PSIII-8 Genetic Parameter Estimates for Bull Prolificacy and Its Relationship with Scrotal Circumference in a Commercial Beef Cattle Population

The commercial beef cattle industry relies heavily on the use of natural service sires. Either due to the size of breeding herds or to safe-guard against injury during the breeding season, multiple-sire breeding pastures are utilized. Although each bull might be given an equal opportunity to produce offspring, evidence suggest that there is substantial variation in the number of calves sired by each bull in a breeding pasture. DNA-based paternity assignment enables correct assignment of calves to their respective sires in multi-sire pastures and presents an opportunity to investigate the degree to which this trait complex is under genetic control. Field data from a large commercial ranch were used to estimate genetic parameters for calf count (CC; n=623) and yearling scrotal circumference (SC; n=1962) using univariate and bivariate animal models. Average CC and SC were 12.1±11.1 calves and 35.4±2.30 cm, respectively. Average number breeding seasons per bull and bulls per contemporary group were 1.40 and 24.9, respectively. The model for CC included fixed effects of age during the breeding season (in years) and contemporary group (concatenation of breeding pasture and year). Random effects included additive genetic and permanent environmental effects, and a residual. The model for SC included fixed effects of age (in days) and contemporary group (concatenation of month and year of measurement). Random effects included an additive genetic effect and a residual. Univariate model heritability estimates for CC and SC were 0.237±0.156 and 0.456±0.072, respectively. Similarly, the bivariate model resulted in heritability estimates for CC and SC of 0.240±0.155 and 0.461±0.072, respectively. Repeatability estimates for CC from univariate and bivariate models were 0.517±0.054 and 0.518±0.053, respectively. The estimate of genetic correlation between CC and SC was 0.270±0.220. Parameter estimates suggest that both CC and SC would respond favorably to selection and that CC is moderately repeatable.

Genomewide association study of reproductive efficiency in female cattle

Reproductive efficiency is of economic importance in commercial beef cattle production, as failure to achieve pregnancy reduces the number of calves marketed per cow exposed. Identification of genetic markers with predictive merit for reproductive success would facilitate early selection of sires with daughters having improved reproductive rate without increasing generation intervals. To identify regions of the genome harboring variation affecting reproductive success, we applied a genomewide association study (GWAS) approach based on the >700,000 SNP marker assay, using a procedure based on genotyping multianimal pools of DNA to increase the number of animals that could be genotyped with available resources. Cows from several populations were classified according to reproductive efficiency, and DNA was pooled within population and phenotype prior to genotyping. Populations evaluated included a research population at the U.S. Meat Animal Research Center, 2 large commercial ranch populations, and a number of smaller populations (<100 head) across the United States. We detected 2 SNP with significant genomewide association (P ≤ 1.49 × 10(-7)), on BTA21 and BTA29, 3 SNP with suggestive associations (P ≤ 2.91 × 10(-6)) on BTA5, and 1 SNP with suggestive association each on BTA1 and BTA25. In addition to our novel findings, we confirmed previously published associations for SNP on BTA-X and all autosomes except 3 (BTA21, BTA22, and BTA28) encompassing substantial breed diversity including Bos indicus and Bos taurus breeds. The study identified regions of the genome associated with reproductive efficiency, which are being targeted for further analysis to develop robust marker systems, and demonstrated that DNA pooling can be used to substantially reduce the cost of GWAS in cattle.

Use of robust multivariate linear mixed models for estimation of genetic parameters for carcass traits in beef cattle

Assumptions of normality of residuals for carcass evaluation may make inferences vulnerable to the presence of outliers, but heavy-tail densities are viable alternatives to normal distributions and provide robustness against unusual or outlying observations when used to model the densities of residual effects. We compare estimates of genetic parameters by fitting multivariate Normal (MN) or heavy-tail distributions (multivariate Student's t and multivariate Slash, MSt and MS) for residuals in data of hot carcass weight (HCW), longissimus muscle area (REA) and 12th to 13th rib fat (FAT) traits in beef cattle using 2475 records from 2007 to 2008 from a large commercial operation in Nebraska. Model comparisons using deviance information criteria (DIC) favoured MSt over MS and MN models, respectively. The posterior means (and 95% posterior probability intervals, PPI) of v for the MSt and MS models were 5.89 ± 0.90 (4.35, 7.86) and 2.04 ± 0.18 (1.70, 2.41), respectively. Smaller values of posterior densities of v for MSt and MS models confirm that the assumption of normally distributed residuals is not adequate for the analysis of the data set. Posterior mean (PM) and posterior median (PD) estimates of direct genetic variances were variable with MSt having the highest mean value followed by MS and MN, respectively. Posterior inferences on genetic variance were, however, comparable among the models for FAT. Posterior inference on additive heritabilities for HCW, REA and FAT using MN, MSt and MS models indicated similar and moderate heritability comparable with the literature. Posterior means of genetic correlations for carcass traits were variable but positive except for between REA and FAT, which showed an antagonistic relationship. We have demonstrated that genetic evaluation and selection strategies will be sensitive to the assumed model for residuals.

Deletion on chromosome 5 associated with decreased reproductive efficiency in female cattle

Reproductive efficiency is arguably the most economically important trait in commercial beef cattle production, as failure to achieve pregnancy reduces the number of calves marketed per cow exposed to breeding. Identification of variation in the genome with predictive merit for reproductive success would facilitate accurate prediction of daughter pregnancy rate in sires enabling effective selection of bulls producing daughters with improved fertility. Copy number variation (CNV) is one form of structural variation that results in abnormal copies of DNA in the genome. Our lab previously reported a region between 25 and 70 Mb on chromosome 5 associated with reproductive efficiency. To further evaluate this region for genomic variations such as CNV, we initially applied a genomewide association approach based on the >700,000 SNP marker assay and PennCNV analysis to 68 Bos indicus cross females from a large commercial ranch in central Florida. A genomic segment located on chromosome 5, spanning the region of approximately 58.37 to 58.44 Mb (Bovine UMD3.1 assembly) was identified as containing a deletion associated with decreased reproductive efficiency. To verify this deletion, a quantitative real-time PCR test was developed to evaluate additional females in the central Florida and U.S. Meat Animal Research Center (USMARC) populations. The frequency of the homozygous deletion was 7% (23/319) in the central Florida population (Bos indicus cross) for females with 2 consecutive failed breeding seasons and 0% in the USMARC population (predominantly Bos taurus) of low reproductive females. To date, we have not identified the deletion in Bos taurus cattle, suggesting that the deletion is specific to Bos indicus cattle. From these data, we have identified a deletion on chromosome 5 associated with reproductive efficiency in Bos indicus-influenced cattle.

A simulation-based approach for evaluating and comparing the environmental footprints of beef production systems

A methodology was developed and used to determine environmental footprints of beef cattle produced at the U.S. Meat Animal Research Center (MARC) in Clay Center, NE, with the goal of quantifying improvements achieved over the past 40 yr. Information for MARC operations was gathered and used to establish parameters representing their production system with the Integrated Farm System Model. The MARC farm, cow-calf, and feedlot operations were each simulated over recent historical weather to evaluate performance, environmental impact, and economics. The current farm operation included 841 ha of alfalfa and 1,160 ha of corn to produce feed predominately for the beef herd of 5,500 cows, 1,180 replacement cattle, and 3,724 cattle finished per year. Spring and fall cow-calf herds were fed on 9,713 ha of pastureland supplemented through the winter with hay and silage produced by the farm operation. Feedlot cattle were backgrounded for 3 mo on hay and silage with some grain and finished over 7 mo on a diet high in corn and wet distillers grain. For weather year 2011, simulated feed production and use, energy use, and production costs were within 1% of actual records. A 25-yr simulation of their current production system gave an average annual carbon footprint of 10.9±0.6 kg of CO2 equivalent units per kg BW sold, and the energy required to produce that beef (energy footprint) was 26.5±4.5 MJ/kg BW. The annual water required (water footprint) was 21,300±5,600 L/kg BW sold, and the water footprint excluding precipitation was 2,790±910 L/kg BW. The simulated annual cost of producing their beef was US$2.11±0.05/kg BW. Simulation of the production practices of 2005 indicated that the inclusion of distillers grain in animal diets has had a relatively small effect on environmental footprints except that reactive nitrogen loss has increased 10%. Compared to 1970, the carbon footprint of the beef produced has decreased 6% with no change in the energy footprint, a 3% reduction in the reactive nitrogen footprint, and a 6% reduction in the real cost of production. The water footprint, excluding precipitation, has increased 42% due to greater use of irrigated corn production. This proven methodology provides a means for developing the production data needed to support regional and national full life cycle assessments of the sustainability of beef.

Application of multivariate heavy-tailed distributions to residuals in the estimation of genetic parameters of growth traits in beef cattle

Assumptions of normality in most animal breeding applications may make inferences vulnerable to the presence of outliers. Heavy-tail densities are viable alternatives to normal distributions and provide robustness against unusual or outlying observations when used to model the densities of residual effects. Our objective is to compare estimates of genetic parameters by fitting multivariate normal (MN) or heavy-tail distributions [multivariate Student's t (MSt) and multivariate slash (MS)] for residuals in data of body birth weight (BBW), weaning (WW), and yearling (YW) weight traits in beef cattle. A total of 17,019 weight records for BBW, WW, and YW from 1998 through 2010 from a large commercial cow/calf operation in the sand hills of Nebraska were analyzed. Models included fixed effects of contemporary group and sire breed whereas animal and maternal effects were random and the degrees of freedom (v) was treated as unknown for MSt and MS. Model comparisons using deviance information criteria (DIC) favored MSt over MS and MN models, respectively. The posterior means [and 95% posterior probability intervals (PPI)] of v for the MSt and MS models were 5.28 (4.80, 5.85) and 1.88 (1.76, 2.00), respectively. Smaller values of posterior densities of v for MSt and MS models confirm that the assumption of normally distributed residuals is not adequate for the analysis of BBW, WW, and YW datasets. Posterior mean (PM) and posterior median (PD) estimates of direct and maternal genetic variances were the same and posterior densities of these parameters were found to be symmetric. The 95% PPI estimates from MN and MSt models for BBW did not overlap, which indicates significant difference between PM estimates from MN or MSt models. The observed antagonistic relationship between additive direct and additive maternal effects indicated that genetic evaluation and selection strategies will be sensitive to the assumed model for residuals.

Genomics and the global beef cattle industry

After two decades of developing DNA-based tools for selection, we are at an interesting juncture. Genomic technology has essentially eliminated the potentially large negative impact of spontaneous single-mutation genetic defects as the management of recent examples in beef cattle have demonstrated. We have the ability to perform more accurate selection based on molecular breeding values (MBVs) for animals closely related to the discovery population. Yet the amount of genetic variation explained falls short of expectations held for the technology. Tests are less effective in distant relatives within a breed and are not robust enough for across-breed use. It is hypothesised that ‘larger single-nucleotide polymorphism (SNP) panels’ will help extend the effective use of tests to more distantly related animals and across breeds. Sequencing and imputing sequences across individuals will enable us to discover causative mutations or SNPs in perfect harmony with the mutation. However, the investment to revisit discovery populations will be large. We can ill afford to duplicate genotyping or sequencing activities for prominent individuals. Hence, a global strategy for genotyping and sequencing becomes an attractive proposition as many of our livestock populations are related. As we learned more of the complexities of the genome, the number of animals in discovery populations necessary to achieve high levels of predictability has grown dramatically. No one organisation has the resources to assemble the animals needed, especially for novel, expensive or hard to measure phenotypes. This scenario is fertile ground for increased international collaboration in all livestock species.

Genetic evaluation of retail product percentage in Simmental cattle

The objective of this study was to estimate genetic parameters required for genetic evaluation of retail product percentage (RPP) in Simmental cattle. Carcass weight (HCW), subcutaneous fat thickness (FAT), longissimus muscle area (REA) and kidney, pelvic, and heart fat (KPH) records were available to compute RPP on steers (n = 5171) and heifers (n = 1400) from the American Simmental Association database; animals were sired by 561 Simmental bulls and out of 5886 crossbred dams. Genetic parameters were estimated using residual maximal likelihood and a four trait animal model for the components of RPP including fixed harvest contemporary group effects, random animal genetic effects, and a linear covariate for age at harvest. Heritability estimates were 0.51 +/- 0.05, 0.36 +/- 0.05, 0.46 +/- 0.05, and 0.18 +/- 0.05 for HCW, FAT, REA and KPH respectively. Non-zero genetic correlations were estimated between HCW and REA (rg = 0.51 +/- 0.06) and between REA and FAT (rg = -0.43 +/- 0.08), but other genetic correlation estimates among the component traits were low. As a linear function of its components, heritability and genetic correlations involving RPP were estimated using index methods. The heritability estimate for RPP was 0.41, and genetic correlations were -0.17, -0.83, 0.67, and 0.01 with HCW, FAT, REA and KPH respectively. Therefore, RPP was strongly associated with muscle and fat deposition, but essentially independent of carcass weight and internal body cavity fat. Genetic evaluation of RPP would be straightforward using multiple trait index methods and genetic regression, although the inclusion of KPH would be of marginal value.

DNA-based paternity analysis and genetic evaluation in a large, commercial cattle ranch setting1

Deoxyribonucleic acid-based tests were used to assign paternity to 625 calves from a multiple-sire breeding pasture. There was a large variability in calf output and a large proportion of young bulls that did not sire any offspring. Five of 27 herd sires produced over 50% of the calves, whereas 10 sires produced no progeny and 9 of these were yearling bulls. A comparison was made between the paternity results obtained when using a DNA marker panel with a high (0.999), cumulative parentage exclusion probability (P(E)) and those obtained when using a marker panel with a lower P(E) (0.956). A large percentage (67%) of the calves had multiple qualifying sires when using the lower resolution panel. Assignment of the most probable sire using a likelihood-based method based on genotypic information resolved this problem in approximately 80% of the cases, resulting in 75% agreement between the 2 marker panels. The correlation between weaning weight, on-farm EPD based on pedigrees inferred from the 2 marker panels was 0.94 for the 24 bulls that sired progeny. Partial progeny assignments inferred from the lower resolution panel resulted in the generation of EPD for bulls that actually sired no progeny according to the high-P(E) panel, although the Beef Improvement Federation accuracies of EPD for these bulls were never greater than 0.14. Simulations were performed to model the effect of loci number, minor allele frequency, and the number of offspring per bull on the accuracy of genetic evaluations based on parentage determinations derived from SNP marker panels. The SNP marker panels of 36 and 40 loci produced EPD with accuracies nearly identical to those EPD resulting from use of the true pedigree. However, in field situations where factors including variable calf output per sire, large sire cohorts, relatedness among sires, low minor allele frequencies, and missing data can occur concurrently, the use of marker panels with a larger number of SNP loci will be required to obtain accurate on-farm EPD.

Genetic evaluation of beef carcass data using different endpoint adjustments

Carcass data from 6,795 Simmental-sired animals born from 1992 to 2001 were used to determine whether adjustment to a constant age, back-fat, HCW, or marbling score would result in differences in heritability of the carcass traits and, correspondingly, if EPD calculated using those variance components and adjustments would result in sire reranking. The endpoints were age (EPA), backfat (EPF), HCW (EPC), or marbling (EPM). The traits analyzed were 12th-rib backfat (FAT), HCW, marbling (MRB), LM area (LMA), and percentage retail cuts (PRC). The data were analyzed using an animal model, where contemporary group was included as a fixed effect and was composed of slaughter date, sex, and herd. Random effects included in the model were direct genetic and residual. Estimates of heritability ranged from 0.12 to 0.14, 0.32 to 0.34, and 0.26 to 0.27 for FAT, HCW, and LMA, respectively, for the corresponding endpoints. Heritability for MRB was estimated to be 0.27 at all endpoints. For PRC, estimates of heritability were more variable, with estimates of 0.23 +/- 0.05, 0.32 +/- 0.05, 0.21 +/- 0.05, and 0.20 +/- 0.04 for EPA, EPF, EPC, and EPM, respectively. However, because the EPF and EPC adjustments adjust for a component trait of PRC (FAT and HCW, respectively), they may be altering the trait to one different from PRC. Spearman rank correlations between EPD within a trait using EPA compared with the other endpoints were >0.90 (P < 0.01) for FAT, HCW, MRB, and LMA. For PRC, Spearman rank correlations with EPA EPD were 0.73 (P < 0.01), 0.93 (P < 0.01), and 0.95 (P < 0.01) for EPF, EPC, and EPM, respectively. For most traits and endpoints, there was little reranking among sires when alternative endpoints were used. However, adjusting PRC to EPF appears to result in a greater heritability and substantial re-ranking of sires, potentially due to the adjustment changing the trait to one other than PRC.

Phenotypic ranges and relationships among carcass and meat palatability traits for fourteen cattle breeds, and heritabilities and expected progeny differences for Warner-Bratzler shear force in three beef cattle breeds1,2

Carcass and Warner-Bratzler shear force (WBSF) data from strip loin steaks were obtained from 7,179 progeny of Angus, Brahman, Brangus, Charolais, Gelbvieh, Hereford, Limousin, Maine-Anjou, Red Angus, Salers, Shorthorn, Simbrah, Simmental, and South Devon sires. Trained sensory panel (TSP) evaluations were obtained on 2,320 steaks sampled from contemporary groups of progeny from one to five sires of each breed. Expected progeny differences for marbling and WBSF were developed for 103 Simmental sires from 1,295 progeny, 23 Shorthorn sires from 310 progeny, and 69 Hereford sires from 1,457 progeny. Pooled phenotypic residual correlations, including all progeny, showed that marbling was lowly correlated with WBSF (-0.21) and with TSP overall tenderness (0.18). The residual correlation between WBSF and TSP tenderness was -0.68, whereas residual correlations for progeny sired by the three Bos indicus breeds were only slightly different than for progeny sired by Bos taurus breeds. The phenotypic range of mean WBSF among sires across breeds was 6.27 kg, and the phenotypic range among breed means was 3.93 kg. Heritability estimates for fat thickness, marbling score, WBSF, and TSP tenderness, juiciness, and flavor were 0.19, 0.68, 0.40, 0.37, 0.46, and 0.07, respectively. Ranges in EPD for WBSF and marbling were -0.41 to +0.26 kg and +0.48 to -0.22, respectively, for Simmentals; -0.41 to +0.36 kg and 0.00 to -0.32, respectively, for Shorthorns; and -0.48 to +0.22 kg and +0.40 to -0.24, respectively, for Herefords. More than 20% of steaks were unacceptable in tenderness. Results of this study demonstrated that 1) selection for marbling would result in little improvement in meat tenderness; 2) heritability of marbling, tenderness, and juiciness are high; and 3) sufficient variation exists in WBSF EPD among widely used Simmental, Shorthorn, and Hereford sires to allow for genetic improvement in LM tenderness.

Application and impact of new genetic technologies on beef cattle breeding: a 'real world' perspective

Molecular genetics is a maturing discipline with innovations that are finding application in animal breeding. Currently, DNA tests are available for parent identification or verification, and markers tests also exist for quantitative trait loci affecting important traits in beef cattle. The beef industry is, however, a particularly challenging industry in which to design breeding programs that fully capitalise on the potential of this technology. Hence, adoption within this industry to date has been below expectation. This paper examines several applications that are being investigated and will include discussion on issues constraining the transfer of DNA technology. An example of using DNA parentage testing for expanding the reach of selection programs into the commercial sector of the beef industry is explored in some depth, as it represents a potential high impact application. Use of molecular information in selection programs and in genetic evaluations is also discussed.

Heritability and correlation estimates of Warner-Bratzler shear force and carcass traits from Angus-, Charolais-, Hereford-, and Simmental-sired cattle

Heritabilities and correlations of Warner-Bratzler shear force (WBSF), marbling score (MS), hot carcass weight (HCW),12–13th rib-fat (FAT), and ribeye area (REA) were calculated from 3360 Angus-, Charolais-, Hereford-, and Simmental-sired cattle in the C attleman’s Beef Board Carcass Merit Project. The heritabilities (± SE) for WBSF, MS, HCW, FAT, and REA were 0.34 ± 0.25, 0.43 ± 0.28, 0.73 ± 0.35, 0.16 ± 0.19, and 0.56 ± 0.31 in Angus; 0.43 ± 0.22, 0.30 ± 0.18, 0.21 ± 0.16, 0.35 ± 0.20, and 0.23 ± 0.16 in Charolais; 0.12 ± 0.11, 0.55 ± 0.22, 0.20 ± 0.14, 0.25 ± 0.15 and 0.34 ± 0.17 in Hereford; and 0.16 ± 0.14, 0.44 ± 0.20, 0.45 ± 0.20, 0.23 ± 0.16, and 0.30 ± 0.18 in Simmental. The genetic correlations, averaged across analysis type, for WBSF-MS, WBSF-HCW, WBSF-FAT, WBSF-REA, MS-HCW, MS-FAT, MS-REA, HCW-FAT, HCW-REA, and FAT-REA were -0.17, 0.32, -0.23, 0.30, 0.10, -0.17, 0.39, -0.15, 0.68, and -0.86 in Angus; -0.42, 0.77, 0.52, -0.05, -0.44, -0.22, -0.19, 0.66, -0.05, and -0.24 in Charolais; -0.43, -0.04, -0.33, 0.09, 0.08, 0.79, -0.14, -0.26, 0.50, and -0.38 in Hereford; and 0.55, 0.08, 0.62, -0.08, 0.30, 0.61, -0.14, 0.06, 0.65, and -0.48 in Simmental. Key words: Beef cattle, genetic parameters, carcass quality, tenderness

Evaluation of Simmental carcass EPD estimated using live and carcass data

This study was conducted to compare carcass EPD predicted using yearling live animal data and/or progeny carcass data, and to quantify the association between the carcass phenotype of progeny and the sire EPD. The live data model (L) included scan weight, ultrasound fat thickness, longissimus muscle area, and percentage of intramuscular fat from yearling (369 d of age) Simmental bulls and heifers. The carcass data model (C) included hot carcass weight, fat thickness, longissimus muscle area, and marbling score from Simmental-sired steers and cull heifers (453 d of age). The combined data model (F) included live animal and carcass data as separate but correlated traits. All data and pedigree information on 39,566 animals were obtained from the American Simmental Association, and all EPD were predicted using animal model procedures. The genetic model included fixed effects of contemporary group and a linear covariate for age at measurement, and a random animal genetic effect. The EPD from L had smaller variance and range than those from either C or F. Further, EPD from F had highest average accuracy. Correlations indicated that evaluations from C and F were most similar, and L would significantly (P < 0.05) re-rank sires compared with models including carcass data. Progeny (n = 824) with carcass data collected subsequent to evaluation were used to quantify the association between progeny phenotype and sire EPD using a model including contemporary group, and linear regressions for age at slaughter and the appropriate sire EPD. The regression coefficient was generally improved for sire EPD from L when genetic regression was used to scale EPD to the appropriate carcass trait basis. The EPD from C and F had similar linear associations with progeny phenotype, although EPD from F may be considered optimal because of increased accuracy. These data suggest that carcass EPD based on a combination of live and carcass data predict differences in progeny phenotype at or near theoretical expectation.

Genetic parameters for carcass traits and their live animal indicators in Simmental cattle

The objective of this study was to estimate parameters required for genetic evaluation of Simmental carcass merit using carcass and live animal data. Carcass weight, fat thickness, longissimus muscle area, and marbling score were available from 5,750 steers and 1,504 heifers sired by Simmental bulls. Additionally, yearling ultrasound measurements of fat thickness, longissimus muscle area, and estimated percentage of intramuscular fat were available on Simmental bulls (n = 3,409) and heifers (n = 1,503). An extended pedigree was used to construct the relationship matrix (n = 23,968) linking bulls and heifers with ultrasound data to steers and heifers with carcass data. All data were obtained from the American Simmental Association. No animal had both ultrasound and carcass data. Using an animal model and treating corresponding ultrasound and carcass traits separately, genetic parameters were estimated using restricted maximum likelihood. Heritability estimates for carcass traits were 0.48 +/- 0.06, 0.35 +/- 0.05, 0.46 +/- 0.05, and 0.54 +/- 0.05 for carcass weight, fat thickness, longissimus muscle area, and marbling score, respectively. Heritability estimates for bull (heifer) ultrasound traits were 0.53 +/- 0.07 (0.69 +/- 0.09), 0.37 +/- 0.06 (0.51 +/- 0.09), and 0.47 +/- 0.06 (0.52 +/- 0.09) for fat thickness, longissimus muscle area, and intramuscular fat percentage, respectively. Heritability of weight at scan was 0.47 +/- 0.05. Using a bivariate weight model including scan weight of bulls and heifers with carcass weight of slaughter animals, a genetic correlation of 0.77 +/- 0.10 was obtained. Models for fat thickness, longissimus muscle area, and marbling score were each trivariate, including ultrasound measurements on yearling bulls and heifers, and corresponding carcass traits of slaughter animals. Genetic correlations of carcass fat thickness with bull and heifer ultrasound fat were 0.79 +/- 0.13 and 0.83 +/- 0.12, respectively. Genetic correlations of carcass longissimus muscle area with bull and heifer ultrasound longissimus muscle area were 0.80 +/- 0.11 and 0.54 +/- 0.12, respectively. Genetic correlations of carcass marbling score with bull and heifer ultrasound intramuscular fat percentage were 0.74 +/- 0.11 and 0.69 +/- 0.13, respectively. These results provide the parameter estimates necessary for genetic evaluation of Simmental carcass merit using both data from steer and heifer carcasses, and their ultrasound indicators on yearling bulls and heifers.

An autoregressive repeatability animal model for test-day records in multiple lactations

Test-day (TD) models are becoming a standard for genetic evaluation of production traits in dairy cattle. Various approaches to model covariances between TD records include random regression, autoregressive repeatability, orthogonal polynomials, and models based on character processing. The applicability of these models is mainly associated with the number of parameters to estimate, incorporation of multiple lactations, and the accuracy of correlations generated by the cow's repeated expression of milking performance (TD yields) within and across lactations. We define and evaluate a multiple-lactation, autoregressive-repeatability model that disentangles environmental effects due to cow within and between lactations. Simulated records either included or ignored a long-term environmental effect between lactations. Our autoregressive TD animal model correctly detected presence and the absence of this effect and accurately recovered the assumed variance components and correlations underlying the data (10 parameters for three lactations). Estimates of variance components and autocorrelation coefficients were obtained using DFREML-simplex methodology. Given the value of this approach to reduce the size of residual variance components, autoregressive animal models are a preferable alternative to classical methods based on cumulative lactation yield to improve milk production in dairy cattle.

Genetic antagonism between body weight and milk production in beef cattle

Korean cattle have an unusually short suckling period (4 mo) due to poor milking ability, and this is a hindrance to growth of calves. Therefore, Korean cattle breeders have shown interest in genetic improvement of milking ability. In this study, body weight (birth weight, weaning weight, and yearling weight) and five daily milk yields by period in Korean cattle (Hanwoo) were analyzed using a two-trait sire and maternal grandsire mixed model. The milk yields used were actually measured at sequential intervals from 1 to 4 mo after calving. Posterior means of the parameters were estimated using Gibbs sampling. Heritability estimates (0.25 to 0.26) for daily milk yield at weaning were larger than those with other periods. Genetic impact on daily milk yield, especially at weaning, was emphasized in order to lengthen the suckling period of Korean cattle. Genetic correlation estimates between BW and daily milk yield were all negative (-0.08 to -0.16 for birth weight, -0.04 to -0.21 for weaning weight, and -0.12 to -0.19 for yearling weight), whereas environmental correlation estimates were all positive (0.20 to 0.39 for birth weight, 0.34 to 0.51 for weaning weight, and 0.30 to 0.45 for yearling weight). The negative estimates of genetic correlation between weight and milk yield implied genetic antagonism between direct and maternal effects for weaning weight of beef cattle.

Genetic analysis of Holstein cattle populations in Brazil and the United States

Genetic relationships between Brazilian and US Holstein cattle populations were studied using first-lactation records of 305-d mature equivalent (ME) yields of milk and fat of daughters of 705 sires in Brazil and 701 sires in the United States, 358 of which had progeny in both countries. Components of(co)variance and genetic parameters were estimated from all data and from within herd-year standard deviation for milk (HYSD) data files using bivariate and multivariate sire models and DFREML procedures distinguishing the two countries. Sire (residual) variances from all data for milk yield were 51 to 59% (58 to 101%) as large in Brazil as those obtained from half-sisters in the average US herd. Corresponding proportions of the US variance in fat yield that were found in Brazil were 30 to 41% for the sire component of variance and 48 to 80% for the residual. Heritabilities for milk and fat yields from multivariate analysis of all the data were 0.25 and 0.22 in Brazil, and 0.34 and 0.35 in the United States. Genetic correlations between milk and fat were 0.79 in Brazil and 0.62 in the United States. Genetic correlations between countries were 0.85 for milk, 0.88 for fat, 0.55 for milk in Brazil and fat in the US, and 0.67 for fat in Brazil and milk in the United States. Correlated responses in Brazil from sire selection based on the US information increased with average HYSD in Brazil. Largest daughter yield response was predicted from information from half-sisters in low HYSD US herds (0.75 kg/kg for milk; 0.63 kg/kg for fat), which was 14% to 17% greater than estimates from all US herds because the scaling effects were less severe from heterogeneous variances. Unequal daughter response from unequal genetic (co)variances under restrictive Brazilian conditions is evidence for the interaction of genotype and environment. The smaller and variable yield expectations of daughters of US sires in Brazilian environments suggest the need for specific genetic improvement strategies in Brazilian Holstein herds. A US data file restricting daughter information to low HYSD US environments would be a wise choice for across-country evaluation. Procedures to incorporate such foreign evaluations should be explored to improve the accuracy of genetic evaluations for the Brazilian Holstein population.

Variation in the volume of zebra finch song control nuclei is heritable: developmental and evolutionary implications

In many songbird species, females prefer males that sing a larger repertoire of syllables. Males with more elaborate songs have a larger high vocal centre (HVC) nucleus, the highest structure in the song production pathway. HVC size is thus a potential target of sexual selection. Here we provide evidence that the size of the HVC and other song production nuclei are heritable across individual males within a species. In contrast, we find that heritabilities of other nuclei in a song-learning pathway are lower, suggesting that variation in the sizes of these structures is more closely tied to developmental and environmental differences between individuals. We find that evolvability, a statistical measure that predicts response to selection, is higher for the HVC and its target for song production, the robustus archistriatalis (RA), than for all other brain volumes measured. This suggests that selection based on the functions of these two structures would result in rapid major shifts in their anatomy. We also show that the size of each song control nucleus is significantly correlated with the song related nuclei to which it is monosynaptically connected. Finally, we find that the volume of the telencephalon is larger in males than in females. These findings begin to join theoretical analyses of the role of female choice in the evolution of bird song to neurobiological mechanisms by which the evolutionary changes in behaviour are expressed.

Application of an autoregressive process to estimate genetic parameters and breeding values for daily milk yield in a tropical herd of Lucerna cattle and in United States Holstein herds

The objectives of this study were to estimate from test day records the genetic and environmental (co)variance components, correlations, and breeding values to increase genetic gain in milk yield of Lucerna and US Holstein cattle. The effects of repeated observations (within cow) were explained by first-order autoregressive processes within and across lactations using an animal model. Estimates of variance components and correlation coefficients between test days were obtained using derivative-free REML methodology. The autoregressive structure significantly reduced the model error component by disentangling the short-term environmental effects. The additional information and the more heterogeneous environmental variances between lactations in the multiple-lactation test day model than in the first lactation model provided substantially larger estimates of additive genetic variance (0.62 kg2 for Lucerna; 14.73 kg2 for Holstein), heritability (0.13 for Lucerna; 0.42 for Holstein), and individual genetic merit. Rank correlations of breeding values from multiple lactations and from first lactations ranged from 0.18 to 0.37 for females and from 0.73 to 0.89 for males, respectively. Consequently, more selection errors and less genetic gain would be expected from selection decisions based on an analysis of first lactation only, and greater accuracy would be achieved from multiple lactations. Results indicated that substantial genetic gain was possible for milk yield in the Lucerna herd (34 kg/yr). Estimates of genetic variance for Holsteins were larger than previously reported, which portends more rapid genetic progress in US herds also; under our assumptions, increases would be from 173 to 197 kg/yr.

Influence of sire misidentification on sire x year interaction variance and direct-maternal genetic covariance for weaning weight in beef cattle

Biased estimates of the genetic correlation between direct and maternal effects may occur when sire x year interaction (SY) effects are ignored in analytical models used to estimate (co)variance components for weaning weight in beef cattle. Using simulation, sire misidentification was explored as a source contributing to estimates of SY variance. Identifications were falsified for 20% of sires of nonparents only or for 20% of sires of all animals. Sire misidentification influenced estimates of genetic and environmental parameters. In populations in which misidentification occurred only in nonparents, heritability estimates for direct growth were reduced, and heritability estimates of maternal effects were inflated. Also, spurious SY variance and direct-maternal covariance were produced. Direct-maternal covariance was biased in a positive direction, and SY variance was on the order of 1 to 3% of the phenotypic variance.

Estimation of genetic variance and covariance components for weaning weight in Simmental cattle

The objectives of this study were to estimate genetic parameters for weaning weight of Simmental cattle from data without selective reporting and to examine heterogeneity of parameters with a multiple trait approach. Heterogeneity of (co)variance components (VC) by sex is accounted for in national genetic evaluations for Simmental cattle. Completely reported data were split into bull, heifer, and steer populations to obtain VC estimates. Estimates of direct-maternal genetic correlation were negative, which suggests that selective reporting was not a cause of a negative correlation in Simmental data. However, analyzing only data for males does not account for selection on females and vice versa. Heterogeneous VC for sex were evaluated by analyzing Simmental data using a multiple trait model where male and female data were treated as two traits. Estimates of heritability of direct (maternal) effects were .19 (.07) and .25 (.12) and estimates of the direct-maternal genetic correlation were -.05 and -.20 for males and females, respectively. The multiple trait model fit the data better (P < .01) than the model under the assumption of homogeneous VC.

Influence of partitioning data by sex on genetic variance and covariance components for weaning weight in beef cattle

Heterogeneity of (co)variance components (VC) by sex is currently accounted for in national genetic evaluations for Simmental cattle. Parameters used in the national evaluation program are estimated from data split into male, female, and steer populations. Analyzing only male data does not account for selection of females, and vice versa. To determine the impact of selection, a Monte Carlo simulation was used, and estimates of VC for weaning weight were obtained when data were partitioned by sex. Weaning weight data were simulated using homogeneous VC for males and females for random and selected populations. Restricted maximum likelihood estimates were obtained for direct and maternal genetic and permanent and temporary environmental variances and genetic covariance between direct and maternal effects by analyzing complete or split data. Estimates differed (P < .01) from input values in data from selected populations split by sex, yielding a spurious heterogeneity of VC for sex. The heterogeneity was reduced in models using genetic groups but not completely removed. Splitting data by sex also influenced VC estimates in data simulated with heterogeneous VC for males and females.

Relationship between sire x year interactions and direct-maternal genetic correlation for weaning weight of Simmental cattle

The interrelation of sire x year interactions (SY) and direct-maternal genetic correlation (rdm) for weaning weight was examined for bias in estimating rdm. Weaning weight records were simulated using models containing SY (D1), rdm (D2), or both (D3). When D1 data were analyzed ignoring SY, a nonzero rdm was observed, and direct and maternal genetic variance estimates were inflated. Analysis of D2 data ignoring rdm did not reveal a spurious SY, and direct and maternal genetic variance estimates were deflated. On application to weaning weights of Simmental cattle, the model ignoring SY resulted in a direct-maternal genetic correlation estimate of -.29. The model using both SY and rdm fit the data better (P < .01). The SY variance represented only 3% of phenotypic variance but explained 62% of the covariance between direct and maternal genetic effects estimated ignoring SY. However, a negative estimate of the genetic correlation (-.14) was still obtained.

Comparison of Landim and Africander cattle in southern Mozambique: II. Female fertility, reproduction, and beef offtake

Fertility and reproductive performance of Landim and Africander females were compared using data collected from 1968 to 1981 at the Chobela Research Station in Mozambique. Breeds were managed together and grouped by age and sex, except when separated for breeding. Traits were relative fertility (probability of fertile females calving from the first breeding season), age at first calving, first calving interval, and subsequent calving intervals. calving rates were tested by x2 procedures with equal expected frequencies in each subclass. The statistical model included breed, the random effect of sire within breed, year-season of birth or calving, and calving group within breed. Landim survivors were more fertile (P < .05) than the Africander ones throughout their recorded lifetimes. Landim females were 1.32 +/- .21 mo (or 3%) younger at first calving and had a 48 +/- 12 d (or 11%) shorter interval between first and second calving than the Africander average of 473 d. When reproductive and growth information were combined to compute an annual index of beef offtake expressed as 18-mo calf yield per unit of dam's weight at first calving, Landim cows annually yielded 30% more calf weight (P < .001) than Africander cows per kilogram of their own body maintenance despite lighter body weights at 18 mo. Superior fertility of Landim females led to greater beef offtake from higher calving rates. Greater fertility and relatively less feed to maintain the reproducing herd are probable mechanisms for a population to adapt to nutrient-limiting environments such as the one in southern Mozambique.

Comparison of Landim and Africander cattle in southern Mozambique: I. Body weights and growth

The growth performance of Landim and Africander breeds was compared using data collected from 1968 to 1981 at the Chobela Research Station in Mozambique. Animals from both breeds were managed together in groups by age and sex, except when separated for breeding. Growth traits were body weights at birth, weaning at 7 mo, 18 mo, and first calving, and pre- and postweaning daily growth rates. These traits were analyzed using a mixed-effects least squares model containing breed, year-season of birth, sex, the nested effect of parity within breed, a linear regression on dam's age, and the random effect of sire within breed. Africander calves were 16, 9, and 7% heavier (P < .01) than Landim calves at birth, weaning, and 18 mo (18 +/- 6 kg heavier than the 237-kg Landim average). However, there was no detectable difference for age-adjusted weight at first calving and postweaning daily growth rate. Diminishing weight and growth differences with advancing age may indicate adaptation by the Landim to the prevailing environmental limitations in southern Mozambique, especially through younger ages at puberty and at first calving.

Multiplicative factors for estimation of daily milk and component yields from single morning or afternoon tests

Prediction of daily yield from single a.m. or p.m. milkings requires factors that are the reciprocal of the proportion of total yield expected from single milkings given the milking interval. Further adjustments to estimated milk yield account for DIM. Factors used by the Cornell Dairy Records Processing Lab were estimated from data collected from August 1983 to November 1984. These factors appear to be biased. Inconsistent estimates of daily yield were observed monthly. New factors were developed using recent data. Factors from a.m. milkings for milk and protein yield were smaller than those currently in use. The reverse was true for fat yield. Covariants for DIM were larger than those currently used. Differences were observed when factors using data with known and assumed milking intervals were compared. Factors for a.m. milkings with known intervals were smaller than those from p.m. milkings with the same known intervals. Use of covariants for DIM were compared with covariants for single milk yield. The latter explained more variation in yield. Factors were tested on independent data. New factors with covariants for single milk yield performed best for estimation of total daily yield.

Determining the minimum sample size required to obtain sufficient progeny with a desired genotype at two quantitative trait loci

In this paper we determine the minimum progeny sample size n needed to obtain, with probability α, at least m individuals of a desired two-locus genotype [Symbol: see text] affecting quantitative traits. The two quantitative trait loci (QTLs) of interest may be linked or independent, with or without epistatic interaction between them. Parental genotypes may be known or unknown, and gene action at either locus may range from additive to overdominance. To reduce the required sample size, mating patterns that will produce a high proportion of desired progeny are suggested for different progeny genotypes and dominance levels. Based on the assumption of normally distributed quantitative trait expression, individuals can be classified into a genotype or genotypic group according to their phenotypic expressions. This technique is used to select both parents and progeny with unknown genotypes. Choice of parental classification criteria for a given quantitative trait affects classification accuracy, and hence the probability of obtaining progeny of the desired genotype. The complexity of this probability depends on the dominance level at each locus, the recombination fraction, and the awareness of parental genotypes. The procedure can be expanded to deal with more than two loci.

Parameter estimation for carcass traits including growth information of Simmental beef cattle using restricted maximum likelihood with a multiple-trait model

(Co)variance component estimates were computed for retail cuts per day of age (kilograms per day), cutability (percentage of carcass weight), and marbling score (1 through 11) using a multiple-trait sire model. Restricted maximum likelihood estimates of (co)variance components were obtained via an expectation-maximization algorithm. Carcass data consisted of 8,265 progeny records collected by U.S. Simmental producers. Growth trait information (birth weight, weaning weight, and[or] postweaning gain) for those progeny with carcass data and an additional 5,405 contemporaries formed the complete data set for analysis. A total of 420 sires were represented. Three models differing in number of traits were investigated: 1) carcass traits with growth traits, 2) carcass traits only, and 3) single trait. The final models did not include postweaning gain because of convergence problems. Parameter estimates for all three models were essentially the same. Heritability estimates were .30, .18, and .23 for retail cuts per day, cutability, and marbling score, respectively. Correlations between growth and carcass traits were low except for those with retail cuts per day, which were moderate and positive. The additional information gained by adding growth traits to the carcass-traits-only evaluation lowered prediction error variances most for retail cuts per day. Little change in prediction error variances was found for cutability and marbling score. Inclusion of growth traits in future sire evaluations for carcass traits will benefit the evaluation of retail cuts per day but have considerably less effect on cutability and marbling score.

Variance heterogeneity in direct and maternal weight traits by sex and percent purebred for Simmental-sired calves

Phenotypic variances for linear and transformed weight traits were partitioned into residual, direct genetic (D) and maternal genetic (M) components using REML techniques with American Simmental Association data from calves born 1969 to 1985. Variance components were estimated separately from subclasses defined by sex (male, female) and percent Simmental (50, greater than or equal to 75). The model included fixed effects of contemporary group and age-of-dam (less than 3, 3 to 5, greater than 5 yr). Additive relationships among sires and maternal grandsires were included. Results follow for a sire-maternal grandsire model for greater than or equal to 75% Simmental untransformed data based on 143,280 male and 281,805 female weaning weights (WW) representing 4,763 and 7,406 sires, respectively. Female results are bracketed. For computational simplification, 47,650 [30,909] postweaning gain (PW) records were included in the analysis only for 114,404 [182,255] calves with birth weight (BW). Phenotypic standard deviations (kg) were: BW, 4.5 [4.1]; WW, 26.9 [23.2]; and PW, 25.9 [19.9]. Heritabilities were: BWD, .40 [.45]; WWD, .32 [.39]; PWD, .26 [.32]; BWM, .13 [.15]; WWM, .20 [.16]; and PWM, .01 [.01]. These heritabilities are higher than previously used for genetic evaluations in this breed. Moderate and positive correlations .26 to .50, existed between direct effects and were similar for both sexes. Direct and maternal effects on the same trait were correlated negatively: BW, -.45 [-.31]; and WW, -.27 [-.34]. Genetic correlation between BWM and WWM was .53 [.49]. First-cross progeny exhibited less genetic and residual variation and had lower heritabilities than Simmental calves of higher percent. Correlations between sire evaluations on the subsets were consistent with those expected given a perfect genetic correlation between traits for each sex and percent Simmental. Logarithmic transformed records were no more homogeneous than untransformed records.

Describing interactions in dystocia scores with a threshold model

Field data on calving difficulty scores provided by the American Simmental Association were subjected to two methods of analysis: ordinary least-squares analysis and maximum likelihood with an assumed threshold model. In each analysis, the model included the interaction of sex of calf X age of dam. This interaction was readily apparent in the data (observed scale): within the youngest dams 58% of the heifer calves and 37% of the bull calves were born unassisted vs 96% and 92%, respectively, in the oldest dams. The objective was to determine if this interaction would be greatly reduced or would disappear on the underlying scale of a threshold model. The least-squares estimate of the sex difference was greatest within the youngest age-of-dam group (18 to 24 mo) and steadily declined with increasing age of dam, approaching zero for dams 6 yr and older. In contrast, the estimates of the sex difference from the threshold analysis were remarkably similar across ages of dam. It was concluded that observed interactions in calving ease data could be adequately described by a threshold model in which the effects of age of dam and sex of calf act additively on the underlying variable.

Analysis of gestation length in American Simmental cattle

Records of gestation length (71,461) for Simmental cattle were distributed with mean 284.3 d and standard deviation 5.52 d. Gestation length was found to increase with percent Simmental and was 1.9 d longer for calves born to mature dams than for those born to heifer dams. Bull calves experienced gestation lengths 1.5 d longer than heifer calves. Sire, maternal grandsire, residual and total variances were estimated to be 2.42, .58, 22.78 and 25.78 d2, respectively, by Henderson's Method III. Heritability of gestation length was calculated to be .374 from the sire variance and .09 from the maternal grandsire variance. Direct additive genetic variance was considered to be of greater importance than maternal additive genetic variance. Correlations between the evaluations of sires for gestation length and heifer calving ease, birth weight and weaning weight were .26, .26 and .13, respectively.

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.

Estimation of genetic trend in a selected population with and without the use of a control population

Data from a selection experiment conducted with sheep at Massey University, New Zealand, were analyzed to obtain an evaluation of selection response. Selection was for heavy 14-mo greasy fleece weight. Approximately seven generations of selection were represented in the data. Three estimates of genetic superiority of the selected line to the control line were obtained. All three estimates were obtained from a mixed model evaluation using the individual animal model for predicting breeding values from own and relatives' records. The estimators were 1) deviation of selected line predicted yearly phenotypes from control line predicted yearly phenotypes, 2) deviation of the predicted yearly phenotype for the selected line from the year estimate in the control line and 3) the mean yearly breeding value from the analysis of the selected line only. The realized heritability using the first approach was .20. However, the control line was found to have a slight positive drift; hence, this estimate was biased downward. Using Approach 2, accounting for drift, the realized heritability was .23. The same realized heritability, .23, was obtained from an analysis of the selected line ignoring the control (Approach 3), when a prior heritability of .30 was assumed for the mixed model evaluation. The estimate of genetic trend from predicted breeding values in the latter approach is, however, quite dependent on the assumed heritability.

Interrelationships of parturition problems, production of subsequent lactation, reproduction, and age at first calving

Data of 22,691 observations on parturition related problems (dystocia, calf mortality, milk fever, retained placenta, and mastitis) were collected from 27 cooperating California dairy herds. Age at first calving did not affect calving difficulty; thus, an optimal age for first calving was not identified. Decisions on breeding virgin heifers should be based on size of cow because of the effect of size of cow on difficulty at first parity. Small calves experienced greatest mortality at parities greater than one; however, large calves had greater mortality at first parity. Greater mortality for large calves at first parity was partially due to the increased difficulty associated with larger calves. Calving difficulty resulted in impaired reproductive performance (more days open, more services, and more days to first breeding) and decreased 30-day milk production but had no effect on 90-day milk production and 305-day mature-equivalent milk production. Dystocia, milk fever, and retained placenta occurred as a complex. Incidence of dystocia and calf mortality decreased with parity, and all other problems increased with parity.

Maternal influences on growth of twin and single calves

Milk production was measured at 28-d intervals by the calf weight change method in 30 dams with twins and in 28 dams with single calves. Average adjusted 170-d weaning weights for twins were between 41 and 38 kg less than for singles (depending on linear contrast). Yet dams with twins weaned between 91 and 97 kg more calf and produced substantially more milk. Significant dam breed and parity differences in calf growth and weaning weight were observed among twins. Dam breeds ranked in the order of decreasing productivity were Hereford-Angus crossbred, Angus and Hereford. Cows outproduced heifers. Among singles, such differences were small. As indicated by linear contrasts, maternal effects were larger in twins than in singles; however, these differences were generally not significant. Only milk production in the first half of lactation by dams with twins was found to be a significant predictor of calf growth and weaning weight. For every 1-kg increase in 6-h milk production in early lactation, 170-d adjusted weaning weight of twins increased (P less than .01) by 18.8 kg. Among singles, regression estimates for growth on milk yield were small and nonsignificant.