Browsing by Person "Stock, Joana"

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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.
Improving the accuracy of multi-breed prediction in admixed populations by accounting for the breed origin of haplotype segments
(2022) Schmid, Markus; Stock, Joana; Bennewitz, Jörn; Wellmann, Robin
Numerically small breeds have often been upgraded with mainstream breeds. This historic introgression predisposes the breeds for joint genomic evaluations with mainstream breeds. The linkage disequilibrium structure differs between breeds. The marker effects of a haplotype segment may, therefore, depend on the breed from which the haplotype segment originates. An appropriate method for genomic evaluation would account for this dependency. This study proposes a method for the computation of genomic breeding values for small admixed breeds that incorporate phenotypic and genomic information from large introgressed breeds by considering the breed origin of alleles (BOA) in the evaluation. The proposed BOA model classifies haplotype segments according to their origins and assumes different but correlated SNP effects for the different origins. The BOA model was compared in a simulation study to conventional within-breed genomic best linear unbiased prediction (GBLUP) and conventional multi-breed GBLUP models. The BOA model outperformed within-breed GBLUP as well as multi-breed GBLUP in most cases.
Is heat stress a growing problem for dairy cattle husbandry in the temperate regions? A case study of Baden-Württemberg in Germany
(2024) Leandro, Miguel António; Stock, Joana; Bennewitz, Jörn; Chagunda, Mizeck G. G.
Heat stress with measurable effects in dairy cattle is a growing concern in temperate regions. Heat stress in temperate regions differs between environments with different geophysical characteristics. Microclimates specific to each environment were found to greatly impact at what level heat stress occurs and will occur in the future. The landlocked state of Baden-Württemberg, Germany, provides several different environments, hence, a good case-study. Temperature–Humidity Index (THI) from 17 weather stations for the years 2003 to 2022 was calculated and milking yields from 22 farms for the years 2017 to 2022 were collected. The occurrences and evolving patterns of heat stress were analyzed with the use of a THI, and the effect of heat stress on milk yield was analyzed based on milking records from Automated Milking Systems. Daily average THI was calculated using hourly readings of relative humidity and ambient temperature, disregarding solar radiation and wind, as all animals were permanently stabled. Based on studies conducted in Baden-Württemberg and neighboring regions, cited ahead in the section of THI, THI = 60 was the threshold for heat stress occurrence. Findings show that the heat stress period varied between stations from 64 to 120 d with THI ≥ 60 in a year. This aligns with yearly and summer averages, also steadily increasing from May to September. The length of the heat stress period was found to increase 1 extra day every year. Extreme weather events such as heat waves did not increase the heat stress period of that year in length but increased the average THI. Milk yield was found to be significantly (α = 0.05) different between counties grouped into different zones according to heat stress severity and rate of increase in daily average THI. Future attempts at managing heat stress on dairy cattle farms in the temperate regions should account for microclimate, as geographical proximity does not mean that the increase in heat stress severity will be the same in the 2 neighboring areas.