The NextGen Project: Whole Genome Data to Optimize Methods to Maintain Farm Animal Biodiversity

The NextGen project is an international collaboration between groups from Europe, Africa and Asia, investigating the genomic variation of important livestock species. The project sampled cattle, sheep and goat from defined regions in Morocco, Uganda and Iran, including animals from industrial and traditional breeds, and the wild-type ancestors.  Whole genome sequencing data was generated and is being used to identify all types of genetic varation.  NextGen is producing variation data on an unprecedented scale for a livestock genomics project. This will aid in the design of breeding programmes that maximise genetic progress in farm animal populations while preserving biodiversity.

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

We present the bioinformatics tools and methods of analysis being used in the NextGen project.  We describe the particular challenges of running variant discovery pipelines for livestock species, where of known variation data sets are incomplete, and reference genomes must be treated with a degree of uncertainty.

http://nextgen.epfl.ch