Genomic approaches with natural fish populations from polluted environments

Abstract

Transcriptomics and population genomics are two complementary genomic approaches that can be used to gain insight into pollutant effects in natural populations. Transcriptomics identify altered gene expression pathways while population genomics approaches more directly target the causative genomic polymorphisms. Neither approach is restricted to a pre-determined set of genes or loci. Instead, both approaches allow a broad overview of genomic processes. Transcriptomics and population genomic approaches have been used to explore genomic responses in populations of fish from polluted environments and have identified sets of candidate genes and loci that appear biologically important in response to pollution. Often differences in gene expression or loci between polluted and reference populations are not conserved among polluted populations suggesting a biological complexity that we do not yet fully understand. As genomic approaches become less expensive with the advent of new sequencing and genotyping technologies, they will be more widely used in complimentary studies. However, while these genomic approaches are immensely powerful for identifying candidate gene and loci, the challenge of determining biological mechanisms that link genotypes and phenotypes remains. Keywords Fundulus heteroclitus; Genomics; Natural populations; Pollution Genomics with natural populationsThe power of genomic tools is the ability to simultaneously query large portions of the genome of an organism. These tools are just beginning to be harnessed for studies of aquatic toxicology in natural populations. The advantage of genomic approaches used in aquatic toxicology studies of natural populations is that an a priori choice of biomarkers of adverse effect is not necessary. This can be particularly important when organisms are exposed to mixtures of chemicals, as is often the case in environmental studies. Since the biological targets of pollutants often are not fully known, the global view gained with genomic approaches can be particularly valuable.Two complementary genomic approaches that are becoming easier and cheaper to implement with non-model, natural populations are microarrays and population genomics.

Effects of Anthropogenic Pollution on the Oxidative Phosphorylation Pathway of Hepatocytes from Natural Populations of Fundulus heteroclitus

“…Importantly, it is of high concentration in sediments and water from the Elizabeth River Superfund site (Vogelbein et al, 1990;Bozinovic and Oleksiak 2010) and thus relevant for investigating the Elizabeth River population. We also used the PCB congener, 3,3 ,4,4 ,5-pentachlorobiphenyl (PCB126) as a representative PCB.…”

Detecting genome-wide gene transcription profiles associated with high pollution burden in the critically endangered European eel

“…Such approaches have been used to explore transcriptomic responses in populations from polluted environments and have identified sets of candidate genes and loci that appear biologically important in response to pollution (Hoffmann and Willi, 2008;Bozinovic and Oleksiak, 2010). Understanding the effects of chronic exposure to environmental pollutants on the transcriptome is crucial to safeguard the adaptive potential of natural populations under heavy anthropogenic pressure (Cheung and Spielman, 2002;Hoffmann and Willi, 2008;Oleksiak, 2008).…”

Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel

“…Genome-scale approaches have the potential for identifying genes and genetic networks that underlie ecologically important traits, such as those linked to adaptation to cold temperatures [5], defense mechanisms [6] or response to pollutants [7,8]. Changes in gene expression can be linked to phenotypic and environmental variation, hence advancing our understanding of the adaptive importance of gene functions and their ecological and evolutionary consequences [9].…”