S.J. Hiemstra

Local cattle breeds in Europe : development of policies and strategies for self-sustaining breeds

Which policies and strategies are required to successfully maintain our European Farm Animal Genetic Resources? The European local cattle populations were a target in the EURECA project, co-funded by the European Commission (EU AGRI GENRES 870/04). The general aim was to better understand the state of the breeds, to identify factors that contribute to their success or failure, and to recommend decision-making tools for development of ambitious and sound strategies and policies

Short communication: Milk fat composition of 4 cattle breeds in the Netherlands

Milk fatty acid (FA) composition was compared among 4 cattle breeds in the Netherlands: Dutch Friesian (DF; 47 animals/3 farms), Meuse-Rhine-Yssel (MRY; 52/3), Groningen White Headed (GWH; 45/3), and Jersey (JER; 46/3). Each cow was sampled once between December 2008 and March 2009 during the indoor housing season, and samples were analyzed using gas chromatography. Significant breed differences were found for all traits including fat and protein contents, 13 major individual FA, 9 groups of FA, and 5 indices. The saturated fatty acid proportion, which is supposed to be unfavorable for human health, was smaller for GWH (68.9%) compared with DF (74.1%), MRY (72.3%), and JER (74.3%) breeds. The proportion of conjugated linoleic acid and the unsaturation index, which are associated positively with human health, were both highest for GWH. Differences in milk fat composition can be used in strategies to breed for milk with a FA profile more favorable for human health. Our results support the relevance of safeguarding the local Dutch breeds.

The potential of cryopreservation and reproductive technologies for animal genetic resources conservation strategies

Ex situ conservation of genetic material from livestock and fish through cryopreservation is an important strategy to conserve genetic diversity in these species. Conservation strategies benefit from advances in cryopreservation and reproductive technologies. Choice of type of genetic material to be preserved for different species highly depends on objectives, technical feasibility (e.g., collection, cryoconservation), costs, and practical circumstances.

Ex situ conservation of Holstein-Friesian cattle: Comparing the Dutch, French, and US germplasm collections

Holstein-Friesian (HF) gene bank collections were established in France, the Netherlands, and the United States to conserve genetic diversity for this breed. Genetic diversity of HF collections within and between countries was assessed and compared with active male HF populations in each country by using pedigree data. Measures of genetic diversity such as probability of gene origin inbreeding and kinship were calculated. The cryobanks have captured substantial amounts of genetic diversity for the HF compared with the current populations. A substantial part of the US, French, and Dutch collections seems to be genetically similar. On the other hand, the US collection in particular represents an interesting reservoir of HF genes of the past. Gene banks can play an important role in conserving genetic diversity within livestock breeds over time, and may support industry in the future when needed.

How Developments in Cryobiology, Reproductive Technologies and Conservation Genomics Could Shape Gene Banking Strategies for (Farm) Animals

Many local breeds are currently at risk because of replacement by a limited number of specialized commercial breeds. Concurrently, for many breeds, allelic diversity within breeds declines because of inbreeding. Gene banking of germplasm may serve to secure the breeds and the alleles for any future use, for instance to recover a lost breed, to address new breeding goals, to support breeding schemes in small populations to minimize inbreeding, and for conservation genetics and genomics research. Developments in cryobiology and reproductive technology have generated several possibilities for preserving germplasm in farm animals. Furthermore, in some mammalian and bird species, gene banking of material is difficult or impossible, requiring development of new alternative methods or improvement of existing methods. Depending on the species, there are interesting possibilities or research developments in the use of epididymal spermatozoa, oocytes and embryos, ovarian and testicular tissue, primordial germ cells, and somatic cells for the conservation of genetic diversity in farm- and other animal species. Rapid developments in genomics research also provide new opportunities to optimize conservation and sampling strategies and to characterize genome-wide genetic variation. With regard to gene banks for farm animals, collaboration between European countries is being developed through a number of organizations, aimed at sharing knowledge and expertise between national programmes. It would be useful to explore further collaboration between countries, within the framework of a European gene banking strategy that should minimize costs of conservation and maximize opportunities for exploitation and sustainable use of genetic diversity.

Domesticated Animal Biobanking: Land of Opportunity.

In the past decade, biobanking has fuelled great scientific advances in the human medical sector. Well-established domesticated animal biobanks and integrated networks likewise harbour immense potential for great scientific advances with broad societal impacts, which are currently not being fully realised. Political and scientific leaders as well as journals and ethics committees should help to ensure that we are well equipped to meet future demands in livestock production, animal models, and veterinary care of companion animals.

The use of SWOT analysis to explore and prioritize conservation and development strategies for local cattle breeds.

SWOT (Strengths, Weaknesses, Opportunities and Threats) analysis is a tool widely used to help in decision making in complex systems. It suits to exploring the issues and measures related to the conservation and development of local breeds, as it allows the integration of many driving factors influencing breed dynamics. We developed a quantified SWOT method as a decision-making tool for identification and ranking of conservation and development strategies of local breeds, and applied it to a set of 13 cattle breeds of six European countries. The method has four steps: definition of the system, identification and grouping of the driving factors, quantification of the importance of driving factors and identification and prioritization of the strategies. The factors were determined following a multi-stakeholder approach and grouped with a three-level structure. Animal genetic resources expert groups ranked the factors, and a quantification process was implemented to identify and prioritize strategies. The proposed SWOT methodology allows analyzing the dynamics of local cattle breeds in a structured and systematic way. It is a flexible tool developed to assist different stakeholders in defining the strategies and actions. The quantification process allows the comparison of the driving factors and the prioritization of the strategies for the conservation and development of local cattle breeds. We identified 99 factors across the breeds. Although the situation is very heterogeneous, the future of these breeds may be promising. The most important strengths and weaknesses were related to production systems and farmers. The most important opportunities were found in marketing new products, whereas the most relevant threats were found in selling the current products. The across-breed strategies utility decreased as they gained specificity. Therefore, the strategies at European level should focus on general aspects and be flexible enough to be adapted to the country and breed specificities.

Value of the Dutch Holstein Friesian germplasm collection to increase genetic variability and improve genetic merit

National gene bank collections for Holstein Friesian (HF) dairy cattle were set up in the 1990s. In this study, we assessed the value of bulls from the Dutch HF germplasm collection, also known as cryobank bulls, to increase genetic variability and improve genetic merit in the current bull population (bulls born in 2010-2015). Genetic variability was defined as 1 minus the mean genomic similarity (SIMSNP) or as 1 minus the mean pedigree-based kinship (fPED). Genetic merit was defined as the mean estimated breeding value for the total merit index or for 1 of 3 subindices (yield, fertility, and udder health). Using optimal contribution selection, we minimized relatedness (maximized variability) or maximized genetic merit at restricted levels of relatedness. We compared breeding schemes with only bulls from 2010 to 2015 with schemes in which cryobank bulls were also included. When we minimized relatedness, inclusion of genotyped cryobank bulls decreased mean SIMSNP by 0.7% and inclusion of both genotyped and nongenotyped cryobank bulls decreased mean fPED by 2.6% (in absolute terms). When we maximized merit at restricted levels of relatedness, inclusion of cryobank bulls provided additional merit at any level of mean SIMSNP or mean fPED except for the total merit index at high levels of mean SIMSNP. Additional merit from cryobank bulls depended on (1) the relative emphasis on genetic variability and (2) the selection criterion. Additional merit was higher when more emphasis was put on genetic variability. For fertility, for example, it was 1.74 SD at a mean SIMSNP restriction of 64.5% and 0.37 SD at a mean SIMSNP restriction of 67.5%. Additional merit was low to nonexistent for the total merit index and higher for the subindices, especially for fertility. At a mean SIMSNP of 64.5%, for example, it was 0.60 SD for the total merit index and 1.74 SD for fertility. In conclusion, Dutch HF cryobank bulls can be used to increase genetic variability and improve genetic merit in the current population, although their value is very limited when selecting for the current total merit index. Anticipating changes in the breeding goal in the future, the germplasm collection is a valuable resource for commercial breeding populations.

The impact of using old germplasm on genetic merit and diversity - A cattle breed case study

Artificial selection and high genetic gains in livestock breeds led to a loss of genetic diversity. Current genetic diversity conservation actions focus on long-term maintenance of breeds under selection. Gene banks play a role in such actions by storing genetic materials for future use and the recent development of genomic information is facilitating characterization of gene bank material for better use. Using the Meuse-Rhine-Issel Dutch cattle breed as a case study, we inferred the potential role of germplasm of old individuals for genetic diversity conservation of the current population. First, we described the evolution of genetic merit and diversity over time and then we applied the optimal contribution (OC) strategy to select individuals for maximizing genetic diversity, or maximizing genetic merit while constraining loss of genetic diversity. In the past decades, genetic merit increased while genetic diversity decreased. Genetic merit and diversity were both higher in an OC scenario restricting the rate of inbreeding when old individuals were considered for selection, compared to considering only animals from the current population. Thus, our study shows that gene bank material, in the form of old individuals, has the potential to support long-term maintenance and selection of breeds.

The effects of recent changes in breeding preferences on maintaining traditional Dutch chicken genomic diversity

Traditional Dutch chicken breeds are marginalised breeds of ornamental and cultural-historical importance. In the last decades, miniaturising of existing breeds (so called neo-bantam) has become popular and resulted in alternatives to original large breeds. However, while backcrossing is increasing the neo-bantams homozygosity, genetic exchange between breeders may increase their genetic diversity. We use the 60 K SNP array to characterise the genetic diversity, demographic history, and level of inbreeding of Dutch heritage breeds, and particularly of neo-bantams. Commercial white layers are used to contrast the impact of management strategy on genetic diversity and demography. A high proportion of alleles was found to be shared between large fowls and neo-bantams, suggesting gene flow during neo-bantams development. Population admixture analysis supports these findings, in addition to revealing introgression from neo-bantams of the same breed and of phenotypically similar breeds. The prevalence of long runs of homozygosity (ROH) confirms the importance of recent inbreeding. A high diversity in management, carried out in small breeding units explains the high heterogeneity in diversity and ROH profile displayed by traditional breeds compared to commercial lines. Population bottlenecks may explain the long ROHs in large fowls, while repetitive backcrossing for phenotype selection may account for them in neo-bantams. Our results highlight the importance of using markers to inform breeding programmes on potentially harmful homozygosity to prevent loss of genetic diversity. We conclude that bantamisation has generated unique and identifiable genetic diversity. However, this diversity can only be preserved in the near future through structured breeding programmes.