ORCID Profile
0000-0002-2029-9893
Current Organisations
Sutherland Bioinformatics
,
University of Victoria
,
Vancouver Island University
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Publisher: Cold Spring Harbor Laboratory
Date: 07-07-2023
DOI: 10.1101/2023.07.07.548145
Abstract: Pacific oysters ( Magallana gigas, also known as Crassostrea gigas ), the most widely farmed oysters, are under threat from climate change and emerging pathogens. In part, their resilience may be affected by their microbiome, which, in turn, may be influenced by ocean warming and acidification. Consequently, for three weeks, we exposed early-development Pacific oyster spat to different temperatures (18 and 24 °C) and p CO 2 levels (800, 1600 and 2800 µ atm) in a fully crossed design. Under all conditions, the microbiome developed over time, with potentially pathogenic ciliates ( Uronema marinum ) greatly reduced in all treatments, suggesting that the spat’s microbiome undergoes adaptive shifts as the oysters age. The microbiome composition also differed significantly with temperature, but not acidification, indicating that M. gigas spat microbiomes can be altered by ocean warming but resilient to ocean acidification in our experiments. These findings highlight the spat microbiome’s flexibility to environmental changes as well as its “protective” capability against potentially pathogenic microbes.
Publisher: Cold Spring Harbor Laboratory
Date: 06-2023
DOI: 10.1101/2023.05.31.540437
Abstract: The Yesso scallop Mizuhopecten yessoensis is an important aquaculture species that was introduced to Western Canada from Japan to establish an economically viable scallop farming industry. This highly fecund species has been propagated in Canadian aquaculture hatcheries for the past 40 years, raising questions about genetic ersity and genetic differences among hatchery stocks. In this study, we compare cultured Canadian and wild Japanese populations of Yesso scallop using double-digest restriction site-associated DNA (ddRAD)-sequencing to genotype 21,048 variants in 71 wild-caught scallops from Japan, 65 scallops from the Vancouver Island University breeding population, and 37 scallops obtained from a commercial farm off Vancouver Island, British Columbia. The wild scallops are largely comprised of equally unrelated in iduals, whereas cultured scallops are comprised of multiple families of related in iduals. The polymorphism rate estimated in wild scallops was 1.7%, whereas in the cultured strains it varied between 1.35% and 1.07%. Interestingly, heterozygosity rates were highest in the cultured populations, which is likely due to shellfish hatchery practices of crossing ergent strains to gain benefits of heterosis and to avoid inbreeding. Evidence of founder effects and drift were observed in the cultured strains, including high genetic differentiation between cultured populations and between cultured populations and the wild population. Cultured populations had effective population sizes ranging from 9-26 in iduals whereas the wild population was estimated at 25-50K in iduals. Further, a depletion of low frequency variants was observed in the cultured populations. These results indicate significant genetic ersity losses in cultured scallops in Canadian breeding programs.
Publisher: Cold Spring Harbor Laboratory
Date: 28-08-2023
DOI: 10.1101/2023.08.26.554329
Abstract: Maintaining genetic ersity in cultured shellfish can be challenging due to high variance in in idual reproductive output, founder effects, and rapid genetic drift. However, it is important to consider for retaining adaptive potential and avoiding inbreeding depression, particularly in species with high mutational load. To support management of genetic ersity and selective breeding efforts in cultured Pacific oyster ( Crassostrea gigas a.k.a. Magallana gigas ), we developed an licon panel comprising 592 licons positioned throughout the genome with an average of 50 markers per chromosome. Markers were selected based on high heterozygosity or high differentiation in Pacific oyster populations from the eastern Pacific Ocean. The developed panel was tested in a pilot study on 371 unique in iduals, including those from hatcheries and farms (n = 72) and from three generations of the Vancouver Island University (VIU) breeding program (n = 181), as well as from naturalized or wild populations in the Northern Hemisphere (n = 118). High repeatability was observed in technical replicate s les on average, 97.5% of typed markers were concordant between s les (n = 68 replicate s le pairs). In the pilot dataset, following quality filters, 463 markers were retained for analysis (average observed heterozygosity = 0.29 +/- 0.19 and FST = 0.040 +/- 0.046). Principal components analysis showed separate clustering of the Japan translocation lineage, China, and a commercial aquaculture population. Parentage analysis of the VIU breeding program identified 84% and 66% of the possible parent-offspring assignments in two spawning events involving 98 and 40 offspring each, respectively. Results were strongest in in iduals with the highest genotyping rates, highlighting the value of s le and target SNP quality. The analysis identified pedigree errors that were then corrected. All code required to analyze the data is provided, including litools , a repository to move the panel target SNP output through parentage analysis. Collectively, these advances will enable rapid, consistent, and cost-effective genotyping of Pacific oyster.
Location: Canada
No related grants have been discovered for Ben J. G. Sutherland.