Browsing by Subject "Animal breeding"

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Breeding for resilient cows
(2025) Keßler, Franziska; Bennewitz, Jörn
Dairy cows are an indispensable part of modern livestock farming and make a significant contribution to human nutrition with producing a high-quality protein. At the same time, they are influenced by environmental factors and must maintain their performance, stay healthy, and remain fertile under given environmental conditions. In recent decades, we have faced an increasing number of new or suddenly emerging environmental stressors: extreme weather events, heatwaves, invasive species, and constantly changing requirements for housing conditions are just a few examples. This demands a high level of robustness and resilience from our dairy cows. While comprehensive research has been conducted on adaptation to changing environmental conditions, there is still a lack of knowledge about coping with short-term disturbances. Resilience is the ability of an individual to respond to these disturbances, recover from them, and return to its previous physiological equilibrium while maintaining the same level of performance. This study examines the concept of resilience in German dairy cattle breeds, analyzes genetic parameters, and discusses possibilities for future breeding strategies. The first chapter describes interactions between organisms and the environment, as well as statistical approaches to assessing the influence of environmental gradients on livestock. The concepts of resilience and robustness were distinguished, and methods for measuring and phenotyping resilience were explored. A promising approach is the analysis of variance and autocorrelation of daily milk yields during lactation. Under the assumption that resilient animals maintain a stable performance level along a natural lactation curve, low variance and an autocorrelation close to zero indicate high resilience. The genetic parameters of these resilience indicator traits were studied in the second chapter for the three most important German dairy breeds: German Holstein, German Fleckvieh, and German Brown Swiss. Within each breed and across breeds, low to moderate heritabilities were observed, along with desirable phenotypic and genetic correlations with performance traits. A comparison between breeds revealed only minimal differences, with no clear trend across all resilience indicator traits studied. Next, correlations between resilience indicator traits and functional as well as health traits were analyzed. While hardly any significant correlations were found for autocorrelation, the variance of daily milk yield correlated in a desirable direction with these traits. Resilient animals appear to be healthier and more long-lived. Chapter three also discusses the design of a selection index for resilience. This requires economic weighting factors, which cannot yet be determined. Therefore, optimizing the selection index resilience by maximizing breeding response in the selection index health was proposed. It was shown that breeding for resilience would lead to genetic progress in overall health. In the German Holstein breed, which was exclusively considered in this context, a selection index consisting of two different variance-based resilience indicator traits was recommended. The adaptation of the methodology to optimize a selection index to the German Fleckvieh and German Brown Swiss breeds was subsequently addressed in the general discussion and considered feasible. The fourth chapter analyzes the genetic architecture of resilience using genome-wide association studies within the three dairy breeds. The results indicated that the resilience indicator traits are polygenic traits. SNPs that significantly influence resilience are located near to QTLs known to affect performance, fertility, or health. Additionally, population structure was examined using linkage disequilibrium analysis. The final general discussion applied the methods from chapter three to the German Fleckvieh and German Brown Swiss breeds. Significant negative, undesirable correlations between autocorrelation and functional and health traits were found in German Fleckvieh. In contrast, variance-based resilience indicator traits correlated positively with most known traits, which is desirable. A selection index resilience was proposed for both breeds, consisting of two to three individual indicator traits, similar to the German Holstein breed. To better understand resilience, differences in breeding values were translated into milk loss per lactation, the number of disturbances an individual suffered from, and the impact on test-day results for milk ingredients. Finally, an outlook was provided on potential future research directions for resilience in livestock.
Investigations on methodological and strategic aspects of genomic selection in dairy cattle using real and simulated data
(2018) Plieschke, Laura Isabel; Bennewitz, Jörn
In Chapter one a method was developed to separate the genomic relationship matrix into two independent covariance matrices. Here, the base group component describes the covariance that results from systematic differences in allele frequencies between groups at the pedigree base. The remaining segregation component describes the genomic relationship that is corrected for the differences between base populations. To investigate the proposed decomposition three different models were tested on six traits, where the covariance between animals was described either only by the segregation component or by a combination of the two components. An additional variant examining the effect of a fixed modeling of the group effects was included. In total, 7965 genotyped Fleckvieh and 4257 genotyped Brown Swiss and 143 genotyped Original Braunvieh bulls were available for this study. The proposed decomposition of the genomic relationship matrix helped to examine the relative importance of the effects of base groups and segregation component in a given population. It was possible to estimate significant differences between the means of base groups in most cases for both breeds and for the traits analyzed. Analysis of the matrix of base group contributions to the populations investigated revealed several general breed-specific aspects. Comparing the three models, it was concluded that the segregation component is not sufficient to describe the covariance completely. However, it also was found that the model applied has no strong impact on predictive power if the animals used for validation show no differences in their genetic composition with respect to the base groups and if the majority of them have complete pedigrees of sufficient depth. The subject of the chapter two was investigation to systematically increase the reliability of genomic breeding values by integrating cows into the reference population of genomic breeding value estimation. For this purpose a dataset was generated by simulation resembling the German-Austrian dual-purpose Fleckvieh population.. The concept investigated is based on genotyping a fixed number of daughters of each AI bull of the last or last two generation of the reference population and, together with their phenotypic performance, to integrate them into the reference population of the genomic evaluation. Different scenarios with different numbers of daughters per bull were compared. In the base scenario the reference population was made up of 4200 bulls. In the extended scenarios, more and more daughters were gradually integrated in the reference population. The reference population of the most extended scenario contained 4200 bulls and 420,000 cows. It was found that the inclusion of genotypes and phenotypes of female animals can increase the reliabilities genomic breeding values considerably. Changes in validation reliability of 6-54% for a trait with a heritability of 0.4 depending on scenario were found. As the number of daughters increased, the validation reliability increased as well. It should be noted that the composition of the daughter samples had a very great influence on whether the additional genotyped and phenotyped animals in the reference population can have a positive effect on the reliability of genomic breeding values. If pre-selected daughter samples were genotyped, the mean validation reliability decreased significantly compared to a correspondingly large unselected daughter sample. In addition, a higher bias was observable in these cases. Chapter three expands the investigations of chapter two by a low-heritability trait, as well as the aspect of so called new traits. The results found in chapter two were confirmed in chapter three for a low-heritability trait. Changes in validation reliability of 5-21% for a heritability of 0.05 depending on scenario were found. The negative effects of pre-selected daughter samples were even more pronounced in chapter three. In the case of an ‘old’ trait, the number of phenotypes is expected to be (nearly) unlimited, since a recording system is well established. In the case of a new trait recording of phenotypes just started, therefore the number of phenotypes is limited. Two different genotyping strategies were compared for new traits. On the one hand, the sires of the phenotyped cows were genotyped and on the other hand the phenotyped cows were genotyped themselves. It was found in all compared scenarios that it is more sensible to genotype cows themselves instead of the genotyping their sires. However, if usual strategy of phenotyping female animals and genotyping of males is applied, it is at least important to ensure that many daughters are phenotyped in a balanced system. If different numbers of daughters per bull are phenotyped and unbalancedness becomes severe, the average validation reliability decreased significantly.