Abstract
We designed a genotyping panel for the investigation of the genetic underpinnings of inter-individual differences in aggression and the physiological stress response. The panel builds on single nucleotide polymorphisms (SNPs) in genes involved in the three subsystems of the hypothalamic-pituitary-adrenal (HPA)-axis: the catecholamine, serotonin and corticoid metabolism. To promote the pipeline for use with wild animal populations, we used non-invasively collected faecal samples from a wild population of Assamese macaques (Macaca assamensis). We targeted loci of 46 previously reported SNPs in 21 candidate genes coding for elements of the HPA-axis and amplified and sequenced them using next-generation Illumina sequencing technology. We compared multiple bioinformatics pipelines for variant calling and variant effect prediction. Based on this strategy and the application of different quality thresholds, we identified up to 159 SNPs with different types of predicted functional effects among our natural study population. This study provides a massively parallel sequencing panel that will facilitate integrating large-scale SNP data into behavioural and physiological studies. Such a multi-faceted approach will promote understanding of flexibility and constraints of animal behaviour and hormone physiology.
Highlights
Recent developments in molecular techniques enable researchers to include large-scale investigations of genetic impacts on behavioural or endocrine variables at reasonable costs[1,2]
Enhancing the approach of behavioural genetics and physiogenetics in wild animals would extend our knowledge of the factors that contribute to the still not completely understood variation within and between populations under natural selection pressures[8]
Behavioural studies often investigate the impacts of personality, age, sex or external factors such as social environment, group size and dominance hierarchy to explain inter-individual differences in HPA-axis related traits and probably misrepresent the amount of variation to be explained by such factors because they neglect genetic impacts[59,60,61,62] or focus only on one or two gene variants[31,32,33], but see[34,63,64]
Summary
Recent developments in molecular techniques enable researchers to include large-scale investigations of genetic impacts on behavioural or endocrine variables at reasonable costs[1,2]. Three main metabolic circuits contribute to the HPA-axis: the serotonin, the catecholamine and the corticoid Genes associated with these metabolic circuits have been repeatedly targeted in human clinical stress[23,24] and aggression[4,25,26] research. Behavioural studies on natural animal populations, commonly target one or a few gene loci associated with aggression and HPA-axis activity[31,32,33], whereas high-throughput multi-locus approaches are rather rare but see[1,34]. Due to the high number of genes involved in physiological pathways such as the HPA-axis, the simultaneous assessment of multiple loci known to affect certain traits promises a much more comprehensive understanding of the investigated physiological and behavioural parameters[35,36]. The generated data provide high coverage of amplicons or genomes and a large and still growing body of different bioinformatics applications helps to investigate multiple loci in a fast and parallel way (e.g. Genome Analysis Toolkit – GATK37, SAMtools[38] and UCSC genome browser[39])
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