Browsing by Subject "Rinderzucht"

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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.
Pedigreeanalysen zur Beschreibung der populations- und quantitativgenetischen Situation von baden-württembergischen Lokalrinderrassen
(2014) Hartwig, Sonja; Bennewitz, Jörn
The challenge of a conservation breeding program is to solve a conflict of goals: genetic variability and genetic autonomy should be maintained, and on time a certain amount of breeding progress has to be realized to ensure the ability to compete. The aim of the present study was to analyse the situation concerning the targets mentioned above for traditional cattle breeds of Baden-Württemberg. Furthermore, methods for the consolidation and development of these breeds should be reconsidered. In chapter 1 the organisation of a breeding program for small cattle breeds is discussed. The challenge of such a program is the conservation of agrobiodiversity, culture and traditions and the progress of traditional local breeds. Number and extend of these breeds declined due to the increasing popularity of high-yielding breeds. Additionally, some of the local breeds are used in different branches of production compared to their original usage. Breeding programs have to be fitted. The establishment of individual adapted breeding methods is required for a sophisticated solution of the conflict mentioned above. Federal support is requested. Nowadays the implementation of genomic selection is not yet practicable for small breeds. But future opportunities should be analysed. The establishment of performance tests concerning breed specific product and efforts is demanded to improve these characteristics. In the following genetic variability of Vorderwald, Hinterwald and Limpurg cattle was examined. In chapter 2 for each breed two reference populations were defined that enable to observe the development over the years. Animals within the reference population comply with restrictions concerning racial origin and completeness of pedigree. Effective population size and the effective number of founders, and ancestors were estimated. The interpretation of the results was done with regard to the history of the breeds. The absolute population size of Vorderwald cattle is the biggest one. The number of Hinterwald cattle is intermediate; Limpurg cattle have the smallest population size. Whereas the management of Hinterwald cattle seemed to maintain genetic variability, the management of Vorderwald cattle was not that target-orientated. With an effective population size greater than 100 there is enough genetic variability within Vorderwald and Hinterwald. In contrast the values of Limpurg cattle are too low. Besides genetic variability, genetic autonomy and breeding progress are the targets of a conservation breeding program. Cross-breeding was carried out to mitigate the risk of inbreeding depression and to improve the performance of local breeds. However, breeding activities for local breeds were not as intensive and target oriented as for popular high yielding breeds. While the gap between the performance of high-yielding and local breeds increase, genetic autonomy of local breeds declined due to migrant influences. Chapter 3 examined the importance of migrant breed influences for the realization of breeding progress of beef traits of Vorderwald and Hinterwald cattle. The results show that there is a high amount of migrant contributions and their effects on performance are substantial for most traits. Breeding values adjusted for the effects of the migrant breeds showed little genetic trend for beef traits. The subject of chapter 4 is the development of milk yield and the associated migrant influences. Yield deviations for milk, fat, and protein content were analysed. Migrant contributions to Vorderwald cattle were high and even rose in the latest past. All the effects of foreign breeds were positive and in most cases highly significant. Most influential breed was Montbéliard. The influences of migrant breeds were substantial for the development of milk performance. However, the trend of milk yield traits for both breeds was positive even without foreign breeds’ influences. In comparison the number of analysed Hinterwald cows was small due to the reason that just a few Hinterwald husbandries take part at the official milk performance recording. Migrant breed contributions were moderate and nearly constant over the time. The most influential migrant breed was the Vorderwald cattle. The development of milk yield shows a flat trend. Influences of migrant breeds were low. The thesis ends with a general discussion.