Models with nuclear,cytoplasmic, and environmental effects for production traits of Columbia sheep

Statistical models (16) were compared for birth weight of 24,741 Columbia lambs recorded at the U.S. Sheep Experiment Station (USSES; 1950 to 1998). The goal was to estimate fractions of variance due to cytoplasmic line (c2; n = 590) and sire x cytoplasmic line interaction (sc2; n = 12,831) with other nuclear and environmental effects included in the model. The basic model included direct genetic (fractional variance, a2; n = 26,623), maternal genetic (m2, with direct-maternal correlation ram), and maternal permanent environmental (p2m; n = 6,385) effects. The model with sc2 was significantly (P < 0.05) better than the basic model with c2, but with other random effects added, sc2 became zero. Significant (P < 0.05) variance components were associated with random dam x year (dy2) and dam x number born (dn2) interaction effects. Estimates with all effects in the model were: a2, 0.26; m2, 0.24; ram, -0.05; p2m, 0.02; c2, 0.00; dn2, 0.04; dy2, 0.08; sd2, 0.04; sc2, 0.00. Estimates for a2, m2, and ram were the same for all models. Estimate of p2 changed when other effects were added to the model. The largest estimates for nongenetic effects were: p2m, 0.06; c2, 0.00; dy2, 0.14; sd2, 0.13; and sc2, 0.04. Parameter estimates were similar regardless of whether fixed genetic groups (n = 84) were in the model. For weaning weight (120 d, n = 23,903), estimates of variances of effects added to the basic model were all near zero (a2, 0.14; m2, 0.09; ram, 0.23; p2m, 0.04). For fleece weight (FW, n = 29,024) and number born (NB, n = 29,688), animal permanent environmental effects were added to the model (p2a; n = 7,741 and 7,840) and ram was dropped. For these traits, effects not in the basic model had small variances. For FW, estimates with the full model were: a2, 0.52; m2, 0.01; p2m, 0.00; p2a, 0.06; c2, 0.00; dy2, 0.00; sd2, 0.02; and sc2, 0.06, and for NB they were: a2, 0.08; m2, 0.00; p2m, 0.00; p2a, 0.02; c2, 0.00; dy2, 0.00; sd2, 0.00; and sc2, 0.01. Cytoplasmic effects were not important. Unusual random effects in the model did not change estimates for basic parameters. Although some effects were significant, especially for BW, effects on genetic evaluations are likely to be small.     

Number of calves born, number of calves weaned, and cumulative weaning weight as measures of lifetime production for Hereford cows

Genetic parameters for lifetime production for cows with the opportunity to produce from 2 through 7 yr of age, as measured by the number of calves born (NB2, ..., NB7), the number of calves weaned (NW2, ..., NW7), and cumulative weaning weight (CW2, ..., CW7), were estimated using data from 3,064 Hereford cows from a selection experiment with a control line (CTL) and three lines selected for weaning weight (WWL), yearling weight (YWL), and an index of yearling weight and muscle score (IXL). Weaning weights were adjusted to 200 d of age and for sex and age of dam. Estimates of heritability and genetic and environmental correlations were obtained by restricted maximum likelihood with bivariate animal models, with year of birth of the cow as a fixed effect and direct genetic and residual as random effects. Genetic trends were estimated by regressing means of estimated breeding values by year of birth and line on birth year. Estimates of heritability (SE) for opportunity groups of 2 to 7 yr of age ranged from 0.08 (0.03) to 0.16 (0.05) for NB; from 0.05 (0.02) to 0.16 (0.05) for NW; and from 0.06 (0.02) to 0.16 (0.05) for CW. Estimates of genetic correlations (SE) among NB traits ranged from 0.60 (0.14) to 1.00 (0.00), and estimates of environmental correlations (SE) ranged from 0.67 (0.02) to 0.99 (0.00). For NW, estimates of genetic and environmental correlations ranged from 0.98 (0.11) to 1.00 (0.00) and from 0.65 (0.02) to 0.99 (0.00), respectively. Estimates of genetic correlations (SE) among CW traits ranged from 0.94 (0.08) to 1.00 (0.00). Estimates of environmental correlations (SE) ranged from 0.66 (0.02) to 0.99 (0.00). Estimates of genetic correlations for NB2 with all definitions of NW ranged from 0.47 (0.18) to 0.71 (0.12), and with all definitions of CW ranged from 0.55 (0.16) to 0.80 (0.11). Estimates of genetic correlations between NW2 and all definitions for CW ranged from 0.95 (0.02) to 0.99 (0.06). Estimates of annual genetic (SE) change were negligible for NB2, NB6, NW2, and NW6 for all lines. Estimates of annual genetic (SE) change for CW2 were 0.85 (0.11), 0.79 (0.14), 0.51 (0.10), and 0.52 (0.18) kg/yr, and for CW6 were 5.01 (1.25), 2.64 (1.75), 3.67 (1.16), and 3.33 (2.37) kg/yr for WWL, YWL, IXL, and CTL, respectively. Selection for lifetime production as measured by NB, NW, or CW could be effective but would be relatively slow due to low estimates of heritability and to increased generation intervals.     

Estimation of additive and nonadditive genetic variances in Hereford, Gelbvieh, and Charolais by Method R.

Parameters for direct and maternal dominance were estimated in models that included non-additive genetic effects. The analyses used weaning weight records adjusted for age of dam from populations of Canadian Hereford (n = 467,814), American Gelbvieh (n = 501,552), and American Charolais (n = 314,552). Method R estimates of direct additive genetic, maternal additive genetic, permanent maternal environment, direct dominance, and maternal dominance variances as a proportion of the total variance were 23, 12, 13, 19, and 14% in Hereford; 27, 7, 10, 18, and 2% in Gelbvieh; and 34, 15, 15, 23, and 2% in Charolais. The correlations between direct and maternal additive genetic effects were -0.30, -0.23, and -0.47 in Hereford, Gelbvieh, and Charolais, respectively. The correlations between direct and maternal dominance were -0.38, -0.02, and -0.04 in Hereford, Gelbvieh, and Charolais, respectively. Estimates of inbreeding depression were -0.20, -0.18, and -0.13 kg per 1% of inbreeding for Hereford, Gelbvieh, and Charolais, respectively. Estimates of the maternal inbreeding depression were -0.01, -0.02, and -0.02 kg, respectively. The high ratio of direct dominance to additive genetic variances provided some evidence that direct dominance effects should be considered in beef cattle evaluation. However, maternal dominance effects seemed to be important only for Hereford cattle.     

Variance components and breeding values for growth traits from different statistical models.

Estimates of genetic parameters resulting from various analytical models for birth weight (BWT, n = 4,155), 205-d weight (WWT, n = 3,884), and 365-d weight (YWT, n = 3,476) were compared. Data consisted of records for Line 1 Hereford cattle selected for postweaning growth from 1934 to 1989 at ARS-USDA, Miles City, MT. Twelve models were compared. Model 1 included fixed effects of year, sex, age of dam; covariates for birth day and inbreeding coefficients of animal and of dam; and random animal genetic and residual effects. Model 2 was the same as Model 1 but ignored inbreeding coefficients. Model 3 was the same as Model 1 and included random maternal genetic effects with covariance between direct and maternal genetic effects, and maternal permanent environmental effects. Model 4 was the same as Model 3 but ignored inbreeding. Model 5 was the same as Model 1 but with a random sire effect instead of animal genetic effect. Model 6 was the same as Model 5 but ignored inbreeding. Model 7 was a sire model that considered relationships among males. Model 8 was a sire model, assuming sires to be unrelated, but with dam effects as uncorrelated random effects to account for maternal effects. Model 9 was a sire and dam model but with relationships to account for direct and maternal genetic effects; dams also were included as uncorrelated random effects to account for maternal permanent environmental effects. Model 10 was a sire model with maternal grandsire and dam effects all as uncorrelated random effects. Model 11 was a sire and maternal grandsire model, with dams as uncorrelated random effects but with sires and maternal grandsires assumed to be related using male relationships. Model 12 was the same as Model 11 but with all pedigree relationships from the full animal model for sires and maternal grandsires. Rankings on predictions of breeding values were the same regardless of whether inbreeding coefficients for animal and dam were included in the models. Heritability estimates were similar regardless of whether inbreeding effects were in the model. Models 3 and 9 best fit the data for estimation of variances and covariances for direct, maternal genetic, and permanent environmental effects. Other models resulted in changes in ranking for predicted breeding values and for estimates of direct and maternal heritability. Heritability estimates of direct effects were smallest with sire and sire-maternal grandsire models.     

Age of dam and sex of calf adjustments and genetic parameters for gestation length in Charolais cattle

To estimate adjustment factors and genetic parameters for gestation length (GES), AI and calving date records (n = 40,356) were extracted from the Canadian Charolais Association field database. The average time from AI to calving date was 285.2 d (SD = 4.49 d) and ranged from 274 to 296 d. Fixed effects were sex of calf, age of dam (2, 3, 4, 5 to 10, > or = 11 yr), and gestation contemporary group (year of birth x herd of origin). Variance components were estimated using REML and 4 animal models (n = 84,332) containing from 0 to 3 random maternal effects. Model 1 (M1) contained only direct genetic effects. Model 2 (M2) was G1 plus maternal genetic effects with the direct x maternal genetic covariance constrained to zero, and model 3 (M3) was G2 without the covariance constraint. Model 4 (M4) extended G3 to include a random maternal permanent environmental effect. Direct heritability estimates were high and similar among all models (0.61 to 0.64), and maternal heritability estimates were low, ranging from 0.01 (M2) to 0.09 (M3). Likelihood ratio tests and parameter estimates suggested that M4 was the most appropriate (P < 0.05) model. With M4, phenotypic variance (18.35 d2) was partitioned into direct and maternal genetic, and maternal permanent environmental components (hd2 = 0.64 +/- 0.04, hm2 = 0.07 +/- 0.01, r(d,m) = -0.37 +/- 0.06, and c2 = 0.03 +/- 0.01, respectively). Linear contrasts were used to estimate that bull calves gestated 1.26 d longer (P < 0.02) than heifers, and adjustments to a mature equivalent (5 to 10 yr old) age of dam were 1.49 (P < 0.01), 0.56 (P < 0.01), 0.33 (P < 0.01), and -0.24 (P < 0.14) d for GES records of calves born to 2-, 3-, 4-, and > or = 11-yr-old cows, respectively. Bivariate animal models were used to estimate genetic parameters for GES with birth and adjusted 205-d weaning weights, and postweaning gain. Direct GES was positively correlated with direct birth weight (BWT; 0.34 +/- 0.04) but negatively correlated with maternal BWT (-0.20 +/- 0.07). Maternal GES had a low, negative genetic correlation with direct BWT (-0.15 +/- 0.05) but a high and positive genetic correlation with maternal BWT (0.62 +/- 0.07). Generally, GES had near-zero genetic correlations with direct and maternal weaning weights. Results suggest that important genetic associations exist for GES with BWT, but genetic correlations with weaning weight and postweaning gain were less important.     

Maternal effects on docility in Limousin cattle

The objective of this study was to quantify the role of maternal effects on docility in Limousin cattle. Docility scores were obtained at weaning while animals were restrained in a squeeze chute. Scores 1 through 6 represented a docile to aggressive temperament, respectively, and were provided by the North American Limousin Foundation. Observations with unknown age of dam, contemporary groups containing less than 10 observations, contemporary groups with no variation, and single-sire contemporary groups were removed, leaving 21,932 observations. A 2-generation pedigree file compiled from animals with observations contained 49,459 animals. Fixed effects were weaning contemporary group and age of dam (2, > or =3 yr). Six animal models encompassed combinations of random factors: direct genetic, maternal genetic, and maternal permanent environmental effects. The model D was the most basic, containing direct genetic and residual effects, and it resembled the method currently used by the North American Limousin Foundation for genetic evaluation of docility. Maternal genetic or permanent environmental effects were separately added to the model D, denoted as models DM and DC, respectively. Model DMC contained all random factors. Models DM-Zero and DMC-Zero were equivalent to models DM and DMC, respectively, but with zero direct-maternal genetic covariance. Direct heritability estimates were moderate for all models (0.29 +/- 0.02 to 0.38 +/- 0.03). Maternal heritability estimates were low, ranging from 0.01 +/- 0.01 (DM-Zero) to 0.05 +/- 0.02 (DM). Negative direct-maternal genetic correlations of -0.41 +/- 0.09 and -0.55 +/- 0.09 were estimated for models DM and DMC, respectively. The proportion of phenotypic variance accounted for by maternal permanent environmental effects was 0.03 +/- 0.01, 0.04 +/- 0.01, and 0.02 +/- 0.01 for models DC, DMC, and DMC-Zero, respectively. Likelihood ratio tests indicated that model DMC best fit the data. Although maternal genetic and maternal permanent environmental effects were significant, they accounted for only 8% (model DMC) of the phenotypic variance, and a Spearman rank correlation of 0.99 between models D and DMC showed sires did not rank differently with or without inclusion of these effects. Given these results, inclusion of maternal effects to the genetic evaluation of docility in Limousin cattle does not seem warranted.     

Parameter estimates for direct and maternal genetic effects on yearling, eighteen-month, and slaughter weights of Korean native cattle

Data collected by the National Livestock Research Institute of the Rural Development Administration of Korea were used to estimate genetic parameters for yearling (YWT, n = 5,848), 18-mo (W18, n = 4,585), and slaughter (SWT, n = 2,279) weights for Korean Native cattle. Nine animal models were used to obtain REML estimates of genetic parameters: DP-2 included genetic, uncorrelated dam, and residual random effects; DQ-2 included genetic, sire x region x year-season interaction, and residual random effects; DPQ-2 was based on DQ-2 but included both interaction and dam effects; DMP-2 was based on DP-2 but with dam effect partitioned to include maternal genetic and permanent environmental effects; and DMPQ-2 was based on DMP-2 but also included sire interaction effects. Those five models included two fixed factors: region x year-season and age of dam x sex effects. Models DP-3, DQ-3, DPQ-3, and DMPQ-3 were based on DP-2, DQ-2, DPQ-2, and DMPQ-2 but included as a third fixed factor whether or not identification of the sire was known. Estimates of heritability with DMPQ-3 for YWT, with DPQ-3 for W18 and SWT when analyzed with single-trait analyses were .14, .11, and .17, respectively, and were nearly the same with bivariate analyses. Estimate of maternal heritability for YWT from single-trait analysis was .04, with estimates for other traits near zero. For bivariate analyses, the estimate for YWT was .01. With single trait analysis, estimate of the direct-maternal genetic correlation for YWT was negative (-.81). Estimates of direct genetic correlations between YWT and W18, YWT and SWT, and W18 and SWT were .99, 1.00, and .97, respectively. Estimates of environmental correlations varied from .60 to .81; the largest was between W18 and SWT. Including a fixed factor for whether sire identification was missing or not missing reduced the estimate of heritability for slaughter weight. The results suggest that the sire x region x year-season interaction is important for yearling weight and may be needed in a model for slaughter weight. Maternal effects may be of slight importance for yearling weight but of no importance for W18 and SWT. Models for national cattle evaluations for Korean Native cattle for YWT should be considered that include maternal genetic and permanent environmental as well as sire x region x year-season interaction effects, but those effects seem not to be needed for models for W18 and SWT. Not much reranking of sires occurred when ranked was based on the different models for W18 and SWT.     

Genetic parameters and trends for litter traits in U.S. Yorkshire,Duroc, Hampshire,and Landrace pigs

Records on 251,296 Yorkshire, 75,262 Duroc, 83,338 Hampshire, and 53,234 Landrace litters born between 1984 and April of 1999 in herds on the National Swine Registry Swine Testing and Genetic Evaluation System were analyzed. Animal model and restricted maximum likelihood procedures were used to estimate variances of animal genetic (a), maternal genetic (m), permanent environmental, and service sire, and the covariances between a and m for number born alive (NBA), litter weight at 21 d (L21WT), and number weaned (NW). Fixed effects of contemporary groups were included in the analysis. Based on a single-trait model, estimates of heritabilities were 0.10, 0.09, 0.08, and 0.08 for NBA; 0.08, 0.07, 0.08, and 0.09 for L21WT; and 0.05, 0.07, 0.05, and 0.05 for NW in the Yorkshire, Duroc, Hampshire, and Landrace breeds, respectively. Estimates of maternal genetic effects were low and ranged from 0.00 to 0.02 for all traits and all breeds. Estimates of permanent environmental effects ranged from 0.03 to 0.08. Estimates of service sire effects ranged from 0.02 to 0.05. A bivariate analysis was used to estimate the genetic correlations among traits. Average genetic correlations over the four breeds were 0.13, 0.15, and 0.71 for NBA with L21WT, NBA with NW, and L21WT with NW, respectively. Average genetic trends were 0.018 pigs/yr, 0.114 kg/yr, and 0.004 pigs/yr for NBA, L21WT, and NW, respectively. Although estimates of heritabilities for litter traits were low and similar across breeds, genetic variances for litter traits were sufficiently large to indicate that litter traits could be improved through selection. This study presents the first set of breed-specific estimates of genetic parameters available from large numbers of field records. It provides information for use in national genetic evaluations.     

Genetic parameters for intramuscular fat percentage, marbling score, scrotal circumference, and heifer pregnancy in Red Angus cattle

Selection criteria for yearling bulls commonly include indicators of fertility and carcass merit, such as scrotal circumference (SC) and intramuscular fat percentage (IMF). Genetic correlation estimates between ultrasound traits such as IMF and carcass marbling score (MS) with fertility traits SC and heifer pregnancy (HP) have not been reported. Therefore, the objective of this study was to estimate the genetic parameters among the indicator traits IMF and SC, and the economically relevant traits MS and HP. Records for IMF (n=73,051), MS (n=15,260), SC (n=43,487), and HP (n=37,802) were obtained from the Red Angus Association of America, and a 4-generation ancestral pedigree (n=10,460) was constructed from the 8,915 sires represented in the data. (Co)variance components were estimated using a multivariate sire model and average information REML to obtain estimates of heritability and genetic correlations. Fixed effects included contemporary group and the linear effect of age at measurement for all traits, and an additional effect of age of dam for both HP and SC. The random effect of sire was included to estimate additive genetic effects, which were assumed to be continuous for IMF, MS, and SC, but a probit threshold link function was fitted for HP. Generally moderate heritability estimates of 0.29 ± 0.01, 0.35 ± 0.06, 0.32 ± 0.02, and 0.17 ± 0.01 were obtained for IMF, MS, SC, and HP on the underlying scale, respectively. The confidence interval for the estimated genetic correlation between MS and HP (0.10 ± 0.15) included zero, suggesting a negligible genetic association. The genetic correlation between MS and IMF was high (0.80 ± 0.05), but the estimate for HP and SC (0.05 ± 0.09) was near zero, as were the estimated genetic correlations of SC with MS (0.01 ± 0.08) and IMF (0.05 ± 0.06), and for HP with IMF (0.13 ± 0.09). These results suggest that concomitant selection for increased fertility and carcass merit would not be antagonistic.     

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.     

Increasing accuracy in estimation of economic values for resistance to gastrointestinal helminths in meat sheep

The impact of utilising different indices and numbers of index traits in estimation of economic values (EVs) for resistance to gastrointestinal (GI) helminths were investigated. Seven indices based on yearling weight (YW), litter size (LS) and ewe live weight (ELW) were evaluated under a scheme that considered individual records (Scheme 1) and one that utilised extra information from individual’s relatives (Scheme 2). Under an objective where index response in YW was maximum (R_IYW = max) economic values were US$ 0.00, 0.41, 0.35 and 1.58 in scheme 1 and −0.07, 0.25, −1.10 and −0.02 in scheme 2 for indexes 1, 2, 3 and 4 respectively. In the determining the effect of the number of index traits on the estimates of EVs, calculations were done for five breeding objectives. Eight scenarios (indices) under each objective that differed in the number of traits considered were evaluated. In all scenarios, EVs under R_IYW = max were positive and were US$ 0.00, 0.41, 0.35 and 1.58 in scheme 1 and −0.07, 0.25, −1.10 and −0.02 in scheme 2 for indexes 1, 2, 3 and 4 respectively. In the determining the effect of the number of index traits on the estimates of EVs, calculations were done for five breeding objectives. Eight scenarios (indices) under each objective that differed in the number of traits considered were evaluated. In all scenarios, EVs under R_IYW = max were positive and were US 0.00, 0.79, 2.68, 2.66, 2.66, 2.62, 2.44 and 2.62 for scenarios 1–8 respectively. Generally, economic value estimates varied across breeding schemes and objectives.     

Genetic relationships between scrotal circumference and female reproductive traits

Records for yearling scrotal circumference (SC; n = 7,580), age at puberty in heifers (AP; n = 5,292), age at first calving (AFC; n = 4,835), and pregnancy, calving, or weaning status following the first breeding season (PR1, CR1, or WR1, respectively; n = 7,003) from 12 Bos taurus breeds collected at the Meat Animal Research Center (USDA) between 1978 and 1991 were used to estimate genetic parameters. Age at puberty (AP) was defined as age in days at first detected ovulatory estrus. Pregnancy (calving or weaning) status was scored as one for females conceiving (calving or weaning) given exposure during the breeding season and as zero otherwise. The final model for SC included fixed effects of age of dam at breeding (AD), year of breeding (Y), and breed (B) and age in days at measurement as a covariate. Fixed effects in models for AP and AFC were AD, Y, B, and month of birth. Fixed effects in models for PR1, CR1, and WR1 included AD, Y, and B. For all traits, random effects in the model were direct genetic, maternal genetic, maternal permanent environmental, and residual. Analyses for a three-trait animal model were carried out with SC, AP, and a third trait (the third trait was AFC, PR1, CR1, or WR1). A derivative-free restricted maximum likelihood algorithm was used to estimate the (co)variance components. Direct and maternal heritability estimates were 0.41 and 0.05 for SC; 0.16 and 0.03 for AP; 0.08 and 0.00 for AFC; 0.14 and 0.02 for PR1; 0.14 and 0.03 for CR1; and 0.12 and 0.01 for WR1. Genetic correlations between direct and maternal genetic effects within trait were -0.26, -0.63, -0.91, -0.79, -0.66, and -0.85 for SC, AP, AFC, PR1, CR1, and WR1, respectively. Direct genetic correlations between SC and AP and between those traits and AFC, PR1, CR1, and WR1 ranged from -0.15 (between SC and AP) to 0.23 (between AP and WR1). Estimates of heritability indicate that yearling SC should respond to direct selection better than AP, AFC, PR1, CR1, and WR1. Variation due to maternal genetic effects was small for all traits. No strong genetic correlations were detected between SC and female reproductive traits or between AP and the other female traits. These results suggest that genetic response in female reproductive traits through sire selection on yearling SC is not expected to be effective.     

Estimation of direct, maternal, and grandmaternal genetic effects for weaning weight in several breeds of beef cattle.

Weaning weights from nine parental breeds and three composites were analyzed to estimate variance due to grandmaternal genetic effects and to compare estimates for variance due to maternal genetic effects from two different models. Number of observations ranged from 794 to 3,465 per population. Number of animals in the pedigree file ranged from 1,244 to 4,326 per population. Two single-trait animal models were used to obtain estimates of covariance components by REML using an average information method. Model 1 included random direct and maternal genetic, permanent maternal environmental, and residual environmental effects as well as fixed sex x year and age of dam effects. Model 2 in addition included random grandmaternal genetic and permanent grandmaternal environmental effects to account for maternal effects of a cow on her daughter's maternal ability. Non-zero estimates of proportion of variance due to grandmaternal effects were obtained for 7 of the 12 populations and ranged from .03 to .06. Direct heritability estimates in these populations were similar with both models. Existence of variance due to grandmaternal effects did not affect the estimates of maternal heritability (m2) or the correlation between direct and maternal genetic effects (r(am)) for Angus and Gelbvieh. For the other five populations, magnitude of estimates increased for both m2 and r(am) when estimates of variance due to grandmaternal effects were not zero. Estimates of the correlation between maternal and grandmaternal genetic effects were large and negative. These results suggest that grand-maternal effects exist in some populations, that when such effects are ignored in analyses maternal heritability may be underestimated, and that the correlation between direct and maternal genetic effects may be biased downward if grandmaternal effects are not included in the model for weaning weight of beef cattle.     

Maternal birth weight breeding value as an additional factor to predict calf birth weight in beef cattle

A total of 1,028 birth weight (BWT) and gestation length (GL) records were collected for calves from 1994 to 1997 in five U.S. Angus herds. Parental BWT EPD and dam BWT maternal breeding values (MBV) computed from the entire U.S. Angus data base after each breeding season were also available. A full model was fit to BWT that contained contemporary group (CG), sire BWT EPD, dam BWT EPD, and dam BWT MBV. A reduced model that dropped dam BWT MBV was also fit. The full model had smaller (P < .01) sum of squares for error than the reduced model. Calf BWT records were then adjusted for CG. Two data sets were formed to include adjusted BWT progeny records from sires with BWT EPD > or = .75 or > or = 1.0 SD above the mean of sires in the data set. Adjusted birth weights were assigned to either > or = .75 or other < .75 SD and > or = 1.0 or < 1.0 SD categories based on the mean BWT of calves in the entire data set. Dams were assigned to either > or =2 .75 or < .75 SD and > or = 1.0 or < 1.0 SD categories based on dam BWT EPD, MBV, or total maternal genetic contribution (TMGC = EPD + MBV). Chi-square analyses showed that dam BWT EPD, MBV, or TMGC categories were not independent (P < .10) of BWT SD categories, indicating that both dam BWT EPD and BWT MBV provide useful information to attenuate calf BWT. Calf BWT records were then adjusted for the overall mean, CG, sire and dam BWT EPD, and dam BWT MBV. Dams were then assigned to five categories: high dam EPD and MBV (HH), high dam EPD and low MBV (HL), low dam EPD and high MBV (LH), low dam EPD and MBV (LL), and other (OTH). High was > or = .75 or > or = 1.0 SD and low was < .75 or < 1.0 SD based on the mean BWT EPD or MBV of dams in the data set. In all adjusted BWT analyses, HH, HL, and LH categories did not differ (P > .05) from each other; however, the LL category was less (P < .05) than all other categories, indicating that calves from LL dams were lighter at birth than expected. For GL, LL was significantly different (P < .05) from only HH. The large differences in birth weight for the LL dams compared to other groups did not seem to be primarily due to shorter GL. Results showed that MBV provided additional information to control BWT; however, when both dam MBV and EPD were low, birth weight of calves was less than expected. Future research should focus on explanations for this interaction.     

Genetic evaluation of an index of birth weight and yearling weight to improve efficiency of beef production

The CGC population is a stabilized composite of 1/2 Red Angus, 1/4 Charolais, and 1/4 Tarentaise germplasm. The objectives of this research were to estimate genetic parameters for weight traits of CGC and to evaluate genetic responses resulting from selection based on the following index: I = 365-d weight 3.2(birth weight). Phenotypes evaluated were birth weight (n = 5,083), 200-d weight (n = 4,902), 365-d weight (n = 4,626), and the index. In addition, there were 1,433 cows with at least one recorded weight, and 4,375 total observations of cow weight collected at the time their calves were weaned. In 1989, a randomly selected control line and a line selected for greater values of the index were established. Average generation intervals were 3.16 +/- 0.04 and 3.90 +/- 0.08 yr in the index and control lines, respectively. The index selection line (n = 950) accumulated approximately 212 kg more selection differential than the control line over three generations (n = 912). Heritability estimates for direct effects were 0.32 +/- 0.04, 0.49 +/- 0.05, 0.49 +/- 0.05, 0.30 +/- 0.04, and 0.70 +/- 0.04 for the index, birth weight, 365-d weight, 200-d weight, and cow weight, respectively. Heritability estimates for maternal effects were 0.05 +/- 0.02, 0.11 +/- 0.03, 0.04 +/- 0.02, and 0.19 +/- 0.04 for the index, birth weight, 365-d weight, and 200-d weight, respectively. In the control line, direct genetic changes for the index and its components were small. For the index selection line, direct genetic changes for the index, birth weight, 365-d weight, 200-d weight, and cow weight were 6.0 +/- 0.3, 0.45 +/- 0.09, 7.74 +/- 0.55, 3.42 +/- 0.25, and 6.3 +/- 0.9 kg/generation, respectively. Maternal genetic changes were generally small for both the control and index selection lines. Thus, selection for the index produced positive correlated responses for direct genetic effects on BW traits at all ages, with only minor effects on maternal genetic effects. Results demonstrate that despite a genetic antagonism that compromises selection response for decreased birth weight and increased postnatal growth, favorable genetic responses can be achieved with the selection index used in this study.     

Symmetric differences squared and analysis of variance procedures for estimating genetic and environmental variances and covariances for beef cattle weaning weight: I. Comparison via simulation

Analysis of variance (ANOVA) and symmetric differences squared (SDS) methods for estimating genetic and environmental variances and covariances associated with beef cattle weaning weight were compared via simulation. Simulation was based on the pedigree and record structure of 503 beef weaning weights collected over 19 yr from a university herd. The SDS methodology was used with four models. The simplest model included direct (g) and maternal (gm) additive genetic effects, 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 obtained using 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 obtained using sire, dam, within dam and maternal grandsire variances, covOD and either covOS or covOGD. Two sets of 1,000 replicates of the data were simulated. These data were used to compare precision and accuracy of SDS and ANOVA estimators, to estimate correlations among SDS and ANOVA estimators, and to study the importance of taking inbreeding into account with SDS methodology. All ANOVA estimators for rho ggm were biased downward. The SDS procedure had a clear advantage over ANOVA. Averages of SDS estimates were closer to parameter values used to simulate the data and their standard deviations were generally smaller. The standard deviations of both SDS and ANOVA estimates of rho ggm were very large. It is important to allow for a nonzero sigma mem (at least when it is negative) when using SDS methods; otherwise estimators of sigma 2gm and sigma ggm are biased upward and downward, respectively.     

Genetic parameter estimates for scrotal circumference and semen characteristics of Line 1 Hereford bulls

The objectives of this study were to estimate heritability for scrotal circumference (SC) and semen traits and their genetic correlations (rg) with birth weight (BRW). Semen traits were recorded for Line 1 Hereford bulls (n = 841), born in 1963 or from 1967 to 2000, that were selected for use at Fort Keogh (Miles City, MT) or for sale. Semen was collected by electroejaculation when bulls were a mean age of 446 d. Phenotypes were BRW, SC, ejaculate volume, subjective scores for ejaculate color, swirl, sperm concentration and motility, and percentages of sperm classified as normal and live or having abnormal heads, abnormal midpieces, proximal cytoplasmic droplets (primary abnormalities), bent tails, coiled tails, or distal cytoplasmic droplets (secondary abnormalities). Percentages of primary and secondary also were calculated. Data were analyzed using multiple-trait derivative-free REML. Models included fixed effects for contemporary group, age of dam, age of bull, inbreeding of the bull and his dam, and random animal and residual effects. Random maternal and permanent maternal environmental effects were also included in the model for BRW. Estimates of heritability for BRW, SC, semen color, volume, concentration, swirl, motility, and percentages of normal, live, abnormal heads, abnormal midpieces, proximal cytoplasmic droplets, bent tails, coiled tails, distal cytoplasmic droplets, and primary and secondary abnormalities were 0.34, 0.57, 0.15, 0.09, 0.16, 0.21, 0.22, 0.35, 0.22, 0.00 0.16, 0.37, 0.00 0.34 0.00, 0.30, and 0.33, respectively. Estimates of rg for SC with color, volume, concentration, swirl, motility, and percentages of live, normal, and primary and secondary abnormalities were 0.73, 0.20, 0.77, 0.40, 0.34, 0.63, 0.33, -0.36, and -0.45, respectively. Estimates of rg for BRW with SC, color, volume, concentration, swirl, motility, and percentages live, normal, and primary and secondary abnormalities were 0.28, 0.60, 0.08, 0.58, 0.44, 0.21, 0.34, 0.20, -0.02, and -0.16, respectively. If selection pressure was applied to increase SC, all of the phenotypes evaluated would be expected to improve. Predicted correlated responses in semen characteristics per genetic SD of selection applied to SC were 0.87 genetic SD or less. If selection pressure was applied to reduce BRW, the correlated responses would generally be smaller but antagonistic to improving all of the phenotypes evaluated. Predicted correlated responses in SC and semen characteristics per genetic SD of selection applied to BRW were less than 0.35 genetic SD.     

Evaluation of birth and weaning traits of Romosinuano calves as purebreds and crosses with Brahman and Angus

The objectives of this work were to evaluate birth and weaning traits, to estimate genetic effects, including heterosis and direct and maternal breed effects, and to evaluate calving difficulty, calf vigor at birth, and calf mortality of Romosinuano as purebreds and as crosses with Brahman and Angus. Calves (n = 1,348) were spring-born from 2002 through 2005 and weaned in the fall of each year at about 7 mo of age. Traits evaluated included birth and weaning weight, ADG, BCS, and weaning hip height. Models used to analyze these traits included the fixed effects of year, sire and dam breeds, management unit, calf sex, cow age, and source of Angus sire (within or outside of the research herd). Calf age in days was investigated as a covariate for weaning traits. Sire within sire breed and dam within dam breed were random effects. Estimates of Romosinuano-Brahman and Romosinuano-Angus heterosis (P < 0.05) were 2.6 +/- 0.3 (8.6%) and 1.4 +/- 0.3 kg (4.7%) for birth weight, 20.5 +/- 1.5 (9.5%) and 14.6 +/- 1.4 kg (7.4%) for weaning weight, 79.2 +/- 6.1 (9.8%) and 55.1 +/- 6.0 g (7.5%) for ADG, 0.16 +/- 0.03 (2.7%) and 0.07 +/- 0.03 (1.2%) for BCS, and 2.77 +/- 0.32 cm (2.4%) and 1.87 +/- 0.32 cm (1.7%) for hip height. Heterosis for Brahman-Angus was greater (P < 0.05) than all Romosinuano estimates except those for Romosinuano-Brahman and Romosinuano-Angus BCS. Romosinuano direct effects were negative and lowest of the breeds, except for the Angus estimate for hip height. Romosinuano maternal effects were the largest of the 3 breeds for birth weight and hip height but intermediate to the other breeds for weaning weight and ADG. A large proportion of Brahman-sired calves from Angus dams (0.09 +/- 0.03; n = 11) was born in difficult births and died before 4 d of age. Brahman and Angus purebreds and Romosinuano-sired calves from Brahman dams also had large proportions of calves that died before weaning (0.09 or greater). Results indicated that Romosinuano may be used as a source of adaptation to subtropical environments and still incorporate substantial crossbred advantage for weaning traits, although not to the extent of crosses of Brahman and Angus.     

Comparison of models for estimation of genetic parameters for mature weight of Hereford cattle

Genetic parameters of mature weight are needed for effective selection and genetic evaluation. Data for estimating these parameters were collected from 1963 to 1985 and consisted of 32,018 mature weight records of 4,175 Hereford cows that were in one control and three selection lines that had been selected for weaning weight, for yearling weight, or for an index combining yearling weight and muscle score for 22 yr. Several models and subsets of the data were considered. The mature weight records consisted of a maximum of three seasonal weights taken each year, at brand clipping (February and March), before breeding (May and June), and at palpation (August and September). Heritability estimates were high (0.49 to 0.86) for all models considered, which suggests that selection to change mature weight could be effective. The model that best fit the data included maternal genetic and maternal permanent environmental effects in addition to direct genetic and direct permanent environmental effects. Estimates of direct heritability with this model ranged from 0.53 to 0.79, estimates of maternal heritability ranged from 0.09 to 0.21, and estimates of the genetic correlation between direct and maternal effects ranged from -0.16 to -0.67 for subsets of the data based on time of year that mature weight was measured. For the same subsets, estimates of the proportions of variance due to direct permanent environment and maternal permanent environment ranged from 0.00 to 0.09 and 0.00 to 0.06, respectively. Using a similar model that combined all records and included an added fixed effect of season of measurement of mature weight, direct heritability, maternal heritability, genetic correlation between direct and maternal effects, proportion of variance due to direct permanent environmental effects, and proportion of variance due to maternal permanent environmental effects were estimated to be 0.69, 0.13, -0.65, 0.00, and 0.04, respectively. Mature weight is a highly heritable trait that could be included in selection programs and maternal effects should not be ignored when analyzing mature weight data.     

Analysis of founder-specific inbreeding depression on birth weight in Ripollesa lambs

Although inbreeding (F) is a topic of major concern in animal breeding, estimates of inbreeding depression are usually obtained by modeling the overall F coefficient of each individual, without considering that the recessive (deleterious) genetic load of a given population may be unevenly distributed among the founder genomes. The founder-specific partial F coefficient is calculated as the identity-by-descent probability at any given autosomal locus related to a particular founder and allows a more detailed analysis of inbreeding depression on productive traits. Within this context, birth BW data from 2,459 Ripollesa lambs were analyzed under a hierarchical animal model without F-related covariates (model 0), with inbreeding depression modeled by the overall F coefficient (model F1), or by the partial F coefficient of 9 founders that made a relevant contribution to the population inbreeding (model F2). A straightforward empirical Bayes factor (BF) was developed for testing statistical relevance of each F-related covariate, in which greater-than-1 values favored the model including the covariate. The deviance information criterion (DIC) clearly supported model F1 (5,767.8) rather than model 0 (5,771.2), suggesting that inbreeding depression had a relevant influence on birth BW data. The linear effect of inbreeding depression was statistically relevant in model F1 (BF = 2.52 x 10(35)), with lamb birth BW declining by -13.6 g with each 1% F increase. The quadratic effect of inbreeding depression was almost null in model F1 (BF = 0.02), as suggested by the reduction in DIC (5,766.9) when this effect was removed from model F1. On the other hand, model F2 provided a similar DIC (5,767.9) value, with this parameter decreasing to 5,764.7 when nonrelevant founder-specific inbreeding depression effects were removed. Substantial heterogeneity in founder-specific inbreeding depression was reported by model F2, in which estimates for 4 of the 9 founders did not differ from zero (BF between 0.05 and 0.42), whereas 5 founders originated moderate (-8.2 g for each 1% F increase; BF = 1.42) to large inbreeding depression (-96.2 g for each 1% F increase; BF = 8.80 x 10(19)). The substantial variability between founder estimates suggested that inbreeding depression effects may mainly be due to a few alleles with major deleterious effects. These results contribute valuable information that should help to achieve more accurate management of inbreeding in the Ripollesa breed.