BIBI: Bayesian inference of breed composition.

The aim of this paper was to develop statistical models to estimate individual breed composition based on the previously proposed idea of regressing discrete random variables corresponding to counts of reference alleles of biallelic molecular markers located across the genome on the allele frequencies of each marker in the pure (base) breeds. Some of the existing regression-based methods do not guarantee that estimators of breed composition will lie in the appropriate parameter space, and none of them account for uncertainty about allele frequencies in the pure breeds, that is, uncertainty about the design matrix. To overcome these limitations, we proposed two Bayesian generalized linear models. For each individual, both models assume that the counts of the reference allele at each marker locus follow independent Binomial distributions, use the logit link and pose a Dirichlet prior over the vector of regression coefficients (which corresponds to breed composition). This prior guarantees that point estimators of breed composition such as the posterior mean pertain to the appropriate space. The difference between these models is that model termed BIBI does not account for uncertainty about the design matrix, while model termed BIBI2 accounts for such an uncertainty by assigning independent Beta priors to the entries of this matrix. We implemented these models in a data set from the University of Florida's multibreed Angus-Brahman population. Posterior means were used as point estimators of breed composition. In addition, the ordinary least squares estimator proposed by Kuehn et al. () (OLSK) was also computed. BIBI and BIBI2 estimated breed composition more accurately than OLSK, and BIBI2 had a 7.69% improvement in accuracy as compared to BIBI.

Gaussian covariance graph models accounting for correlated marker effects in genome-wide prediction.

Several statistical models used in genome-wide prediction assume uncorrelated marker allele substitution effects, but it is known that these effects may be correlated. In statistics, graphical models have been identified as a useful tool for covariance estimation in high-dimensional problems and it is an area that has recently experienced a great expansion. In Gaussian covariance graph models (GCovGM), the joint distribution of a set of random variables is assumed to be Gaussian and the pattern of zeros of the covariance matrix is encoded in terms of an undirected graph G. In this study, methods adapting the theory of GCovGM to genome-wide prediction were developed (Bayes GCov, Bayes GCov-KR and Bayes GCov-H). In simulated data sets, improvements in correlation between phenotypes and predicted breeding values and accuracies of predicted breeding values were found. Our models account for correlation of marker effects and permit to accommodate general structures as opposed to models proposed in previous studies, which consider spatial correlation only. In addition, they allow incorporation of biological information in the prediction process through its use when constructing graph G, and their extension to the multi-allelic loci case is straightforward.

Stochastic dynamic simulation modeling including multitrait genetics to estimate genetic, technical, and financial consequences of dairy farm reproduction and selection strategies.

The objective of this study was to develop a daily stochastic dynamic dairy simulation model that included multitrait genetics and to evaluate the effects of reduced genetic models and various reproduction and selection strategies on the genetic, technical, and financial performance of a dairy herd. The 12 correlated genetic traits included in the 2014 lifetime net merit (NM$) index were modeled for each animal. For each animal, a true breeding value (TBV) for each trait was calculated as the average of the sire's and dam's TBV, plus a fraction of the inbreeding and Mendelian sampling variability. Similarly, an environmental component for each trait was calculated and was partitioned into a permanent and a daily (temporary) effect. The combined TBV and environmental effects were converted into the phenotypic performance of each animal. Hence, genetics and phenotypic performances were associated. Estimated breeding values (EBV) were also simulated. Genetic trends for each trait for the service sire were based on expected trends in US Holsteins. Surplus heifers were culled based on various ranking criteria to maintain a herd size of 1,000 milking cows. In the first 8 scenarios, culling of surplus heifers was either random or based on the EBV of NM$. Four different genetic models, depending on the presence or absence of genetic trends or genetic and environmental correlations, or both, were evaluated to measure the effect of excluding multitrait genetics on animal performance. In the last 5 scenarios, the full genetic model was used and culling of surplus heifers was either random or based on the EBV of NM$ or the EBV of milk. Sexed semen use and reliability of the EBV were also varied. Each scenario was simulated for 15yr into the future. Results showed that genetic models without all 12 genetic trends and genetic and environmental correlations provided biased estimates of the genetic, technical, and financial performance of the dairy herd. Average TBV of NM$ of all cows in the herd was $263 greater in yr 15 in a scenario that combined sexed semen use in heifers and culling of surplus heifers with the lowest EBV of NM$, compared with a scenario that used only conventional semen and surplus heifers were culled randomly. The average TBV of daughter pregnancy rate of all cows in the herd was 1.25 percentage points greater in yr 15 in a scenario that combined using sexed semen in heifers as well as culling of surplus heifers ranked by EBV of NM$, compared with a scenario using conventional semen only as well as culling surplus heifers ranked by EBV of milk. In conclusion, the multitrait genetics model resulted in improved estimates of genetic, technical, and financial effects and appears useful to evaluate consequences of various reproduction and selection strategies within a dairy farm.

Single nucleotide polymorphisms associated with carcass traits in a population of Brahman and Brahman-influenced steers.

Brahman cattle are important in tropical regions due to their ability to tolerate excessive heat and parasites. However, Brahman cattle exhibit lower carcass quality characteristics when compared to Bos taurus breeds. The objective of this study was to evaluate potential associations between single nucleotide polymorphisms (SNPs) in six candidate genes for carcass quality and composition traits in a population of Brahman and Brahman-influenced steers. Steers were evaluated through the American Brahman Breeders Association carcass evaluation project in Gonzales, Texas. Carcass traits measured included hot carcass weight, ribeye area, marbling score, yield grade, quality grade, dressing percent, and Warner-Bratzler shear force score. Six previously described candidate genes were chosen for SNP analysis based on their previous association with growth and carcass traits. Candidate genes utilized in the current study included calpastatin (CAST), calpain (CAPN3), thyroglobulin (TG), growth hormone, insulin growth factor 1, and adiponectin. Six unique SNPs from three candidate genes (TG, CAST, and CAPN3) were significantly associated (P < 0.001) with carcass quality traits (marbling score and quality grade). A genotypic effect was observed for all significant SNPs, with differing levels of performance observed for animals inheriting different genotypes. Although multiple SNPs in the current study were significantly (P < 0.001) associated with growth and carcass traits, they should be validated in larger populations prior to implementation in selection strategies.

Effect of Brahman genetic influence on collagen enzymatic crosslinking gene expression and meat tenderness.

The objective of the study was to examine the effect of Brahman genetics on collagen enzymatic crosslinking gene expression and meat tenderness. Steers were randomly selected to represent a high percentage Brahman genetics (n = 13), Half-Blood genetics (n = 13), Brangus genetics (n = 13), and a high percentage Angus genetics (n = 13). Muscle samples from the Longissimus lumborum muscle were collected at weaning and harvest and reverse transcription quantitative PCR (qPCR) analysis was conducted to measure the mRNA expression of lysyl oxidase (LOX), bone morphogenetic protein 1 (BMP1), and cystatin C (CYS). Steaks from subject animals were collected at harvest, aged for 14 d and subjected to collagen analysis, Warner-Bratzler Shear Force (WBS) and trained sensory panel analysis (tenderness, juiciness, and connective tissue). Data indicated that Half-Blood and Brahman steers had greater (P<0.05) WBS values and tended to receive decreased (P < 0.06) panel tenderness scores than Angus and Brangus steers. Panelists tended to detect more connective tissue in Brahman and Half-Blood steaks when compared to Angus and Brangus steaks (P < 0.07). Crosslinking gene expression data revealed that at weaning Half-Blood steers had more (P < 0.05) mRNA expression of CYS and LOX than Angus and Brangus steers. At weaning and harvest, all genetic groups had similar mRNA expression of BMP1 (P > 0.10). At harvest, Brangus and Angus steers had greater LOX mRNA expression than Brahman cattle (P < 0.05). Pearson's correlation coefficients indicated that only weaning CYS mRNA expression was correlated to WBS, panel tenderness and connective tissue scores (P < 0.05). Expression of LOX was only correlated to these measures at harvest, and BMP1 was correlated to these traits at both time periods (P < 0.05). These results indicate that collagen crosslinking enzyme activity, as indicated by mRNA levels, early in an animal's life may account for some of the variation seen in steak tenderness due to Brahman genetic influence.

Somatic Cells Count and Its Genetic Association with Milk Yield in Dairy Cattle Raised under Thai Tropical Environmental Conditions.

Somatic cells count (SCC), milk yield (MY) and pedigree information of 2,791 first lactation cows that calved between 1990 and 2010 on 259 Thai farms were used to estimate genetic parameters and trends for SCC and its genetic association with MY. The SCC were log-transformed (lnSCC) to make them normally distributed. An average information-restricted maximum likelihood procedure was used to estimate variance components. A bivariate animal model that considered herd-yr-season, calving age, and regression additive genetic group as fixed effects, and animal and residual as random effects was used for genetic evaluation. Heritability estimates were 0.12 (SE = 0.19) for lnSCC, and 0.31 (SE = 0.06) for MY. The genetic correlation estimate between lnSCC and MY was 0.26 (SE = 0.59). Mean yearly estimated breeding values during the last 20 years increased for SCC (49.02 cells/ml/yr, SE = 26.81 cells/ml/yr; p = 0.08), but not for MY (0.37 kg/yr, SE = 0.87 kg/yr; p = 0.68). Sire average breeding values for SCC and MY were higher than those of cows and dams (p<0.01). Heritability estimates for lnSCC and MY and their low but positive genetic correlation suggested that selection for low SCC may be feasible in this population as it is in other populations of dairy cows. Thus, selection for high MY and low SCC should be encouraged in Thai dairy improvement programs to increase profitability by improving both cow health and milk yield.

Association between cow reproduction and calf growth traits and ELISA scores for paratuberculosis in a multibreed herd of beef cattle.

The objective of this research was to assess the association between 4 cow reproductive and weight traits, and 2 preweaning calf traits and ELISA scores for paratuberculosis (0 = negative, 1 = suspect, 2 = weak-positive, and 3 = positive) in a multibreed herd of cows ranging from 100% Angus (A) to 100% Brahman (B). Cow data were 624 gestation lengths (GL), 358 records of time open (TO), 605 calving intervals (CI), and 1240 weight changes from November to weaning in September (WC) from 502 purebred and crossbred cows. Calf data consisted of 956 birth weights (BWT), and 923 weaning weights adjusted to 205 d of age (WW205) from 956 purebred and crossbred calves. Traits were analyzed individually using multibreed mixed models that assumed homogeneity of variances across breed groups. Covariances among random effects were assumed to be zero. Fixed effects were year, age of cow, sex of calf, year x age of cow interaction (except WC), age of cow x sex of calf interaction (only for WC), and covariates for B fraction of sire and cow, heterosis of cow and calf, and ELISA score. Random effects were sire (except for TO and CI), dam, and residual. Regression estimates of cow and calf traits on ELISA scores indicated that lower cow fertility (longer TO), lower ability of cows to maintain weight (negative WC), lower calf BWT, and lower calf WW205 were associated with higher cow ELISA scores. Further research on the effects of subclinical paratuberculosis in beef cattle at regional and national levels seems advisable considering the large potential economic cost of this disease.

Effect of Brahman genetics on myofibrillar protein degradation, collagen crosslinking, and tenderness of the longissimus lumborum.

The objective of this study was to examine the effect of percent Brahman genetics on Warner-Bratzler shear force (WBSF), desmin and troponin-T (TnT) degradation, hydroxylysyl pyridinoline (HP) crosslink content, and perimysial collagen melting temperature. Steers ( = 131) produced in 2012 and 2013 were harvested at 1.27 cm of visual s.c. back fat thickness. Steers were divided into 4 genetic categories consisting of steers that contained 6/32 or less Brahman genetics, 12/32 Brahman genetics, 14/32 to 18/32 Brahman genetics, and 23/32 to 32/32 Brahman genetics. Twenty-four hours after harvest, a 7.62-cm piece of the longissimus lumborum beginning at the 13th rib was collected and aged for 14 d. Following aging, three 2.54-cm steaks were cut for WBSF, trained sensory panel, and laboratory analyses. Laboratory analyses steaks were used to determine protein degradation, HP crosslink analysis, and perimysial collagen melting temperature. Data were analyzed using a polynomial regression for unequally spaced treatments. As the percent Brahman genetics increased, WBSF increased (linear, = 0.01). As percent Brahman genetics increased, tenderness score decreased (less tender) and connective tissue score increased (more connective tissue; linear, = 0.01). As the percentage of Brahman genetics increased, the amount of degraded desmin (38 kDa) and TnT (34 and 30 kDa) decreased (linear, < 0.03) whereas the amount of immunoreactive 36 kDa TnT increased (linear, = 0.04). Percent Brahman genetics had no effect ( = 0.14) on HP crosslink content but did tend to increase ( = 0.07) perimysial collagen melting temperature as the percent Brahman increased. The percentage of Brahman genetic influence was positively correlated to WBSF ( = 0.25), 36 kDa immunoreactive TnT ( = 0.26), and perimysial collagen melting temperature ( = 0.25, = 0.01). Sensory panel tenderness ( = -0.44), juiciness ( = -0.26), and connective tissue scores ( = -0.63); 38 kDa degraded desmin ( = -0.34), 34 ( = -0.36) and 30 kDa degraded TnT ( = -0.29); and HP collagen crosslinks ( = -0.20) were negatively correlated to percent Brahman genetic influence ( < 0.03). Increasing Brahman genetic influence in steers negatively affects tenderness, partially through a reduction in degradation of desmin and TnT. Although HP collagen crosslinks are unaffected by Brahman genetics, a tendency for increased perimysium melting temperature indicates that other collagen-stabilizing crosslinks may be affected.

Restricted maximum likelihood procedures for the estimation of additive and nonadditive genetic variances and covariances in multibreed populations.

Restricted maximum-likelihood procedures were developed to estimate additive and nonadditive genetic and environmental covariances for multiple traits in multibreed populations. The computational procedure follows the expectation-maximization (EM) algorithm, where the set of equations in the maximization step is solved by successive approximations. This computational procedure does not guarantee convergence to a symmetric positive-definite covariance matrix. Thus, computer programs will need to incorporate restrictions in the maximization step to ensure positive definiteness of each covariance matrix. Additive genetic and environmental covariances were modeled in subclass form (zeros and ones in the design matrices). Nonadditive genetic covariances were modeled in regression form (any value between and including zero and one in the design matrices). Computational requirements will be larger than for intrabreed analyses. Appropriate simplifying assumptions and numerical techniques (e.g., sparse and iterative numerical techniques) will be required for the implementation of these multibreed covariance estimation procedures. Number of iterations (5 to 12) and computing times (57 to 113 min) to achieve convergence when estimating 21 genetic and environmental covariances in five small simulated multibreed data sets (two breeds, 25,200 to 50,400 calves, 120 to 135 unrelated bulls) suggest that these procedures are computationally feasible.

Covariances among sire by breed group of dam interaction effects in multibreed sire evaluation procedures.

In multibreed populations, bulls need to be evaluated for additive and nonadditive genetic effects. When the nonadditive genetic effects associated with a bull are defined as sire x breed-group-of-dam interactions, they can be expressed as linear combinations of interactions between alleles of one or more breeds at one or more loci. If these specific allelic interactions are assumed to be independent, then variances and covariances between sire x breed-group-of-dam interaction subclasses can be shown to be linear combinations of variances and covariances of specific intra- and interlocus intra- and interbreed allelic interactions. Furthermore, covariances between sire x breed-group-of-dam interactions due to specific interactions at one, two, or more loci are zero. If dams are assumed to be unrelated to bulls and among themselves, except through their sires and maternal grandsires, efficient procedures to compute the inverse of the covariance matrices of nonadditive genetic effects can be devised, both in subclass and in regression models. Recursive procedures developed make possible the evaluation of large numbers of bulls for nonadditive genetic effects using mixed-model methodology. For completeness, recursive procedures to compute nonadditive covariance matrices in subclass and in regression models also were developed. The prediction of nonadditive genetic values for bulls, in addition to their additive genetic values, will help plan matings, make selection decisions more accurate and, possibly, make economic projections better.

Unconstrained procedures for the estimation of positive definite covariance matrices using restricted maximum likelihood in multibreed populations.

Two unconstrained procedures to ensure that intrabreed and interbreed genetic and environmental covariance estimates for multibreed populations are computed within the permissible ranges were developed. These procedures were called Partial Scoring and Cholesky Maximization. The Partial Scoring procedure uses partial steps to keep estimates of covariance matrices positive definite at each expectation-maximization (EM) iteration, and the Cholesky Maximization procedure achieves the same goal by computing the elements of the Cholesky Decomposition of each intrabreed and interbreed genetic and environmental covariance matrix. Groups of small simulated data sets containing either direct genetic effects of two traits (90 bulls, 13,500 calves) or direct and maternal genetic effects for a single trait (135 bulls, 32,400 calves) were used to test the computational feasibility of these two procedures. The overall means (and ranges) of the numbers of expectation-maximization iterations, times to convergence, and accuracy of estimation were 10 (2 to 184), 26.2 min (4.1 to 773.2 min), and 40.1% (12.7 to 81.9%) for the Partial Scoring procedure and 7 (3 to 37), 16.7 min (9.5 to 64.6 min), and 37.8% (3.1 to 67.8%) for the Cholesky Maximization procedure. Although the overall accuracy of both procedures was similar, the Cholesky Maximization procedure should be preferred because it converged faster and its covariance estimates were less affected by the values of the covariance priors than those computed using the Partial Scoring strategy. Application to large unbalanced multibreed data sets will require an iterative version of these procedures.

Covariance components and prediction for additive and nonadditive preweaning growth genetic effects in an Angus-Brahman multibreed herd.

Estimates of covariances and sire expected progeny differences of additive and nonadditive direct and maternal genetic effects for birth and weaning weights were obtained using records from 1,581 straightbred and crossbred calves from the Angus-Brahman multibreed herd at the University of Florida. Covariances were estimated by Restricted Maximum Likelihood, using a Generalized Expectation-Maximization algorithm applied to multibreed populations. Estimates of heritabilities and additive genetic correlations for straightbred and crossbred groups were within the ranges of values found in the literature for these traits. Maximum values of interactibilities (ratios of nonadditive genetic variances to phenotypic variances) and nonadditive correlations were somewhat smaller than heritabilities and additive genetic correlations. Sire additive and total direct and maternal genetic predictions for birth and weaning weight tended to increase with the fraction of Brahman alleles, whereas nonadditive direct and maternal genetic predictions were similar for sires of all Angus and Brahman fractions. These results showed that it is feasible to evaluate sires for additive and nonadditive genetic effects in a structured multibreed population. Data from purebred breeders and commercial producers will be needed to accomplish the same goal at a national level.

Additive and nonadditive genetic variability for growth traits in the Turipaná Romosinuano-Zebu multibreed herd.

Intrabreed additive genetic, environmental, and phenotypic variances and covariances for Romosinuano (R) and Zebu (Z), as well as interbreed nonadditive genetic variances and covariances (sire x breed-group-of-dam interactions), for birth weight (BWT), weaning weight (WW), and postweaning gain (GW) were computed using a Romosinuano-Zebu multibreed data set from the Turipaná Experiment Station in Colombia. Covariances were estimated with a sire-maternal grandsire model, using a multibreed REML procedure. The computing algorithm was a generalized expectation-maximization (GEM) algorithm. This algorithm yields no asymptotic standard errors as part of its computations. Because of the small size of the data set (2,546 calves), these REML covariance estimates should be viewed with caution. Estimates of intrabreed heritabilities were similar to the ratios of interbreed nonadditive to phenotypic variances (interactibilities) for direct and maternal effects of the growth traits evaluated in this study. Intrabreed heritability estimates for BWT, WW, and GW direct genetic effects were .16, .09, and .14, for R and .24, .10, and .14 for Z. Corresponding heritability values for maternal effects were .18, .09, and .23 for R and .14, .13, and .07 for Z. Interactibility estimates were .21, .05, and .12, for direct and .26, .04, and .11, for maternal BWT, WW, and GW. Negative correlations between additive maternal weaning weight and direct and maternal postweaning gain, as well as between environmental weaning weight and postweaning gain, suggested that there was compensatory postweaning gain in this herd. Estimates of genetic variation and predictions of expected progeny differences showed that Romosinuano animals competed well against Zebu and RZ crossbred animals under the tropical environmental conditions at Turipaná.

Direct and maternal genetic effects due to the introduction of Bos taurus alleles into Brahman cattle in Florida: I. Reproduction and calf survival.

Pregnancy rate, calf survival rate to weaning and calf age at weaning of several types of crossbred cows (2/3 or more Brahman) were compared to those of straightbred Brahman and Angus cows over a 12-yr period at Subtropical Agricultural Research Station near Brooksville, FL. The purpose of this study was to determine the relative importance of additive vs nonadditive genetic effects on reproductive and calf survival traits in a population of cattle whose foundation was selected on the basis of superior reproductive performance under harsh environmental conditions. Best linear unbiased estimates (BLUE) of direct additive effect (measured as the deviation of Brahman additive breed effect from Angus) for pregnancy rate and calf age, measured as traits of the dam, were 6 +/- 3% and -7.2 +/- 2.1 d, respectively. Thus, Bos taurus germ plasm did not increase pregnancy rate but resulted in an earlier calving date. The BLUE of nonadditive (intralocus) direct genetic effects measured as deviations from intralocus group genetic effects in the parental breeds on pregnancy rate and calf age at weaning were 25 +/- 4% and -6.4 +/- 2.5 d. Nonadditive effects on pregnancy rate were the primary cause of the superior reproductive rates observed in Brahman crossbred cows. Calf survival was considered to be a trait of the calf, and BLUE of direct additive, direct nonadditive, maternal additive and maternal nonadditive genetic effects was obtained. Only maternal nonadditive genetic effects were found to have a significant effect on survival rate (9 +/- 4%).

Direct and maternal genetic effects due to the introduction of Bos taurus alleles into Brahman cattle in Florida: II. Preweaning growth traits.

Records of birth weight (BW), weaning weight (WW) and condition score (CS) from 1,467 Brahman and Brahman X Angus crossbred calves from Brahman and crossbred Brahman sires and Brahman, crossbred Brahman and Angus dams were collected at the Subtropical Agricultural Research Station, Brooksville, Florida, from 1971 to 1982. Best linear unbiased estimates (BLUE) of Brahman sire and dam group additive genetic effects (as deviations from Angus) and Brahman X Angus dam and calf group nonadditive (intralocus) genetic effects (as deviations from intralocus group genetic effects in the parental breeds) were obtained. Linear combinations of these were used to compute direct and maternal Brahman additive and Brahman X Angus nonadditive (intralocus) group genetic effects. The respective BLUE of these four effects were 5.99 +/- 2.08, -5.70 +/- 1.91, .52 +/- 1.81 and 2.85 +/- .72 kg for BW; 9.60 +/- 10.29, 8.76 +/- 9.47, 9.47 +/- 8.96 and 20.95 +/- 3.56 kg for WW; and -1.10 +/- .55, 1.64 +/- .50, 1.47 +/- .47 and .05 +/- .19 units for CS. Linear combinations of the BLUE of sire, dam and calf group genetic effects can be used to predict the genetic worth of crossbred groups composed of any combination of Brahman and Angus breeding. Nonadditive maternal group genetic effects were the most important factor for BW and WW, whereas nonadditive direct group genetic effects were the most important for CS.

Genetic and environmental factors affecting serum macrominerals and weights in an Angus-Brahman multibreed herd: I. Additive and nonadditive group genetic effects of serum calcium, phosphorus, and magnesium and weight at weaning.

Amounts of serum calcium, phosphorus, and magnesium at weaning (WCa, WP, and WMg, respectively) and weaning weights (WW) were obtained from 380 Angus (A), Brahman (B), and A x B calves of various expected A and B fractions reared at the Pine Acres Research Station of the University of Florida, Citra from 1989 to 1990. Calves were produced by mating A, .75A, .25B, .5A .5B, .25A .75B, B, and Brangus (.625A .375B) sires to dams of the same expected breed fractions, except for .25A .75B dams. Best linear unbiased estimates (BLUE) of genetic effects, expressed as regression coefficients, were 1) -15.07 +/- 13.65 mg of WCa, -11.21 +/- 12.07 mg of WP, -1.23 +/- 2.99 mg of WMg, and .66 +/- 1.18 kg of WW for the difference between A and B additive direct; 2) 9.79 +/- 6.94 mg of WCa, -5.72 +/- 6.14 mg of WP, 1.64 +/- 1.52 mg of WMg, and .52 +/- .60 kg of WW for the difference between A and B additive maternal; 3) 242.21 +/- 51.56 mg of WCa, 66.67 +/- 45.62 mg of WP, 52.16 +/- 11.27 mg of WMg, and 22.61 +/- 4.44 kg of WW for A x B nonadditive direct; and 4) 373.63 +/- 38.44 mg of WCa, 93.96 +/- 34.02 mg of WP, 69.90 +/- 8.41 mg of WMg, and 36.83 +/- 3.31 kg of WW for A x B nonadditive maternal. Nonadditive (A x B) effects were the main factors affecting total (sum of additive plus nonadditive) genetic effects in this multibreed population. Total genetic effects were used to rank breed group of sire x breed group of dam combinations.(ABSTRACT TRUNCATED AT 250 WORDS)

Genetic and environmental factors affecting serum macrominerals and weights in an Angus-Brahman multibreed herd: II. Heritabilities of and genetic, environmental, and phenotypic correlations among serum calcium, phosphorus, and magnesium and weight at weaning.

Heritabilities of and genetic, environmental, and phenotypic correlations among serum amounts of calcium, phosphorus, and magnesium and weight at weaning (WCa, WP, WMg, and WW, respectively) were estimated for an Angus (A)-Brahman(B) multibreed herd located at the Pine Acres Research Station of the University of Florida, Citra. Records were obtained from 380 calves produced by mating A, .75A .25B, .5A .5B, .25A .75B, B, and Brangus sires across dams of the same breed groups, except for .25A .75B, during 1989 and 1990. Restricted maximum likelihood procedures were used to compute variance and covariance components. Estimates of heritability were .39 (WCa), .40 (WP), .36 (WMg), and .35 (WW). Estimates of genetic, environmental, and phenotypic correlations were .66, .55, .57 (WCa, WP), .70, .71, .70 (WCa, WMg), 1.00, .86, .88 (WCa, WW), .50, .51, .51 (WP, WMg), .78, .60, .63 (WP, WW), and .86, .73, .75 (WMg, WW). These correlations indicate that serum Ca, P, and Mg could be used in multiple-trait genetic evaluation procedures to help identify animals that require low amounts of these macrominerals for preweaning growth. This may prove advantageous in mineral-deficient regions.

Genetic parameters and relationships between hip height and weight in Brahman cattle.

Genetic parameters for weaning hip height (WHH), weaning weight (WWT), postweaning hip height growth (PHG), and hip height at 18 mo of age (HH18) and their relationships were estimated for Brahman cattle born from 1984 to 1994 at the Subtropical Agricultural Research Station, Brooksville, FL. Records per trait were 889 WHH, 892 WWT, and 684 HH18. (Co)variances were estimated using REML with a derivative-free algorithm and fitting three two-trait animal models (i.e., WHH-WWT, WHH-PHG, and WWT-HH18). Heritability estimates of WHH direct effects were 0.73 and 0.65 for models WHH-WWT and WHH-PHG and were 0.29 and 0.33 for WWT direct for models WHH-WWT and WWT-HH18, respectively. Estimates of heritability for PHG and HH18 direct were 0.13 and 0.87, respectively. Heritability estimates for maternal effects were 0.10 and 0.09 for WHH for models WHH-WWT and WHH-PHG and 0.18 and 0.18 for WWT for models WHH-WWT and WWT-HH18, respectively. Heritability estimates for PHG and HH18 maternal were 0.00 and 0.03. Estimates of the genetic correlation between direct effects for the different traits were moderate and positive; they were also positive between WHH and WWT maternal and WWT and HH18 maternal but negative (-0.19) between WHH and PHG maternal, which may indicate the existence of compensatory growth. Negative genetic correlations existed between direct and maternal effects for WHH, WWT, PHG, and HH18. The correlation between direct and WWT maternal effects was low and negative, moderate and negative between WHH direct and PHG maternal, and high and negative (-0.80) between WWT direct and HH18 maternal. There is a strong genetic relationship between hip height and weight at weaning that also affects hip height at 18 mo of age. Both product-moment and rank correlations between estimated breeding values (EBV) for direct values indicate that almost all of the same animals would be selected for PHG EBV if the selection criterion used was WHH EBV, and that it is possible to accomplish a preliminary selection for HH18 EBV using WHH EBV. Correlations between breeding values for WHH, WWT, and HH18 indicate that it will be possible to identify animals that will reduce, maintain, or increase hip height while weaning weight is increased. Thus, if the breeding objective is to manipulate growth to 18 mo of age, implementation of multiple-trait breeding programs considering hip height and weight at weaning will help to predict hip height at 18 mo of age.

Genetic variation and prediction of additive and nonadditive genetic effects for six carcass traits in an Angus-Brahman multibreed herd.

Estimates of covariances and sire expected progeny differences of additive and nonadditive genetic effects for six carcass traits were obtained using records from 486 straightbred and crossbred steers from 121 sires born between 1989 and 1995 in the Angus-Brahman multibreed herd of the University of Florida. Steers were slaughtered at a similar carcass composition end point. Covariances were estimated by REML procedures, using a generalized expectation-maximization algorithm applied to multibreed populations. Straightbred and crossbred estimates of heritabilities and additive genetic correlations were within ranges found in the literature for steers slaughtered on an age- or weight-constant basis for hot carcass weight, longissimus muscle area, and shear force but equal to or less than the lower bound of these ranges for fat-related traits. Maximum values of interactibilities (i.e., ratios of nonadditive variances to phenotypic variances in the F1) and nonadditive genetic correlations were smaller than heritabilities and additive genetic correlations in straightbreds and crossbred groups. Sire additive and total direct genetic predictions for longissimus muscle area, marbling, and shear force tended to decrease with the fraction of Brahman alleles, whereas those for hot carcass weight and fat thickness over the longissimus were higher, and those for kidney fat were lower in straightbreds and F1 than in other crossbred groups. Nonadditive genetic predictions were similar across sire groups of all Angus and Brahman fractions. These results suggest that slaughtering steers on a similar carcass composition basis reduces variability of fat-related traits while retaining variability for non-fat-related traits comparable to slaughtering steers on a similar age or weight basis. Selection for carcass traits within desirable (narrow) ranges and slaughter of steers at similar compositional end point seems to be a good combination to help produce meat products of consistent quality.

Influence of frame size and body condition score on performance of Brahman cattle.

The effects of frame size (FS) and body condition score (BCS) on performance of Brahman cows were evaluated using records collected from 1984 to 1994 at the Subtropical Agricultural Research Station, Brooksville, Florida. Age at puberty (AP), calving rate (CR), calving date (CD), survival rate (SR), weaning rate (WR), birth weight (BWT), weaning weight (WWT), preweaning ADG, and kilograms of calf produced per cow exposed (PPC) were obtained from first- (n = 215), second- (n = 130), and third or greater-parity (n = 267) dams. Based on hip height at 18 mo of age, heifers were assigned to three FS groups: small (115 to 126 cm), medium (127 to 133 cm), or large (134 to 145 cm). Small and medium FS heifers attained puberty at younger (P<.05) ages (633.2+/-12.3 and 626.4+/-12.0 d) than large FS heifers (672.3+/-17.1 d). Calving rate in large FS second-parity dams was 27% less (P<.05) than in small and medium FS dams. In third or greater-parity dams, CR was greater (P<.05) for small FS cows than for medium and large FS cows. Across the three parity groups, CR improved with increasing BCS. Except for the first-parity dams, animals with better fall BCS calved earlier (P<.05). In first-parity dams, SR was less (P<.01) in large (47.9+/-11.0%) than in small (80.7 +/-5.2%) and medium (83.4+/-4.7%) FS groups. Weaning rates of large FS first- and second-parity dams were less (P<.05) than those of small and medium FS dams. Second-parity dams with BCS 3 had lower (P<.05) WR than dams with BCS 4 and 5. Within first- and third or greater-parity dams, BWT of calves born to small FS cows were the lightest, and those born to large FS dams were the heaviest; those born to medium FS dams were intermediate (P<.05). In second-parity dams, BWT of calves of large FS dams were greater (P<.05) than those of small and medium FS dams. In first-parity dams, calves weaned by small FS cows had lower (P<.05) WWT than those weaned by higher FS cows. In the third or greater-parity group, large FS dams weaned heavier calves (P<.05) than other dams. In all parity groups of dams, calves out of large FS cows had greater ADG (P<.05) than those from small and medium FS cows. In first-parity dams, PPC was comparable between small and medium FS dams, but both tended to be greater (P<.10) than PPC of large FS dams. Small and medium FS females reached puberty at an earlier age, calved earlier, and had greater calving, survival, and weaning rates, as well as greater kilograms of calf produced per cow exposed than the large FS females. As the large FS cows matured, they seemed to have overcome the negative effects imposed by FS that were observed at younger ages. Their performance traits were generally all comparable to those of smaller cows once they had reached maturity.