In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Abstract

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

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

“…Thus, the new SNP panel represents an optimised compromise between the needed non-invasive sampling method, cost-efficiency needed for the application in conservation and the resulting informative accuracy, which is demonstrably and reasonably sufficient for the purpose it was developed for. While other recently presented SNP panels lack implementation in appropriate assays 3 , 11 , 28 , 29 , 34 , 79 the presented marker panel is non-invasive genotyping approach for the European bison ready to be used in conservation and monitoring studies. Ongoing real-world application comprises dung-based genetic monitoring of the reintroduced European bison in the Țarcu Mountains, Romania (LIFE RE-Bison; LIFE14 NAT/NL/000987).…”