Proceedings of the ASEM workshop on Domestication and Breeding,

Bangkok 16-18 May 2005.

Objectives of the Workshop:

1. To identify problem areas in the field of genetic management and improvement  of aquatic animals
2. To prioritize these problem areas
3. Discuss how the problems could be solved and develop an action-oriented agenda
4. Prioritize a set of recommendations as a base for future cooperative actions

Problem areas are to be discussed in the context of food security and sustainable economic development. This means thinking beyond technical issues to include such issues as societal constraints, historical preferences and future economic developments.

1. To identify problem areas in the field of genetic management and improvement of aquatic animals

The discussion was initiated by identifying major areas around which problems could be grouped. Three areas were identified, namely "Resource use", "Species tools and methods" and "Environmental and societal impact". Within each of these areas specific problems were identified.

Resource Use

• 1. In the context of the workshop, domestication was broadly defined as "a process whereby reproduction and further rearing becomes feasible under human control". Little is known of the effects of domestication of aquatic species on (loss of) genetic diversity. Domestication should be carried out with a view to conserving genetic diversity and across a range of culture system environments taking GxE interactions into account
• 2. There is a need for cooperation through consortia (eg. Universities and DoFs) to work with industry to apply selective breeding programs. The knowledge base concerning genetics of aquatic animals and the principles of selective breeding needs to be strengthened for both University and State sectors.
• 3. There is an urgent need for support services and means to improve understanding of selective breeding and population genetics to make the technologies more accessible and applicable.
• 4. There may, in circumstances where seed producers cannot be expected to play the major role in production of improved seed, be a need for centralized national seed production and management centers.
• 5. There are some species (e.g. those species difficult to breed or maintain in captivity or those in which domestic seed production is not economically feasible) in which aquaculture could be continued with sustainable harvest of wild caught seed. For such species there is a need for recommendations on utilization of wild stocks.

Species tools and methods

• 6. QTL (quantitative trait loci) are used in livestock mainly as marketing tools; there are not many examples of their effective use for improving traits (e.g. marbling in beef). Initial work with fish has yet to produce results. Few aquatic species have comprehensive genetic linkage maps. There are high density genetic linkage maps for zebrafish and medaka and medium density linkage maps are being developed for salmonids, tilapia, Japanese flounder, fugu and tetraodon. Fully sequenced genomes are available for fugu and tetraodon and are under development for zebrafish and medaka. High density genetic linkage maps should be developed for some additional commercially important species (e.g. shrimp).
• 7. There is a need to address the limitations imposed by the biology of some species (reproduction, physiology, disease control) to remove key constraints to domestication and genetic improvement. Geneticists, breeders (reproductive biologists) and veterinarians should collaborate in the early stages of domestication and research on captive breeding.
• 8. There is a need for the development and comparative analysis of more basic genetic management and selection protocols that can be used where the higher level breeding programs (e.g. those using pedigreed animals and BLUP-EBV) are not feasible due to resource limitations.
• 9. We need codes of practice for genetic management of domesticated stocks (e.g. for introduction of new species, stock transfers, domestication etc.)

Impact on environment

• 10. We do need more understanding of environmental impact of aquaculture on genetic diversity (both by exotic species and by "genetic pollution")
• 11. Genetic user restricted technology (GURT) can be applied to render genetically improved breeds infertile. There is a clear advantage to aquaculture of having 100% efficient GURTs to reduce the risk of crossbreeding of cultured exotic species/strains with native stocks and thus there is a demand for the development of these technologies. GURT reduces environmental impact of exotics and genetically improved strains and permit brand control and protection.
• 12. Restocking programs can be used for increasing aquatic production but there is a need to recognize the potential impacts on biodiversity caused by the genetic effects of domestication.
• 13. Live "gene" or "strain" banks and (cryopreserved) gamete banks should be fundamental to conserving genetic diversity, and additionally can provide reference material (e.g. for estimating genetic gains) and act as back ups for genetic improvement programs.
• 14. There is a need to develop genetic conservation protocols to enable safer exchange of genetic material through frozen sperm etc. Cryo-technologies need to be further adapted for fish (especially for new species) and better developed for crustaceans.

Impact on society

• 15. Genetically improved stock often does not reach the end user due to problems with dissemination. Over the years, several attempts have been made to distribute improved stock to farmers. There is a need for a critical review of successful and unsuccessful dissemination programs to better understand the issues involved.
• 16. There may be a need for development of certification programs for improved fish varieties, probably based on livestock industry approaches. However, to date there is no experience in this area in aquaculture. In order to asses the importance of the problem a review of the role certification strategies for livestock is needed.

2. Discussion and prioritization of problem areas.

The discussion of the problem areas made it clear that problems and priorities are different depending on the scale of the breeding operation and the stage of maturation of the industry. Therefore the prioritization of problems was devided up into three categories:

1:  Natural populations (restocking programs, impact of aquaculture and use of wild caught seed)

For many new species there are still reproductive bottlenecks which inhibit successful domestication. In other cases, cultural preferences and the scale of the market (local, regional) constrain the development of an aquaculture industry and dictate that animals are to be harvested from the wild. In both cases sustainable aquaculture relies on the appropriate utilization of wild caught broodstock or seed.  In some cases there is also a need to restock hatchery reared animals back into the natural environment.  Where domesticated stocks are used for this purpose there are important issues relating to the genetic pollution of wild stocks and potential loss of genetic diversity in the wild.  Escapes from aquaculture, which can occur in large numbers, can have smilar effects on natural populations.

2:  Small scale breeding operations

The majority of aquatic species in S-E Asia are farmed on a regional or national scale, and production levels are typically small. For these species there is little or no capital investment available to set up large scale sophisticated breeding programs and genetic management and improvement will thus rely on tailor made small-scale breeding programs. 

3:  Large scale breeding operations

Finally there are species which have an economic importance beyond the national or regional level. For these global commodity species, such as shrimp and tilapia, breeding is or is likely to be in the hands of a few specialized large companies. A large number of farmers directly or indirectly will rely on the success of these companies in genetically improving their seed stock in terms of growth rate, disease resistance and other economically relevant traits.

Based on these considerations it was decided that the problem areas would need to be reformulated and prioritized for each category. The workshop members formed three working groups to develop a set of recommendations for each category, which were then centrally discussed and fine-tuned. Prioritization was based on the consensus view from the workshop group and final weightings were set by specialists within each category. The recommendations are summarized below, for each category separately (natural populations, small scale aquaculture, large scale aquaculture).

3. Development of an action-oriented agenda

 "Natural Populations" (impact of Aquaculture, restocking programs and use of wild caught seed in aquaculture)

•1.        Support the establishment of restocking strategies including:

- Support and encourage ASEM members to initiate research on population biology of aquatic resources including the characterization of life cycles in relation to local environmental condition and the elucidation of stock structure using genetic markers.

- Support and encourage ASEM members to conduct socio-economical research on coastal communities to understand issues with candidates for restocking. Basic studies on the population structure, genetic variability and ecology of selected species are important.

•2.        Support to R&D on hatchery-technology to minimize possible impacts on biodiversity caused by using limited number of broodstock animals and genetic changes in hatchery reared stock. Support capacity-building in broodstock development of major aquatic species

•3.        Support the development of cooperative networks for exchange of information on trading and using wild caught seed. Promote the collaboration of scientists (geneticists, physiologist etc.) and breeders to improve culture methods and address constraints of current breeding practices. Disseminate available information on genetic variability of major species. (e.g. stock enhancement working group of FAO)

•4.        Promote and intensify research into new alternative resources to reduce pressure on traditional resources including the domestication of new candidate species. 

•5.        Recommendations of genetic protocols related to restocking should take into account the capabilities of the parties involved and where necessary include support to overcome resource constraints.

"Small-scale breeding operations"

1. Accessibility of selective breeding

Develop support services that will make the application of genetic technologies feasible in situations in which local capacity is a limiting factor.

1. Need for more basic breeding programs

Develop genetic improvement programs that can be implemented with limited resources and in the absence of individual identification, but that are scientifically sound and sustainable in the long term (i.e. for durations of 10 years or more).

1. Domestication environments and strain performance

Support the conduct of domestication of new species and of genetic improvement programs of cultured species in a range of logical environments in order to detect genotype by environment interactions in case they are important, and encourage the conduct of strain evaluations of cultured species in a range of environments, by an independent body or organization.

1. Genetics taken into account in domestication

Encourage the involvement of geneticists in the initial stages of domestication, specifically in using strategies that avoid subjecting the population to bottlenecks that may result in reduced genetic variability.

1. Cooperation and knowledge base

Support capacity building activities such as conduct of training programs in genetics (population, quantitative, molecular), development of manuals and software on the theory and practice of genetics applied to aquatic animal improvement, the development of data base information on resource groups and persons in different areas, and the establishment of networks of relevant subject matter areas.  Practically, the strengthening and broadening of services provided by existing networks such as NACA or INGA could be contemplated.  Typical services would be the provision of a discussion forum in which users could post questions and get answers, or the listing of useful linked sites on the subject.

1. Need for structured seed production

Support the development of structured and technically regulated seed production that will capitalize on the genetic improvement made in breeding centers. This will prevent genetic deterioration of the improved stock, and will enable effective and equitable dissemination of high quality seed of the superior genetic material.

1. Need for review of case studies of dissemination of improved stock

Encourage the conduct of studies documenting and evaluating the success or failure of different cases of dissemination of newly developed and improved strains, when possible to the point of assessing impact at the farmer and consumer level.  Studies need to be conducted at different levels, namely, national or regional depending on the particular circumstances.  Information thus generated will converge to a common platform from where it will be readily available.  This will provide a fruitful field of multidisciplinary work between aquaculturists and socio-economists.

1. Environmental impact

Encourage the conduct of environmental impact studies related to the development and deployment of genetically improved strains of aquatic animals.

1. Use of sperm cryopreservation

Encourage the development of sperm cryopreservation protocols and use of frozen sperm for conservation, insurance, strain dissemination and estimation of genetic change purposes.

 "Large scale breeding operations"

1. Central or regional facilities

Central/regional facilities should be set up in ASEM countries (see the example of National Broodstock Centers in Vietnam) and used to implement codes of good practice, including breeding, genetic improvement, biosafety and water management. These facilities could serve also as back up, through live or cryopreserved "gene" and gamete banks, to the public and private sector.  They should also serve as training centres for all the above areas, including advanced breeding methods.

1. R&D efforts addressing persisting biological constraints to improve current technologies

There is a need to address the limitations imposed by the biology of some species (e.g. reproduction, physiology and disease control) to remove key constraints to genetic improvements. Geneticists, breeders (reproductive biologists) and veterinarians should collaborate in the early stages of domestication and research on captive breeding.

Specific target areas are:

• - P. monodon

reproduction and nutrition in captivity; gamete preservation.

• - O. niloticus

Increased fillet yield, salt and stress tolerance; Synchronization of spawning; Hormone-free production technology.

1. The need for quarantine facilities

For some of the species (e.g. shrimp) it is desirable to set up national or regional quarantine facilities. They should be built by the government and they could be operated as commercial facilities.

1. R&D for the generation and/or improvement of genetic linkage maps

Efforts should be directed at the development of a medium (at least) density genetic linkage map for all aquaculture species used at large scale breeding operations. Such maps are essential for identification of genes coding for important monogenic traits and for QTL searches as well.

For those species, where the genetic linkage map is not available, the best option is comparative genomics, especially in case of finfish, where several medium to high density linkage maps (e.g. zebrafish, medaka, salmonids, etc.), as well as fully sequenced (Japanese fugu, Tetraodon) or partially sequenced genomes (zebrafish and medaka) are available in the public domain. These two approaches should also be extended to some of the invertebrate species such as Artemia, which is used as live feed in large scale breeding operations but for which the strains are not characterized or selected. The potential for Artemia to be used as a Crustacean model organism should be explored

1. Genome Projects

It is desirable to initiate genome projects for some of the most important species depending on their economical importance and evolutionary position. They could be initiated similarly to the mapping efforts, however due to their high cost they would need the support of international grant agencies and research community. One such forming project is the Shrimp Genome Project, which is aiming to sequence fully the genome of Penaeus species.

1. Environmental Impact Assessment (EIA) studies

More research is needed on the environmental impact of aquaculture on the genetic diversity of natural populations. Such studies should be conducted in parallel on the potential effects of introduced exotic species and "genetic pollution" caused by farmed strains. They should be performed by specialized academic institutions from international or state-financed grants.

1. R&D on GURT technologies

The possibility of "genetic pollution" caused by the farms should be minimized. GURT technologies leading to sterility of marketed specimen or restricting their viability to special conditions (e.g. dependence on certain amino acids) should be developed.

Since such technologies would provide clear advantages to the companies running large scale breeding programs, we propose that private companies should tightly collaborate with academic institutions to work out potential solutions.

1. Certification program

A certification program which includes independent assessment of the health and performance of genetically improved strains should be set up in every ASEM country by the government, using examples from the livestock industry.