Defining valid breeding goals for animal breeds

BACKGROUND

The objective of any valid breeding program is to increase the suitability of a breed for its future purposes. The approach most often followed in animal breeding for optimizing breeding goals assumes that the sole desire of the owners is profit maximization. As this assumption is often violated, a generalized approach is needed that does not rely on this assumption.

RESULTS

The generalized approach is based on the niche concept. The niche of a breed is a set of environments in which a small population of the breed would have a positive population growth rate. Its growth rate depends on demand from prospective consumers and supply from producers. The approach involves defining the niche that is envisaged for the breed and identifying the trait optima that maximize the breed's adaptation to its envisaged niche within the set of permissible breeding goals. The set of permissible breeding goals is the set of all potential breeding goals that are compatible with animal welfare and could be reached within the planning horizon of the breeding program. In general, the breed's adaptation depends on the satisfaction of the producers with the animals and on the satisfaction of the consumers with the products produced by the animals. When consumers buy live animals, then the breed needs to adapt to both the environments provided by the producers, and the environments provided by the consumers. The profit function is replaced by a more general adaptedness function that measures the breed's adaptation to its envisaged niche.

CONCLUSIONS

The proposed approach coincides with the traditional approach if the producers have the sole desire to maximize their income, and if consumer preferences are well reflected by the product prices. If these assumptions are not met, then the traditional approach to breeding goal optimization is unlikely to result in a valid breeding goal. Using the example of companion breeds, this paper shows that the proposed approach has the potential to fill the gap.

Genomic and Phenotypic Udder Evaluation for Dairy Cattle Selection: A Review

The traditional point of view regarding dairy cattle selection has been challenged by recent genomic studies indicating that livestock productivity prediction can be redefined based on the evaluation of genomic and phenotypic data. Several studies that included different genomic-derived traits only indicated that interactions among them or even with conventional phenotypic evaluation criteria require further elucidation. Unfortunately, certain genomic and phenotypic-derived traits have been shown to be secondary factors influencing dairy production. Thus, these factors, as well as evaluation criteria, need to be defined. Owing to the variety of genomic and phenotypic udder-derived traits which may affect the modern dairy cow functionality and conformation, a definition of currently important traits in the broad sense is indicated. This is essential for cattle productivity and dairy sustainability. The main objective of the present review is to elucidate the possible relationships among genomic and phenotypic udder evaluation characteristics to define the most relevant traits related to selection for function and conformation in dairy cattle. This review aims to examine the potential impact of various udder-related evaluation criteria on dairy cattle productivity and explore how to mitigate the adverse effects of compromised udder conformation and functionality. Specifically, we will consider the implications for udder health, welfare, longevity, and production-derived traits. Subsequently, we will address several concerns covering the application of genomic and phenotypic evaluation criteria with emphasis on udder-related traits in dairy cattle selection as well as its evolution from origins to the present and future prospects.

Preferences of European dairy stakeholders in breeding for resilient and efficient cattle: A best-worst scaling approach

Including resilience in the breeding objective of dairy cattle is gaining increasing attention, primarily as anticipated challenges to production systems, such as climate change, may make some perturbations more difficult to moderate at the farm level. Consequently, the underlying biological mechanisms by which resilience is achieved are likely to become an important part of the system itself, increasing value on the animal's ability to be unperturbed by variable production circumstances, or to quickly return to pre-perturbed levels of productivity and health. However, because the value of improving genetic traits to a system is usually based on known profit functions or bioeconomic models linked to current production conditions, it can be difficult to define longer-term value, especially under uncertain future production circumstances and where nonmonetary values may be progressively more important. We present the novel application of a discrete choice experiment, used to investigate potential antagonisms in the values of genetic improvements for 8 traits to dairy cattle system stakeholders in Europe when the production goal was either efficiency or resilience. A latent class model was used to identify heterogeneous preferences within each production goal, and postestimation was used to identify associations between these preferences and sociodemographic characteristics of respondents. Results suggested 3 distinct latent preference classes for each production goal. For the efficiency goal, yield and feed efficiency traits were generally highly valued, whereas for the resilience goal, health and robustness traits were generally highly valued. In both cases, these traits generally carried a low value in the other production scenario. Overall, in both scenarios, longevity was highly valued; however, the value of this trait in terms of resilience will depend on phenotyping across diverse environments to sufficiently capture performance under various anticipated system challenges. Additionally, results showed significant associations between membership of latent preference classes with education level and profession. In conclusion, as resilience becomes increasingly important, it is likely that a continued reliance on the short-term economic value of traits alone will lead decision makers to misrepresent the importance of some traits, including those with substantial contextual values in terms of resilience.

Genotype-by-environment interactions at the trait level and total merit index level for milk production and functional traits in Brown Swiss cattle

The production environments of the German-Austrian Brown Swiss population show a wide range due to differences in topography, landscapes, local climates, and different farm management systems. Extensive production systems such as organic farming have become increasingly popular in recent decades because of interest in sustainability and consumer preferences. Compared with conventional farmers, organic farmers put more weight on fitness traits. Besides the official total merit index (TMI), a selection index applying relative economic weights (REWs) suitable for organic production systems is provided for Brown Swiss cattle in Germany. The aim of the study was to investigate genotype-by-environment interactions (GxE) for milk production traits and functional traits (including longevity, fertility traits, and calving traits) in a sample of the German-Austrian Brown Swiss population housed in Baden-Wuerttemberg (southern Germany) by applying bivariate and random regression sire models. For bivariate analyses, the production environment was binary classified by farm management system (organic and conventional) and altitude of farm location (above or below 800 m above sea level (ASL)). Milk energy yields (MEY) obtained from herd effects were used as continuously scaled environmental descriptor in the reaction norm approach. The TMIs for sires were calculated based on breeding values estimated with different models and environment-specific REWs to determine possible GxE at TMI levels and rerankings of sires. In bivariate analyses, genetic correlations at the trait level were high and ranged from r_g = 0.99 (calving to first insemination, cystic ovaries, and maternal stillbirth rate) to r_g = 0.79 (first insemination to conception for altitude). Except for the latter, no severe GxE were found at the trait level using the bivariate models. Fat yield was the only trait showing minor GxE in the reaction norm model approach. Investigating the environmental sensitivity at the TMI level revealed rank correlations between the different environment-specific TMIs that were close to unity, implying no severe reranking effects. The results show no need to account for different environments in Brown Swiss cattle breeding programs.

Genomic analysis of perinatal sucking reflex in German Brown Swiss calves

A healthy sucking reflex is essential for newborn calves to ensure sufficient colostrum intake in the first few hours postpartum. In recent decades, European Brown Swiss breeders have repeatedly reported that some calves lack the ability to consume colostrum directly after birth due to an absent sucking reflex. In this study, we collected the phenotypes of more than 5,500 German Brown Swiss calves and performed variance component estimation with sire threshold models using Markov chain Monte Carlo algorithms. The 50K (777K) genotypes of nearly 2,000 (200) calves were collected, and an imputation was performed for all 50K genotypes up to 777K. Genome-wide association studies (GWAS) for the trait sucking reflex were conducted for all 777K genotypes. Depending on the trait coding, a low heritability was estimated to range from 0.08 to 0.11. The GWAS results identified 34 trait-associated SNP on 6 different chromosomes. Post-GWAS analyses showed significant overrepresentation of Gene Ontologies for central nervous development and several regulative processes. Functional annotation clustering and pathway analysis revealed relations to lipid metabolism, immune and endocrine systems, and signal transduction. The results of this study suggest that breeding for an improved sucking reflex is possible but requires large data sets for the estimation of reliable breeding values (either large progeny testing groups or a large reference genome in a genomic selection program).