Estimates of heritabilities and correlations of traits associated with pelvic area in beef cattle

Pelvic measurements, cow weights and cow ages were obtained on 703 Angus- and Hereford-sired cows from five Louisiana Agricultural Experiment Station herds. Cows were either purebred or crossbred, ranging in age from 1 to 14 yr, and sired by 52 Angus and 63 Hereford bulls. All pelvic measurements were obtained via the rectum by the same technician. Paternal half-sib heritability estimates and genetic (rG) and phenotypic (rP) correlations were computed for pelvic height (PH), pelvic width (PW), pelvic area (PA-I; the product of PH X PW), the ratio of PH to PW and cow weight (CW). Pelvic area was also calculated as an ellipse using the formula PA-II = pi (PH/2)(PW/2). Mean PA-I was 298.5 cm2 while PA-II averaged 234.4 cm2. The pooled heritability estimate for PA-I was .68 +/- .34, indicating that pelvic area is a highly heritable trait and should respond to selection. The estimate for PA-II was similar (.66 +/- .34). The heritability of PW was higher than for PH or PA-I. The heritability of CW was .57 +/- .34 and CW was positively correlated (rG2 = .47 and rP = .40) with PA-I. Direct selection for PA-I was estimated to yield a response of 12.2 cm2 in one generation with a correlated response for CW of 12.5 kg. If change in CW was held at zero using a restricted selection index, about 90% as much increase in PA-I was estimated compared with ignoring CW in the index. Therefore, selection for increased pelvic area can be accomplished without causing large increases in cow size. This should aid in reducing calving difficulty.     

Estimates of covariances between reproduction and growth in Australian beef cattle

Estimates of covariance components between scrotal circumference, serving capacity, days to calving, and yearling and final weight were obtained for Hereford, Angus, and Zebu cross cattle in temperate and tropical Australia. Analyses were carried out by REML employing a derivative-free algorithm and fitting bivariate animal models. Aspects of modeling and computational requirements related to the use of this method are discussed. Estimates of heritabilities agreed closely with those from univariate analyses, being low for female reproductive performance and moderate to high for male reproduction and growth. Estimates of genetic correlation between male and female fertility traits were low but favorable, being -.25, -.28, and -.41 between scrotal circumference and days to calving for Herefords, Angus, and Zebu crosses, respectively. Genetic correlations between male reproductive traits and weights ranged from .24 to .52 for the temperate breeds and were higher (.65 to .69) for Zebu crosses. Phenotypic correlations between scrotal circumference and weights were similar for all breeds, ranging from .32 to .47, whereas serving capacity and weights were phenotypically unrelated. Estimates of correlations between days to calving and weights were less consistent. Phenotypically, there was little association between the two traits. Genetic correlations for Zebu crosses were negative and low to moderate (-.36 to -.66) and estimates for Angus were close to zero.     

Direct and maternal variances and covariances and maternal phenotypic effects on preweaning growth of beef cattle

Birth weights (BW) and weaning weights (WW) of 4,423 non-creep-fed Hereford calves were used to estimate direct and maternal sources of variation and maternal phenotypic effects (fm). Seventeen different (co)variances among relatives were estimated through Henderson's Method III and restricted estimated maximum likelihood procedures. Direct and maternal (co)variances and fm were evaluated by multiple regression procedures. Estimates of h2 for BW and WW were .28 and .28 respectively, by the paternal half-sib procedure and .45 and .88, respectively, based on full-sibs. Repeatability estimates were .21 for BW and .30 for WW. Heritabilities based on regression of offspring on dam and offspring on sire were .45 and .21 for BW and .28 and .06 for WW, respectively. Negative correlations were found between solutions for additive genetic direct and additive maternal effects (rG). Estimates of rG ranged from -.86 to -1.05 for BW and from -.57 to -.79 for WW. Estimates of heritability for direct effects (h2o), for maternal effects (h2m) and for total additive genetic effects (h2T) were .16 to .27, .18 to .63 and -.02 to .05 for BW and .26 to .32, .27 to .67 and .10 to .20 for WW. Dominance affected both direct and maternal effects for BW and WW. Values of -.15 (BW) and -.25 (WW) were found for fm (path coefficient between the maternal phenotypes of dam and daughter). These results indicated that selection response would be decreased due to the negative genetic correlation between direct and maternal effects.     

Alternative contemporary group structure to maximize the use of field records: Application to growth traits of composite beef cattle

The objective of the present study was to define an alternative contemporary group structure that would permit an increase in the number of records to be included in genetic evaluations with minimal bias. For this purpose, using different criteria as goodness of fit measured by percentages of squared bias, correlations between predicted and observed records, residual variances, genetic trends, rank correlations, and a practical situation of genetic evaluation, an animal model with standard contemporary group structure was compared with a model with alternative contemporary group structure including weaning management group (WMG) as an additional uncorrelated random effect for postweaning growth traits of composite beef cattle. The present study showed that the inclusion of WMG as a random effect in the statistical model for postweaning growth traits has only a small impact on animal ranking and a small or no impact on the estimation of genetic parameters and genetic trends. On the other hand, this approach leads to an important increase in the number of records available for the prediction of genetic merit with minimal or even no bias. Therefore, the model proposed here can be recommended to overcome problems related to loss of data of model with standard contemporary group structure.     

An evaluation of bias in estimated breeding values for weaning weight in Angus beef cattle field records. I. Estimates of within herd genetic trend

Genetic trends for weaning weight were evaluated in 15 purebred herds in the United States participating in the Angus Herd Improvement. Records production testing program. Regression techniques were used for separate estimates of sire and dam contributions that were summed to estimate total herd trend. Sire contributions, calculated as the pooled within sire regression of weaning weight ratio on year of calf birth, ranged from .01 +/- .23 to 1.30 +/- .24 across the herds and average .51 ratio units/yr. Dam contributions, estimated as the pooled within dam regression of offspring weaning weight ratio, deviated from the contemporary paternal half-sib average ratio, on year of calf birth, ranged from .06 +/- .06 to .68 +/- .11 and averaged .34 ratio units/yr. A positive trend in direct effects was associated with a possible negative trend in maternal effects. The annual trend within herds ranged from .21 to 1.50 ratio units and averaged .85 units over all herds, representing 1.8 kg annual genetic gain in weaning weight.     

Symmetric differences squared and analysis of variance procedures for estimating genetic and environmental variances and covariances for beef cattle weaning weight: II. Estimates from a data set

Analysis of variance (ANOVA) and symmetric differences squared (SDS) methods were used to estimate additive genetic and environmental variances and covariances associated with weaning weight. The two methods were applied to 503 beef records collected over 19 yr from a relatively unselected university Angus herd. The SDS methodology was used with four models. The first model included direct (g) and maternal (gm) additive genetic effects, the genetic covariance between direct and maternal additive genetic effects (sigma ggm), permanent maternal environmental effects (m) and temporary environmental effects (e). The second model also allowed for a nonzero environmental covariance (sigma mem) between dam and offspring weaning weights. Models 3 and 4 were models 1 and 2, respectively, expanded to include a grandmaternal genetic effect (gn) and covariances sigma ggn and sigma gmgn. Two ANOVA solution sets for the parameters of model 4 were based on sire, dam, maternal grandsire, maternal grandam and phenotypic variances and offspring-dam (covOD), offspring-sire (covOS), offspring-grandam (covOGD) and offspring-maternal half-aunt or uncle (covOMH) covariances. Four ANOVA solution sets for the parameters of model 2 were based on sire, dam, within dam and maternal grandsire variances, covOD and either covOS or covOGD. Symmetric differences squared estimates of h2g and h2gm averaged .30 and .16, respectively. All SDS estimates of rho ggm (correlation between direct and maternal genetic effects) were less than -1. Estimates of sigma mem were positive. Both SDS estimates and one of the two ANOVA estimates of the grandmaternal variance were negative. The ANOVA model 4 estimates of h2g were .33. The estimates of h2gm were .44 and .39, while the estimates for rho ggm were -.88 and -.80. Both estimates of sigma mem were positive. The four ANOVA model 2 estimates of h2g and h2gm averaged .33 and .48, respectively. Three of the four estimates of rho ggm were less than -.97; the fourth was .35. Three of the four estimates of sigma mem were positive. Expectations show the extent to which SDS and ANOVA estimators were biased by nonzero grandmaternal components that were not accounted for. The extent to which dominance components bias the ANOVA estimators also is shown. Nonzero grandmaternal effects need to be taken into account in either SDS or ANOVA solution sets, or important biases occur with most of the estimators. More numerous, and generally more severe, biases occur with ANOVA estimators than with SDS estimators in solution sets that do not account for grandmaternal effects.     

Comparison of methods for handling censored records in beef fertility data: field data

The purpose of this study was to compare methods for handling censored days to calving records in beef cattle data, and verify results of an earlier simulation study. Data were records from natural service matings of 33,176 first-calf females in Australian Angus herds. Three methods for handling censored records were evaluated. Censored records (records on noncalving females) were assigned penalty values on a within-contemporary group basis under the first method (DCPEN). Under the second method (DCSIM), censored records were drawn from their respective predictive truncated normal distributions, whereas censored records were deleted under the third method (DCMISS). Data were analyzed using a mixed linear model that included the fixed effects of contemporary group and sex of calf, linear and quadratic covariates for age at mating, and random effects of animal and residual error. A Bayesian approach via Gibbs sampling was used to estimate variance components and predict breeding values. Posterior means (PM) (SD) of additive genetic variance for DCPEN, DCSIM, and DCMISS were 22.6d2 (4.2d2), 26.1d2 (3.6d2), and 13.5d2 (2.9d2), respectively. The PM (SD) of residual variance for DCPEN, DCSIM, and DCMISS were 431.4d2 (5.0d2), 371.4d2 (4.5d2), and 262.2d2 (3.4d2), respectively. The PM (SD) of heritability for DCPEN, DCSIM, and DCMISS were 0.05 (0.01), 0.07 (0.01), and 0.05 (0.01), respectively. Simulating trait records for noncalving females resulted in similar heritability to the penalty method but lower residual variance. Pearson correlations between posterior means of animal effects for sires with more than 20 daughters with records were 0.99 between DCPEN and DCSIM, 0.77 between DCPEN and DCMISS, and 0.81 between DCSIM and DCMISS. Of the 424 sires ranked in the top 10% and bottom 10% of sires in DCPEN, 91% and 89%, respectively, were also ranked in the top 10% and bottom 10% in DCSIM. Little difference was observed between DCPEN and DCSIM for correlations between posterior means of animal effects for sires, indicating that no major reranking of sires would be expected. This finding suggests little difference between these two censored data handling techniques for use in genetic evaluation of days to calving.     

Estimates of genetic and phenotypic covariance functions for postweaning growth and mature weight of beef cows

Annual weights of cows from 19 to 119 months of age in two herds were analysed fitting a random regression model, regressing on orthogonal polynomials of age in months. Estimates of covariances between random regression coefficients were obtained by restricted maximum likelihood, and the resulting estimates of covariance functions were used to construct covariance matrices for all ages in the data. Analyses were carried out fitting regression coefficients corresponding to overall animal effects only and fitting regressions for animals' additive genetic and permanent, environmental effects. Different definitions of fixed effects subclasses were examined. Models were compared using likelihood ratio tests and estimated standard deviations for the ages in the data. Cubic regressions were sufficient to model both population trajectories and individual growth curves. Random regression coefficients were highly correlated, so that estimation forcing their covariance matrices to have reduced rank (2 or 3) did not reduce likelihoods significantly, allowing parsimonious modelling. Results showed that records were clearly not repeated measurements of a single trait with constant variances. As cows grew up to about 5 years of age, variances. As cows grew up to about 5 years of age, variances increased. Estimates of genetic correlations between 3-year-old and older cows were close to unity in one herd but more erratic in the other. For both herds, genetic correlations between weights on 2-year-old cows and older animals were clearly less than unity.     

An evaluation of bias in estimated breeding values for weaning weight in Angus beef cattle field records. III. Estimates of bias due to nonrandom mating

Field records from 15 herds involved in the Angus Herd Improvement Records program of the American Angus Association indicated that positive assortative mating for weaning weight estimated breeding value (EBV) was being practiced. For each dam, a separate EBV was calculated from information on each progeny with all other progeny data deleted. Individual, paternal and maternal half-sib data available in all years were included in each calculation and thus, were held constant. Bias in cow EBV caused by nonrandom mating was measured as the pooled within dam regression of dam EBV on progeny's sire EBV deviated from the contemporary site average EBV. Across herds, the average estimated bias associated with positive assortative mating ranged from .05 to .08 ratio units.     

An evaluation of bias in estimated breeding values for weaning weight in Angus beef cattle field records. II. Estimates of bias due to genetic trend

Field records (53,989) from the American Angus Association were used to evaluate the impact of bias associated with genetic trend in estimated breeding values for weaning weight. Annual estimates of breeding values were calculated using the reported weaning weight ratios and ratios adjusted for estimated genetic trend. Genetic gains were assumed to be consistently linear. Bias was estimated as the difference between the two estimates, and herd averages across years for dam's bias ranged from .38 to 3.86 ratio units. The bias was a function of the magnitude of the estimated trend and the generation interval. The impact of this bias was small in young cows, but increased rapidly after diet fourth or fifth calves. When annual genetic trend was less than .75 ratio units, the loss in selection response (based upon selecting the top 10 and 50% of males and females, respectively) did not exceed 2.5%. In herds with trends between .75 and 1.1 units/yr, the loss was 6 to 8%. In the five herds where estimated trend exceeded 1.1 units/yr, the loss ranged from 10.8 to 25.2%).     

Estimates of beef carcass intermuscular fat.

Three experienced persons evaluated 158 carcasses 24 h postmortem for USDA yield grade (YG) and quality grade factors, nine subcutaneous (SC) fat indicators, and four intermuscular (IM) fat indicators. Forty sides (YG 1.1 to 3.8) were selected for determination of chemical composition, two measures of cutability, and total IM fat from the round, loin, rib, and chuck. The IM fat estimates at the 12th rib, rib-plate juncture, and 5th rib were correlated with percentage of chemical fat (r = -.72, -.70, and -.55, respectively). Simultaneous consideration of YG factors accounted for 61% of the variation in chemical fat. Substituting the IM fat estimate at the 12th rib for adjusted fat thickness (AFT) in the equation explained 60% of the variation in percentage of chemical fat. An equation containing two IM fat estimates, marbling score and longissimus muscle area explained 68% of the variation in chemical fat. Simultaneous consideration of the YG factors accounted for 59% of the variation in boneless, closely trimmed (6 mm SC fat and no IM fat) retail cuts from the round, loin, rib, and chuck. Substituting the IM fat estimate at the 12th rib for AFT in the equation accounted for 65% of the variation. These data from a fairly uniform set of steer carcasses show that percentage of chemical fat and cutability can be reliably predicted from IM fat estimates and other traits that can be visually estimated on hot-fat trimmed carcasses.     

Studies on multiple trait and random regression models for genetic evaluation of beef cattle for growth

A simulation study examined issues important for genetic evaluation of growth in beef cattle by random regression models with cubic Legendre polynomials (RRML) and linear splines with three knots (RRMS) compared with multiple-trait models (MTM). Parameters for RRML were obtained by conversion from covariance functions. Parameters for MTM and RRMS were extracted from RRML at 1, 205, and 365 d; parameters for RRMS were the same as MTM for all effects except the permanent environment and the residual. Four data sets were generated assuming RRML included records at 1, 205, and 365 d; at 1, 160 to 250, and 320 to 410 d; at 1, 100, 205, 300, and 365 d; and at 1, 55 to 145, 160 to 250, 275 to 325, and 320 to 410 d. Accuracies were computed as correlations between the true (simulated) and predicted breeding values. With the first data set, excellent agreement in accuracy was obtained for all models. With the second data set, the accuracy of MTM dropped by up to 1.5% compared with the first data set, but accuracy was unchanged for both RRML and RRMS. With the third (fourth) data set, accuracies of RRML were up to 2.4% (2.5%) higher than with the first (second) data set. Small differences in accuracy between RRML and RRMS were found with the third and fourth data sets, which were traced to inflated correlations especially between 1 and 205 d in RRMS; inflation could be decreased by adding one extra knot at 100 d to RRMS. Diagonalization of random coefficients was crucial for RRML but not for RRMS, resulting in approximately six (two) times faster convergence with RRML (RRMS). Reduction of dimensionality in RRML associated with small eigenvalues caused a less accurate evaluation for birth weight. Genetic evaluation of growth by RRM requires careful implementation. The RRMS is simpler to implement than the RRML.     

Genomic imprinting variances of beef carcass traits and physiochemical characteristics in Japanese Black cattle

The objective of this study was to estimate variance components related to imprinting for carcass traits and physiochemical characteristics in Japanese Black cattle. The carcass records obtained from 4,220 Japanese Black feedlot cattle included carcass weight (CW), rib eye area (REA), rib thickness, subcutaneous fat thickness, and beef marbling score (BMS), and the physiochemical characteristics were fat, moisture, glycogen per proportion of moisture content, oleic acid, and monounsaturated fatty acids (MUFA). To detect gametic effects, an imprinting model was fitted. High additive heritabilities were estimated for all traits (from 0.516 for glycogen to 0.853 for fat) and were reduced in Mendelian heritability. The range of the differences was from 0.002 (CW) to 0.331 (fat and moisture), and the reductions were due to their imprinting variances. The ratio of the imprinting variance to the total additive genetic variance for REA (0.374), BMS (0.291), fat (0.387), moisture (0.388), and MUFA (0.337) were large (p < 0.05). These imprinting variances were due to the maternal contribution and suggested the existence of maternally expressed genomic imprinting effects on the traits in Japanese Black cattle. Therefore, maternal gametic effects should be considered in breeding programs for Japanese Black cattle.     

Search for quantitative trait loci affecting growth and carcass traits in a cross population of beef and dairy cattle

A genome scan to detect QTL influencing growth and carcass-related traits was conducted in a Charolais x Holstein crossbred cattle population. Phenotypic measurements related to growth and carcass traits were made on the 235 second-generation crossbred males of this herd (F2 and reciprocal backcrosses), which were born in 4 consecutive annual cohorts. Traits measured in vivo were related to birth dimensions, growth rates, and ultrasound measurements of fat and muscle depth. The animals were slaughtered near a target BW of 550 kg, and a wide range of postmortem traits were measured: visual assessment of carcass conformation and carcass fatness, estimated subcutaneous fat percentage, weights of kidney knob and channel fat, and weights of carcass components after commercial and full-tissue dissections. The whole population, including grandparents, parents, and the crossbred bulls, was genotyped initially for 139 genome-wide microsatellite markers. Twenty-six additional markers were subsequently analyzed to increase marker density on some of the chromosomes where QTL had been initially identified. The linear regression analyses based on the 165 markers revealed a total of 51 significant QTL at the suggestive level, 21 of which were highly significant (F-value >or=9; based on the genome-wide thresholds obtained in the initial scan). A large proportion of the highly significant associations were found on chromosomes 5 and 6. The most highly significant QTL was localized between markers DIK1054 and DIK082 on chromosome 6 and explained about 20% of the phenotypic variance for the total bone proportion estimated after the commercial dissection. In the adjacent marker interval on this chromosome, 2 other highly significant QTL were found that explain about 30% of the phenotypic variance for birth dimension traits (BW and body length at birth). On chromosome 5, the most significant association influenced the lean:bone ratio at the forerib joint and was flanked by markers DIK4782 and BR2936. Other highly significant associations were detected on chromosomes 10 (estimated subcutaneous fat percentage), 11 (total saleable meat proportion), 16 (prehousing growth rate), and 22 (bone proportion at the leg joint). These results provide a useful starting point for the identification of the genes associated with traits of direct interest to the beef industry, using fine mapping or positional candidate gene approaches.     

Estimation of genetic parameters for beef traits from field data

Data of the progeny testing for meat production of the Swiss A.I.-Federation were used in order to estimate genetic parameters. A heritability of carcass gain between 0.21 and 0.25 was found. Very small heritabilities of carcass grades were found (<0.1). Positive genetic correlations between carcass gain and carcass grades seem to exist.The average coefficient of relationship among the sires ($\text{R}$) can be considered in the estimation of the heritability by dividing the variance component of sires (σ_s²) by 1 — R. In this analysis the results were hardly influenced at all, due to the very small average relationship of only 1%.     

Estimates of genetic parameters for live animal ultrasound, actual carcass data, and growth traits in beef cattle

Growth and carcass measurements were made on 2,411 Hereford steers slaughtered at a constant weight from a designed reference sire program involving 137 sires. A second data set consisted of ultrasound measures of backfat (USFAT) and longissimus muscle area (USREA) from 3,482 yearling Hereford cattle representing 441 sires. Restricted maximum likelihood procedures were used to estimate genetic parameters among carcass traits and live animal weight traits from these two separate data sets. Heritability estimates for the slaughter weight constant steer carcass backfat (FAT) and longissimus muscle area (REA) were .49 and .46, respectively. In addition, FAT had a negative genetic correlation with REA (-.37), weaning weight (-.28), and yearling weight (-.13) but positive with marbling (.19) and carcass weight (.36). Marbling was moderately heritable (.35) and highly correlated with total postweaning average daily gain (.54) and feedlot relative growth rate (.62). Heritability estimates for weight constant USFAT and USREA were .26 and .25, respectively. The genetic correlation between weight constant USFAT and USREA was positive (.39), indicating that in these young animals USFAT does not seem to be an indication of maturity. Mean USFAT measures and variability were small (.48 +/- .17 cm, n = 3,482). Results indicate that carcass fat on slaughter steers and ultrasound measures of backfat on young breeding animals may have different relationships with growth and muscling. These relationships need to be explored before wide scale selection based on ultrasound is implemented.     

Genetic and phenotypic parameters estimated from Nebraska specific-pathogen-free swine field records

Records collected during 1971 through 1979 from 101,606 hogs raised in 18 Nebraska Specific Pathogen Free herds were analyzed. Traits considered were backfat at 100 kg (BF), weight at 140 d of age (WT) and, in some analyses, number of live pigs/litter at birth (NBA). The phenotypic correlation of BF and WT, averaged across herds, was -.07. The correlations between BF and NBA and between WT and NBA were .04 and -.05, respectively. Average phenotypic standard deviations for BF, WT and NBA were 2.6 mm, 8.8 kg and 2.0 pigs. Estimates of the heritability of BF and WT were lower than most estimates reported from university research herds. Within breed, herd and sex estimates of heritability ranged from -.22 and .51 (unweighted mean = .16 +/- .025) for BF and ranged from -.28 to .49 (mean = .16 +/- .016) for WT. Estimates of the genetic correlation between BF and WT were extremely variable (mean = -.62 +/- 14.3, range = -9.42 to 1.30) among breed-herd-sex subclasses.     

Interval mapping of growth quantitative trait loci in Japanese Black beef cattle using microsatellite DNA markers and half-sib regression analysis

A confirmatory scan for the regions of bovine chromosome 1 segregating the quantitative trait loci (QTL) influencing birthweight, weaning weight, yearling weight, and preweaning and postweaning average daily gains was performed by genotyping half‐sib progeny of four Japanese Black sires using microsatellite DNA markers. Data were analyzed by generating an F‐statistic every 1 cM on a linkage map by the regression of phenotype on the probabilities of inheriting an allele from the sire after adjusting for the fixed effects of sire, sex, parity and season of birth as well as age as a covariate. Permutation tests at chromosome‐wide significance thresholds were carried out over 10 000 iterations. A significant QTL for birthweight at 114 cM was detected in the sire 2 family. This identification of a birthweight QTL in Japanese Black cattle may be useful for the implementation of marker‐assisted selection.     

A field study of culling and mortality in beef cows from western Canada

The objectives were to describe the pattern of losses through culling, sales of breeding stock, mortality, and disappearance, and to characterize the causes of mortality of cows and replacement heifers of breeding age from Western Canadian beef herds. Cows and replacement heifers from 203 herds were observed for a 1-year period starting June 1, 2001. Veterinarians examined dead animals on-farm using a standard postmortem protocol. The incidence of culling in cows and replacements heifers was 14.3 per 100 cow-years at risk, and the frequencies of sales for breeding stock, mortality, and cows reported missing per cow-years at risk were 4.0, 1.1, and 0.4, respectively. During the study, 355 animals died or were euthanized, 209 were examined postmortem, and the requested tissues were submitted for histopathologic examination from 184. A cause of death was determined for 70% (128/184) of the cows with complete gross postmortem and histopathologic examinations. Hardware disease (traumatic reticuloperitonitis), malignant neoplasia (cancer), calving-associated injury, rumen tympany (bloat), myopathy, and pneumonia accounted for 56% (72/128) of the animals where a cause of death was determined. Twenty-three other causes of death accounted for the remaining 44% (56/128). Factors relating to cow nutrition accounted for 25% of the deaths, emphasizing the importance of feeding management as a determinant of cow health in western Canada.     

Scaling to account for heterogeneous variances in a Bayesian analysis of broiler quantitative trait loci

A Bayesian method for QTL analysis that is capable of accounting for heterogeneity of variance between sexes, is introduced. The Bayesian method uses a parsimonious model that includes scaling parameters for polygenic and QTL allelic effects per sex. Furthermore, the method employs a reduced animal model to increase computational efficiency. Markov Chain Monte Carlo techniques were applied to obtain estimates of genetic parameters. In comparison with previous regression analyses, the Bayesian method 1) estimates dispersion parameters and polygenic effects, 2) uses individual observations instead of offspring averages, and 3) estimates fixed effect levels and covariates and heterogeneity of variance between sexes simultaneously with other parameters, taking uncertainties fully into account. Broiler data collected in a feed efficiency and a carcass experiment were used to illustrate QTL analysis based on the Bayesian method. The experiments were conducted in a population consisting of 10 full-sib families of a cross between two broiler lines. Microsatellite genotypes were determined on generation 1 and 2 animals and phenotypes were collected on third-generation offspring from mating members from different families. Chromosomal regions that seemed to contain a QTL in previous regression analyses and showed heterogeneity of variance were chosen. Traits analyzed in the feed efficiency experiment were BW at 48 d and growth, feed intake, and feed intake corrected for BW between 23 and 48 d. In the carcass experiment, carcass percentage was analyzed. The Bayesian method was successful in finding QTL in all regions previously detected.