From Wisent to the Lab and Back Again—A Complex SNP Set for Population Management as an Effective Tool in European Bison Conservation

Abstract

Proper management and genetic monitoring of the modern European bison (Bison bonasus) population is one of the most important responsibilities for this species’ conservation. Up-to-date, complex genetic analysis performed using a consistent molecular method is needed for population management as a tool to further validate and maintain the genetic diversity of the species. The identification of the genetic line when pedigree data are missing, as well as the identification of parentage and individuals, are crucial for this purpose. The aim of our research was to create a small but informative panel of SNP (single-nucleotide polymorphism) markers that can be used for routine genotyping of the European bison at low cost. In our study, we used a custom-designed microarray to genotype a large number of European bison, totaling 455 samples from two genetic lines. The results of this analysis allowed us to select highly informative markers. In this paper, we present an effective single nucleotide polymorphism set, divided into separate panels to perform genetic analyses of European bison, which is needed for population monitoring and management. We proposed a total of 20 SNPs to detect hybridization with Bos taurus and Bison bison, a panel of 50 SNPs for individuals and parentage identification, as well as a panel of 30 SNPs for assessing membership of the genetic line. These panels can be used together or independently depending on the research goal and can be applied using various methods.

A reduced SNP panel optimised for non-invasive genetic assessment of a genetically impoverished conservation icon, the European bison

“…A 100 SNP panel has been published for parental assignment for LL exclusively 29 , of which a portion of markers were included in the current panel. Wojciechowska et al 3 developed a subset of 50 SNPs for parental assignment applied for both breeding lines. With the reduced 63 SNP subset in our study, parental assignment was also successful for LC and additionally proved effective for non-invasively collected samples.…”

“…For this we selected 63 autosomal unlinked loci in HWE found to be polymorphic in the European bison. The SNPs utilised in this panel were originally detected in domestic cattle 3,11,28,29,34,[36][37][38][39] . Though common practice [40][41][42] , it is obvious that such a reduced number of SNPs found in a related species as well as an ascertainment bias from selecting for high polymorphism in our target species will not allow for unbiased estimates of genetic diversity 43,44 .…”

“…Ex situ and in situ population management is based on the world's first studbook for a threatened species (European Bison Pedigree Book; EBPB) established for conservation purposes 1 . Today's global population size of > 9,500 is the result of this successful population management during the last almost 100 years [1][2][3] . Despite this success, the species is still threatened by genetic erosion due to a small gene pool resulting from a total of only 12 founders with uneven founder representations [4][5][6] .…”

“…F-statistics were calculated using either arithmetic averages 1 or based on the average HS and HT over loci 2 . Pedigree-based genetic diversity values in PMx were calculated based on kinship matrix3 or gene drop4 . A more detailed table including genetic diversity values of each both breeding lines is provided in the Supplementary TableS4.Breeding line discriminationA subset of 18 SNP markers provided the lowest false-positive rate in breeding line assignments.…”

Wisent genome assembly uncovers extended runs of homozygosity and a large deletion that inactivates the thyroid hormone responsive gene

“…Wisent genetic research had long relied on mitochondrial genome sequences and microsatellite markers (Soubrier et al, 2016; Tokarska et al, 2011, 2009). More recent investigations into genome-wide genetic diversity in wisent have utilized a taurine cattle ( Bos taurus taurus ) reference genome and bovine microarrays (Druet et al, 2020; Gautier et al, 2016; Wojciechowska et al, 2023). Considering that wisent and taurine cattle diverged between 1.7 and 0.85 million years before present (Gautier et al, 2016), this methodological approach likely introduces reference bias (Chen et al, 2021; Günther and Nettelblad, 2019).…”