90 CADERNOS DE ANÁLISE E PROSPETIVA CULTIVAR N.º 30 ABRIL 2024 – Melhoramento e técnicas genómicas plex multifactorial traits. An important approach extensively applied in livestock species has been the identification of quantitative trait loci (QTL). Although numerous studies have contributed to a collection of thousands of QTL, identification of the actual genes underlying these QTL has proven to be extremely difficult (Andersson and Purugganan 2022). The analysis of livestock populations from distinct biogeographical regions for which comprehensive phenotypes and environmental information are available (see text box) has an enormous potential to improve the power of landscape genomics and selective sweep analysis to detect adaptation. These include traits like disease, heat and water and food shortage tolerance in the traditional/native breeds across continental regions (e.g., north vs south). The bioinformatics and modelling approaches portrayed above and validated for different organisms should allow us to: i) identify selective sweeps (i.e. genes under strong selection) for a variety of traits; ii) capture genome-environment interactions within and across breeds; iii) provide scientific information on the evolution, adaptation, and selection of livestock to aid conservation of highly diverse and resilient breeds from the Iberian Peninsula. The identification of genetic variants associated with adaptation and selection processes can contribute to the sustainable management of biodiversity that is essential for dealing with the impact of ongoing climate change. For example, the genes detected in these selective sweeps can be characterised and the associated variants used in the improvement of other breeds (e.g., less diverse transboundary commercial breeds). The results for health-related traits have the potential to contribute to a reduction in major disease outbreaks. The identification of deleterious variants, in particular potential lethal ones, should allow pruning them from the populations. This should result in more viable animals/herds and directly contribute to a reduction of poverty in rural areas. Concluding remarks The association of phenotypic diversity with underlying genetic variability is now greatly facilitated by the development of sequencing technologies and genomic analyses methods. Combining the genomic data produced on several domesticated species, particularly on autochthonous breeds, with inferential approaches should provide very interesting and original avenues of research. In our opinion, there is now great opportunity to develop interdisciplinary 8 https://cordis.europa.eu/project/id/727715 9 https://leap-agri.com/?page_id=291 10 https://subsites.wur.nl/en/optibov-project.htm research projects among laboratories in the Iberian Peninsula to generate these genomes, identify the most appropriate methods to analyse the data and overcome computational limitations to assure the continued sustainable utilisation of locally adapted farm animal genetic resources. Example of an integrated project using genomic tools OPTIBOV: Genetic characterization of cattle populations for an optimised performance in African ecosystems OPTIBOV is a ERA-Net Cofund project within LEAP-Agri8,9,10 a joint Europe-Africa Research and Innovation initiative related to Food and Nutrition Security and Sustainable Agriculture. The project was initiated in September 2018 and ended in August 2022, but the huge dimension of the data collected will impact the team research in the long term. The team is developing association studies of well-defined phenotypes under local conditions with whole genome sequence data. What makes OPITIBOV so unique and innovative is the fact that phenotypes were collected in a specific ecotype under local conditions with their own stressors across different countries and continents. The main idea underlying the project was to generate such data across a North-South transect for sampling local cattle breeds in Finland, The Netherlands, Portugal, Egypt, Uganda and South Africa. In total, approximately 500 animals of 26 autochthonous breeds and the Holstein-Friesian commercial breed were sampled in detail. A combination of sequence data (whole genome, expression, microbiome) and many phenotypic traits is being used to identify biomarkers for adaptation, resilience, and disease resistance. The focus of OPTIBOV was on smallholder farmers and the knowledge of these local breeders. Contacts and meetings with breeder associations were established to identify those interested in participating and organizing material and data sharing among partners according to the Nagoya Protocol. Specifically, project meetings were organized in South Africa, Uganda and Egypt to promote the training of farmers, young scientists, rural developers and breed associations pertaining OPTIBOV-phenotype protocols and data analyses. The Portuguese team developed flyers in several languages with contributions from all partners for project announcement and dissemination. A centralised biobank is being maintained at Wageningen University in The Netherlands for duplicates of
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