7 Genomic Approaches in Aquaculture and Fisheries
215
Despite the enormous, worldwide development of aquaculture in the last decade,
the application of genomics to aquaculture remains poorly exploited. Improving
state-of-the-art genomics research in various aquaculture systems, and its industrial
applications remain major challenges and must be the focus of the next generation
of projects. This chapter will discuss the application of genomic approaches to the
improvement of fish and shellfish aquaculture, including the evaluation of stock
diversity and the use of selection procedures. The chapter will also discuss the use
of genomic methods to study and monitor natural fish and shellfish populations and
to understand interactions within their ecosystems (Fig. 7.1).
7.2 Genomic Tools and Resources
In this section, available (or soon-to-be available) tools for structural and functional
genomics in marine fish and shellfish will be described. As the reader will note, most
of these tools have been developed for farmed or fished species. One obvious reason for this limitation is the fact that the development of genomic tools requires
a relevant economic investment, which has been possible so far only for commercially important species and model species. However, the introduction of new
technologies, e.g. ultra high-throughput DNA sequencing (Margulies et al. 2005),
has dramatically lowered the costs of EST production, generation of BAC clones,
and whole-genome sequencing, therefore more and more marine fish and shellfish
species are expected to enter the genomic arena.
7.2.1 Genetic Linkage Maps
Historically, the first portrait of an animal genome was obtained in the form of a
genetic linkage map. Any polymorphic locus, i.e. a locus where at least two distinguishable alleles are observed, can be positioned on a genetic map (Fig. 7.2). In the
last 30 years, different types of markers have been successively used: allozymes,
minisatellites, RAPDs (Random Amplification of Polymorphic DNAs), AFLP
(Amplified Fragment Length Polymorphisms), SSRs (Simple Sequence Repeats)
and SNPs (Single-Nucleotide Polymorphisms) (Schlötterer 2004; see Glossary and
Chapter 3 for detailed explanations about these markers). Allozyme markers have
been widely used as they are highly polymorphic in most species, especially bivalve
shellfish (Solé-Cava and Thorpe 1991). They have permitted a large number of population genetic studies and are still used, notably in combination with other types
of markers (e.g. Nikula et al. 2008). Heterozygote deficiencies and relationships
between their heterozygosity and fitness-related traits have been frequently observed
in wild or farmed populations using these markers (Raymond et al. 1997, Bierne
et al. 2000). Consequently, the non-neutrality of allozyme markers has been strongly
debated in bivalves (e.g. McDonald et al. 1996).
To date, most markers are based on DNA technologies. At present, the most
popular types are the microsatellites, also known as SSR loci. SSR loci consist of
215
Despite the enormous, worldwide development of aquaculture in the last decade,
the application of genomics to aquaculture remains poorly exploited. Improving
state-of-the-art genomics research in various aquaculture systems, and its industrial
applications remain major challenges and must be the focus of the next generation
of projects. This chapter will discuss the application of genomic approaches to the
improvement of fish and shellfish aquaculture, including the evaluation of stock
diversity and the use of selection procedures. The chapter will also discuss the use
of genomic methods to study and monitor natural fish and shellfish populations and
to understand interactions within their ecosystems (Fig. 7.1).
7.2 Genomic Tools and Resources
In this section, available (or soon-to-be available) tools for structural and functional
genomics in marine fish and shellfish will be described. As the reader will note, most
of these tools have been developed for farmed or fished species. One obvious reason for this limitation is the fact that the development of genomic tools requires
a relevant economic investment, which has been possible so far only for commercially important species and model species. However, the introduction of new
technologies, e.g. ultra high-throughput DNA sequencing (Margulies et al. 2005),
has dramatically lowered the costs of EST production, generation of BAC clones,
and whole-genome sequencing, therefore more and more marine fish and shellfish
species are expected to enter the genomic arena.
7.2.1 Genetic Linkage Maps
Historically, the first portrait of an animal genome was obtained in the form of a
genetic linkage map. Any polymorphic locus, i.e. a locus where at least two distinguishable alleles are observed, can be positioned on a genetic map (Fig. 7.2). In the
last 30 years, different types of markers have been successively used: allozymes,
minisatellites, RAPDs (Random Amplification of Polymorphic DNAs), AFLP
(Amplified Fragment Length Polymorphisms), SSRs (Simple Sequence Repeats)
and SNPs (Single-Nucleotide Polymorphisms) (Schlötterer 2004; see Glossary and
Chapter 3 for detailed explanations about these markers). Allozyme markers have
been widely used as they are highly polymorphic in most species, especially bivalve
shellfish (Solé-Cava and Thorpe 1991). They have permitted a large number of population genetic studies and are still used, notably in combination with other types
of markers (e.g. Nikula et al. 2008). Heterozygote deficiencies and relationships
between their heterozygosity and fitness-related traits have been frequently observed
in wild or farmed populations using these markers (Raymond et al. 1997, Bierne
et al. 2000). Consequently, the non-neutrality of allozyme markers has been strongly
debated in bivalves (e.g. McDonald et al. 1996).
To date, most markers are based on DNA technologies. At present, the most
popular types are the microsatellites, also known as SSR loci. SSR loci consist of