Functional Genomics in Aquaculture

Aquaculture is a billion dollar industry. In 2010 more than 150 billion kg of fish, crustaceans, mollusks, and plants was harvested from aquaculture, almost twice that caught in the wild. As with any new venture, aquaculture maintains both advantages and weaknesses. With the global decline in fish and invertebrates, and an increasing demand for human consumption, farming of these species provides a potentially sustainable method to satiate demand and help slow or even reverse population declines. However, domestication comes with its own set of problems: low fecundity and growth rates, high levels of disease and parasitism, and the risk of introducing non-native species to an environment through escape. Recent studies have turned to functional genomics to address many of these problems. While some key commercial species have been studied extensively, we see here how comparative studies can be used to look at a non-model organism with few genomic resources. Through the use of next generation sequencing and microarray analysis, as well as many other techniques, the authors here address issues such as how captivity may affect the genome, whether there is evidence for growth-related genes, what genes are associated with infection, disease, or deformity, and how the use of dietary supplementation affects gene expression.