Conservation & local programs

Advancing Bison (Bison bison) Genomics to Strengthen Herd and Metapopulation Health and Resiliency

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Abstract

Genomic data on North American bison (Bison bison) lags behind many livestock species but may be leading the way for many wildlife species. The Bison Management System is widely variable, including private production, federal and state public wildlife agencies, nonprofit NGOs, and Tribal nations sectors. Each sector often implements vastly different management strategies specifically relating to bison (i.e., provisioning, regulating, supporting, and cultural ecosystem services). The whole genome of only a few bison has been sequenced, and existing SNP panels are largely derived from SNP discovered first in cattle; hindering development of genomic tools specifically for bison management tailored for either production, conservation, or both. Our objectives were to 1) develop a de novo genome assembly of the bison genome, 2) discover novel bison genetic variants through analysis of whole genomes and 3) estimate amount of inbreeding in a bison herd managed for conservation purposes using these variants. The DNA and RNA from liver and muscle tissue were isolated from bison (n=2; one male and one female) slaughtered at a South Dakota private ranch. Using DNA from the male, Oxford Nanopore Technologies (ONT) long-reads were sequenced, producing over 8.1 million reads with >97% reads having an average Phred score ≥ 20, totaling 51.5 Gb (~20X coverage). Genome assembly quality was compared among CLC Genomics Workbench Long Read assembler (which implements RAVEN) and phased and unphased HIFIASM. The non-phased genome assembled by HIFIASM (total length = 3.0 Gb, N50 = 87 Mb) produced the highest quality genome assembly. Using gVOLANTE, 97% of the 9,226 BUSCO genes from Mammalia orthologs were identified in this reference genome. 1.9 billion reads in pairs from transcriptome samples (n=27; both publicly available and from our data) were mapped to this reference genome, resulting in annotation of 33,772 genes and 278,507 putative transcripts. An additional 94 bison sampled from Custer State Park, Custer, SD, were sequenced using an Illumina Novaseq X+ (short reads; 6 lanes on a 25B reads flow cell) to an average coverage of 30X. Variants were aligned to the TAMU_BisBis_3.0 reference genome and called using the CLC Genomics Read Mapping and Variant Calling tools, identifying 23.5 million putative variants. Using PLINK, these variants were filtered to >460,000 high-quality SNP Preliminary examination of linkage disequilibrium maps revealed that LD varied within and among chromosomes. The proportion of the genome with runs of homozygosity (≥ 500 kb and 50 SNP minimum) were used to estimate inbreeding among bison at Custer State Park - a state park that has managed this bison herd since 1914 and kept as a closed herd since the 1950s. The FROH of 0.38 suggest significant loss of genetic diversity.

Keywords: 2026

How to Cite:

Gonzalez Hernandez, J., Boehm, F., Martin, J., Gonda, M. & Urso, P., (2026) “Advancing Bison (Bison bison) Genomics to Strengthen Herd and Metapopulation Health and Resiliency”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286385. doi: https://doi.org/10.31274/wcgalp.23973

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