Location: National Cold Water Marine Aquaculture Center
Project Number: 8030-31000-005-003-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 24, 2018
End Date: Sep 23, 2023
Objective:
To improve the eastern oyster genome assembly and annotation through bioinformatic analysis and experimental work. To characterize patterns of polymorphism and gene expression in genetic lines and selected families used in aquaculture. To utilize gene expression data to understand functional responses to environmental stress (including pathogen exposure, low pH, and hypoxia). To associate polymorphisms with stress-response phenotypes and facilitate enhanced genetic improvement.
Approach:
The eastern oyster genome assembly produced by the eastern oyster genome consortium, as well as gene expression and genome re-sequencing data will be collected and analyzed to characterize functional mechanisms underlying stress response phenotypes and identify SNPs associated with specific phenotypes and the effects of artificial selection. RNAseq and genome re-sequencing data from phenotyped oysters sourced from multiple selectively-bred families and collected during ARS-led disease challenge experiments and URI-led low pH/hypoxia challenges will be mapped to the genome assembly and analyzed to:
1) further annotate the eastern oyster genome,
2) assess genetic variation for Dermo resistance and low pH tolerance within selected breeding populations, and
3) associate specific SNPs, genes, and gene pathways with the stress-response phenotypes. Identification of markers, genes, and pathways associated with commercially important traits will expose novel targets for selection and enhance current oyster breeding practices.
