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.     

(Co)variance components, genetic parameters and annual trends for calf weights in a pedigree Brahman herd under selection for three decades

A 300 cow Brahman herd kept on improved pasture was subjected to a selection and management programme based on a limited breeding season. Artificial insemination using mainly progeny tested bulls was used in part of the herd and the rest were bred in single sire herds. Of the 200 sires used during the 30 year period, 82% were homebred and selected principally for high estimated breeding value of 18-month weight. Variance components of birth (BW), weaning (205 W) and 18-month (548 W) weights of 6130 calves born 1968 through to 1997 were estimated by the Restricted Maximum Likelihood method (REML) using uni- and bivariate animal models. For each weight the animal's direct and maternal genetic and the dam's permanent environmental effects were considered random and those of sex, year and month of birth and age of cow were considered fixed, but the models differed as far as the number of significant interactions included. Adjusted least squares means for BW, 205 W and 548 W were 28, 158 and 292 kg. Phenotypic and direct and maternal genetic trends from univariate analysis were for BW: 0.156, 0.061 and −0.001 kg; for 205 W: 0.471, 0.126 and 0.044 kg; for 548 W: 1.973, 0.486 and 0.251 kg per year. Direct and maternal heritabilities from univariate analyses were for BW, 205 W and 548 W, 0.33 and 0.08; 0.07 and 0.14; 0.13 and 0.08, respectively. Genetic direct-maternal correlations for the three weights were −0.37, −0.13 and 0.49 and permanent environmental variance of the dam as proportion of phenotypic variance (c²) had values of 0.03, 0.16 and 0.01, respectively. Direct and maternal genetic correlations were for BW: 205 W, 0.64 and 0.74; for BW: 548 W, 0.35 and 0.74; and for 205 W: 548 W, 0.64 and 0.96. Future genetic work in the herd should put more emphasis on the improvement of cow efficiency for sustainable beef production on native and improved pasture.     

Variation in direct and maternal genetic effects for meat production traits in Egyptian Zaraibi goats

Multi-trait analyses were carried out to quantify the (co)variation in meat production traits in Zaraibi goats. The data were obtained from a research station. There were birth weight records on 6610 kids, of which 5970 and 5237 had also pre-and postweaning gain record, respectively. The kids were progeny of 115 bucks and 1387 does, which had altogether 3603 litter size and milk yield records in different parities and which were daughters of 109 sires and 721 dams. Single-trait analyses were carried out as preliminary to a three-trait (litter size, birth weight, early growth) and five-trait (litter size, milk and growth traits) analyses. The analyses containing birth weight data required the highest number of iteration rounds in estimating the variance components using AI REML. The maternal genetic component was important for the genetic variation of birth weight and preweaning gain. In general, direct heritability was low (0.03–0.12) for growth traits, possibly due to the low-input environment. The estimates on genetic correlation between direct and maternal effects within these traits indicated mostly favourable relationship. Genetic antagonism was found between birth weight and early growth. Heritability (repeatability) for 90-day and total milk yield was 0.16–0.23 and 0.23–0.24 (0.28 and 0.39–0.40), respectively and 0.04–0.05 (0.10–0.11) for litter size. The genetic correlation between 90-day (total) milk yield and litter size was 0.45 (0.22). The correlation between the milk yield and the maternal genetic effects for the preweaning gain was very high (0.94). Selection schemes aiming to improve meat (litter size and growth) and milk production simultaneously are feasible. The increased milk production serves also for the acceleration of early growth in kids.     

Estimates of direct and maternal (co)variance components as well as genetic parameters of growth traits in Nellore sheep

In the present study, (co)variance components and genetic parameters in Nellore sheep were obtained by restricted maximum likelihood (REML) method using six different animal models with various combinations of direct and maternal genetic effects for birth weight (BW), weaning weight (WW), 6-month weight (6MW), 9-month weight (9MW) and 12-month weight (YW). Evaluated records of 2075 lambs descended from 69 sires and 478 dams over a period of 8 years (2007–2014) were collected from the Livestock Research Station, Palamaner, India. Lambing year, sex of lamb, season of lambing and parity of dam were the fixed effects in the model, and ewe weight was used as a covariate. Best model for each trait was determined by log-likelihood ratio test. Direct heritability for BW, WW, 6MW, 9MW and YW were 0.08, 0.03, 0.12, 0.16 and 0.10, respectively, and their corresponding maternal heritabilities were 0.07, 0.10, 0.09, 0.08 and 0.11. The proportions of maternal permanent environment variance to phenotypic variance (Pe²) were 0.07, 0.10, 0.07, 0.06 and 0.10 for BW, WW, 6MW, 9MW and YW, respectively. The estimates of direct genetic correlations among the growth traits were positive and ranged from 0.44(BW-WW) to 0.96(YW-9MW), and the estimates of phenotypic and environmental correlations were found to be lower than those of genetic correlations. Exclusion of maternal effects in the model resulted in biased estimates of genetic parameters in Nellore sheep. Hence, to implement optimum breeding strategies for improvement of traits in Nellore sheep, maternal effects should be considered.     

Genetic parameter estimation for pre- and post-weaning traits in Brahman cattle in Brazil

Beef cattle producers in Brazil use body weight traits as breeding program selection criteria due to their great economic importance. The objectives of this study were to evaluate different animal models, estimate genetic parameters, and define the most fitting model for Brahman cattle body weight standardized at 120 (BW120), 210 (BW210), 365 (BW365), 450 (BW450), and 550 (BW550) days of age. To estimate genetic parameters, single-, two-, and multi-trait analyses were performed using the animal model. The likelihood ratio test was verified between all models. For BW120 and BW210, additive direct genetic, maternal genetic, maternal permanent environment, and residual effects were considered, while for BW365 and BW450, additive direct genetic, maternal genetic, and residual effects were considered. Finally, for BW550, additive direct genetic and residual effects were considered. Estimates of direct heritability for BW120 were similar in all analyses; however, for the other traits, multi-trait analysis resulted in higher estimates. The maternal heritability and proportion of maternal permanent environmental variance to total variance were minimal in multi-trait analyses. Genetic, environmental, and phenotypic correlations were of high magnitude between all traits. Multi-trait analyses would aid in the parameter estimation for body weight at older ages because they are usually affected by a lower number of animals with phenotypic information due to culling and mortality.     

Estimation of Genetic Parameters and Variance Components for Growth Traits of Nguni Cattle in Limpopo Province,South Africa

Estimates of (co)variance and genetic parameters of birth, weaning (205 days) and yearling (365 days) weight were obtained using single-trait animal models. The data were analysed by restricted maximum likelihood, fitting an animal model that included direct and maternal genetic and permanent environmental effects. The data included records collected between 1976 and 2001. The pedigree information extended as far back as early 1960s. The heritabilities for direct effects of birth, weaning and yearling weights were 0.36, 0.29 and 0.25, respectively. Heritability estimates for maternal effects were 0.13, 0.16 and 0.15 for birth, weaning and yearling weights, respectively. The correlations between direct and maternal additive genetic effects were negative for all traits analysed. The results indicate that both direct and maternal effects should be included in a selection programme for all the traits analysed.     

Technical note: Calculation of standard errors of estimates of genetic parameters with the multiple-trait derivative-free restricted maximal likelihood programs

The multiple-trait derivative-free REML set of programs was written to handle partially missing data for multiple-trait analyses as well as single-trait models. Standard errors of genetic parameters were reported for univariate models and for multiple-trait analyses only when all traits were measured on animals with records. In addition to estimating (co)variance components for multiple-trait models with partially missing data, this paper shows how the multiple-trait derivative-free REML set of programs can also estimate SE by augmenting the data file when not all animals have all traits measured. Although the standard practice has been to eliminate records with partially missing data, that practice uses only a subset of the available data. In some situations, the elimination of partial records can result in elimination of all the records, such as one trait measured in one environment and a second trait measured in a different environment. An alternative approach requiring minor modifications of the original data and model was developed that provides estimates of the SE using an augmented data set that gives the same residual log likelihood as the original data for multiple-trait analyses when not all traits are measured. Because the same residual vector is used for the original data and the augmented data, the resulting REML estimators along with their sampling properties are identical for the original and augmented data, so that SE for estimates of genetic parameters can be calculated.     

Genetic parameters for growth traits for a composite terminal sire breed of sheep.

Records of 9,055 lambs from a composite population originating from crossing Columbia rams to Hampshire x Suffolk ewes at the U.S. Meat Animal Research Center were used to estimate genetic parameters among growth traits. Traits analyzed were weights at birth (BWT), weaning (7 wk, WWT), 19 mo (W19), and 31 mo (W31) and postweaning ADG from 9 to 18 or 19 wk of age. The ADG was also divided into daily gain of males (DGM) and daily gain of females (DGF). These two traits were analyzed with W19 and with W31 in three-trait analyses. (Co)variance components were estimated with REML for an animal model that included fixed effects of sex, age of dam, type of birth or rearing, and contemporary group. Random effects were direct and maternal genetic of animal and dam with genetic covariance, maternal permanent environmental, and random residual. Estimates of direct heritability were .09, .09, .35, .44, .19, .16, and .23 for BWT, WWT, W19, W31, ADG, DGM, and DGF, respectively. Estimates of maternal permanent environmental variance as a proportion of phenotypic variance were .09, .12, .03, .03, .03, .06, and .02, respectively. Estimates of maternal heritability were .17 and .09 for BWT and WWT and .01 to .03 for other traits. Estimates of genetic correlations were large among W19, W31, and ADG (.69 to .97), small between BWT and W31 or ADG, and moderate for other pairs of traits (.32 to .45). The estimate of genetic correlation between DGM and DGF was .94, and the correlation between maternal permanent environmental effects for these traits was .56. For the three-trait analyses, the genetic correlations of DGM and DGF with W19 were .69 and .82 and with W31 were .67 and .67, respectively. Results show that models for genetic evaluation for BWT and WWT should include maternal genetic effects. Estimates of genetic correlations show that selection for ADG in either sex can be from records of either sex (DGM or DGF) and that selection for daily gain will result in increases in mature weight but that BWT is not correlated with weight at 31 mo.     

Estimation of genetic parameters and prediction of breeding values for multivariate threshold and continuous data in a simulated horse population using Gibbs sampling and residual maximum likelihood

Simulated horse data were used to compare multivariate estimation of genetic parameters and prediction of breeding values (BV) for categorical, continuous and molecular genetic data using linear animal models via residual maximum likelihood (REML) and best linear unbiased prediction (BLUP) and mixed linear-threshold animal models via Gibbs sampling (GS). Simulation included additive genetic values, residuals and fixed effects for one continuous trait, liabilities of four binary traits, and quantitative trait locus (QTL) effects and genetic markers with different recombination rates and polymorphism information content for one of the liabilities. Analysed data sets differed in the number of animals with trait records and availability of genetic marker information. Consideration of genetic marker information in the model resulted in marked overestimation of the heritability of the QTL trait. If information on 10,000 or 5,000 animals was used, bias of heritabilities and additive genetic correlations was mostly smaller, correlation between true and predicted BV was always higher and identification of genetically superior and inferior animals was - with regard to the moderately heritable traits, in many cases - more reliable with GS than with REML/BLUP. If information on only 1,000 animals was used, neither GS nor REML/BLUP produced genetic parameter estimates with relative bias 50% for all traits. Selection decisions for binary traits should rather be based on GS than on REML/BLUP breeding values.     

Choice of statistical model for estimating genetic parameters using restricted maximum likelihood in swine

Summary Restricted maximum likelihood (REML) was used to determine the choice of statistical model, additive genetic maternal and common litter effects and consequences of ignoring these effects on estimates of variance–covariance components under random and phenotypic selection in swine using computer simulation. Two closed herds of different size and two traits, (i) pre‐weaning average daily gain and (ii) litter size at birth, were considered. Three levels of additive direct and maternal genetic correlations (r_dm) were assumed to each trait. Four mixed models (denoted as GRM1 through GRM4) were used to generate data sets. Model GRM1 included only additive direct genetic effects, GRM2 included only additive direct genetic and common litter effects, GRM3 included only additive direct and maternal genetic effects and GRM4 included all the random effects. Four mixed animal models (defined as EPM1 through EPM4) were defined for estimating genetic parameters similar to GRM. Data from each GRM were fitted with EPM1 through EPM4. The largest biased estimates of additive genetic variance were obtained when EPM1 was fitted to data generated assuming the presence of either additive maternal genetic, common litter effects or a combination thereof. The bias of estimated additive direct genetic variance (VA_d) increased and those of recidual variance (VE) decreased with an increase in level of r_dm when GRM3 was used. EPM1, EPM2 and EPM3 resulted in biased estimation of the direct genetic variances. EPM4 was the most accurate in each GRM. Phenotypic selection substantially increased bias of estimated additive direct genetic effect and its mean square error in trait 1, but decreased those in trait 2 when ignored in the statistical model. For trait 2, estimates under phenotypic selection were more biased than those under random selection. It was concluded that statistical models for estimating variance components should include all random effects considered to avoid bias.     

Estimates of genetic correlations between days to calving and reproductive and weight traits in Nelore cattle

Data comprising 53,181 calving records were analyzed to estimate the genetic correlation between days to calving (DC), and days to first calving (DFC), and the following traits: scrotal circumference (SC), age at first calving (AFC), and weight adjusted for 550 d of age (W550) in a Nelore herd. (Co)variance components were estimated using the REML method fitting bivariate animal models. The fixed effects considered for DC were contemporary group, month of last calving, and age at breeding season (linear and quadratic effects). Contemporary groups were composed by herd, year, season, and management group at birth; herd and management group at weaning; herd, season, and management group at mating; and sex of calf and mating type (multiple sires, single sire, or AI). In DFC analysis, the same fixed effects were considered excluding the month of last calving. For DC, a repeatability animal model was applied. Noncalvers were not considered in analyses because an attempt to include them, attributing a penalty, did not improve the identification of genetic differences between animals. Heritability estimates ranged from 0.04 to 0.06 for DC, from 0.06 to 0.13 for DFC, from 0.42 to 0.44 for SC, from 0.06 to 0.08 for AFC, and was 0.30 for W550. The genetic correlation estimated between DC and SC was low and negative (-0.10), between DC and AFC was high and positive (0.76), and between DC and W550 was almost null (0.07). Similar results were found for genetic correlation estimates between DFC and SC (-0.14), AFC (0.94), and W550 (-0.02). The genetic correlation estimates indicate that the use of DC in the selection of beef cattle may promote favorable correlated responses to age at first mating and, consequently, higher gains in sexual precocity can be expected.     

Direct and maternal (co)variance components and genetic parameters for growth and reproductive traits in the Boran cattle in Kenya

Direct and maternal (co)variance components and genetic parameters were estimated for growth and reproductive traits in the Kenya Boran cattle fitting univariate animal models. Data consisted of records on 4502 animals from 81 sires and 1010 dams collected between 1989 and 2004. The average number of progeny per sire was 56. Direct heritability estimates for growth traits were 0.34, 0.12, 0.19, 0.08 and 0.14 for birth weight (BW), weaning weight (WW), 12-month weight (12W), 18-month weight (18W) and 24-month weight (24W), respectively. Maternal heritability increased from 0.14 at weaning to 0.34 at 12 months of age but reduced to 0.11 at 24 months of age. The maternal permanent environmental effect contributed 16%, 4% and 10% of the total phenotypic variance for WW, 12W and 18W, respectively. Direct-maternal genetic correlations were negative ranging from −0.14 to −0.58. The heritability estimates for reproductive traits were 0.04, 0.00, 0.15, 0.00 and 0.00 for age at first calving (AFC), calving interval in the first, second, and third parity, and pooled calving interval. Selection for growth traits should be practiced with caution since this may lead to a reduction in reproduction efficiency, and direct selection for reproductive traits may be hampered by their low heritability.     

Genetic correlations between body weight,scrotal circumference and visual evaluation scores in Bos indicus cattle

The objective was to estimate genetic correlations between body weight (BW), scrotal circumference and visual evaluation scores of body conformation measured at standard ages in Guzerat cattle. All measurements were performed at 205 (weaning age), 365, 450 and 550 days of age; for BW, two additional measurements (at birth and 120 days of age) were realized. The data utilized in this study were retrieved from a database of the Brazilian Association of Zebu Breeders that contained information of registered Guzerat animals born between 1970 and 2013. Genetic parameters were estimated in bi‐trait analyses by using Bayesian inference. Genetic correlations between BW at 205 and 450 days of age with other traits were high and positive, whereas the correlations between visual evaluation scores with other traits were moderate. Based on correlations herein obtained, we conclude that selection based on BW results in increased visual scores and scrotal circumference, leading to improvements in productive performance and animals with best body conformation.     

Estimation of variance and covariance components to determine heritabilities and repeatability of weaning weight in American Simmental cattle

Components of (co)variance for weaning weight were estimated from field data provided by the American Simmental Association. These components were obtained for the observational components of variance corresponding to a sire, maternal grandsire, and dam within maternal grandsire model. From these estimates, direct additive genetic variance (Sigma2A), maternal additive genetic variance (Sigma2M), covariance between direct and maternal additive genetic effects (SigmaAM), variance of permanent environment(Sigma2pe) and temporary environment variance(Sigma2te) were determined. A procedure to approximate restricted maximum likelihood (REML) estimates of the observational components of variance based on the expectation-maximization (EM) algorithm is described. From these results, phenotypic variance ( ) of weaning weight was 667.88 kg2. Values forSigma2A, Sigma2M, Sigma2pe and Sigma2te were 79,30,58,38,49.45, and 469.97 kg2, respectively. Genetic correlation between direct and maternal additive genetic effects was .16.     

应用多性状动物模型及DFREML法对罗曼褐壳蛋鸡纯系的遗传分析

采用多性状动物模型BLUP和非求导约束最大似然法（MTDFREML）估计了引进罗曼蛋鸡纯系配套组合中4个品系9个性状的方差组分和遗传参数,并估计了固定效应的BLUE值和动物个体的加性遗传效应值（育种值）,分析了测定性状的世代间遗传趋势和表型趋势。结果表明,4个系各性状的遗传力基本一致,体重、蛋重以及不同周期的产蛋量之间存在显著的正相关。蛋重与产蛋量存在较强的遗传负相关。六个世代选育后,各品系蛋重、产蛋量的平均育种值均有提高,表明对产蛋量和蛋重的选择是有效的。     

Genetic (co)variance components for ewe productivity traits in Katahdin sheep

The objective of this study was to estimate genetic parameters, in Katahdin sheep, for total weight of litter weaned per ewe lambing (TW) and its components, number of lambs born (NB), number of lambs weaned (NW), and average weight of lambs weaned (AW) measured as traits of the ewe. Weaning weights of lambs (WW) were adjusted to 60 d of age and for effects of ewe age, lamb sex, and type of birth and rearing and averaged over all lambs in the litter to obtain AW. The 60-d age-adjusted WW were adjusted for ewe age and lamb sex and summed over all lambs in the litter to obtain TW. A total of 2,995 NB and NW records, 2,622 AW, and 2,714 TW records were available from 1,549 ewes (progeny of 235 sires) over 4 yr. Heritabilities were initially estimated for each trait from univariate REML analyses. Estimates of genetic correlations were obtained from bi- and trivariate analyses. Models for NB, NW, AW, and TW included random ewe additive and permanent environmental effects. A random service sire effect was also fit for AW and TW. Heritabilities of TW, NB, NW, and AW from univariate analyses were 0.12, 0.12, 0.09, and 0.13 (all P < 0.01), respectively. Permanent environmental effects were significant (P < 0.01) for TW and AW. Genetic correlations of TW with NB, NW, and AW ranged from 0.27 to 0.33, 0.88 to 0.91, and 0.72 to 0.76, respectively; those of NB with NW and AW ranged from 0.70 to 0.75 and -0.01 to 0.02, respectively; and that between NW and AW ranged from 0.40 to 0.55. Genetic parameters were also obtained for lamb survival to weaning (LS) and WW measured as traits of the lamb, and the relationships between WW of the ewe as a lamb and her subsequent records for NB and NW were also estimated. A total of 5,107 LS and 5,444 WW records were available. Models for WW and LS included random animal and maternal genetic, maternal permanent environmental, and litter effects. Heritability of WW ranged from 0.15 to 0.20. There was no evidence of genetic effects on LS. Direct genetic correlations of WW with NB and NW were not significantly different from zero. The correlation between maternal genetic effects on WW, and animal genetic effects on NW, averaged 0.35. Results of this study indicate that there are no major antagonisms among TW and its components, so that selection for TW would not have adverse effects on any component traits and vice versa. Maternally superior ewes for WW appear to also be somewhat superior for NW.     

Estimates of genetic parameters for worm resistance,wool and growth traits in Merino sheep of Uruguay

The genotype of an individual and the environment as the maternal ability of its dam have substantial effects on the phenotype expression of many production traits. The aim of the present study was to estimate the (co)variance components for worm resistance, wool and growth traits in Merino sheep, testing the importance of maternal effects and to determine the most appropriate model for each trait. The traits analyzed were Greasy Fleece Weight (GFW), Clean Fleece Weight (CFW), average Fibre Diameter (FD), Coefficient of Variation of FD (CVFD), Staple Length (SL), Comfort Factor (CF30), Weaning Weight (WWT), Yearling Body Weight (YWT) and Faecal worm Egg Count (FEC). The data were recorded during a 15-year period from 1995 to 2010, from Uruguayan Merino stud flocks. A Bayesian analysis was performed to estimate (co)variance components and genetic parameters. By ignoring or including maternal genetic or environmental effects, five different univariate models were fitted in order to determine the most effective for each trait. For CVFD and YWT, the model fitting the data best included direct additive effects as the only significant random source of variation. For GFW, CFW, FD, SL and CF30 the most appropriate model included direct-maternal covariance; while for FEC included maternal genetics effects with a zero direct-maternal covariance. The most suitable model for WWT included correlated maternal genetic plus maternal permanent environmental effects. The estimates of direct heritability were moderate to high and ranged from 0.15 for log transformed FEC to 0.74 for FD. Most of the direct additive genetic correlation (rg) estimations were in the expected range for Merino breed. However, the estimate of rg between FEC and FD was unfavourable (−0.18±0.03). In conclusion, there is considerable genetic variation in the traits analyzed, indicating the potential to make genetic progress on these traits. This study showed that maternal effects are influencing most of traits analyzed, thus these effects should be considered in Uruguayan Merino breeding programs; since the implementation of an appropriate model of analysis is critical to obtain accurate estimates.     

Genetic associations of sow longevity with age at first farrowing, number of piglets weaned, and wean to insemination interval in the Finnish Landrace swine population

The objective of the study was to estimate genetic parameters for length of productive life (LPL), and determine its genetic correlation with age at first farrowing (AFF), number of piglets weaned at first farrowing (NW), and first wean-to-insemination interval (W2I) in the Finnish Landrace swine population. Data from the Finnish national litter recording scheme were utilized to estimate the genetics of LPL, and genetic associations between LPL, AFF, NW, and W2I. Data from the Finnish Landrace sow records were utilized from farms that farrowed more than 20 gilts annually from 2000 through 2005. The data set included information from 11,222 sows, all of which had AFF and NW information available. The sows producing the records evaluated were daughters of 1,267 sires, and there were 3,684 animals in the pedigree when all of the sires were traced back to founder animals. All data were obtained from FABA Breeding (Vantaa, Finland). Multivariate Bayesian analysis of Gaussian, right censored Gaussian, and categorical traits was utilized to estimate (co)variance parameters of LPL, AFF, NW, and W2I of the sow. From these traits, AFF and NW were treated as Gaussian, LPL as right-censored Gaussian, and W2I as categorical traits. Estimated posterior means of heritabilities were 0.22, 0.16, 0.09, and 0.08 for LPL, AFF, NW, and W2I, respectively. A relatively large proportion of variance due to farm-year interaction was observed (posterior means of f(2) ranged between 0.03 and 0.26). The LPL was moderately genetically correlated with NW and AFF (posterior means were -0.20 and 0.36, respectively), whereas no clear association was found between W2I and LPL. Favorable genetic correlations between AFF and W2I and between NW and W2I were also observed. Additionally, an unfavorable genetic correlation between AFF and NW was observed in the present data set. Because LPL is genetically associated with other economically important prolificacy traits, it should be included in a multiple trait swine breeding value estimation system.     

"Quasi-REML" correlation estimates between production and health traits in the presence of selection and confounding: a simulation study

Performance of the "quasi-REML" method for estimating correlations between a continuous trait and a categorical trait, and between two categorical traits, was studied with Monte Carlo simulations. Three continuous, correlated traits were simulated for identical populations and three scenarios with either no selection, selection for one moderately heritable trait (Trait 1, h2 = .25), and selection for the same trait plus confounding between sires and management groups. The "true" environmental correlations between Traits 2 (h2 = .10) and 3 (h2 = .05) were always of the same absolute size (.20), but further data scenarios were generated by setting the sign of environmental correlation to either positive or negative. Observations for Traits 2 and 3 were then reassigned to binomial categories to simulate health or reproductive traits with incidences of 15 and 5%, respectively. Genetic correlations (r(g12), r(g13), and r(g23) and environmental correlations (r(e12), r(e13), and r(e23)) were estimated for the underlying continuous scale (REML) and the visible categorical scales ("quasi-REML") with linear multiple-trait sire and animal models. Contrary to theory, practically all "quasi-REML" genetic correlations were underestimated to some extent with the sire and animal models. Selection inflated this negative bias for sire model estimates, and the sign of r(e23) noticeably affected r(g23) estimates for the animal model, with greater bias and SD for estimates when the "true" r(e23) was positive. Transformed "quasi-REML" environmental correlations between a continuous and a categorical trait were estimated with good efficiency and little bias, and corresponding correlations between two categorical traits were systematically overestimated. Confounding between sires and contemporary groups negatively affected all correlation estimates on the underlying and the visible scales, especially for sire model "quasi-REML" estimates of genetic correlation. Selection, data structure, and the (co)variance structure influences how well correlations involving categorical traits are estimated with "quasi-REML" methods.     

Calculating economic weights for sheep sire breeds used in different breeding systems

The objective of this paper was to adapt gene-flow methodology for the calculation of economic weights (EW) for direct and maternal traits and trait components in sheep and to apply this methodology to the Suffolk breed in the Czech Republic. Computer programs were developed in which annual-lambing sheep production systems with purebreeding or partial terminal crossing were simulated. Using these programs, the EW for 12 production and functional traits were estimated for i) Suffolk sires whose sons were used both in purebreeding and in terminal crossing with the 4 dual-purpose breeds, Romanov, Sumavska, Romney, and Merinolandschaf; and ii) Suffolk sires used only for terminal crossing. For case (i), the EW were at first calculated separately for the purebreeding system and for the crossing systems with the 4 dual-purpose breeds in dam position. Compound EW for the general breeding goal for Suffolk were then estimated as weighted averages from the EW in the 5 subsystems. Standardized EW were calculated by multiplying the marginal EW with the genetic SD of the trait, and relative EW were defined as absolute values of the standardized EW expressed as percentage of the sum of the absolute values of the standardized EW over all traits. The 5 most important trait components for Suffolk sires whose sons were used both in purebreeding and in terminal crossing were (relative EW given in parentheses): the direct components of survival rate until weaning (21.0%), daily BW gain until weaning (14.1%), survival rate at birth (14.0%), the maternal component of survival rate until weaning (10.7%), and litter size at lambing (7.6%). There were only small differences between the relative EW calculated for the whole system with pure- and crossbreeding and the relative EW for the purebred system within the Suffolk breed. Therefore, selection of Suffolk rams using a selection index based on the compound EW is expected to be of high efficiency in all of the simulated breeding systems. Only direct traits were relevant for Suffolk sires used only for terminal crossing; the most important (range of relative EW calculated for the 4 crossing systems given in parentheses) were survival rate until weaning (35.2 to 36.5%), daily BW gain until weaning (24.2 to 26.3%), and survival rate at birth (23.7 to 24.8%).