Biodiversidade dos animais domésticos da Península Ibérica: uma perspetiva genómica 91 the OPTIBOV samples. In Portugal, there is now a sample bank for the three autochthonous breeds included in this project – Barrosã, Mirandesa and Mertolenga (in addition to the sample bank already established by C. Ginja’s team with most Portuguese native cattle breeds represented, as well as native dogs and some sheep breeds). Analyses pipelines were developed and tested and are being used for the metadata inferences. In addition, long read references are being built for all 26 traditional breeds which will create a unique dataset for the search for adaptation biomarkers. The potential for improved performance will be analysed while maintaining biodiversity and adaptive phenotypes. Furthermore, blood expression profiles of each breed on a selection of animals will enable us to detect the immune and energy status of each of these animals. The microbiome analysis of the faecal samples of all the OPTIBOV animals is being used in the animal health analysis but will also give insights on the GreenHouse Gas emissions of the animals in different ecosystems. The results of our research can be communicated to policy makers through technical reports. Indeed, this is the case of the technical guidelines11 published in 2023 by the Food and Agriculture Organization of the United Nations with major contributions from OPTIBOV researchers. Acknowledgments The authors would like to thank the breeder associations and farmers for their collaboration over the years. We would also like to thank our colleagues Lounès Chikhi, Gabriel Marais and Raquel Tavares for fruitful discussions on evolutionary biology and population genetics, and for their careful reading of the manuscript. We also gratefully acknowledge funding for our research from the following entities: Fundação para a Ciência e a Tecnologia (FCT), Portugal, ARIES project (reference: https://doi.org/10.54499/2022.04843.PTDC); Programa Ibero-americano de Ciência e Tecnologia para o Desenvolvimento (CYTED), through the REZGEN-IBA network, Red iberoamericana sobre los recursos zoogenómicos y su resiliencia (reference: https://www.cyted.org/web_redes. php?id_rede=511); and the LEAP-Agri programme, OPTIBOV project (reference: https://leap-agri.com/?page_id=291). 11 https://doi.org/10.4060/cc3079en 12 https://www.genome.gov/genetics-glossary 13 https://evolution.berkeley.edu/glossary/ Glossary12,13 Admixture: it occurs when individuals from two or more previously isolated populations interbreed, admixed or hybrid individuals have mixed ancestry. Autosome: one of the numbered pairs of chromosomes, as opposed to the sex chromosomes. Gene flow: is any movement of genetic material from one population to another (e.g., through migration) and is an important source of genetic variation. Genetic drift: is a mechanism of evolution characterized by random fluctuations in the frequency of a particular version of a gene (allele) in a population. Genome: all the genetic information an organism carries. A reference genome is used to map sequencing reads and identify the exact position of each nucleotide base. Genome coverage: the average number of reads that align to, or “cover,” known bases in a reference genome. For high coverages, each base is confirmed by a greater number of aligned sequence reads, so base calls can be made with high confidence. Genome Wide Association Study: abbreviated GWAS, is a research approach used to identify genomic variants that are statistically associated with a risk for a disease or a particular phenotypic trait. Genotyping: a genotype is a scoring of the type of variant present at a given location (i.e., a locus) in the genome. Haplotype: is a physical grouping of genomic variants (or polymorphisms) that tend to be inherited together. Inbreeding: Mating between relatives, defined as a pattern of mating in which mates are more closely related than two individuals selected at random from the population. Introgression: the transfer of genetic material from one species to another through hybridization, e.g., from the wild ancestor species to the domestic counterparts, or vice versa, co-existing in the same territory. Landscape genomics: aims to identify the environmental factors that shape adaptive genetic variation and the gene variants that drive local adaptation. Microbiome: is the community of microorganisms (e.g., fungi, bacteria and viruses) that exists in a particular environment.
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