**6. Conclusion**

140 Aquaculture

Salmoniformes or the Gadiformes. However, work on the genomes of Atlantic salmon (Davidson et al., 2010) and Atlantic cod (Johansen et al., 2009) is in progress, and the results are eagerly anticipated by the aquaculture community that breeds these and related species.

The availability of a complete genome sequence for Atlantic salmon will have a major impact on all sectors of the international salmonid community. For the aquaculture industry it will provide a complete suite of genetic markers for the identification of the genes and alleles responsible for production traits. Companies will be able to develop tailored broodstock using nucleotide or allele assisted selection rather than the more general marker assisted selection. In conjunction with traditional breeding practices, this approach promises rapid gains that will make companies who embrace this technology

The conventional approach to sequencing whole genomes is to break the genome into small parts, and sequence each part using Sanger sequencing (reviewed in Hutchison, 2007). Although this approach remains the gold standard for sequence and assembly quality, limitations with respect to cost, labor-intensiveness and speed have fueled the demand for new approaches to DNA sequencing. In recent years, several novel high-throughput sequencing platforms, or 'next generation' sequencing approaches have entered the market (for a review, see Metzker, 2010). Most of these are targeted to the goal of re-sequencing an entire human genome for <\$1,000, and their capabilities with respect to sequencing whole genomes *de novo* (i.e., for the first time, and without a reference sequence for comparative assembly), remain unknown. This is complicated by the diverse, highly repetitive and overall complex nature of the fish genomes given that, these technologies are currently limited by their sequence read lengths and difficulties with specific types of repetitive sequences. Generally, the next generation sequencing platforms are capable of producing vast amounts of sequence data in very short periods of time for significantly lower cost than traditional Sanger sequencing, but the bottleneck lies in developing the computational tools to handle the data, and ultimately, to assemble the short sequence reads into contiguous (gap-free) stretches of DNA sequence when no reference genome is available (Quinn et al.,

Aside from their potential contribution to whole genome sequencing, next generation sequencing technologies have countless implications for genomics. One of the most common uses for next generation sequencing in human genomics is re-sequencing, i.e., sequencing the genomes of individuals for which there is a full reference sequence. This could be applied to aquaculture to look for allelic variations between individuals of the same species that show differences in characteristics of interest (e.g., disease resistance or growth). Similarly, next generation sequencing has been used for "transcriptome sequencing" (also referred to as "transcriptomics") i.e., sequencing the entire repertoire of transcribed RNA of a species. This is a form of expression profiling, as the relative number of transcripts of genes can be compared against one another, thus providing insight into the expression

**5. Role of whole genome sequencing (WGS) in genomics** 

**5.2 Methods and approaches to whole genome sequencing** 

**5.1 Benefits of whole genome sequences** 

more competitive.

2008).

Genomics has become an increasingly powerful field with far-reaching implications from medicine to pharmacology to industry to ecology. When applied to aquaculture, genomics has vast potential to improve factors such as production, efficiency, animal welfare, sustainability, reducing inbreeding, and increasing the profitability of the industry. The current genomics tools for fish, and specifically for aquaculture species, have already enabled drastic improvements to characteristics such as growth and disease resistance, and show great promise for future developments; however, their utility remains limited by the lack of whole genome sequences for a few key species, which could provide reference sequences for other aquaculture species. As these sequences, particularly those of Atlantic salmon, rainbow trout and Atlantic cod, become available over the next several years, which will certainly correspond to further advances in technology and computational tools, the potential for genomics to facilitate major developments in aquaculture is enormous.
