Dobson, Lauren K (2015-08). Sequencing the Genome of the North American Bison. Doctoral Dissertation. Thesis uri icon

abstract

  • American bison (Bison bison) is a well-known iconic species with a history and legacy intertwined with the Plains of North America. Unfortunately, the American colonization of North America in the late 1800's resulted in the almost complete destruction of the American bison and subsequent population bottleneck. Bison were also faced with forced hybridization of domestic cattle genetics (Bos taurus), through failed experiments of some ranchers to produce a hardier beef animal for the greatplains. The hybridization of domestic cattle into bison presents challenges in the management and conservation of American bison today, primarily because it is difficult to differentiate between hybrid cattle-bison and purebred bison within a population.



    Whole genome sequencing provides the next step in advancing bison management and conservation. A 2.82-Gb de novo reference assembly of the American bison genome was produced using approximately 75X coverage, utilizing both mate pair and pair-end sequencing. Illumina, Inc. and 454 Life Sciences Technologies raw sequence reads were mapped to both nuclear and mitochondrial sequences of the domestic cattle reference UMD3.1 (Ensembl GCA_000003055.3), in order to detect genetic variants, including single nucleotide variants (SNVs) and insertion and deletions (INDELs). An additional 14 re-sequenced bison genomes were also aligned to the UMD3.1 domestic cattle reference sequence to identify genomic variants. These variants were determined and annotated to examine their effect on gene structure and function in bison.



    With the completed de novo plains bison reference genome sequence a comparison of historic and modern bison sequences identified genomic variants and were compared across bison populations. Historic bison samples that predate cattle and bison introgression were sequenced and conserved genomic regions between historic and current bison were identified. Identified variants between modern and historic bison provided an outline of the genetic architecture of bison that existed before the population bottleneck. This genomic analysis of North American bison provides insight into the genetic history, taxonomy, and inheritance of important genetic traits in bison that have allowed them to not only survive but thrive in their recovery from this population bottle neck that occurred 130 years ago.
  • American bison (Bison bison) is a well-known iconic species with a history and legacy intertwined with the Plains of North America. Unfortunately, the American colonization of North America in the late 1800’s resulted in the almost complete destruction of the American bison and subsequent population bottleneck. Bison were also faced with forced hybridization of domestic cattle genetics (Bos taurus), through failed experiments of some ranchers to produce a hardier beef animal for the greatplains. The hybridization of domestic cattle into bison presents challenges in the management and conservation of American bison today, primarily because it is difficult to differentiate between hybrid cattle-bison and purebred bison within a population. Whole genome sequencing provides the next step in advancing bison management and conservation. A 2.82-Gb de novo reference assembly of the American bison genome was produced using approximately 75X coverage, utilizing both mate pair and pair-end sequencing. Illumina, Inc. and 454 Life Sciences Technologies raw sequence reads were mapped to both nuclear and mitochondrial sequences of the domestic cattle reference UMD3.1 (Ensembl GCA_000003055.3), in order to detect genetic variants, including single nucleotide variants (SNVs) and insertion and deletions (INDELs). An additional 14 re-sequenced bison genomes were also aligned to the UMD3.1 domestic cattle reference sequence to identify genomic variants. These variants were determined and annotated to examine their effect on gene structure and function in bison. With the completed de novo plains bison reference genome sequence a comparison of historic and modern bison sequences identified genomic variants and were compared across bison populations. Historic bison samples that predate cattle and bison introgression were sequenced and conserved genomic regions between historic and current bison were identified. Identified variants between modern and historic bison provided an outline of the genetic architecture of bison that existed before the population bottleneck. This genomic analysis of North American bison provides insight into the genetic history, taxonomy, and inheritance of important genetic traits in bison that have allowed them to not only survive but thrive in their recovery from this population bottle neck that occurred 130 years ago.

publication date

  • August 2015