Identifying Farm Animal Genetic Resources by Using Whole Genome Data

NEXTGEN is an ongoing project based on a comparative analysis of whole genome data at the intraspecific level to optimise genetic management of livestock diversity. A bioinformatics pipeline has been set to take advantage of whole genome sequences that are produced at a 10 X coverage. Adaptation in sheep and goats is investigated by studying for each species 164 individuals sampled in places representative of contrasting environmental conditions in Morocco. Resistance to vector born disease is studied on cattle in Uganda, where disease endemic areas are well defined. These adaptations are studied through a spatially-explicit analysis of genome diversity that is a powerful alternative to linkage or association studies for identifying genomic regions associated with key traits for sustainable breeding. Moreover, an evaluation of the potential of wild ancestors and traditional breeds as reservoirs of genetic variation for sheep and goats is conducted by analysing the genomes of 80 individuals of the species ancestral range (i.e. asiatic mouflons, bezoars and local Iranian domestic sheep and goats). Finally, a novel freeze-drying approach is proposed for bio-banking cells and gametes at very low cost. Thus, NEXTGEN aims at providing the necessary tools for the exploitation of new generation genomic and reproductive technologies for Farm Animal Genetic Resources characterization and conservation.