Genomic and chromosomal context provides valuable information in genetic analyses, such as during genome-wide association studies, population genetics, and gene expression. Salmonids are a model species for whole genome duplication followed by a return to a diploid state for a majority of the genome and some residual tetraploidy. Working in the lab of Louis Bernatchez with Céline Audet, we developed a high-density genetic map for Brook Charr Salvelinus fontinalis and integrated this map with all other salmonids (via the tool MapComp), providing insight in the large-scale chromosome rearrangements throughout the rediploidization process (Sutherland et al. 2016). Among other benefits, this enabled investigation into the changing sex chromosomes in the salmonids (Sutherland et al. 2017).
Oyster Genomics and Population Health
Pacific oyster has been faced with severe mortality events, leaving the industry with significant losses. Understanding the climatic, microbial, and/ or genetic factors involved in these mortalities is part of an ongoing project with Kristi Miller (Pacific Biological Station, DFO-MPO) and Curtis Suttle (UBC), funded by the Moore Foundation and Hakai. Understanding the genetic similarity of oysters around British Columbia on farms and self-recruiting in the wild has been explored and compared to those elsewhere through the introduced and native range (Sutherland et al. 2020). Alleles associated with survival to mortality events, or differences in overall genetic diversity, could be valuable to mitigate these mortality events.
Genetic Stock Identification
Genetic stock identification through microsatellite or SNP markers is a useful technique for assigning stock of origin to unknown origin individuals. This has proven to be a highly useful method for many commercial species of salmonids in British Columbia. As next-generation sequencing approaches are increasingly applied (e.g., RAD-sequencing and amplicon sequencing), it enables the application towards non-model species and can increase the interoperability of baselines between labs (e.g., eulachon Thaleichthyes pacificus; Sutherland et al. 2021). These single nucleotide polymorphism (SNP)-based approaches can also include potentially adaptive markers, and may be amenable to portable genotyping techniques for remote application (e.g., Nanopore sequencing; Deeg et al. submitted).
Environmental DNA (eDNA)
eDNA is a promising and non-invasive tool for characterizing biodiversity, disturbances, range changes, and detection of invasive species. Recently, we applied metabarcoding to evaluate the presence of different species in algal blooms (Esenkulova et al. 2020). This technique is increasingly being applied by agencies such as the Government of Canada (Baillee et al. 2018). To demonstrate use in biodiversity studies, the CanadaC3 expedition sampled throughout all three coasts of Canada, including in highly remote locations (see Vancouver Sun article). This technique also shows great promise for remote sampling.
Transcriptomics provides an integrative view of the response of an organism to its biotic and abiotic environment. Working in the lab of Prof. Ben Koop I applied this approach to the question of salmon and infective agents such as sea lice or viruses. In collaboration with Simon Jones (DFO), we have demonstrated species- and life stage-specific variation in sea lice infection rates and host responses to infection (Sutherland et al. 2011; Sutherland et al. 2014). Applying these approaches, we have also investigated the louse responses to Pacific and Atlantic salmonids, highlighting the possibility of co-evolution resulting in different infection dynamics in the responses of lice to different species of hosts (Braden, Sutherland et al., 2017). Transcriptomics work has also indicated energetic trade-offs in responses, for example the suppression of the innate immune system during smoltification (Sutherland et al. 2014), or during responses of sea lice to different levels of abiotic stress (Sutherland et al., 2012). Sea lice transcriptomics has also been used to investigate the differences in sexual dimorphism in lice (Poley et al. 2016), different expression patterns associated with antiparasiticide drug resistance (Sutherland et al. 2015) and sea lice responses to a naturally occurring microsporidian parasite (Poley , Sutherland et al. 2017).
Method Development: MapComp
Presentation from Coastwide Salmonid Genetics Meeting (2018)
Method Development: GO Trimming
© Ben J G Sutherland 2021 All rights reserved