Environmental and Comparative Genomics - Research Projects
Shrimp

Dr. Acacia Warren leads a genome mapping effort in shrimp that is branching out into other aquatic species, wildlife, and horses. Supported by the USDA-CREES, Tufts University, NIH Short Training Grants and other agencies and foundations, the laboratory is elucidating a great deal of information about the genetics of important traits such as resistance to viral diseases, sex determination, and bioaccumulation of cadmium, among others. Also, faculty, staff and students in this section are studying the complex interactions between aquaculture and the environment. Her well-supported laboratory also trains some of our students interested in applying advanced molecular techniques to their projects.

Shrimp Genomics and Comparative Genomics

• US Marine Shrimp Farming Program (USMSFP)
  Tufts University is a member of the USMSFP. The specific tasks performed under this project are: tracing the pedigree of specific pathogen free (SPF) shrimp lines maintained at the Oceanic Institute, constructing a genetic linkage map for P. vannamei, searching for candidate quantitative trait loci (QTLs) responsible for resistance to Taura Syndrome Virus (TSV) and high growth, and estimating allele diversity in USMSFP germplasm.

• International Marine Shrimp Environmental Genomics Initiative (IMSEGI): Monitoring Ecosystems, Animal and Public Health
  Worldwide, marine shrimp populations in their natural habitat are threatened by a variety of pressures including habitat destruction, pollution, diseases, and gene pool depletion. To conserve penaeid shrimp species and develop a sustainable shrimp aquaculture industry, the International Marine Shrimp Environmental Genomics Initiative (IMSEGI) was initiated with the purpose of monitoring the structure of the meta-population of wild penaeid penaeid shrimp species, the levels of genetic diversity and differentiation of selected species, and the presence of pollutants such as pathogens, heavy metals, pesticides and antibiotics in penaeid shrimp populations along their natural range in Asia and Latin America.

Environmental Genomics Applied to Aquatic Species
There is a high level of concern regarding impacts of transgenic stocks on natural populations. Application of genomics technologies may yield new inferences on the impacts of transgenic fish and shellfish in particular, and aquaculture and fisheries management practices in general, on native stocks. Availability of genetic linkage maps for aquatic species allows researchers with the opportunity to address some important questions:

1. What are the molecular mechanisms or pathways by which animals respond to stress or to environmental cues?
2. Which are the fitness-related genes?
3. How the genetic composition of a population changes in response to selection pressures such as abiotic environmental stressors, disease, or introgression of genes from outside the population?
4. What are the potential genetic impacts to wild populations caused by interbreeding of selectively bred (potentially inbred and disease susceptible), inter-specific hybrids, and transgenic stocks with indigenous populations?
• will they establish new populations outside their natural range?
• transgenic research focus mostly on studying the fitness of transgenics using empirical experimentation and models of single and multiple genes on net fitness
• should a more holistic approach to environmental issues be considered?

Genomics tools such as microarrays and QTL mapping will allow aquaculturists and fisheries managers to better understand and minimize potential population-level impacts of transgenics.