Bison Genome Project

North American bison experienced a severe population bottleneck in the late 1800's that coincided with man-mediated hybridization experiments with domestic cattle. In the ensuing 125 years, populations of bison exposed to these hybrids have experienced hybrid swarm and now retain low levels of the introgressed domestic cattle nuclear and mitochondrial genomes. We have detected low levels of introgression of domestic cattle DNA in the bison at Custer State Park, SD. To study historic introgressive hybridization in this population we obtained DNA samples from every individual (N=1,660) present in the park and we propose to genotype the entire population for 3,072 species diagnostic SNP loci.

Additionally, we will genotype representative samples from two bison populations that have no evidence of hybridization (pure bison), one additional population with historic hybridization, 45 "beefalo" and several ancient (12-60K years old) bison samples. Using an approach based upon linkage disequilibrium, the SNP genotypes will identify regions of the bison genome that harbor introgressed cattle DNA as well as regions in which no cattle DNA is present. Leveraging the resources invested in the Bovine Genome Sequencing Project, we shall characterize the genomic organization of these regions in terms of size (Mb) and gene content. A Bayesian approach will be used to identify the size of each extant introgressed genomic fragment and the distribution of these fragment locations and sizes will be tested for deviations from expectation under a model of selective neutrality.

This project will produce a large amount of data (~5.9 million SNP genotypes) that shall be used to answer fundamental questions of hybridization. Results of this project will have applicability to other less well characterized genomes by providing a framework for determining the number of loci needed to detect historic hybridization and the potential genetic forces that impact regions of the genome capable of accepting introgressed DNA and those impermeable to introgression in which selection has removed introgressed DNA. All of the raw data produced in this project will be made publicly available including: 1) Animal genotypes, 2) Marker information (chromosomal position and allele frequencies), and 3) Pedigree and phenotype information, allowing others to use it to develop new approaches and test existing or novel hypotheses regarding hybridization. The results of this project will impact the management of both the Custer State Park bison as well as other public and private bison populations by providing additional loci for testing hybridization and will increase the public's perception of an American symbol.