Sexual dimorphism in livestock species selected for economically important traits.

Most breeding companies evaluate economically important traits in males and females as a single trait, assuming genetic correlation of 1 between phenotypes measured in both sexes. This assumption may not be true because genes may be differently expressed in males and females. We estimated genetic correlations between males and females for growth and efficiency traits in broiler chickens, growth traits in American Angus beef cattle, and birth weight and preweaning mortality in purebred pigs; therefore, each trait was treated differently in males and females. Variance components were estimated in single- and multiple-trait models, jointly or separated into both sexes. Furthermore, we calculated traditional and genomic evaluations, and we correlated EBV or genomic EBV (GEBV) from joint and separate evaluations for males and females. For broiler chickens, genetic correlations ranged from 0.86 to 0.94. For Angus cattle, genetic correlations ranged from 0.86 to 0.98 for early growth traits and were less, ranging from 0.68 to 0.84, for postweaning gain. In pigs, genetic correlations ranged from 0.98 to 0.99 for birth weight and from 0.71 to 0.73 for preweaning mortality. For some models in all 3 animal species, the joint and separate analyses had different heritabilities. Despite differences in heritability, the correlations within the sex-specific trait EBV and between the sex-specific and the joint trait EBV were very strong, regardless of the model or inclusion of genomic information. Males and females differed for traits measured late in the animal's life; however, strong traditional EBV correlations and also GEBV correlations indicate that considering the traits equal in males and females may have no negative impact on selection.

Crossbreed evaluations in single-step genomic best linear unbiased predictor using adjusted realized relationship matrices.

Combining purebreed and crossbreed information is beneficial for genetic evaluation of some livestock species. Genetic evaluations can use relationships based on genomic information, relying on allele frequencies that are breed specific. Single-step genomic BLUP (ssGBLUP) does not account for different allele frequencies, which could limit the genetic gain in crossbreed evaluations. In this study, we tested the performance of different breed-specific genomic relationship matrices () in ssGBLUP for crossbreed evaluations; we also tested the importance of genotyping crossbred animals. Genotypes were available for purebreeds (AA and BB) and crossbreeds (F) in simulated and real pig populations. The number of genotyped animals was, on average, 4,315 for the simulated population and 15,798 for the real population. Cross-validation was performed on 1,200 and 3,117 F animals in the simulated and real populations, respectively. Simulated scenarios were under no artificial selection, mass selection, or BLUP selection. Two genomic relationship matrices were constructed based on breed-specific allele frequencies: 1) , a genomic relationship matrix centered by breed-specific allele frequencies, and 2) , a genomic relationship matrix centered and scaled by breed-specific allele frequencies. All (the across-breed genomic relationship matrix), , and were also tuned to account for selective genotyping. Using breed-specific allele frequencies reduced the number of negative relationships between 2 purebreeds, pulling the average closer to 0, as in the pedigree-based relationship matrix. For simulated populations that included mass selection, genomic EBV (GEBV) in F, when using and , were, on average, 10% more accurate than ; however, after tuning to account for selective genotyping, provided the same accuracy as for breed-specific genomic relationship matrices. For the real population, accuracies for litter size in F were 0.62 for , , and , and tuning had no impact on accuracy, except for , which was 1 percentage point less accurate. Accuracy of GEBV for number of stillborns in F1 was 0.5 for all tested genomic relationship matrices with no changes after tuning. We observed that genotyping F increased accuracies of GEBV for the same animals by up to 39% compared with having genotypes for only AA and BB. In crossbreed evaluations, accounting for breed-specific allele frequencies promoted changes in G that were not influential enough to improve accuracy of GEBV. Therefore, the best performance of ssGBLUP for crossbreed evaluations requires genotypes for pure- and crossbreeds and no breed-specific adjustments in the realized relationship matrix.

Genetic analyses of stillbirth in relation to litter size using random regression models.

Estimates of genetic parameters for number of stillborns (NSB) in relation to litter size (LS) were obtained with random regression models (RRM). Data were collected from 4 purebred Duroc nucleus farms between 2004 and 2008. Two data sets with 6,575 litters for the first parity (P1) and 6,259 litters for the second to fifth parity (P2-5) with a total of 8,217 and 5,066 animals in the pedigree were analyzed separately. Number of stillborns was studied as a trait on sow level. Fixed effects were contemporary groups (farm-year-season) and fixed cubic regression coefficients on LS with Legendre polynomials. Models for P2-5 included the fixed effect of parity. Random effects were additive genetic effects for both data sets with permanent environmental effects included for P2-5. Random effects modeled with Legendre polynomials (RRM-L), linear splines (RRM-S), and degree 0 B-splines (RRM-BS) with regressions on LS were used. For P1, the order of polynomial, the number of knots, and the number of intervals used for respective models were quadratic, 3, and 3, respectively. For P2-5, the same parameters were linear, 2, and 2, respectively. Heterogeneous residual variances were considered in the models. For P1, estimates of heritability were 12 to 15%, 5 to 6%, and 6 to 7% in LS 5, 9, and 13, respectively. For P2-5, estimates were 15 to 17%, 4 to 5%, and 4 to 6% in LS 6, 9, and 12, respectively. For P1, average estimates of genetic correlations between LS 5 to 9, 5 to 13, and 9 to 13 were 0.53, -0.29, and 0.65, respectively. For P2-5, same estimates averaged for RRM-L and RRM-S were 0.75, -0.21, and 0.50, respectively. For RRM-BS with 2 intervals, the correlation was 0.66 between LS 5 to 7 and 8 to 13. Parameters obtained by 3 RRM revealed the nonlinear relationship between additive genetic effect of NSB and the environmental deviation of LS. The negative correlations between the 2 extreme LS might possibly indicate different genetic bases on incidence of stillbirth.

Estimation of genetic parameters of feed intake and daily gain in Durocs using data from electronic swine feeders.

Genetic parameters for daily feed intake (DFI, g/day) and daily gain (DG, g/day) were estimated using records of 1916 Duroc boars from electronic feeder stations. Management was limited and resulted in varied ranges of age and weight on test. Boars were housed in 102 pens, each equipped with one feeder, and allowed ad libitum feeding. Weekly averages of DFI and DG were used due to large variation in daily records. Six traits were defined as DFI and DG during 85-106 (period 1), 107-128 (period 2) and 129-150 days of age (period 3). A six-trait model included age as a linear and a quadratic covariate for DFI and a linear covariate for DG with a fixed effect of year-week-pen and random effects of litter, additive genetic animal and permanent environmental animal. Variance components were estimated by a Bayesian approach using Gibbs sampling algorithm. Estimates of heritability for respective periods were 18%, 12% and 10% for DFI and 21%, 11% and 10% for DG. Genetic correlations between DFI and DG in the same period were 0.70, 0.73 and 0.32 for the respective periods. DFI and DG obtained from automatic feeders can be analysed to reveal variation across testing periods by using weekly averages when many monthly averages are incomplete.

Use of serial pig body weights for genetic evaluation of daily gain.

This study examined the utility of serial weights from FIRE (Feed Intake Recording Equipment, Osborne Industries, Inc., Osborne, KS, USA) stations for an analysis of daily gain. Data included 884 132 body weight records from 3888 purebred Duroc pigs. Pigs entered the feeder station at age 77-149 days and left at age 95-184 days. A substantial number of records were abnormal, showing body weight close to 0 or up to twice the average weight. Plots of body weights for some animals indicated two parallel growth curves. Initial editing used a robust regression, which was a two-step procedure. In the first step, a quadratic growth curve was estimated assuming small or 0 weights for points far away from the curve; the process is iterative. In the second step, weights more than 1.5 SD from the estimated growth curve were treated as outliers. The retained body weight records (607,597) were averaged to create average daily weight (170,443) and then used to calculate daily gains (152,636). Additional editing steps included retaining only animals with >or=50 body weight records and SD of the daily gain

Influence of heritable social status on daily gain and feeding pattern in pigs.

Social genetic relationships among average daily gain (ADG, g) and feeding pattern as daily feed intake (DFI, g), daily feeder occupation time (DOT, min), and daily feeding rate (DFR, g/min) were examined using records of 547 Duroc boars. Single-trait animal models were fitted differently for traits, including or excluding social genetic effects, random or fixed pen effects, with covariates of pen sizes and initial age or weight. Genetic parameters for feeding pattern were estimated by restricted maximum likelihood. Six sets of parameters for ADG based on literature estimates were used due to difficulty in untangling confounded effects. Positive and negative signs of direct-social genetic covariances were interpreted as heritable cooperation and competition, respectively. Dominant and subordinate pigs were classified as pigs with higher direct and social genetic values, respectively. Correlations of estimated breeding values between ADG and DFI, DOT, and DFR were 0.46, 0.04 and 0.29 for dominant pigs. Given heritable cooperation, subordinate pigs tended to increase feed intake (r = 0.36) and eating rate (r = 0.25). Given heritable competition, subordinate pigs fail to compensate for the competition with decreased feed intake (r = -0.53). The slow eating rate (r = -0.31) was considered as a consequence of eating during less busy hour of feeding.

Genetic and environmental parameters for steer ultrasound and carcass traits.

Carcass measurements for weight, longissimus muscle area, 12-13th-rib fat thickness, and marbling score, as well as for live animal measurements of weight at the time of ultrasound, ultrasound longissimus muscle area, ultrasound 12-13th-rib fat thickness, and ultrasound-predicted percentage ether extract were taken on 2,855 Angus steers. The average ages for steers at the time of ultrasound and at slaughter were 391 and 443 d, respectively. Genetic and environmental parameters were estimated for all eight traits in a multivariate animal model. In addition to a random animal effect, the model included a fixed effect for contemporary group and a covariate for measurement age. Heritabilities for carcass weight, carcass longissimus muscle area, carcass fat thickness, carcass marbling score, ultrasound weight, ultrasound longissimus muscle area, ultrasound fat thickness, and ultrasound-predicted percentage ether extract were 0.48, 0.45, 0.35, 0.42, 0.55, 0.29, 0.39, and 0.51, respectively. Genetic correlations between carcass and ultrasound longissimus muscle area, carcass and ultrasound fat thickness, carcass marbling score and ultrasound-predicted percentage ether extract, and carcass and ultrasound weight were 0.69, 0.82, 0.90, and 0.96, respectively. Additional estimates were derived from a six-trait multivariate animal model, which included all traits except those pertaining to weight. This model included a random animal effect, a fixed effect for contemporary group, as well as covariates for both measurement age and weight. Heritabilities for carcass longissimus muscle area, carcass fat thickness, carcass marbling score, ultrasound longissimus muscle area, ultrasound fat thickness, and ultrasound-predicted percentage ether extract were 0.36, 0.39, 0.40, 0.17, 0.38, and 0.49, respectively. Genetic correlations between carcass and ultrasound longissimus muscle area, carcass and ultrasound fat thickness, and carcass marbling and ultrasound-predicted percentage ether extract were 0.58, 0.86, and 0.94, respectively. The high, positive genetic correlations between carcass and the corresponding real-time ultrasound traits indicate that real-time ultrasound imaging is an alternative to carcass data collection in carcass progeny testing programs.

Decreased growth in angus steers with a short TG-microsatellite allele in the P1 promoter of the growth hormone receptor gene.

A polymorphic TG-repeat microsatellite is located 90 base pairs upstream from a major transcription start site in the bovine growth hormone receptor gene. A shorter allele with 11 consecutive TG is common in Bos indicus cattle, whereas longer 16- to 20-TG-repeat alleles predominate in Bos taurus breeds. The purpose of this study was to compare growth and carcass traits between Angus steers that had two of the longer growth hormone receptor alleles with their half-siblings that had one short allele and one of the longer alleles. We genotyped 64 Angus sires with respect to the poly-TG microsatellite and identified six bulls that were heterozygous in that they had one short 11-TG allele and one of the longer alleles. We then grouped 125 steer progeny of these six heterozygous bulls according to their genotypes: only the longer 16- to 20-TG-repeat alleles were found in 73 steer progeny (long/long homozygotes), whereas a short 11-TG allele was paired with one of the longer alleles in 52 progeny (short/long heterozygotes). Contrasts for the long/long homozygotes vs the short/long heterozygotes were significant for weaning weight (17 +/- 4 kg; P < .001) and carcass weight (14 +/- 5 kg; P < .01). Approaching significance (P = .03) was the contrast for USDA marbling score (-.3 +/- .2). No significant differences (P > .05) were detected for contrasts in birth weight (.3 +/- .6 kg), longissimus muscle area (-.2 +/- 1 cm2), or carcass fat depth (-.01 +/- .07 cm). This polymorphism has potential for use in DNA marker-assisted selection programs.

Genetic and environmental parameters for traits derived from the Brody growth curve and their relationships with weaning weight in Angus cattle.

Direct and maternal genetic and environmental variances and covariances were estimated for weaning weight and growth and maturing traits derived from the Brody growth curve. Data consisted of field records of weight measurements of 3,044 Angus cows and 29,943 weaning weight records of both sexes. Growth traits included weights and growth rates at 365 and 550 d, respectively. Maturing traits included the age of animals when they reached 65% of mature weight, relative growth rates, and degrees of maturity at 365 and 550 d. Variance and covariance components were estimated by REML from a set of two-trait animal models including weaning weight paired with a growth or maturing trait. Weaning and cow contemporary groups were defined as fixed effects. Random effects for weaning weight included direct genetic, maternal genetic, and permanent environmental effects. For growth and maturing traits, a random direct genetic effect was included in the model. Direct heritability estimates for growth traits ranged from .46 to .52 and for maturing traits from .31 to .34. Direct genetic correlations between weaning weight and weights and growth rates at 365 and 550 d ranged from .56 to .70. Correlations of maternal weaning genetic effects with direct genetic effects on weights at 365 and 550 d were positive, but those with growth rates were negative. Between weaning weight and degrees of maturity at both 365 and 550 d, direct genetic correlation estimates were .55 and maternal genetic correlations estimates were -.05, respectively. Direct genetic correlations of weaning weight with relative growth rates and age at 65% of mature weight ranged from .04 to .06, and maternal-direct genetic correlation estimates ranged from -.50 to -.56, respectively. These estimates indicate that higher genetic capacity for milk production was related to higher body mass and degrees of maturity between 365 and 550 d of age but was negatively related to absolute and relative growth rates in that life stage.

Genetic and environmental parameters for mature weight in Angus cattle.

Genetic and environmental variances and covariances and associated genetic parameters were estimated for weaning weight, asymptotic mature weight, and repeated mature weights. Data consisted of a set of weight measurements of 3,044 Angus cows born between 1976 and 1990. Mature weight was predicted by individually fitting Brody growth curves (asymptotic weight) and by using weights repeatedly measured after 4 yr of age. Variance and covariance components for mature weight were estimated by REML from a single-trait animal model with asymptotic weight, a two-trait animal model with asymptotic and weaning weight, and a two-trait animal model with repeated weights and weaning weight. Weaning and cow contemporary groups were defined as fixed effects. Random effects for weaning weight included direct genetic, maternal genetic, and permanent environmental effects; and for mature weight, direct genetic and repeated measurements (if in the model). Heritability estimates for weaning weight were similar for both two-trait models (.53 and .59). Estimates of heritability for mature weight were .44, .52, and .53 for the single-trait model with asymptotic weight, two-trait model with asymptotic weight, and two-trait model with repeated measures weights, respectively. The estimate of the genetic correlation between mature and weaning weight was higher for the repeated measures model (.85 vs. .63). A lower heritability estimate for mature weight from the single-trait model was likely due to postweaning culling. Therefore, a genetic evaluation of mature weight from field data should include a trait recorded earlier in life that is less subjected to selective data reporting.

Comparison of four real-time ultrasound systems that predict intramuscular fat in beef cattle.

Eighty-one crossbred steers were used to evaluate four commercially available ultrasound systems that predict intramuscular fat. The software systems represented included Animal Ultrasound Services, Inc., Ithaca, NY; CPEC, Oakley, KS; Critical Vision, Inc., Atlanta, GA (CVIS); and Classic Ultrasound Equipment, Tequesta, FL. Systems were evaluated using marbling scores and percentage ether extractable fat of the longissimus muscle. Before statistical analyses, system predictions were corrected for the respective system's average deviation between the prediction and carcass measurement. The absolute difference between system prediction and percentage ether extract (EEADIFF) or marbling score (MADIFF) converted to ether extract by regression was analyzed with a model accounting for effects of system, technician within system, animal, and animal x system. Steers with USDA marbling scores less than Small00 were assigned to a low marbling class, and all others were assigned to a second class. Data were then analyzed with a subsequent model including marbling class. For EEADIFF in the first model, system, animal, and system x animal were significant (P < .001). For MADIFF, technician within system (P < .05) and all other effects (P < .001) were significant. In the second model, system x marbling class was significant (P < .05) for EEADIFF and approached significance for MADIFF (P = .17). Least squares means for EEADIFF indicated that the systems were more precise measuring animals in the low marbling class. Finally, the CPEC and CVIS systems were the most precise for predicting intramuscular fat.

Evaluation of machine, technician, and interpreter effects on ultrasonic measures of backfat and longissimus muscle area in beef cattle.

Before slaughter, 44 Hereford-sired steers were measured ultrasonically for backfat (UFAT) and longissimus muscle area (ULMA) between the 12th and 13th ribs by three technicians (TECH) using two different machines (MACH) on two consecutive days (DAY). Each TECH interpreted (INT) his own images in addition to other TECH images. The absolute values of the difference between the 2 DAY's ultrasound measurements for ULMA (magnitude of LMAR) and UFAT (magnitude of FATR) were analyzed with a model including fixed effects of MACH and TECH with a random effect of steer and all interactions. For both magnitude of LMAR and magnitude of FATR, MACH x TECH was significant (P < .10). Correlations between the 2 DAY's measurements ranged from .36 to .90 and .69 to .90 for ULMA and UFAT, respectively. Simple statistics to quickly evaluate TECH and MACH were developed. Root mean squared errors (RMSE) and error standard deviations (ESD) between repeated measurements ranged from 3.89 to 11.32 and 3.93 to 11.34 cm2 for ULMA and .12 to .20 cm and .12 to .20 cm for UFAT, respectively. For accuracy, the absolute values of the difference between the ultrasound and carcass measurement for fat (magnitude of FATD) and longissimus muscle area (magnitude of LMAD) were analyzed with a model accounting for fixed effects of DAY, TECH, and MACH and a random effect of steer with all higher-order interactions. For magnitude of LMAD, TECH x MACH was a significant source of variation (P < .001). Also, a similar model was fit that included the fixed effects of TECH, MACH, and INT and a random effect of steer with all interactions. The MACH x INT interaction was found to be significant for magnitude of LMAD (P < .05). From this research, TECH and MACH differences do exist. Ultrasound is a valid means of measuring carcass traits in live steers if appropriate personnel and equipment are selected.

Comparison of live and carcass equations predicting percentage of cutability, retail product weight, and trimmable fat in beef cattle.

Forty-four Hereford-sired steers were measured ultrasonically for backfat and longissimus muscle area between the 12th and 13th ribs before slaughter and visually appraised for fatness, overall muscling, and frame. Carcass measurements associated with USDA yield and quality grades were measured and recorded. Carcasses were fabricated into closely trimmed, boneless subprimals at 1.27- and .32-cm fat trim levels. Cutability percentage (percentage of retail cuts from the cold carcass weight) and kilograms of retail product were defined three ways. The first definition included only retail cuts from the round, loin, rib, and chuck. The second included the above plus adjusted lean trim from the round, loin, rib, and chuck, and, finally, total retail product from the entire carcass. Kilograms (TOTFAT) and percentage (PERFAT) of trimmable fat were also calculated. Stepwise regression procedures were used for live and carcass trait model development predicting cutability percentages, kilograms of retail product, and trimmable fat. Fat measurements accounted for the largest portion of variation in cutability percentage and PERFAT. Weight measurements accounted for the major sources of variation in predicting kilograms of retail product and TOTFAT. Final models using live animal traits ranked the steers equally as well for cutability percentages as the original USDA cutability equation and stepwise, developed carcass equations (P > .10). Final models using live animal or carcass equations ranked the animals equally for kilograms of retail product yield (P > .10).