7 Genomic Approaches in Aquaculture and Fisheries
263
but in the first place selection is identified at specific genomic sites, where crucial
genes or gene complexes are lodged. It provides great promise for understanding
the genomic imprint of man’s actions, such as “fishing down the food web” (Pauly
et al. 1998), for modifications to the trophic cascade (Scheffer et al. 2005), and for
defining biologically meaningful management units and marine protected areas. The
incorporation of genomics allows for realistic “genetic monitoring” of populations
as an integral part of fisheries management.
The analysis of phenotype in the natural environment was historically limited
to the morphotype and some ecophysiological traits. That picture is increasingly
complemented now by a well-documented transcriptome and proteome phenotype
in a number of species. This will aid to understand the functioning and evolution
of fish and their communities. Accordingly, understanding the function and origin
of an ecological adaptation has become feasible (Feder and Mitchell-Olds 2003).
Unfortunately, fully understanding those patterns remains a tedious process. The
bottleneck to fast progress is that information has to be collected from diverse
fields of research and put together in a comprehensive model framework. Still, these
novel insights will benefit the sustainable resource management of fisheries and the
optimisation of aquaculture.
Phenotype is a major focus in aquaculture, where animals ideally feature traits
of preference to the producers (e.g. low food conversion, high survival and long
shelf life) and consumers (e.g. shape, colour and taste). There are two main strategies to achieve this. First, animals can be selected through the well-established and
classical strategies of trait selection (most efficiently through some kind of family
selection). Genetic background information on relatedness, origin and diversity can
be incorporated to support breeding. Second, a genomics supported breeding strategy of marker-assisted selection may accelerate the domestication process. Here
molecular genetic information closely linked to genes of interest serves as selection
target. As most fish have a relatively short history of domestication, few traits have
been maximised for aquaculture production. Using markers linked to well characterised QTL should speed up the process of domestication. Understanding how
genes function and chromosome segments impact traits is high on the breeding
agenda, although few cases have reached the demonstration level in fish breeding
(A. Sonesson, personal communication).
Globalisation of the food market has raised concerns about food quality. Huge
efforts are devoted to monitoring the flow of animal products, including fish and
fisheries products, from “field to fork”. Customers look for certification of origin
and composition; traders and processors prefer guarantees of quality and ownership
(see Section 7.5). It is foreseen that routine monitoring and forensic applications
in fisheries will vastly expand. It involves a legal and organisational framework,
including sampling, genotyping, statistical analysis and interpretation. Genomics
will contribute to the increasing use of DNA based methods as it allows for the
simultaneous analysis of many samples for a high number of loci, and the identification of selected loci with elevated levels of genetic differentiation. So far no
genomic studies of GSI and traceability have been published for marine fish, but
genomics will revolutionise the field of fish forensics in the near future.
263
but in the first place selection is identified at specific genomic sites, where crucial
genes or gene complexes are lodged. It provides great promise for understanding
the genomic imprint of man’s actions, such as “fishing down the food web” (Pauly
et al. 1998), for modifications to the trophic cascade (Scheffer et al. 2005), and for
defining biologically meaningful management units and marine protected areas. The
incorporation of genomics allows for realistic “genetic monitoring” of populations
as an integral part of fisheries management.
The analysis of phenotype in the natural environment was historically limited
to the morphotype and some ecophysiological traits. That picture is increasingly
complemented now by a well-documented transcriptome and proteome phenotype
in a number of species. This will aid to understand the functioning and evolution
of fish and their communities. Accordingly, understanding the function and origin
of an ecological adaptation has become feasible (Feder and Mitchell-Olds 2003).
Unfortunately, fully understanding those patterns remains a tedious process. The
bottleneck to fast progress is that information has to be collected from diverse
fields of research and put together in a comprehensive model framework. Still, these
novel insights will benefit the sustainable resource management of fisheries and the
optimisation of aquaculture.
Phenotype is a major focus in aquaculture, where animals ideally feature traits
of preference to the producers (e.g. low food conversion, high survival and long
shelf life) and consumers (e.g. shape, colour and taste). There are two main strategies to achieve this. First, animals can be selected through the well-established and
classical strategies of trait selection (most efficiently through some kind of family
selection). Genetic background information on relatedness, origin and diversity can
be incorporated to support breeding. Second, a genomics supported breeding strategy of marker-assisted selection may accelerate the domestication process. Here
molecular genetic information closely linked to genes of interest serves as selection
target. As most fish have a relatively short history of domestication, few traits have
been maximised for aquaculture production. Using markers linked to well characterised QTL should speed up the process of domestication. Understanding how
genes function and chromosome segments impact traits is high on the breeding
agenda, although few cases have reached the demonstration level in fish breeding
(A. Sonesson, personal communication).
Globalisation of the food market has raised concerns about food quality. Huge
efforts are devoted to monitoring the flow of animal products, including fish and
fisheries products, from “field to fork”. Customers look for certification of origin
and composition; traders and processors prefer guarantees of quality and ownership
(see Section 7.5). It is foreseen that routine monitoring and forensic applications
in fisheries will vastly expand. It involves a legal and organisational framework,
including sampling, genotyping, statistical analysis and interpretation. Genomics
will contribute to the increasing use of DNA based methods as it allows for the
simultaneous analysis of many samples for a high number of loci, and the identification of selected loci with elevated levels of genetic differentiation. So far no
genomic studies of GSI and traceability have been published for marine fish, but
genomics will revolutionise the field of fish forensics in the near future.