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.

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)

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