The NextGen Project, Next Generation Methods to Preserve Farm Animal Diversity

The NextGen project is working towards the development of methods to preserve farm animal biodiversity by optimising present and future breeding options.  The project is recording data on all major types of genetic variation in the genome of cattle, sheep and goats. These data will aid the design of breeding programmes that maximise genetic progress in livestock populations while maintaining diversity, and will aid the choice of animals for biobanking, to maximise neutral and functional genetic diversity in stored material.

The NextGen comprises three case studies:  The first case study will sequence the genomes of sheep and goat from Morocco, where there is marked regional variation in environmental conditions.  This will allow a study of the relationships between genome and the environment (landscape genomics).  The second case study will sequence sheep and goat samples from wild-type populations as well as domestic breeds in North-Western Iran. The aim is to evaluate the potential of wild ancestors as reservoirs of genetic diversity for the domestic species.  The third case study will sequence the genomes of cattle from Uganda, where vector born diseases are prevalent.  This will allow a study of the biodiversity aspect of disease resistance.

We describe the bioinformatics tools and the methods of analysis being used in the NextGen project.  We describe the particular challenges of running a variant discovery pipeline from whole genome sequencing of livestock.

http://nextgen.epfl.ch/