Genomics and Genome Sequencing: Benefits for Finfish Aquaculture

Introduction 1.1 What is genomics?The central dogma of molecular biology states that DNA is transcribed to RNA, which is translated into proteins (Crick, 1970), the molecules that facilitate all biological functions.A genome comprises all of an organism's DNA, or hereditary information.The field of genomics is the study of whole genomes.Genomics has been defined as "a branch of biotechnology concerned with applying the techniques of genetics and molecular biology to the genetic mapping and DNA sequencing of sets of genes or the complete genomes of selected organisms" (Mirriam-Webster Dictionary).Specifically, whereas genetics is the study of a single gene, or a few genes in isolation, genomics examines all of the genes, as well as the non-coding elements (i.e., regions that do not encode proteins or RNA components of the cell), within the DNA of a genome.Although the term genomics was first used in 1987, the field is relatively new and is growing rapidly as new technologies for exploring genomes emerge.The applications of genomics are vast, spanning realms such as medicine, industry and ecology, with implications for global issues including cancer diagnosis, prevention and treatment, alternative energy sources, agriculture, conservation and sustainable development.Furthermore, given that the fundamental basis of genomics DNAis common across all living organisms, genomics stands to bridge the gaps between these fields of study, with synergistic results as multi-disciplinary approaches to answering biological questions are developed. Genomics in aquaculture: Phenotypic vs. genotypic selectionIn traditional selective breeding practices, individuals showing desirable phenotypic, or visible characteristics are bred to produce new strains of plants or animals that exhibit features such as faster growth, greater size, increased overall robustness, or improved aesthetic appeal.Farmers, through thousands of years of following the mantra "breed the best to the best and hope for the best" (quotation attributed to American Thoroughbred and www.intechopen.com Atlantic salmon: A model aquaculture species for MASThe holy grail of any genomics program for a species is a whole genome sequence that is well assembled and annotated.The advantages of this are many, and are discussed in further detail in subsequent sections, but are mainly centered around two things: 1) the www.intechopen.comGenomics and Genome Sequencing: Benefits for Finfish Aquaculture 129 w e a l t h o f d a t a t h a t i s p r o d u c e d , i n c l u d i n g the full gene repertoire with additional information such as gene location and copy number, and 2) the ability of the sequenced genome to act as a reference genome, both for the sequenced species itself (i.e., such that the genomes of additional individuals can be easily re-sequenced using the original as a reference for assembly), as well as to provide information for other, closely related species.Currently, however, even with the great advances in sequencing technology that have come to light in recent years, obtaining a whole genome sequence remains an extremely difficult, costly and time-consuming undertaking.This is particularly true for fish species simply due to the evolutionary age of fish and the more than 20,000 extant species (Nelson, 2006), factors that make the fish genomes diverse and complex and complicate sequencing.Indeed, only five fish genomes have been reported to date (medaka, Oryzias latipes; tiger pufferfish, Takifugu rubripes; green spotted pufferfish, Tetraodon nigriviridis; zebrafish, Danio rerio and stickleback, Gasterosteus aculeatus), although more are underway.Their sequences, as well as those for the sequenced genomes of other organisms are publically available within the Ensembl database (www.ensembl.org).These fish species were chosen for their abilities to act as model sequences for genetics research, rather than for their utility for aquaculture.Specifically, the medaka and zebrafish genomes were sequenced to provide model organisms for studying developmental biology, while the stickleback genome serves as a model for studying adaptive evolution, and the two pufferfish represent the smallest known vertebrate genomes.Figure 1 illustrates the phylogenetic relationships among these species as well as some key aquaculture species, and shows that the full spectrum of teleosts is not represented by the genome sequences that are currently available. Ensembl Genome Browser: A joint project between EMBL-EBI and the Wellcome TrustSanger Institute to develop a software system that produces and maintains automatic annotation on selected eukaryotic genomes (www.ensembl.org).EST: Expressed sequence tag, which is a short sequence obtained from one shot sequencing of cDNA, corresponding to a fragment (~500 bp) of an expressed gene.Gene: Name given to stretches of DNA that code for a specific protein for a specific characteristic or function.It represents the heredity unit in living organisms. Gene Expression Omibus (GEO):A database repository of high-throughput gene expression data and hybridization arrays, chips and microarrays. Generation time:The average interval between the birth of an individual and the birth of its offspring.Genome: Is the entirety of an organism's hereditary information.It is encoded either in DNA or RNA (some viruses).Genomics: Discipline in genetics concerning the study of the genomes of organisms. Genotype:The total set of alleles possessed by an organism that determines a specific characteristic or trait.It comprises the entire complex of genes inherited from both parents.Heritability: Proportion of phenotypic variation in a population that is due to genetic variation between individuals.High-throughput: Processes usually performed via increased levels of automation and robotics.In sequencing: involves the application of rapid sequencing technology at the scale of whole genomes.Locus: (pl.loci) Specific location of a gene or DNA sequence on a chromosome. Marker-assisted selection (MAS):The use of DNA markers linked to traits of interest to assist in the selection of individuals for breeding purposes.Molecular marker: Specific fragments of DNA that can be identified within the whole genome.These can be associated with the position of a particular gene or the inheritance of a particular characteristic.Molecular pathway: Series of molecular processes that are connected by their intermediates such that the products of one process may trigger or participate in the other. Morphology:The visible form and structure of living organisms.mRNA: Molecule of RNA encoding a specific protein product.mRNA is transcribed from a DNA template in the cell nucleus then moves to the cytoplasm where it is translated by the ribosomes. NCBI:The National Center for Biotechnology Information, which houses the world's biggest sequence datasets in GenBank and an index of biomedical research articles in PubMed. Non-coding:Components of an organism's genome (DNA sequences) that do not encode for protein sequences.www.intechopen.