02 Stock Improvement
The long-term future of the Scottish aquaculture will rely on the timely supply of high quality seed (eggs, fry, smolts, spat) with the traits/characteristics that match the changing requirements of the production, processing and retail sectors. In terrestrial livestock there have been enormous improvements in the performance of chickens, pigs and dairy cattle by the application of pedigree breeding ( i.e. breeding using family information and statistical prediction of performance). This allows efficient breeding for improved performance and the application of new genomic methods. In the major aquaculture species in Scotland pedigree breeding is only used for Atlantic salmon. In the other species of interest in Scotland (cod, halibut, rainbow trout and shellfish), pedigree breeding is not used or is at a very early stage of development and probably not targeted specifically at traits of importance to Scottish industry/conditions. The quality of seed for the industry can also be improved through one-off manipulations in the hatcheries that enable improved strains to achieve their full potential. Environmental manipulation of light, temperature and water chemistry ensures the correct development and timing of the life-cycle of the farmed fish to match the production requirements. The production of single-sex or sterile animals may result in improvements in productivity and could reduce issues related to escapes and welfare. There are however, issues of quality which may need to be addressed. For Scotland to become a global centre for aquaculture the industry will need access to strains that are selected for yield and quality traits and that perform well under Scottish conditions.
Selective improvement has been practiced for millennia by farmers but it is only in the last 30 years, with our increased understanding of genetics, that scientifically based breeding programmes in terrestrial livestock have shown enormous improvements in production (growth performance in broiler chickens >300%). Aquatic species still lag well behind in their potential performance because of the short period of domestication associated with this important animal production system. However, selective improvement in aquatic organisms can be rapid because of the higher selective pressure possible, the greater genetic diversity and the larger family sizes. Increases in growth rate of 100% or more have been seen in in several fish species, including salmon, within 5-6 generations of selection. Atlantic salmon is still the only farmed fish species globally for which virtually all production is based on fish originating from breeding programs, although these will have been running for no more than 10 generations.
The lag in applying selective breeding to other fish species was mainly a result of them having more complicated breeding and early life-cycles that did not lend themselves to the approach used in salmon. However, in the last ten years the rapid development of new and ever more powerful and cost-effective genetic fingerprinting and DNA sequencing techniques has enabled pedigree assignment in many new marine species with complicated larval development, when combined with individual fish ( RFID) tagging systems, has enabled bespoke broodstock management and genetic improvement to be adopted in a wide range of other new and less tractable fish and shellfish species. The rate of technological change in genetics and genomics means that we can now look at many individuals in great detail and identify those with the greatest possible breeding value for a number of commercially important traits. At this stage in the development of the industry growth performance and disease resistance are high priorities but in the future traits related to yield, flesh quality and improved food conversion and retention of nutrients will become important. These are much more difficult and expensive traits to identify and select for because many require the animal to be killed before they can be assessed.
However, developments in functional genomics over the last decade enables us to describe how sequence information can be used to define the heritability and the functioning of genes associated with commercial traits. We now have access to draft genomes for Atlantic salmon and rainbow trout (became available during 2011), which has directly led to improved tools for identifying the genetic basis for performance differences between individuals in production traits. When genomics is undertaken in collaboration with pedigree breeding programmes accurate estimates of the performance differences between different genotypes for the genes that control an individual trait can be assessed. In subsequent generations selection can be based on the presence or absence of a given marker for the trait rather than having to kill or challenge fish to assess the trait as done at present. This has enabled a Marker Assisted Selection ( MAS) approach to be used for some traits ( IPN resistance, muscle yield), so speeding up the rate of improvement in these species. We still do not have full genome sequence or good high definition genetic maps for most farmed Scottish species, sequencing and mapping should be a priority activity as new Next Generation Sequencing technologies now makes this quick and cost effective so we can apply these methodologies across all species. New sequencing technologies have been the cornerstone to many of the new methods, but with such as vast amount of information being generated there is also a need to ensure maximal information can be retrieved. It is essential to develop the bioinformatics capacity - the computational analysis of sequence data and integrating this with phenotypic data - in parallel with the genetic improvement and genomics. We also need to develop new scanning technologies for non-destructive analysis of phenotypic parameters ( e.g. CT scanning for fillet and conformation) to speed up trait identification and selection.
Genomics does not only address breeding potential, but also how the genes are expressed and translated into proteins. Transcriptomics, which examines the expression of tens of thousands of genes in parallel, can reveal how individual fish respond to factors such as disease, nutrition, sexual maturation and environmental changes. It is now recognised that the environment under which an organism develops can have a long-term impact on individual's and its offspring subsequent performance. With a better understanding of these epigenetic effects it should be possible, by manipulating the environment, to programme the fish to maximize their performance under a range of different production environments.
The genetic potential of the fish is of little significance if it cannot be produced when and in the quantities and with the qualities the industry requires. Stock management strategies must be developed to first ensure timely and predictable production of optimal quality eggs and second control sexual maturation of farmed stocks. This involves the development and implementation of environmental regimes to manipulate broodstock spawning and hormonal therapies when required in species either not spawning spontaneously or to meet requirements for a selection program ( e.g. milt volume). While protocols exist in species already established and domesticated to some degree for aquaculture ( e.g. salmon, trout, tilapia), broodstock spawning remains one of the main bottlenecks in most emerging or new candidate species. There is therefore a need to develop such protocols based on basic understanding of reproductive physiology and environmental perception.
Strategies to control sexual reproduction of farmed stock include photoperiodic manipulation as routinely done in salmon ongrowing, sterilisation through triploidy as commercially done in rainbow trout and oyster (under experimentation in salmon), mono-sexing as done in trout, tilapia and recently halibut, and selection although the latter is longer term in species where no selective breeding program has been established yet. Importantly, the control of sex and reproduction is relevant to all aquaculture species. The reproductive containment of fish stock can increase productivity through enhanced growth (energy put towards somatic growth rather than gonad) and flesh quality, reduce downgrading at processing, protect wild stock from potential interbreeding and overall improve fish welfare. All of the above requires fundamental research to better understand light perception and biological efficiency, sex determination systems and ploidy impact on quantitative genetics and gene expression. New means of sterility should also be studied ( e.g. vaccination, PGCs and GnRH inactivation, gene silencing technologies).
This brief outline suggests how the stock used in Scottish aquaculture will need to be managed if the industry is to compete on quality and performance in the global marketplace.