Genome-wide Tests for Adaptive Molecular Variation
in Domestic & Wild Ungulates
Summary:
We are using candidate gene sequencing and genome-wide scans to identify and characterize genes responsible for adaptation and productivity in salmonids and in the three most economically important livestock species (cattle, sheep and goat) and their wild relatives. The approach is based on analysis of exon sequences from thousands of candidate genes in domestic (e.g. hatchery) and wild species including the following for ungulates: gaur, bison, & wild sheep, and wild goats.
We are sequencing nearly 10% of the exome (all exons) using exon capture arrays and Illumina massively parallel sequencing (HiSEQ). This approach will help identify selection signatures, genome regions, haplotypes and perhaps single nucleotide polymorphisms (SNPs) important for fitness and production. The data also will be used to assess the evolutionary history (e.g., domestication process) and adaptation to environmental change.
Collaborators:
S.J. Amish, A. Beja-Pereira, J. Chen., T. Cozart, J. Shendure, S. Porcella et al.
Publications:
- Beja-Pereira, A., G. Luikart, P.R. England, D.G. Bradley, O.C. Jann, G. Bertorelle, A.T. Chamberlain, T.P. Nunes, S. Metodiev, N. Ferrand, and G. Erhardt. 2003. Gene-culture coevolution between cattle milk protein genes and human lactase genes. Nature Genetics, 35:311-313.
- Beja-Pereira, A., G. Luikart et al. 2006. Genetic evidence for multiple origins of European cattle in Near-East, Africa, and Europe. Proceedings of the National Academy of Sciences, USA. 103:8113-8118.
- Chen, S., V. Costa, V., M. Azevedo, G. Luikart, and A. Beja-Pereira. 2008. New alleles of the bovine kappa-casein gene revealed by re-sequencing and haplotype inference analysis. J. Dairy Science, In press.
- Cosart, T, A. Beja-Pereira, J. Johnson, and G. Luikart. In prep. ExonSample: A computer program for genome-wide sequence sampling to facilitate new generation sequencing. In prep.
- Cosart, T, A. Beja-Pereira, S. Chen, J. Shendure, and G. Luikart. Exome-wide DNA capture and sequencing in domestic and wild species. BMC Genomics. Accepted pending minor revision.
- Genome 10K Community of Scientists. Submitted. Genome 10K: A proposition to obtain whole genome sequence for 10,000 vertebrate species. Journal of Heredity. In review.