An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster.

Autor: Sutherland BJG; Sutherland Bioinformatics, Lantzville, BC V0R 2H0, Canada.; Faculty of Science and Technology, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada., Thompson NF; United States Department of Agriculture, Hatfield Marine Science Center, Pacific Shellfish Research Unit, Agricultural Research Service, Newport, OR 97365, USA., Surry LB; Faculty of Science and Technology, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada., Gujjula KR; ThermoFisher Scientific, 2130 Woodward Street, Austin, TX 78744, USA., Carrasco CD; ThermoFisher Scientific, 2130 Woodward Street, Austin, TX 78744, USA., Chadaram S; ThermoFisher Scientific, 2130 Woodward Street, Austin, TX 78744, USA., Lunda SL; Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR 97331, USA., Langdon CJ; Hatfield Marine Science Center, 2030 SE Marine Science Dr., Oregon State University, Coastal Oregon Marine Experiment Station, Newport, OR 97365, USA., Chan AM; Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada., Suttle CA; Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada.; Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada.; Department of Botany, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada.; Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada., Green TJ; Faculty of Science and Technology, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada.
Jazyk: angličtina
Zdroj: G3 (Bethesda, Md.) [G3 (Bethesda)] 2024 Sep 04; Vol. 14 (9).
DOI: 10.1093/g3journal/jkae125
Abstrakt: Maintaining genetic diversity in cultured shellfish can be challenging due to high variance in individual reproductive success, founder effects, and rapid genetic drift, but is important to retain adaptive potential and avoid inbreeding depression. To support broodstock management and selective breeding in cultured Pacific oysters (Crassostrea (Magallana) gigas), we developed an amplicon panel targeting 592 genomic regions and SNP variants with an average of 50 amplicons per chromosome. Target SNPs were selected based on elevated observed heterozygosity or differentiation in Pacific oyster populations in British Columbia, Canada. The use of the panel for parentage applications was evaluated using multiple generations of oysters from a breeding program on Vancouver Island, Canada (n = 181) and families selected for Ostreid herpesvirus-1 resistance from the Molluscan Broodstock Program in Oregon, USA (n = 136). Population characterization was evaluated using wild, naturalized, farmed, or hatchery oysters sampled throughout the Northern Hemisphere (n = 189). Technical replicates showed high genotype concordance (97.5%; n = 68 replicates). Parentage analysis found suspected pedigree and sample handling errors, demonstrating the panel's value for quality control in breeding programs. Suspected null alleles were identified and found to be largely population dependent, suggesting population-specific variation impacting target amplification. Null alleles were identified using existing data without the need for pedigree information, and once they were removed, assignment rates increased to 93.0 and 86.0% of possible assignments in the two breeding program datasets. A pipeline for analyzing the amplicon sequence data from sequencer output, amplitools, is also provided.
Competing Interests: Conflicts of interest B.J.G.S. is affiliated with Sutherland Bioinformatics. The author has no competing financial interests to declare. Some authors affiliated with ThermoFisher Scientific have potential conflicts considering that the AgriSeq Targeted Genotyping by Sequencing solutions and associated Oligo panels that were designed and validated in the study are offered by ThermoFisher Scientific. However, the selection of markers, and data analysis was primarily conducted by other authors. The authors declare that the research was conducted in a scientific manner without any commercial considerations that could be construed as potential conflict of interest and further declare no other conflicts of interest. The other authors declare no competing interests.
(© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)
Databáze: MEDLINE
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