Genomic architecture of artificially and sexually selected traits in a wild cervid

Abstract

22Characterization of the complex genomic architecture underlying quantitative 23 traits can provide valuable insights into the study, conservation, and management of 24 natural populations. This is particularly true for fitness-related traits such as body size 25 and male ornamentation in mammals because as indicators of quality and health, these 26 traits are often subject to sexual and artificial selective pressures. Here we performed 27 high-depth whole genome re-sequencing on pools of individuals representing the 28 phenotypic extremes in our study system for antler and body size in white-tailed deer 29 (Odocoileus virginianus). Samples were selected from a database containing 30 phenotypic data for 4,466 male white-tailed deer from Anticosti Island, Quebec, with 31 four pools representing the extreme phenotypes for antler and body size in the 32 population. Our results revealed a largely panmictic population (F ST ~ 0.01), but also 33 detected diverged regions (F ST > 0.11) between pools for both traits. These regions 34 revealed genomic islands with signatures of positive selection and demographic 35 expansion (negative Tajima's D), and contained putative genes of small-to-moderate 36 effect. Through qPCR analysis we genotyped an intron variant on gene SRP54 that is a 37 potential QTL for antler size, and propose two missense variants on the MYADM and 38 SPATA31E1 genes known to influence body size in mammals and reproductive success 39 as potential QTL. This study revealed the polygenic nature of both antler morphology 40 and body size in white-tailed deer and identified target loci for additional analyses. 41 Study area 126Anticosti Island (49°N, 62°W; 7,943 km 2 ) is located in the Gulf of St. Lawrence, Québec 127 (Canada) at the northeastern limit of the white-tailed deer range (Figure 1). The island is 128 within the balsam fir-white birch bioclimatic region with a maritime sub-boreal climate 129 characterized by cool and rainy summers (630mm/year), and long and snowy winters 130 (406 cm/year;Environment Canada, 2006;Simard et al., 2010). The deer population 131 was introduced in 1896 with ca. 220 animals and rapidly increased. Today, densities are 132 7 >20 deer/km 2 and can exceed 50 deer/km 2 locally (Potvin and Breton 2005) with an 133 estimated population >160,000 individuals. 134 Sample Collection and Modeling 135We collected tissue samples and phenotypic data on 4,466 male deer harvested by 136 hunters from September to early December, 2002-2014. We used cementum layers in 137 incisor teeth to age individuals (Hamlin et al., 2000). Two metrics of antler size were 138 selected: the number of antler tines or points (>2.5 cm) and beam diameter (measured 139

Heritability estimates of antler and body traits in white-tailed deer (Odocoileus virginianus) from genomic-relatedness matrices

“…For a subset of male samples we genotyped the SRP54 locus that was previously found to be associated with antler morphology (Anderson et al ., 2019). 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).…”

“…Similarly, h 2 was estimated between 0.58 and 0.64 for body mass (Williams et al ., 1994). Recent work suggests a highly polygenic nature of these traits (Anderson et al ., 2019), but h 2 has yet to be quantified in a free-ranging population of white-tailed deer. Theoretical and empirical evidence suggests that bottlenecked populations, such as those we might expect to see in captivity, have increased V A (Goodnight, 1988; Whitlock et al ., 1993; van Heerwaarden et al ., 2008; Jarvis et al ., 2011; Taft and Roff, 2012), thus it is unclear how h 2 values transfer from captivity to the wild.…”

Admixture mapping reveals loci for carcass mass in red deer x sika hybrids in Kintyre, Scotland

“…Additionally, based on substantial LD across each linkage group (Table 2), we identified 40 genes that could be functionally associated with carcass mass in deer (Table S1). While none of these genes have been associated with carcass mass in white-tailed deer (Anderson et al 2020) or cattle (cow QTL database) (Bouwman et al 2018;Hu et al 2019), four of them are associated with height in humans (Locke et al 2015) and 12 are associated with body mass index (BMI) or obesity in humans (Comuzzie et al 2012;Danjou et al 2015;Winkler et al 2015;Wojcik et al 2019). Perhaps the strongest evidence we have for carcass mass QTL is where multiple adjacent SNPs indicate an effect.…”

Genomic correlates for migratory direction in a free-ranging cervid

“…The tiered window selection criteria seem to extract primarily functional outliers compared to other pooled genome-wide association studies using statistical thresholds (e.g., Anderson et al, 2020). The 11 genes that occurred on or within 25kb of a divergent window were ADGRB1, BSG, DPPA3, EMC9, FITM1, IKZF3, ITSN2, MAN2A2, PSME1, RNF216, and SETX.…”