88 CADERNOS DE ANÁLISE E PROSPETIVA CULTIVAR N.º 30 ABRIL 2024 – Melhoramento e técnicas genómicas markers for production traits, can be used for breeding in the future and for the continued sustainable utilisation of these locally adapted farm animal genetic resources, by monitoring crossbreeding or breed replacement. Here, we will try to integrate the most recent technological developments with the state-of-the-art regarding the characterization of local farm animal genetic diversity by elaborating on the following aspects: 1. Characterising and protecting farm animals’ biodiversity 2. Investigating the domestication and breed differentiation processes 3. Studying the impact and resilience to climate change 1. Characterising and protecting farm animals’ biodiversity The aim of the Final Conference of the European Science Foundation’s Genomic Resources program (ESF-Science Connect), held in 2014 at Cardiff University and which involved scientists and policy-makers, from South and East Asia, North America, Europe and Africa, was to identify a series of pressing questions for a research and policy agenda for Farm Animal Genetic Resources (FAnGR) conservation for the following decade (Bruford et al. 2015). The overall conclusion was that the livestock sector needed to make a concerted effort to enable the democratisation of the genomic tools available, to ensure they are applied in the context of breed conservation and sustainable development (Bruford et al. 2015). A decade later, there is still a large gap between the current state-of-theart in the use of tools to characterise genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilisation of genetic and genomic data as indicators of genetic erosion (i.e., loss of genetic diversity). An Ibero-American consortium, established in the framework of the Conbiand network4, allowed researchers to carry out one of the most comprehensive genetic studies of worldwide cattle using mitochondrial, Y-chromosome and autosomal microsatellite (STRs, short tandem repeats) markers, showing that Iberian breeds hold high genetic diversity for all markers and left their signature in current Creole populations (Ginja et al. 2020). While this study established the foundations of a continent-wide program for the characterization, conservation and recognition of Ibero-American FAnGR, genomic analyses of such patrimony are still lacking. Whole genome data is key to understanding the consequences of historic breed formation and the putative role of admixture events in the 4 https://conbiand.site/?page_id=518 observed diversity patterns. For example, a pivotal analysis of low coverage genomes of eight Iberian native cattle breeds showed that they display significant gene flow or admixture from African taurine cattle and include mtDNA and Y-chromosome haplotypes from multiple origins (Da Fonseca et al. 2019). Interestingly, a very low differentiation of chromosome X relative to autosomes was detected within all analysed taurine breeds, potentially reflecting male-biased gene flow. In cattle, an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries, however the extent to which this also applies to other domesticated animal species in this territory remains unclear. For instance, the first genomic study of Portuguese native sheep of Merino and intermediate wooltype suggested that these breeds are not genetically compromised, in the sense that they showed moderate diversity and negligible inbreeding (Gaspar et al. 2023). Consistently with historical records, it depicted the Iberian Merino sheep as a well differentiated breed group. Genomic studies set the ground for defining ancestry informative SNPs (Single Nucleotide Polymorphisms) for breed-specific admixture analysis, i.e., a powerful tool for breed assignment and traceability of certified breed-products, but also for genome-wide association studies. Supporting further multidisciplinary collaborative research, involving researchers, governmental agencies, and stakeholders (e.g., Breeder Associations), should provide an excellent framework for the continued sustainable use of local FAnGR by employing up-to-date molecular biology and bioinformatics tools to characterise and manage biodiversity. The development of high-throughput sequencing revolutionized the field of population genetics/animal breeding and genetics, allowing for evolutionary processes to be addressed at unprecedented resolution, and will increasingly be used to be able to cope with climatic challenges. However, these data are still lacking for many native Iberian breeds, thus there is the need to increase awareness of local authorities (e.g., Food and Veterinary Services of the Ministry of Agriculture, DGAV) and stakeholders (Breed Associations) for the utility of generating such data, implement training and science outreach activities to reach large audiences. Contributing population-scale whole-genome sequencing data for Iberian breeds, can help overcome the limitations of classic molecular markers (e.g., “neutral” autosomal STRs) for example for the discovery and genotyping of structural variants. In addition, complementing long- and short-read sequencing data allows us to screen a larger number of animals per breed using low-coverage shotgun sequences and
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