Fresh is best: Accurate SNP genotyping from koala scats

Anthony J Schultz; Romane H Cristescu; Bethan Littleford-Colquhoun; Damian Jaccoud; Celine H Frere

doi:10.1002/ece3.3765

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Fresh is best: Accurate SNP genotyping from koala scats

Journal article

Open access

Peer reviewed

Fresh is best: Accurate SNP genotyping from koala scats

Anthony J Schultz, Romane H Cristescu, Bethan Littleford-Colquhoun, Damian Jaccoud and Celine H Frere

Ecology and Evolution, Vol.8(6), pp.3139-3151

2018

DOI: https://doi.org/10.1002/ece3.3765

PMCID: PMC5869377

PMID: 29607013

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Abstract

diet

disease

koala

scat

SNP Genotyping

Maintaining genetic diversity is a crucial component in conserving threatened species. For the iconic Australian koala, there is little genetic information on wild populations that is not either skewed by biased sampling methods (e.g., sampling effort skewed toward urban areas) or of limited usefulness due to low numbers of microsatellites used. The ability to genotype DNA extracted from koala scats using next-generation sequencing technology will not only help resolve location sample bias but also improve the accuracy and scope of genetic analyses (e.g., neutral vs. adaptive genetic diversity, inbreeding, and effective population size). Here, we present the successful SNP genotyping (1272 SNP loci) of koala DNA extracted from scat, using a proprietary DArTseqâ„¢ protocol. We compare genotype results from two-day- old scat DNA and 14-day- old scat DNA to a blood DNA template, to test accuracy of scat genotyping. We find that DNA from fresher scat results in fewer loci with missing information than DNA from older scat; however, 14-day- old scat can still provide useful genetic information, depending on the research question. We also find that a subset of 209 conserved loci can accurately identify individual koalas, even from older scat samples. In addition, we find that DNA sequences identified from scat samples through the DArTseqâ„¢ process can provide genetic identification of koala diet species, bacterial and viral pathogens, and parasitic organisms.

Details

Title: Fresh is best: Accurate SNP genotyping from koala scats
Authors: Anthony J Schultz (Corresponding Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Romane H Cristescu (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Bethan Littleford-Colquhoun (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Damian Jaccoud (Author) - University of Canberra
Celine H Frere (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Publication details: Ecology and Evolution, Vol.8(6), pp.3139-3151
Publisher: John Wiley & Sons Ltd.
Date published: 2018
DOI: 10.1002/ece3.3765
ISSN: 2045-7758; 2045-7758
PMID: 29607013; PMC5869377
Copyright note: Copyright © 2017 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Organisation Unit: School of Science and Engineering - Legacy; GeneCology Research Centre - Legacy; School of Science, Technology and Engineering
Language: English
Record Identifier: 99451278402621
Output Type: Journal article

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Collaboration types: Domestic collaboration
Web Of Science research areas: Ecology; Evolutionary Biology