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ARS Home » Northeast Area » Orono, Maine » National Cold Water Marine Aquaculture Center » Research » Research Project #435424

Research Project: Leveraging the Eastern Oyster Genome to Facilitate Enhanced Germplasm Improvement

Location: National Cold Water Marine Aquaculture Center

Project Number: 8030-31000-005-03-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 24, 2018
End Date: Sep 23, 2021

Objective:
Improve the eastern oyster genome assembly and annotation through bioinformatic analysis and experimental work. Characterize patterns of polymorphism in genetic lines and selected families used in aquaculture. Associate polymorphisms with traits of commercial interest to facilitate enhanced genetic improvement.

Approach:
The eastern oyster genome assembly produced by the eastern oyster genome consortium, as well as available genome re-sequencing data from 90 individuals derived from wild and selected oyster lines spanning the geographic and ecological range of the species will be analyzed to identify SNPs and assess the effect of artificial selection on patterns of polymorphism. In addition, RNAseq and genome re-sequencing data from phenotyped oysters sourced from multiple selectively-bred families and collected during ARS-led disease challenge experiments will be mapped to the genome assembly and analyze to 1) further annotate the eastern oyster genome, 2) assess genetic variation for Dermo resistance within the selected breeding population and 3) associate specific SNPs, genes, and gene pathways with the resistance phenotypes. Measures of disease-resistant/tolerant phenotypes beyond survival, including gene expression profiles and genetic polymorphisms, can be used to enhance current existing programs by including marker-assisted and genomic selection techniques.