Genetic Heterogeneity of Residual Variance for Production and Functional Traits in American Angus Cattle
| dc.contributor.author | Amorim, Sabrina Thaise | en |
| dc.contributor.committeechair | Morota, Gota | en |
| dc.contributor.committeemember | Chen, Chun-Peng | en |
| dc.contributor.committeemember | Osorio Estevez, Johan | en |
| dc.contributor.committeemember | Holliday, Jason A. | en |
| dc.contributor.department | Animal and Poultry Sciences | en |
| dc.date.accessioned | 2024-08-16T08:00:46Z | en |
| dc.date.available | 2024-08-16T08:00:46Z | en |
| dc.date.issued | 2024-08-14 | en |
| dc.description.abstract | Beef cattle are continuously selected for different traits and the success in improving these traits has been remarkable. However, for certain traits, it is essential not only to improve the average performance, but also to control the variation around the mean. There is evidence that residual variance may be under genetic control, which opens the possibility of selecting for uniformity. In this sense, the objectives of the present dissertation were: 1) to investigate the extent of genetic heterogeneity of residual variance at the pedigree level in birth weight (BW), weaning weight (WW), yearling weight (YW), foot angle (FA), and claw set (CS) in American Angus cattle; 2) to compare the results of different genetic heterogeneity models; 3) to evaluate the effectiveness of Box-Cox transformation in continuous traits; and 4) to address limitations and explore alternative solutions for implementing genetic parameters for residual variance in genetic evaluations. The first study investigated the genetic heterogeneity of residual variances for BW, WW, and YW. Three models were compared: a homoscedastic residual variance model (M1), a double hierarchical generalized linear model (DHGLM, M2), and a genetically structured environmental variance model (MCMC, M3). The results showed significant genetic heterogeneity of residual variances in growth traits, suggesting the possibility of selection for uniformity. The genetic coefficient of variation for residual variance ranged from 0.90 to 0.92 in M2 and 0.31 to 0.38 in M3 for BW, 0.64 in M2 and 0.01 to 0.29 in M3 for WW, and 0.67 to 0.63 in M2 and 0.25 to 0.31 in M3 for YW. Low heritability estimates for residual variance were found, particularly in M2 (0.08 for BW, 0.06 for WW, and 0.09 for YW). The study identified both negative and positive genetic correlations between mean and residual variance, depending on the trait and data transformation. Negative correlations suggest the potential to increase trait means while decreasing residual variance. However, positive correlations indicate that the genetic response to selection for uniformity may be limited unless a selection index is used. Data transformation reduced skewness but did not eliminate genetic heterogeneity of residual variances. The Bayesian approach provided higher estimates of additive genetic variance for residual variance compared to DHGLM. Overall, the findings indicate the potential to reduce variability through selection and lay the groundwork for incorporating uniformity of growth traits into breeding goals. The second study focused on the genetic heterogeneity of residual variance for two foot conformation traits, FA and CS. Using 45,667 phenotypic records collected between 2009 and 2021, three models were compared: a traditional homoscedastic residual variance model (M1), a DHGLM (M2), and a genetically structured environmental variance model (M3). Results showed that heritability estimates for FA and CS means were within expected ranges, although lower in M2. Despite low heritability estimates for residual variance (0.07 for FA and 0.05 for CS in M2), significant genetic coefficients of variation were found, suggesting that selection on trait mean would also influence residual variance. Positive genetic correlations between mean and residual variance in M2 and M3 indicate that selection for uniformity is feasible, but may require additional strategies such as selection indices. The study highlights the potential of FA and CS as indicators for breeding programs aimed at improving production uniformity in beef cattle. Our findings suggest that selection for uniformity in growth and foot score traits in beef cattle may be limited by low heritability of residual variance and moderate to high positive genetic correlations between mean and residual variance. This was observed for most of the traits studied. To overcome these challenges, further research is needed, particularly to explore genomic information to improve the prediction accuracy of estimated breeding values (EBV) for residual variance. Although studies of uniformity using genomic data are limited, they have shown improved EBV accuracy for residual variance. Additionally, alternative methods for measuring uniformity, such as different uniformity or resilience indicators, should be considered, especially with advances in digital phenotyping. Precision livestock farming technologies that allow for extensive data collection on various production traits should be integrated into the development of new uniformity indicators. This dissertation provides valuable insights into the genetic heterogeneity of residual variance in American Angus cattle and highlights the complexity of selecting for uniformity while improving mean traits. Continued research with larger data sets, genomic information, and further methodological refinement will be critical to advance these findings to improve uniformity and productivity in beef cattle breeding. | en |
| dc.description.abstractgeneral | Uniformity in livestock breeding refers to the goal of reducing variability in certain traits within a livestock population to achieve more consistent and predictable outcomes. This is particularly important for traits that affect productivity, economic efficiency, animal welfare, and product quality. By achieving greater uniformity, producers can optimize management practices, improve marketability, and enhance the overall efficiency of animal production systems. Residual variance refers to the variation in traits that is not explained by known genetic or environmental factors. Recent research suggests that residual variance may be under genetic control, meaning that it is possible to select animals that not only have desirable traits, but also have less variability in those traits. Therefore, this dissertation investigates the genetic control of residual variance that may allow selection for uniformity in traits. The research focused on American Angus cattle and aimed to 1) investigate genetic heterogeneity of residual variance in traits, such as birth weight, weaning weight, yearling weight, foot angle, and claw set; 2) compare different genetic models; 3) evaluate the effectiveness of data transformations; and 4) address limitations in genetic evaluations. The first study examined genetic heterogeneity in growth traits using three models. It revealed significant genetic variability, suggesting the potential for selection for uniformity. The study found both positive and negative genetic correlations between trait means and residual variance, indicating varying potential for reducing variance while improving trait means. Data transformations reduced skewness but did not eliminate genetic heterogeneity. A Bayesian approach provided higher estimates of genetic variance than other methods. The second study focused on foot conformation traits with over 45,000 records. The study showed that despite low heritability for residual variance, there was significant genetic variation, indicating the possibility of altering residual variance through selection. Positive genetic correlations suggested that additional strategies, such as selection indices, may be needed to achieve uniformity in practice. Overall, the findings highlight the complexity of selecting for uniformity while improving average traits and underscore the need for further research, particularly using genomic data, to improve prediction accuracy. Integrating precision livestock farming technologies could help develop new indicators of uniformity, improving productivity and uniformity in beef cattle breeding. | en |
| dc.description.degree | Doctor of Philosophy | en |
| dc.format.medium | ETD | en |
| dc.identifier.other | vt_gsexam:41296 | en |
| dc.identifier.uri | https://hdl.handle.net/10919/120943 | en |
| dc.language.iso | en | en |
| dc.publisher | Virginia Tech | en |
| dc.rights | In Copyright | en |
| dc.rights.uri | http://rightsstatements.org/vocab/InC/1.0/ | en |
| dc.subject | beef cattle | en |
| dc.subject | double hierarchical generalized linear model | en |
| dc.subject | genetically structured variance | en |
| dc.subject | genetic heterogeneity of residual variance | en |
| dc.subject | growth trait | en |
| dc.subject | foot score | en |
| dc.title | Genetic Heterogeneity of Residual Variance for Production and Functional Traits in American Angus Cattle | en |
| dc.type | Dissertation | en |
| thesis.degree.discipline | Animal and Poultry Sciences | en |
| thesis.degree.grantor | Virginia Polytechnic Institute and State University | en |
| thesis.degree.level | doctoral | en |
| thesis.degree.name | Doctor of Philosophy | en |
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