Compared with understanding of biological shape and form, knowledge is sparse regarding what regulates growth and body size of a species. For example, the genetic and physiological causes of heterosis (hybrid vigor) have remained elusive for nearly a century. Here, we investigate gene-expression patterns underlying growth heterosis in the Pacific oyster (Crassostrea gigas) in two partially inbred (f ؍ 0.375) and two hybrid larval populations produced by a reciprocal cross between the two inbred families. We cloned cDNA and generated 4.5 M sequence tags with massively parallel signature sequencing. The sequences contain 23,274 distinct signatures that are expressed at statistically nonzero levels and show a highly positively skewed distribution with median and modal counts of 9.25 million and 3 transcripts per million, respectively. For nearly half of these signatures, expression level depends on genotype and is predominantly nonadditive (hybrids deviate from the inbred average). Statistical contrasts suggest Ϸ350 candidate genes for growth heterosis that exhibit concordant nonadditive expression in reciprocal hybrids; this represents only Ϸ1.5% of the >20,000 transcripts. Patterns of gene expression, which include dominance for low expression and even underdominance of expression, are more complex than predicted from classical dominant or overdominant explanations of heterosis. Preliminary identification of ribosomal proteins among candidate genes supports the suggestion from previous studies that efficiency of protein metabolism plays a role in growth heterosis.MPSS ͉ nonadditive expression ͉ factorial cross of partially inbred lines ͉ potence ͉ protein metabolism W hole-genome sequencing has yielded rich insights into the number of genes required to make complex eukaryotic animals (1-4). Surprisingly few genes, however, can effect major changes in body design and shape. For example, elaboration and mutation of a fairly small number of developmentally important regulatory genes, such as the Hox gene cluster, appear to have driven the evolution of the major metazoan body plans (5). Profound changes in shape or morphology, underlying adaptive differences among closely related species, also can be caused by mutations in a very few genes (6-8).Compared with our growing understanding of the evolution of biological shape and form, our understanding of what regulates body size and the rates and efficiencies of physiological functions is much less developed. For example, the genetic and physiological causes of heterosis (hybrid vigor) and its converse, inbreeding depression, have remained elusive for nearly a century, despite the economic and scientific significance of these phenomena (9-12). Major genetic explanations for heterosis are overdominance, the superiority of heterozygotes at genes affecting fitness or economic traits, dominance, the masking, in hybrids, of deleterious recessive mutations by dominant alleles inherited from one or the other inbred parent, and epistasis, the interaction of alleles at differe...