Browsing by Subject "Genomic models"

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Genomic methods for rotational crossbreeding in local dairy cattle breeds
(2022) Stock, Joana; Bennewitz, Jörn
Local dairy breeds, such as German Angler, usually have small population sizes and thus a reduced genetic gain, compared to high-yielding breeds. Especially since genomic selection is widely used in the latter, the performance gap between local breeds and high-yielding breeds increased further, as it requires large reference populations in order to achieve accurate estimated breeding values. As a result, many farmers switched to high-yielding breeds. On the other hand, to increase the performance of local breeds the introgression of high-yielding breeds was a common strategy in the past, which resulted in high amounts of foreign genetic material in many of them. Much of the original genetic background got lost, however, they do not achieve the same performance level as high-yielding breeds. Local breeds are therefore faced with the risk of two types of extinction, i.e. a numerical extinction due to the small and decreasing numbers of breeding animals, and a genetic extinction due to massive introgression from high-yielding breeds. To promote local dairy breeds, the implementation of a genomic rotational crossbreeding scheme can be a promising strategy. Local breeds can benefit from a genomic rotational crossbreeding scheme with a high-yielding breed due to 1) an enlarged reference population including both the local breed and crossbred animals, and 2) the increased performance level of crossbred animals. On the other hand, crossbreeding is particularly known to improve functional traits by the exploitation of heterosis. Thus, it appears to be an appealling option for high-yielding breeds, as well, as they tend to struggle with fitness related problems. This thesis aimed to develop genomic methods for numerically small local dairy breeds in crossbreeding schemes in order to improve their genetic gain, genetic uniqueness, and their ability to compete with high-yielding breeds. In Chapter 2 a review study conducted a comparison of different genomic models which are suitable for crossbred data. Different additive models (such as the parental model, a model with breed-specific allele effects, and a single step model) and dominance models, which were either line-dependent, line-independent or included imprinting were discussed. It was concluded that the model choice needs to be made based on desired accuracies, computational possibilities, and data availability. In general, dominance models showed to result in higher accuracies compared to additive models. A breed of origin of alleles model approach was introduced in Chapter 3, which assumes different SNP effects for different origins of haplotypes. This model is suitable for the multi-breed genomic prediction of breeding values of numerically small breeds (i.e. German Angler) that have experienced introgression from high-yielding breeds in the past. The breed of origin of alleles model approach tended to be advantageous for Angler over multi-breed and within-breed genomic predictions with GBLUP. Chapter 4 contains a simulation study about the implementation of a rotational crossbreeding scheme including German Angler x German Holstein, while introducing genomic selection in Angler. Different sizes and structures of growing reference populations and selection goals of Angler were examined. The results showed that crossbred animals had a small overall superiority to both Holstein and Angler populations. In addition, a reference population containing both Angler and crossbred animals, in combination with a selection based on the purebred performance of Angler, gave the highest response to selection in the purebred Angler population and in the crossbred population. The difference between selection methods for Angler individuals could only be observed in the long term, as the purebred-crossbred correlations decreased. In Chapter 5 a simulation study on rotational crossbreeding was performed including different Optimum Contribution Selection methods, in order to realize genetic gain while regaining the original genetic background of Angler. Different constraints regarding mean kinships, native kinships, and migrant contributions from Holstein were applied to investigate their effects on Angler, crossbred, and Holstein populations. Constraining the amount of migrant contribution in Angler increased their genetic uniqueness. However, it led to a notable reduction of genetic gain and thus a reduced superiority of the crossbred animals. The slowed rate of genetic gain and thus the large difference of the performance between the parental breeds could not be compensated by heterosis effects. In Chapter 6 the thesis ends with a general discussion about further genomic models for crossbreeding, and the practical relevance of crossbreeding in dairy cattle.