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Genotyping‐in‐Thousands by sequencing (GT‐seq) panel development and application to minimally invasive DNA samples to support studies in molecular ecology
Author(s) -
Schmidt Danielle A.,
Campbell Nathan R.,
Govindarajulu Purnima,
Larsen Karl W.,
Russello Michael A.
Publication year - 2020
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.13090
Subject(s) - biology , genotyping , molecular ecology , dna sequencing , evolutionary biology , ecology , computational biology , dna , genetics , genotype , gene , population , demography , sociology
Minimally invasive sampling ( MIS ) is widespread in wildlife studies; however, its utility for massively parallel DNA sequencing ( MPS ) is limited. Poor sample quality and contamination by exogenous DNA can make MIS challenging to use with modern genotyping‐by‐sequencing approaches, which have been traditionally developed for high‐quality DNA sources. Given that MIS is often more appropriate in many contexts, there is a need to make such samples practical for harnessing MPS . Here, we test the ability for Genotyping‐in‐Thousands by sequencing ( GT ‐seq), a multiplex amplicon sequencing approach, to effectively genotype minimally invasive cloacal DNA samples collected from the Western Rattlesnake ( Crotalus oreganus ), a threatened species in British Columbia, Canada. As there was no previous genetic information for this species, an optimized panel of 362 SNP s was selected for use with GT ‐seq from a de novo restriction site‐associated DNA sequencing ( RAD seq) assembly. Comparisons of genotypes generated within and among RAD seq and GT ‐seq for the same individuals found low rates of genotyping error ( GT ‐seq: 0.50%; RAD seq: 0.80%) and discordance (2.57%), the latter likely due to the different genotype calling models employed. GT ‐seq mean genotype discordance between blood and cloacal swab samples collected from the same individuals was also minimal (1.37%). Estimates of population diversity parameters were similar across GT ‐seq and RAD seq data sets, as were inferred patterns of population structure. Overall, GT ‐seq can be effectively applied to low‐quality DNA samples, minimizing the inefficiencies presented by exogenous DNA typically found in minimally invasive samples and continuing the expansion of molecular ecology and conservation genetics in the genomics era.