Content uploaded by Gerrit Wehrenberg
Author content
All content in this area was uploaded by Gerrit Wehrenberg on Mar 02, 2020
Content may be subject to copyright.
Mitglied der
XY
Bullshit makes sense now:
A reduced SNP panel for non-invasive genetic assessment
of a genetically impoverished species, the European bison.
Background
The European bison or wisent (Bos bonasus, LINNAEUS 1758) was saved from the brink of extinction due to
considerable conservation efforts since the early 20th century. The current global population descends from a total
of 12 captive individuals, which represents a severe bottleneck event. Although the population size increased to
more than 7,500 individuals worldwide by successful ex situ-breeding and reintroductions into the wild, the species
is still threatened by an extremely low level of genetic variability and high inbreeding. Due to the low allelic
diversity, traditional molecular toolsets, such as microsatellites, fail to provide sufficient resolution for basic
individual discrimination and consequently, hamper accurate analysis of kinship or genetic diversity. In this
respect, applying genetic information to support ex situ-breeding management or non-invasive population
monitoring was not feasible so far. Here, we present a novel reduced SNP panel that tackles the aforementioned
issues and holds great promise to facilitate the use of genetic data in conservation management of this species.
I. sex determination
Results & Conclusion
•Newly developed 96 SNP panel implemented in a
microfludic chip for non-invasive samples with low-
quality DNA tackles several current questions in
conservation of the European bison with low error
rates (cf. box)
•Provision of a best practice sampling, preservation
and DNA extraction method for bison dung with
subsequent most extensive genotyping of the extant
population of European bison
•Kinship comparison between molecular and pedigree
data from the world‘s oldest studbook of a threatened
species
Methodology
•> 1,000 mostly non-invasive samples (faeces, hairs,
saliva etc.) from > 300 captive and wild individuals all
over Europe
•Comparison with pedigree data from the European
Bison Pedigree Book (EBPB) for kinship validation
GERRIT WEHRENBERG1,2,3, MAŁGORZATA TOKARSKA4, CARSTEN NOWAK1,2 and BERARDINO COCCHIARARO1,2
1Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571 Gelnhausen, Germany, e-mail: gerrit.wehrenberg@senckenberg.de; 2LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25,
60352 Frankfurt am Main, Germany; 3Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany; 4Mammal Research Institute, Polish Academy of Sciences, Waszkiewicza 1, 17‐230 Białowieża, Poland
II. individualisation
V. breeding line discrimination VI. cross-species detection
III. parental assignment
lowland line lowland-Caucasian line
XX
wisent
cattle
IV. assessment of genetic diversity
With a subset of 90 biallelic SNPs represented in the global
population it is possible to assign non-invasive samples to any
European bison worldwide.
With a gonosomal marker, located in the ameloginin gene, the
sex of genotyped non-invasive samples can be determined.
90 ID markers provide the molecular resolution to assign close
relatives like parents with known genotypes. This was
validated with pedigree data from the world‘s oldest studbook
of a threatened species (cf. figure above).
A subset of 61 equally distributed SNPs allows for an
assessment of the genetic diversity. Relevant issues like
inbreeding in reintroduced but isolated populations can now be
monitored non-invasively.
A subset of 29 SNPs, mainly due to unequal allele
frequancies, allows to assign an individual to one of both the
breeding lines important for conservation managemant in the
European bison (cf. figure above).
Five SNPs monomorphic in the European bison but
polymorphic in close related species like domestic cattle or
American bison allow to detect non-invasive samples from non-
target species erroneously collected in the field.
96 SNP panel
Fig. 1: This sampled and successfully genotyped bull
(studbook#11338) near Bad Berleburg (Germany) is part of the
ex situ-conservation breeding program.
WAITS et al. 2001
References: TOKARSKA, M.; PERTOLDI, C.; KOWALCZYK, R. and PERZANOWSKI, K. (2011): Genetic status of the European bison Bison bonasus after extinction in the wild and subsequent recovery. Mammal Review 41. 151–162. DOI: 10.1111/j.1365-2907.2010.00178.x.
WAITS, L. P.; LUIKART, G. and TABERLET, P. (2001): Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol Ecol 10. 249–256. DOI: 10.1046/j.1365-294X.2001.01185.x.
Karl und Marie
Schack-Stiftung
Outlook
•Application in monitoring of reintroduced populations; Genotyping of
historical sample collections to reflect temporal changes in genetic
diversity; informative evaluation of the SNP panel for related species
Fig. 2: Faecal sampling
using swabs in tubes
with lysis buffer.
Fig. 3: PID and PIDsib
for a microsatellite panel
(11 loci) and the SNP
panel (90 loci). PIDsib
msat is outside the
depiced scale. Red
dashed line represents
PID threshold for natural
populations and is only
overcome by the new
SNP panel for the
European bison.