Li, G., S. Hubert, K. Bucklin, V. Ribes, and D. Hedgecock. 2003. Characterization of 79 microsatellite DNA markers in the Pacific oyster Crassostrea gigas. Molecular Ecology Notes 3:228-232.

Hedgecock, D., G. Li, S. Hubert, K. Bucklin, and V. Ribes. 2004. Widespread null alleles and poor cross-species amplification of microsatellite DNA loci cloned from the Pacific oyster (Crassostrea gigas). Journal of Shellfish Research 23:379-385.

Hubert, S., and D. Hedgecock. 2004. Linkage maps of microsatellite DNA markers for the Pacific oyster Crassostrea gigas. Genetics 168:351-362.

Hedgecock, D., P. M. Gaffney, P. Goulletquer, X. Guo, K. Reece, and G. W. Warr. 2005. The case for sequencing the Pacific oyster genome. Journal of Shellfish Research 24:429-441.

This “white paper” was the first to advocate for the sequencing of the Pacific oyster genome. The paper describes the biological and genomic resources available (at that time) to support a genome sequencing project, including the fourth-generation inbred line 51, from which a BAC DNA library was constructed and which ultimately provided the oyster whose genome was sequenced by the Beijing Genome Institute (Zhang et al. 2012). Also mentioned are the 51 × 35 F1 and F2 hybrids, which have been used extensively for research on heterosis and inbreeding depression; this research provided a framework for genomic approaches to understanding heterosis and its applications to shellfish breeding and, thus, a compelling rationale for sequencing the genome.

Hedgecock, D., J.-Z. Lin, S. DeCola, C. Haudenschild, E. Meyer, D. T. Manahan, and B. Bowen. 2007. Transcriptomic analysis of growth heterosis in larval Pacific oysters (Crassostrea gigas). Proceedings of the National Academy of Sciences, U.S.A. 104:2313-2318.

Published in the prestigious journal, Proceedings of the National Academy of Sciences, this paper reported the first analysis of sequences of transcribed or expressed genes in a marine animal. It was one of the first such studies, comparing inbre and hybrid families of any organism.

Curole, J. P., E. Meyer, D. T. Manahan and D. Hedgecock. 2009. Expression of the Pacific oyster mitochondrial genome: Variation among loci and evidence for regulation by nuclear-cytoplasmic interaction. Biological Bulletin 218:122-131.

In this paper, an outgrowth of the transcriptome study (Hedgecock et al 2007, below), we focused on the expression of genes in the oyster mitochondrial genome. We showed that mitochondrial genes, despite being transcribed as a unit, have very different levels of expression (i.e. abundances of messenger RNA vary by orders of magnitude). We also provided evidence that this variation in mitochondrial gene expression depends in part on the nuclear genotype. Such nuclear-cytoplasmic interactions may underlie the significant differences that we often see between reciprocal hybrids (i.e. hybrid AB ≠ hybrid BA), even though both hybrids have, in principle, have very similar nuclear genes. Hedgecock and Davis (2007) provided substantial evidence that reciprocal differences are a significant component of yield variance. This work was supported by grants from the USDA and the NSF.