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SRP54 locus genotypes of white-tailed deer from Jamieson et al.

Citation

Shafer, Aaron (2020), SRP54 locus genotypes of white-tailed deer from Jamieson et al. , Dryad, Dataset, https://doi.org/10.5061/dryad.pzgmsbchr

Abstract

Estimating heritability (h2) is required to predict the response to selection and is useful in species that are managed or farmed using trait information. Estimating h2 in free-ranging populations is challenging due to the need for pedigrees; genomic-relatedness matrices (GRMs) circumvent this need and can be implemented in nearly any system where phenotypic and genome-wide single nucleotide polymorphism (SNP) data are available. We estimated the heritability of five body and three antler traits in a free-ranging population of white-tailed deer (Odocoileus virginianus) on Anticosti Island, Quebec, Canada. We generated classic and robust GRMs from >10,000 SNPs: hind foot length, dressed body mass and peroneus muscle mass had high h2 values of 0.62, 0.44 and 0.55, respectively. Heritability in male-only antler features ranged from 0.07 to 0.33 and had high standard errors. We explored the influence of filtering by minor allele frequency and data completion on h2: GRMs derived from fewer SNPs had reduced h2 estimates and the relatedness coefficients significantly deviated from those generated with more SNPs. As a corollary, we discussed limitations to the application of GRMs in the wild, notably how skewed GRMs, specifically many unrelated individuals, can increase variance around h2 estimates. This is the first study to estimate h2 on a free-ranging population of white-tailed deer and should be informative for breeding designs and management as these traits should respond to selection.

Methods

We custom designed a rhAmp SNP assay and genotyped individuals via qPCR with a QuantStudio 3 Real-Time PCR System (Thermo Fisher Scientific, Waltham, MA, USA). The thermocycling condition was 60 °C for 30 seconds followed by 95 °C for 10 minutes, then 40 cycles of 95 °C for 10 seconds, 60 °C for 30 seconds, and 68 °C for 20 seconds, followed by a final 30 seconds at 60 °C. The qPCR had a 5 µL reaction volume in each 0.1 mL well of a sealed 96-well optical plate. We score the SRP54 locus in an additive framework (0, 1, or 2 alleles)

Usage Notes

Included are four colums, in order: population, ID, age, and allele calls

Funding

Natural Sciences and Engineering Research Council of Canada

ComputeCanada Resources for Research Groups

Canadian Foundation for Innovation

John R. Evans Leaders Fund

Industrial Chairs and Collaborative Research and Development