Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours

Abstract

Strains of red fox (Vulpes vulpes) with markedly different behavioural phenotypes have been developed in the famous long-term selective breeding programme known as the Russian farm-fox experiment. Here we sequenced and assembled the red fox genome and re-sequenced a subset of foxes from the tame, aggressive and conventional farm-bred populations to identify genomic regions associated with the response to selection for behaviour. Analysis of the re-sequenced genomes identified 103 regions with either significantly decreased heterozygosity in one of the three populations or increased divergence between the populations. A strong positional candidate gene for tame behaviour was highlighted: SorCS1, which encodes the main trafficking protein for AMPA glutamate receptors and neurexins and suggests a role for synaptic plasticity in fox domestication. Other regions identified as likely to have been under selection in foxes include genes implicated in human neurological disorders, mouse behaviour and dog domestication. The fox represents a powerful model for the genetic analysis of affiliative and aggressive behaviours that can benefit genetic studies of behaviour in dogs and other mammals, including humans.

Analysis of new retrogenes provides insight into dog adaptive evolution

“…generation time (corresponding to 1.33 × 10 -9 mutations per year) to calculate the divergence time between retrocopies and corresponding parental genes (T = K s /2λ). Thus, a further phylogenetic analysis, by comparing the other genomes such as the gray wolf and the red fox(Gopalakrishnan et al, 2017;Kukekova et al, 2018), would be helpful to validate dog-specific or Canini-specific candidate retrogenes. Consistent with previous studies in other mammals(Marques et al, 2005;Pan & Zhang, 2009), fish(Fu et al, 2010), and plant(Wang et al, 2006), this result confirmed that retrotransposition could play significant roles in both genome remolding and lineage or species differentiation.Interestingly, we detected 14 intact retrogenes with K s values of 0 which might be indicative of very recent retrogenes.…”

Genomic responses to selection for tame/aggressive behaviors in the silver fox (Vulpes vulpes)

“…http://dx.doi.org/10.1101/228544 doi: bioRxiv preprint first posted online Dec. 4, 2017; heterozygosity and increased divergence between populations which was identified in the 157 analysis of re-sequenced genomes (34 (35,36). In our exonic SNP data, GRM3 has a C to G change causing a Wnt4 in the fox had more than one SNP with significant allele frequency changes.…”

Allele frequency dynamics in a pedigreed natural population

“…Also, empirical pedigree calculations have long been used to understand genetic models of human diseases (13) and are increasingly used in natural populations to understand the genetic basis of quantitative trait variation, fitness consequences of inbreeding, and much more (14). To date, empirical pedigrees and gene dropping approaches have been rarely used to study the temporal spread and loss of individual alleles (15)(16)(17)(18).Here, we combine genomic data with a known population pedigree to describe and predict allele frequency change at many loci in an exhaustively sampled free-living population of Florida Scrub-Jays (Aphelocoma coerulescens) at Archbold Biological Station. Intensive study since 1969 has resulted in lifetime fitness measures for thousands of individuals on an extensive pedigree.…”

“…Also, empirical pedigree calculations have long been used to understand genetic models of human diseases (13) and are increasingly used in natural populations to understand the genetic basis of quantitative trait variation, fitness consequences of inbreeding, and much more (14). To date, empirical pedigrees and gene dropping approaches have been rarely used to study the temporal spread and loss of individual alleles (15)(16)(17)(18).…”