GENETIC EVALUATIONS IN BEEF CATTLE

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
303	3310	1080	85%
303	3320	1080	15%

Progress 03/04/98 to 09/30/03

Outputs
The American Simmental Association provided us with data on carcass traits on slaughter animals and ultrasound measures on breeding animals. In collaboration with Denny Crews at Lethridge Research Center of Agriculture and Agri-Food Canada, these two data sets were used to estimate the genetic and environmental parameters associated with paired observations from the ultrasound and carcass data. The parameters from this study were then incorporated in a multitrait, multibreed genetic evaluation for carcass. These evaluations are now available to the industry. A pilot project in commercial ranch genetic evaluation was initiated at the Bell Ranch in New Mexico. DNA samples were collected on commercial bulls and calves from multiple sire breeding pastures. Parent identification was accomplished using software developed as part of this project. Weaning weights on all calves have been collected as have ultrasound measures for carcass quality on all steer calves. Female reproductive success and longevity are now being monitored. Genetic evaluations have been done at this pilot location using a new parent uncertainty model. The study on genetic evaluation for predicted feed efficiency has been expanded to included four breeds. Data are being collected on bulls currently being fed on performance test. These data will be available over the next two years and fall under the new hatch project on feed efficiency started in October 2004.

Impacts
The impact of the implementation of multibreed carcass evaluations using ultrasound information will be to increase the accuracy of genetic predictions for carcass merit characteristics and to increase the number of animals with carcass trait evaluations. This should enhance the efficiency of selection for improving carcass quality. The impact of the commercial ranch project is intended to expand the influence of genetic evaluation to commercial operations. This will allow for selection of bulls that are producing the calves for harvest. This dramatically increases the potential for increasing data on carcass traits and provides information directly on seedstock animals. These evaluations will be used by seedstock producers in selection decisions for improvement of carcass quality and by commercial producers in the selection of replacement herd bulls.

Publications

Crews, D. H., Jr., Pollak, E. J., Weaber, R. L., Quaas, R. L. and Lipsey, R. J. 2003. Genetic parameters for carcass traits and their live animal indicators in Simmental cattle. J. Anim. Sci. 81:1427-1433.

Progress 01/01/02 to 12/31/02

Outputs
The American Simmental Association provided us with data on carcass traits on slaughter animals and ultrasound measures on breeding animals. In collaboration with Denny Crews at Lethridge Research Center of Agriculture and Agri-Food Canada, these two data sets were used to estimate the genetic and environmental parameters associated with paired observations from the ultrasound and carcass data. The parameters from this study were then incorporated in a multitrait, multibreed genetic evaluation for carcass. These evaluations will be made available to the industry during the summer of 2003. A pilot project in commercial ranch genetic evaluation was initiated at the Bell Ranch in New Mexico. DNA samples were collected on commercial bulls and calves from multiple sire breeding pastures. Parent identification was accomplished using software developed as part of this project. Weaning weights on all calves have been collected as have ultrasound measures for carcass quality on all steer calves. The study on genetic evaluation for predicted feed efficiency has been expanded to included four breeds. Data are being collected on bulls currently being fed on performance test.

Impacts
Carcass data are difficult and expensive to collect. Ultrasound may be used on potential breeding animals. This dramatically increases the potential for increasing data on carcass traits and provides information directly on seedstock animals. Genetic evaluation for carcass characteristics using ultrasound data will be released to the industry in summer of 2003. These evaluations will be used by seedstock producers in selection decisions for improvement of carcass quality and by commercial producers in the selection of replacement herd bulls.

Publications

Zhang, Z.W., Quaas, R.L. and Pollak, E.J. 2002. Simulation study on the effects of incorporating external genetic evaluation results. 7th World Congress on Genetics Applied to Livestock Production. Montpellier, France. Communication #20-14.
Cardoso, F.F., Tempelman R.J. and Pollak, E.J. 2002. Bayesian influence on genetic merit with uncertain paternity. 7th World Congress on Genetics Applied to Livestock Production. Montpellier, France. Communication #20-02.
Pollak, E.J. and Kirschten, D.P. 2002. Genetic prediction of efficiency in the future: A U.S. perspective. Presented at the Beef Improvement Federation Annual Convention, July 10-13. Omaha, NE. Pages 107-110.

Progress 01/01/01 to 12/31/01

Outputs
Collection of carcass merit data continues for national carcass merit project sponsored by National Cattlemen's Beef Association and various breed associations. This is the last year of this project. We have used the data from this program to create a genetic evaluation for Warner-Bratzler shear force measures on steaks. This evaluation of Simmental bulls in the project has been made available to the industry. We have started a commercial ranch project to bring genetic evaluations to commercially used bulls. This project is being piloted at the Bell Ranch, New Mexico. We have initiated a project with the Charolais producers and their breed association to evaluate models for predicted feed efficiency. We will evaluate the genetic component of predicted feed consumption. There are 11 producers representing 2000 bulls on test to be used in this study.

Impacts
Carcass merit data will provide a standard regarding the quality of beef products produced. Successful validation of QTL's will provide a selection tool for traits where data collection is difficult and expensive. Feed efficiency is a difficult trait to obtain genetic information on as the collection of data is difficult. A model for the prediction of consumption will be used to study the genetics of feed efficiency.

Publications

Pollak, E. J., M. E. Dikeman, C. Gill, D. W. Moser, T. Holm, and E. Westcott. 2001. Update on the carcass merit project. Reciprocal Meats Conference Proceedings Vol. 1, pages 103-104.
Minick, J. A., D. E. Wilson, M. E. Dikeman, and E. J. Pollak. 2001. Heritability and correlation estimates of carcass data from Angus-sired steers. J. Anim. Sci. 79(Suppl. 2):
Dikeman, M.E., E. J. Pollak, R. D. Green, J. Taylor, S. Davis, T. Holm, S. Koontz, C. Gill, D. Moser, and E. A. Westcott. 2001. Carcass Merit Project:Development of EPDs and Genetic Marker Validation. Kansas Agr. Expt. Sta. Rep. of Prog. 873:4-6.
Dikeman, M. E., E. J. Pollak, S. L. Stroda, R. J. Lipsey, and E. A. Westcott. 2001. Carcass Merit Traits: Development of EPDs for Warner-Bratzler Shear force and DNA Marker Validation. Kansas Agr. Expt. Sta. Rep. of Prog. 873:7-8.

Progress 01/01/00 to 12/31/00

Outputs
Collection of carcass merit data continues for national carcass merit project sponsored by National Cattlemen's Beef Association and various breed associations. There are 12 breeds that have collected carcass information, blood samples and have provided us with pedigree information on bulls in the project. Ten sires from each breed are designated for a DNA study. Fifty progeny from each of these bulls are being scored for carcass characteristics and shear force, while 25 of these are being evaluated additionally for sensory panel data. Over 2000 records on 77 bulls have been report. Eleven bulls have completed data collection for analysis of quantitative trait locus segregation. Data on two bulls has been analyzed and both have been found to be heterozygous for shear force measures. We have done a an analysis of these data to estimate heritability of shear force in the Simmental breed. The estimate based on 800 records of progeny from 47 bulls was 0.21.

Impacts
Carcass merit data will provide a standard regarding the quality of beef products produced. Successful validation of QTL's will provide a selection tool for traits where data collection is difficult and expensive.

Publications

Pollak, E. J. 2000. Beef cattle breeding--past, present, future. In Proceedings, XXXVI Annual Meeting of the Brazilian Society of Animal Science, Vicosa, Minas Gerais, July 24-27.
Zhang, Z, Pollak, E.J, Quaas, R.L., Dikeman, M.E., Green, R.D., Taylor, J., and Davis, S. 2000. (Abstr.) Heritability of Warner Bratzler shear force measures estimated from data on Simmental-sired calves. J. Animal Sci. 78(Suppl. 1):59.

Progress 01/01/99 to 12/31/99

Outputs
Collection of carcass merit data began this year for the national carcass merit project sponsored by National Cattlemen's Beef Association and various breed associations. Sixteen breeds are participating in a project. Ten sires from each breed are designated for a DNA study. Fifty progeny from each of these bulls are being scored for carcass characteristics and shear force, while 25 of these are being evaluated additionally for sensory panel data. The bull and progeny will be DNA tested for segregating markers and analyzed for the association of these markers with QTL's identified in the Texas A&M project involving Brahman and Angus cattle. We have done a preliminary analysis of these data to estimate heritability of shear force in the Simmental breed. The estimate based on 307 records of progeny from 31 bulls was 0.67. In the genetic evaluation project, we have added two major databases to the multibreed genetic evaluation for weight. These breeds are Chianna and Maine-Anjou. We also will be doing a run that includes the Gelbvieh national data set.

Impacts
Carcass merit data will provide a standard regarding the quality of beef products produced. Successful validation of QTL's will provide a selection tool for traits where data collection is difficult and expensive.

Publications

Cunningham, B. E., R. L. Quaas, and E. J. Pollak. 1999. Evaluation of Simmental sires for daughters' length of productive life. Journal of Animal Science 77(Suppl. 1):144.

Progress 01/01/98 to 12/31/98

Outputs
Current research is aimed at redefining the (co)variance structure in the multibreed beef cattle genetic evaluation being used in Simmental-cross cattle. Genetic parameters will be estimated by breed for inclusion in this analysis. We are also in the process of combining analyses of calving ease with the analyses weight and carcass traits. As well, we have received a data set on scrotal circumference measures for Simmental bulls. Interest in this trait is its relationship to female fertility. Genetic parameters necessary for evaluation of this trait are being estimated.

Impacts
(N/A)

Publications

POLLAK, E. J. 1998. Mixed model methodology in genetic evaluation of beef cattle. Pages 197-208 in Proceedings Symposium Series 1, 8th World Conference on Animal Production. Seoul National University, Korea. June 28-July 4, 1998.
QUAAS, R. L., E. J. POLLAK, B. E. CUNNINGHAM and L. KLEI 1998. (Abstr.) Bayesian procedure with an autoregressive prior for smoothing estimated time trends. J. Animal Sci. 76(Suppl. 1):57.
POLLAK, E. J.,R. L., QUAAS, B. E. CUNNINGHAM and L. KLEI 1998. (Abstr.) Multibreed data analysis: Genetic versus gametic trends. J. Animal Sci. 76(Suppl. 1):84.
SCHAFER, S. M. 1998. Scrotal Circumference: A predictor for Reproduction? Proceedings, Beef Improvement Federation Annual Meeting. Calgary, BC, Canada. June, 1998.

Progress 01/01/97 to 12/31/97

Outputs
Current research was aimed at defining the role of various factors on estimation of this covariance in Simmental data. Inclusion of a sire-by-year interaction term was used in the Simmental genetic evaluation model to determine the impact of that effect on the maternal and direct genetic covariance. The inclusion of this term reduced the magnitude of the negative correlation but did not eliminate it. Also of interest was the effect of partitioning data into male and female subsets to estimate genetic and environmental parameters. It was found that such partitioning leads to biased estimates of these parameters and that heterogeneity of variance would be incorrectly concluded. The valid approach to estimating parameters for these subclasses was to treat them as different traits depending on the sex of the individual. In doing so, it was determined that there still exists heterogenous variances by sex of calf subclasses.

Impacts
(N/A)

Publications

LEE,C. & E.J.POLLAK. 1997. Influence of partitioning data by sex on genetic variance and covariance components for weaning weight in beef cattle. J Anim Sci 75:61-67.
LEE,C. & E.J.POLLAK. 1997. Relationship between sire x year interactions and direct-maternal genetic correlation for weaning weight of Simmental cattle. J Anim Sci 75:68-75.
LEE,C, C.P.VAN TASSEL, & E.J.POLLAK. 1997. Estimation of genetic variance and covariance components for weaning weight in Simmental cattle. J Anim Sci 75:325-330.
LEE,C. & E.J.POLLAK. 1997. Influence sire misidentification on sire-by-year interaction variance and direct-maternal genetic covariance for weaning weight in beef cattle. J Anim Sci
LEE,C. & E.J.POLLAK. 1997. Influence inbreeding depression on genetic (co)variance and sire-by-year interaction variance estimates for weaning weight in beef cattle. Asian J Anim Sci 10:510-513.

Progress 01/01/96 to 12/30/96

Outputs
Previous research indicated several factors could be involved in the estimation of a spurious negative genetic correlation between direct and maternal effects for weaning weight in beef cattle. Current research was aimed at defining the role of these factors in the estimation of this covariance in Simmental data. Two factors of interest were the levels of inbreeding and parent misidentification. The Simmental population represents a mildly inbred group of animals. Simulation results indicated ignoring the effect of inbreeding on performance in genetic evaluation models did not contribute to the negative estimate. It was established that parent misidentification was an important factor in biasing the estimate of the genetic correlation.

Impacts
(N/A)

Publications

LEE, C., POLLAK, E. J. 1996. Inbreeding depression in parameter estimation of weaning weight. J. Anim. Sci. 74 (Suppl. 1):115. (Abstr.).

Progress 01/01/95 to 12/30/95

Outputs
Accurate genetic evaluations depend on accurate parameter estimates such as genetic and environmental variances and covariances. The covariance between direct and maternal effects for weaning weight in beef cattle has been the subject of debate. Most estimates from field data are negative. Simulation studies have shown a potential toward biased negative estimates under certain conditions. The results from our own simulation are consistent with these findings. The Simmental data was reanalyzed with a model fitting a sire-by-year interaction, one source of bias. The direct and maternal covariance was still negative but less so. The effect of splitting data by gender was also examined by simulation. Spurious heterogeneity of variance was observed in split data when selection was practiced, not so in random mating populations. Analyses were done with the Simmental data, treating observations in each sex as a separate trait, to obtain new estimates for use in the national evaluation.

Impacts
(N/A)

Publications

Progress 01/01/94 to 12/30/94

Outputs
Genetic evaluations are run to estimate the potential merit of animals as parents. The amount of information available on individuals varies, hence, accuracy of the estimate varies. The Simmental genetic evaluation system consists of evaluation programs for weight traits and calving ease. The weight trait evaluation is a mixed model analysis using linear models while the calving ease evaluation uses the threshold model. Obtaining accuracies for weight trait evaluations is straightforward while obtaining accuracies using the threshold model is not. In a threshold model, data are not normally distributed, resulting in a nonlinear system of equations to solve for genetic merit of animals. Accuracies of estimated genetic values are computed in principle using the inverse of Fisher's observed information matrix. This matrix depends not only on number of records and distribution of records in contemporary and age groups, as in a linear analysis, but also on estimated genetic values. The better use of information leads to an increase in accuracies compared to a linear analysis. The new accuracy procedure for calving ease will be used for the 1995 spring American Simmental genetic evaluation.

Impacts
(N/A)

Publications

Progress 01/01/93 to 12/30/93

Outputs
Genetic evaluation of animals for genetic merit is an ongoing process. As new information is reported, changes occur in evaluations in response to that new information. If, however, there is a systematic bias in the evaluation system, then changes exceed the expected distribution of change. In order to study the stability of the Simmental genetic evaluations using the current multiple trait animal model, a retrospective study was undertaken. Genetic evaluations were done in two-year increments using the historical data up to the cut-off date for that particular evaluation. Comparisons were made between subsequent evaluations of animals as the nature and amount of information for them increased. Comparisons, for examples, of animals' evaluations based on their own performance to those when they have progeny and between pedigree indices and subsequent evaluations were made. The mean change in evaluations at each critical stage of animal's life were at or close to zero, and the distribution of change was close to the expected change based on the accuracy of the previous evaluation.

Impacts
(N/A)

Publications

CUNNINGHAM, B.E. AND KLEI, L. 1993. Performance and genetic trends in Simmentals for regions of the United States. Journal Animal Science 71(Suppl. 1):94 (Abstract).
KLEI, L., DESTEFANO, A.L., QUAAS, R.L. AND POLLAK, E.J. 1993. Creating a list of informative animals for genetic evaluation with an animal model. Journal Animal Science 71(Suppl. 1):98 (Abstract).
WARD, B.J., POLLAK, E.J. AND EVERETT, R.W. 1993. The level of inbreeding and its effect on weight traits in the Simmental cattle breed. Journal Animal Science 71(Suppl. 1):104 (Abstract).
WARD, B. J. 1993. The level of inbreeding and its effect on weight traits in Simmental cattle. Ph.D. thesis, Cornell University, Ithaca, NY.

Progress 01/01/92 to 12/30/92

Outputs
Concern exists as to whether age of dam factors influencing birth weight and weaning weight should be derived on a regional basis or whether factors obtained from the national data set suffice. Analysis of data based on Simmental-sired calves was carried out to test the significance of age of dam by region of country effects. Six regions were used in the analysis, and only calves from Simmental, Angus, and Hereford cows were included in the analysis. Results showed a significant region by age interaction; however, using adjustment factors from each region did not significantly reduce the effect of age on subsequent data. The region defined by Louisiana, Arkansas and eastern Texas showed the greatest difference in age of dam effects. Application of the animal model to the analysis of weight trait data in beef cattle was also investigated. An evaluation system was developed to handle a multiple trait animal model analysis for the Simmental population.

Impacts
(N/A)

Publications

WOODWARD, B.W., POLLAK, E.J. AND QUAAS, R.L. 1992. Parameter estimation for carcass traits including growth information of Simmentals using REML with an MT model. Journal Animal Science 70:1098-1109.
CARVALHEIRA, J., BLAKE, R.W. AND POLLAK, E.J,. 1992. Comparison of Landim & Africander cattle in southern Mozambique. Journal Animal Science 70(Supplment 1):215.

Progress 01/01/91 to 12/30/91

Outputs
Concern exists as to whether evaluations obtained on bulls with progeny located mainly in one geographical region are useful to predict future progeny performance of calves born in different regions and perhaps under different environmental conditions. Genetic evaluations of Simmental bulls based on their progeny's performance in two regions were compared. The data consisted of all Simmental-sired calves of either Hereford (data set 1) or Angus (data set 2) origin; that is, the initial base dam in the pedigree was either Hereford or Angus. The regions were broadly defined as North and South, both being east of the Mississippi River. Evaluations of bulls based on progeny performance in the North were used to predict the performance of calves born in the South and vice versa. The regressions of progeny performance in one region on bull EPD's obtained in the other were all positive and different from zero. Generally, regressions were higher in data set 1 and higher when using EPD's from the South to predict performance in the North. These results indicate that there is not a problem using EPD's from bulls proven regionally to predict performance of future calves in other regions.

Impacts
(N/A)

Publications

DONG, M.C., QUAAS, R.L. and POLLAK, E.J. 1991. Estimation of genetic parameters of calving ease and birth weight by a threshold model. Journal Animal Science 69(Suppl. 1):204.
WRIGHT, D.W. and POLLAK, E.J. 1991. Evaluation of Simmental sires producing crossbred calves in two different geographic locations. Journal Animal Science 69(Suppl. 1):218.
DONG, M.C., POLLAK, E.J. and QUAAS, R.L. 1991. Comparsions of calving ease evaluations by linear model and threshold model with and without birth weight. Journal Animal Science 69(Suppl. 1):220.

Progress 01/01/90 to 12/30/90

Outputs
Genetic evaluations for carcass traits have been receiving increased attention. Analyses were done to estimate the genetic and environmental parameters for three carcass characteristics, which were retail cuts per day of age, cutability, and marbling score. Parameters also were estimated among weight traits and these carcass characteristics to determine if selection for weight traits influenced the population of animals available for slaughter data. Selection was not found to influence the parameter estimates. Research on the stability of evaluations on sires with the addition of new data was investigated. Comparisons were for the pedigree index compared to evaluations when data become available, early progeny test evaluations compared to those based on larger numbers of progeny, and maternal evaluations obtained from correlated weight traits compared to those from daughter-calf performance. The distribution of sire evaluation changes were within the bounds of theoretical expectation. A new project has been started that will examine genotype-by-environment interactions as they influence the ability to predict differences in progeny performance.

Impacts
(N/A)

Publications

PALMER, D. L. 1990. A retrospective study of American Simmental sire evaluations for weight traits. M. S. Thesis. Cornell University, Ithaca, NY 101p.
WOODWARD, B. W. 1990. Parameter estimation for carcass traits including growth information of Simmental beef cattle using REML with a multiple-trait model. Ph.D. Thesis. Cornell University, Ithaca, NY, 143p.
WOODWARD, B. W., POLLAK, E. J. and QUAAS, R. L. 1990. Parameter estimation for carcass traits including growth infomation of Simmental beef cattle using REML with a multiple-trait model. J. Animal Science 68(Suppl. 1):239. (Abs.).

Progress 01/01/89 to 12/30/89

Outputs
Genetic evaluation accounting for heterogeneity of variance was implemented in Simmental cattle for weight traits, including birth weight, weaning weight, yearling weight direct growth, and maternal effects for birth weight and weaning weight. Separate variance components were estimated for large subclasses, defined as sex, of calf and percent Simmental of calf. Work on comparing genetic evaluations as new data are added to the data set was also investigated this year. Comparisons between subsequent year proofs show that in general the estimates were unbiased and the distribution of change observed from one year to the next was not greater than that expected. A project was also initiated to investigate the joint analysis of weight traits with the carcass characteristics. Currently, genetic evaluations are separate for growth characteristics and carcass traits. In this project, genetic and environmental variances and covariances were estimated as well as a study of sire evaluations resulting from this system.

Impacts
(N/A)

Publications

Progress 01/01/88 to 12/30/88

Outputs
Records on birth weight, weaning weight and yearling weight from Simmental-siredcalves were used to investigate the heterogeneity of variance across sex of calf and percent Simmental of calf subclasses in data provided by the American Simmental Association covering the years 1969 through 1985. Variance components wereestimated separately within subclasses using REML techniques. The model included fixed contemporary group and age of dam effects and random sire and maternal grand sire effects. Relationships among sires and maternal grandsires were included. Phenotypic standard deviations (kg) were: weaning weight 26.9 vs. 23.2 for males vs. females; birth weight 4.5 vs. 4.1 (males vs. females); and postweaning gain 25.9 vs. 19.9 (males vs. females). Heritabilities were calculated for weaning weight direct (WWD), birth weight direct (BWD), postweaning gain direct (PWD), weaning weight maternal (WWM), birth weight maternal (BWM), and postweaning gain maternal (PWM). Heritabilities for the direct effects were higher in females than in males. For WWD, heritability for females was .39 vs. .32 for males. For BWD, the heritabilities were .45 vs. .40. For PWD, the heritabilities were .32 vs. .26. The heritabilities for weaning weight and birth weight maternal were comparable in both sexes. For WWM, the heritabilities were .2 for males vs. .16 for females, and for BWM the heritabilities were .13 for males and .15 for females. The heritabilities for PWM in both sexes were 0.

Impacts
(N/A)

Publications

GARRICK, D. J. 1988. Restricted maximum likelihood estimation of variance components for multiple traits with missing observations and an application to beef cattle. Ph.D. Thesis. Cornell Univ., Ithaca, NY.
GARRICK, D. J., POLLAK, E. J., QUAAS, R. L. and VAN VLECK, L. D. 1988. Variance heterogeneity in weight traits by sex-of-calf and percent purebred for Simmental-sired calves. J. Anim. Sci. 66(Suppl. 1):220-221.
WOODWARD, B. W., POLLAK, E. J., and QUAAS, R. L. 1988. Adjusting weaning weights for age at weaning. J. Anim. Sci. In press.