, prevalences of orthopedic health traits decreased in offspring of TIR-selected sires.

Animals↗

PubMed1992

Comparison of selection methods at the same level of inbreeding.

Animal geneticists predict higher genetic responses to selection by increasing the accuracy of selection using BLUP with information on relatives. Comparison of different selection methods is usually made with the same total number tested and with the same number of parents and mating structure so as to give some acceptable (low) level of inbreeding. Use of family information by BLUP results in the individuals selected being more closely related, and the levels of inbreeding are increased, thereby breaking the original restriction on inbreeding. An alternative is to compare methods at the same level of inbreeding. This would allow more intense selection (fewer males selected) with the less accurate methods. Stochastic simulation shows that, at the same level of inbreeding, differences between the methods are much smaller than if inbreeding is unrestricted. If low to moderate inbreeding levels are targeted, as in a closed line of limited size, then selection on phenotype can yield higher genetic responses than selection on BLUP. Extra responses by BLUP are at the expense of extra inbreeding. The results derived here show that selection on BLUP of breeding values may not be optimal in all cases. Thus, current theory and teaching on selection methods are queried. Revision of the methodology and a reappraisal of the optimization results of selection theory are required.

Animals↗

PubMed1995

Maximizing selection efficiency for categorical traits.

Genetic improvement of categorically recorded traits is hampered because information content of categorical records is low and ordinary linear breeding value estimation methods do not apply theoretically. The ordinary animal or linear mixed model (LMM), which ignored the categorical nature of the trait, is compared to a generalized linear mixed model (GLMMp) that assumes a linear mixed model for an underlying continuous variable. The GLMMp takes full account of the categorical nature of the trait and is a straightforward extension of LMM. In a closed nucleus breeding scheme (e.g., cattle, pigs, or poultry), rates of genetic gain increased by 1 to 2%, when GLMMp was used instead of LMM. Rates of genetic gain increased by 7 to 20%, when the best sires were used on the best herds (i.e., when there was some confounding between sire and herd effects). When considering a binary trait (e.g., disease incidence) initial incidences of 25% could be reduced to 2.8% within 10 generations of selection. Rates of gain can be increased by up to 84% by gathering more information on high-incidence categories (i.e., by dividing these categories into subcategories). Subdividing low-incidence categories (e.g., splitting diseased animals into moderately and severely diseased) hardly increased rates of gain. Direct recording of the underlying variable, which requires uncovering of the physiological background of the categorical trait, yielded 109 to 278% more genetic gain than selection for a binary trait.

Animals↗

PubMed1993

Linkage between amylase-1 locus and a major gene for milk fat content in cattle.

Linkage between the amylase-1 (Am-1) locus and a quantitative trait locus influencing fat content in milk was studied in offspring from heterozygous sires of the Swedish Red and White dairy breed. The effect on bull breeding values for fat content was estimated as interactions between sire and paternal Am-1 allele using a model eliminating the direct effects of sire and Am-1 allele. There were strong indications of linkage, confirming results of previous studies. The interaction was caused by strong associations in 7 out of 14 site families. A test for within-family variance heterogeneity performed on the whole population of breeding bulls also supported the presence of a major gene for fat content in milk. The results indicate that there is genetic linkage between the Am-1 locus and a locus with large effect on milk fat content.

Amylases↗

PubMed1996

Systematic error in genetic evaluation of miles city line 1 hereford cattle resulting from preadjustment for age of dam.

Differences in preweaning growth of calves nursing 2- and 3-yr-old dams compared with contemporaries nursing older dams are accentuated in the Miles City Line 1 Hereford herd relative to age-of-dam (AOD) effects implied by preadjustment of 205-d weight in national cattle evaluation. Mixed-model analyses of 205-d weight that fit random individual direct effects and maternal genetic and permanent environmental effects on 4,998 calves were conducted to 1) determine the magnitude of residual AOD effects after preadjustment (PA) using industry-standard procedures and 2) compare changes in genetic predictions resulting from either PA or simultaneous adjustment (SA) for AOD. Expressed as differences from the 5- to 10-yr-old age effect, simultaneously estimated AOD effects were 45 +/- 1, 19 +/- 1, 6 +/- 1, and 19 +/- 3 kg for 2, 3, 4, and 11+ AOD classes, respectively. Comparable estimates of residual AOD effects after PA were 20 +/- 1, 6 +/- 1, 1 +/- 1, and 14 +/- 3 kg. Rank correlations of direct (BVd) and maternal (BVm) breeding values (BV) for 205-d weight from the analysis using PA with BV predicted using SA for AOD were .98 and .77, respectively. Estimated genetic trends were also affected by the method of accounting for AOD effects. One hundred fifty replicate simulations of 205-d weights with pedigree, fixed effect, and variance-covariance structures corresponding to the experimental population were used to establish correlations (r) of predicted BV with underlying true values. The r of predicted BVd with true values were reduced less than .02 by PA compared to SA in accounting for AOD. However, r of predicted BVm with true values were reduced more than .13 by PA compared to SA in accounting for AOD. These data indicate potential for systematic error in genetic evaluations that apply standard adjustments for AOD to 205-d weight.

Aging↗

PubMed2005

Comparison of random regression test-day models for Polish Black and White cattle.

Test-day milk yields of first-lactation Black and White cows were used to select the model for routine genetic evaluation of dairy cattle in Poland. The population of Polish Black and White cows is characterized by small herd size, low level of production, and relatively early peak of lactation. Several random regression models for first-lactation milk yield were initially compared using the "percentage of squared bias" criterion and the correlations between true and predicted breeding values. Models with random herd-test-date effects, fixed age-season and herd-year curves, and random additive genetic and permanent environmental curves (Legendre polynomials of different orders were used for all regressions) were chosen for further studies. Additional comparisons included analyses of the residuals and shapes of variance curves in days in milk. The low production level and early peak of lactation of the breed required the use of Legendre polynomials of order 5 to describe age-season lactation curves. For the other curves, Legendre polynomials of order 3 satisfactorily described daily milk yield variation. Fitting third-order polynomials for the permanent environmental effect made it possible to adequately account for heterogeneous residual variance at different stages of lactation.

Analysis of Variance↗