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Even though genetic resources represent a fundamental reservoir of options to achieve sustainable development goals in a changing world, they are overlooked in the policy agenda and severely threatened. The conservation of genetic resources relies on complementary in situ and ex situ approaches appropriately designed for each type of organism. Environmental and socioeconomic changes raise new challenges and opportunities for sustainable use and conservation of genetic resources.Aiming at a more integrated and adaptive approach, European scientists and genetic resources managers with long experience in the agricultural crop, animal and forestry domains joined their expertise to address three critical challenges: (1) how to adapt genetic resources conservation strategies to climate change, (2) how to promote in situ conservation strategies and (3) how can genetic resources conservation contribute to and benefit from agroecological systems. We present here 31 evidence-based statements and 88 key recommendations elaborated around these questions for policymakers, conservation actors and the scientific community.We anticipate that stakeholders in other genetic resources domains and biodiversity conservation actors across the globe will have interest in these crosscutting and multi-actor recommendations, which support several biodiversity conservation policies and practices.

The Centre for Genetic Resources, the Netherlands (CGN) carries out Statutory Research Tasks (“WOT”) for the Dutch Ministry of Agriculture, Nature and Food Quality. The aim of CGN is to contribute to the conservation and sustainable use of plant, animal, forest and aquatic genetic resources, and to support the implementation and further development of relevant international agreements (CBD, NP, FAO, EU). CGN maintains and develops genebank collections (ex situ), promotes the use of the collections for breeding and research, and contributes to the further development of sustainable and resilient food systems and forestry. Besides management of gene bank collections, CGN also supports the conservation and monitoring of genetic diversity in plants, farm animals, trees and aquatic species in situ and on-farm., De WOT Genetische Bronnen richt zich op behoud en duurzaam gebruik van genetische bronnen voor voedsel, landbouw, aquacultuur, bos, natuur en landschap. De WOT wordt uitgevoerd door het Centrum voor Genetische Bronnen Nederland (CGN) van Wageningen University & Research. Het CGN levert een belangrijke bijdrage aan de implementatie van internationale afspraken en regelgeving (CBD, NP, FAO, EU). De WOT Genetische Bronnen draagt zorg voor instandhouding van een brede genetische basis in genenbankcollecties (ex situ). De collecties zijn beschikbaar voor onderzoek, veredeling en fokkerij, en voor de instandhouding van bio-cultureel erfgoed, de aanleg van bossen, en instandhouding van een aantrekkelijk landschap. Naast het beheer van genenbankcollecties (ex situ) ondersteunt en monitort CGN de instandhouding van genetische diversiteit “in het veld” (in situ en on-farm).

The European Regional Focal Point for Animal Genetic Resources (ERFP), is the European regional platform of National Coordinators (NCs) supporting management of animal genetic resources (AnGR). To assess the performance of the ERFP platform/network and consider options for its further development, a survey was performed among NCs. Twenty-five NCs responded to the survey on the roles, values and future of the platform. The paper provides an analysis of the results of the survey, including a ERFP SWOT analysis. NCs indicated high value of the support of the ERFP in fulfilling their functions at the national level. They highlighted the well-established network and facilitated communication and collaboration among NCs and other AnGR experts in Europe. The NCs appreciated the efficient organizational structure of the ERFP (Working Groups, Task Forces, Ad hoc Actions), and the well-functioning Secretariat. Indicated weak points included discontinuity of NC positions in some countries, and low levels of activities in some countries. NCs saw new opportunities for ERFP development in the context of the EU policy and regulatory framework related to AnGR management, and in strengthening the role of the Secretariat. No immediate threats were identified, however potential future threats included insufficient financing and lack of continuity. The NCs highly appreciated the substantial progress achieved by the ERFP over the last 20 years.

Improvements in ex situ storage of genetic and reproductive materials offer an alternative for endangered livestock breed conservation. This paper presents a dataset for current ex situ collections and in situ population for 179 Spanish livestock breeds of seven species, cattle, sheep, pig, chicken, goat, horse and donkey. Ex situ data was obtained via survey administered to 18 functioning gene banks in Spain and relates to the reproductive genetic materials (semen doses) of 210 livestock breeds distributed across the gene banks. In situ data combines CENSUS information with linear regression techniques and relates to the geographic distribution of 179 Spanish autochthonous livestock breeds (2009-2018), and in situ population projections and extinction probabilities (2019-2060). We use a decision variable defining an “acceptable level of risk” that allows decision makers to specify tolerable levels of in situ breed endangerment when taking ex situ collection and storage decisions.

The Centre for Genetic Resources, The Netherlands, (CGN) of Wageningen University and Research (WUR), carries out Statutory Research Tasks (WOT) for the Dutch Ministry of Agriculture, Nature and Food Quality (LNV) to support the conservation and sustainable use of genetic resources for food and agriculture (www.wur.nl/cgn). With respect to recent developments in the FAO Commission on Genetic Resources for Food and Agriculture on Aquatic genetic resources, LNV asked CGN to explore the need to also include WOT on Aquatic genetic resources in the next 5-year WOT program that runs from 2021 to 2025. The FAO defines aquatic genetic resources as 'farmed aquatic species and their wild relatives'. In the Netherlands these include several relevant species of shellfish, fish and seaweeds. Priorities have been determined based on interviews with experts and representatives from the aquaculture sector, and by using literature sources. Monitoring of genetic diversity in relevant species of shellfish, fish and seaweed, both wild and cultured populations, is a general priority area for aquatic genetic resources in the Netherlands. Next, based on the monitoring data, advise will be formulated for in situ and/or ex situ conservation measures for the most relevant aquatic genetic resources. CGN manages genebank facilities for long term cryoconservation of genetic diversity in livestock species, that can also be used for the purpose of cryoconservation of priority species of shellfish, fish and seaweeds., Het Centrum voor Genetische Bronnen, Nederland (CGN) van Wageningen University & Research voert Wettelijke OnderzoeksTaken (WOT) uit voor het Ministerie van LNV. Deze WOT (www.wur.nl/cgn) richt zich op behoud en duurzaam gebruik van genetische bronnen voor voedsel en landbouw. In verband met recente internationale afspraken over behoud en duurzaam gebruik van aquatische genetische bronnen heeft LNV aan het CGN gevraagd om te verkennen welke WOT voor aquatische genetische bronnen onderdeel zouden moeten zijn van het WOT programma genetische bronnen. FAO definieert aquatische genetische bronnen als 'farmed aquatic species and their wild relatives'. In Nederland zijn daarbij zowel verschillende soorten schelpdier, vis als zeewier relevant. Op basis van interviews met experts, met vertegenwoordigers uit de sector en op basis van literatuurbronnen zijn prioriteiten vastgesteld. Monitoring van genetische diversiteit in relevante schelpdier-, vis- en zeewiersoorten, zowel in het wild als in beheerde populaties, is de eerste prioriteit. Op basis van de monitoringsgegevens kan worden geadviseerd over specifieke maatregelen gericht op in situ en/of ex situ behoud van aquatische genetische bronnen. De WOT genenbankfaciliteiten (cryoconservering) voor landbouwhuisdierrassen kunnen ook worden benut voor lange termijn behoud van genetische diversiteit in schelpdier-, vis- en zeewiersoorten.

Growth of animals is a complex trait, in chicken resulting in a diverse variety of forms, caused by a heterogenous genetic basis. Bantam chicken, known as an exquisite form of dwarfism, have been used for crossbreeding to create corresponding dwarf counterparts for native fowls in the Dutch population. Here we demonstrate the heterogeneity of the bantam trait in Dutch chickens and reveal the underlying genetic causes, using whole-genome sequence data from matching pairs of bantam and normal-sized breeds. During the bantam oriented crossbreeding, various bantam origins were used to introduce the bantam phenotype, three major bantam sources were identified and clustered. The genome-wide association studies revealed multiple genetic variants and genes associated with bantam phenotype, including HMGA2 and PRDM16, genes involved in body growth and stature. The comparison of associated variants among studies illustrated differences related with divergent bantam origins, suggesting a clear heterogeneity among bantam breeds. We show that in neo-bantam breeds, the bantam-related regions underwent a strong haplotype introgression from the bantam source, outcompeting haplotypes from the normal-sized counterpart. The bantam heterogeneity is further confirmed by the presence of multiple haplotypes comprising associated alleles, which suggests the selection of the bantam phenotype is likely subject to a convergent direction across populations. Our study demonstrates that the diverse history of human-mediated crossbreeding has contributed to the complexity and the heterogeneity of the bantam phenotype.

With the ‘genomic revolution’ a continuously increasing amount of data is being generated. The Convention on Biological Diversity refers to this type of data as “Digital Sequence Information (DSI)”. Innovation in different domains and subsectors, ranging from agriculture and biodiversity conservation, to biotechnology and human health, depends on the use of DSI. Access to DSI and related technologies is crucial for any stakeholder and country, in order to reach long term food security objectives, to be able to adapt to climate change, to deal with human health issues, and to contribute to the conservation and sustainable use of biodiversity. Stakeholder consultations in the Netherlands indicate that fair and equitable benefit sharing arrangements - related to the use of DSI - should possibly only be dealt with in a multilateral context.

Ex situ collections offer the potential to reduce extinction risks, affording option to society in maintaining future breeding opportunities for productivity and heritage traits. However, how much should we be seeking to collect and conserve in gene banks, and where? We developed a mathematical model to optimize logistical decisions of breed conservation choices and to evaluate alternative scenarios for efficiently re-allocating genetic materials currently stored in different European gene banks, allowing for cross-country collections, cost and cryogenic capacity differentials. We show how alternative allocations for the breeds that are currently stored in 11 European gene banks could reduce overall conservation costs by around 20% by selecting cryogenic banks that have relatively lower combination of fixed and collection costs, and are geographically closer to collection regions. Our results show that centralizing collections in one gene bank would double the costs, relative to collective European collections approaches. We also calculate marginal costs of collections and show that increasing diversity within the gene banks implies in higher costs per conserved breed.

Breed registries have been established for livestock species to maintain the purity of breeds and to document the ancestry of animals. However, a significant number of animals are unregistered with no or incomplete pedigree data and uncertain ancestral breed origin. Although many local livestock breeds are “at risk” on the basis of the number of purebred breeding females in a breed registry, there is often also a reservoir of unregistered animals that may belong to the same breed. However, due to the missing pedigree it is not possible for breed societies or herd books to include those animals in their breeding program for purebred animals. A genetic test was developed to unequivocally determine the breed origin of cattle without pedigree data. Such a test will open up the possibility to incorporate animals without pedigree data in the breed registry that turn out to be purebred based on the test results. In this study we developed and validated such a test. Genotype data (50k SNP array) were used to compose reference populations for six local Dutch cattle breeds. The combination Principal Component Analysis and Random Forest was used to perform SNP selection. A total of 133 informative SNPs were selected to determine breed composition of individual animals. Overall, 82.0% of the animals in the test population are correctly assigned to the breed in question. For Dutch Red and White Friesian and Deep Red Cattle we suggest that if an animal has a percentage for its own breed <0.775 to use the combined percentage of two breeds (Deep Red Cattle with Meuse‐Rhine‐Yssel and Dutch Red and White Friesian with Dutch Friesian). Using this criteria 88.9% (104 out of 117) of the animals in the test population is correctly assigned. The developed test was successful and will be implemented in practice to identify (partly) unregistered individuals as being purebred (or not) for one of the Dutch local cattle breeds.

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 Dutch Draught horse is a rare Dutch horse breed. To conserve rare breeds, it is of great importance to monitor population size and increase in inbreeding and kinship in a population. When screening the Dutch Draught horse population, it turned out that inbreeding (and potential consequences) should be controlled by the studbook (KVTH) with participation of breeders. During the most recent generation (2010-2017) fewer foals were born annually compared to the generation before. Also, the percentage of foals that is used in breeding at a later age decreased steadily. At the same time there is a considerable increase in the kinship between horses that are used in breeding. The increase in inbreeding passes the FAO threshold of 0.5% per generation. In light of the increase in kinship, we expect that the increase in inbreeding will even be higher in the future. Screening the population clearly showed that genetic management is needed to be able to better control inbreeding (and potential accompanying consequences). It is possible to drastically reduce the inbreeding increase through genetic management., Het Nederlandse Trekpaard is een zeldzaam Nederlands paardenras. Voor de instandhouding van zeldzame rassen is het van groot belang om de populatiegrootte en de toename in inteelt en verwantschap in de populatie te monitoren. Uit het doorlichten van de Nederlandse Trekpaardenpopulatie bleek dat inteelt (en eventuele bijbehorende gevolgen) beter moeten worden beheerst door het stamboek (KVTH) én met medewerking van fokkers. In de meest recente generatie (2010-2017) werden minder veulens geboren dan in de generatie ervoor, er werden verhoudingsgewijs ook minder Trekpaarden ingezet voor de fokkerij terwijl de verwantschap tussen de paarden aanzienlijk toenam. De berekende inteelttoename bevindt zich ruim boven de door de FAO gestelde norm van maximaal 0,5% per generatie. Door aangepast genetisch beheer is het mogelijk de inteelttoename drastisch terug te dringen.