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Intensive aquaculture of Atlantic cod is fast developing in both Northern Europe and Canada. The last six years have seen major improvements in the larval rearing protocols and husbandry techniques for this species. Although breeding programmes are currently being developed by both governmental and private institutions in the main cod producing countries (i.e. Norway, Iceland and Canada), most hatcheries still rely on the mass spawning of their own broodstock. Mass spawning tanks are complex systems where fish are left to spawn naturally and fertilised eggs are collected with the overflowing water, with little or no control over the matings of the animals. Few published studies in other commercial marine species (i.e. turbot and sole) have attempted to analyse the output from such systems using microsatellite markers and several parentage analysis software programs. A review of these publications exposed a lack of consistency in the methods used to analyse such complex datasets. This problem was addressed by carrying out a detailed comparison of two analytical principals (i.e. assignment by strict exclusion and assignment by probabilities) and four parentage software programmes (i.e. FAP, VITASSIGN, CERVUS and PAPA), using the DNA profiles, at 5 loci, from 300 cod fry issued from the mass spawning of a large hatchery cod broodstock tank (consisting of 99 fish). This study revealed large discrepancies in the allocation outcomes between exclusion-based and probability-based assignments caused by the important rate of typing errors present in the dataset. Out of the four softwares tested, FAP (Taggart, 2007) was the most appropriate to use for handling such a dataset. It combined the most conservative method of assignment with the most informative output for the results displayed. In an attempt to study the breeding dynamics in a cod commercial hatchery, parental contributions to five groups of 300 fry (from five single days of spawning and from two commercial mass spawning cod tanks) were analysed, based on the genotyping data from eight loci. The parentage results from the exclusion-based analyses revealed that, on a single day, at least 25 to 30% of the total breeding population contributed to fertilised eggs that resulted in viable offspring at 50 and 83 days post-hatch. Family representations were highly skewed - with the marked dominance of a few males - and effective breeding populations were consistently low (approx. 5% of the total breeding population). Parental contribution to a group of 960 codlings - produced following intensive commercial practices (i.e. including successive size gradings and mixing of batches) and belonging to a single graded group - was also analysed, based on the genotyping data from eleven loci. The effective breeding population size of the juvenile batch (c. 14% of the total broodstock population) was two to three times greater than the effective size observed on a single day of mass spawning. The per-generation rate of inbreeding was however relatively high, for this batch alone, at 2.5%. Based on these results, suggestions were made to manage hatchery cod broodstock populations and implement genetic selection. Early maturation of farmed cod in sea cages (at two or three years old) is a major concern for ongrowers. Understanding the mechanism(s) behind sex determination in cod would probably help the development of a method to control sexual maturation. In an attempt to elucidate sex determination in cod, a protocol to induce gynogenesis was developed. Gynogenetic fish were successfully produced by irradiating cod milt with UV and applying a cold shock (at -6oC) to newly fertilised eggs. However, due to poor survival during larval rearing, only one gynogenetic fish survived long enough to be sexed; not enough to conclude anything on the sex determination mechanism(s) in cod.

This report addresses the problem: how to improve approaches to fish seed production in smallholder aquaculture systems of Northeast Thailand? The work was carried out as a component of the U.K. Government Department for International Development Aquaculture Research Programme funded project, R7052: Improving freshwater fish seed supply and performance in smallholder aquaculture systems in Asia. From 1997 to 2003 the project worked in collaboration with regional partners in Bangladesh, Laos P.D.R., Thailand and Vietnam on constraints to seed production and distribution. The research problem called for improvement, implying that change was required in the way that seed was produced. The hypothesis that active collaboration in research by seed producers and institutional partners, facilitated by project staff would enable all participants to extend their understanding of the situation, contribute to the knowledge base and that resulting accommodations would lead to a continuous process of planning, action and reflection toward changes required for improvement. Reflection on the project outputs indicated that quality of fish seed was variable but there was no agreement on the nature of the problem among stakeholders. The decision was made to shift the research focus away from looking for technical problems and to focus instead on examining ways that existing knowledge could be integrated in a learning process with key stakeholders. The research problem then became to find an appropriate, effective and efficient methodology to achieve this; participatory action research was chosen for evaluation. Participatory action research is a collaborative approach involving the researcher in a facilitative role working with stakeholder groups to enable systematic investigation of issues, planning and action to resolve the issues. Outcomes should be action and public knowledge that feed in to further reflection and action in an ongoing learning cycle. Implementation of the methodology was carried out over two stages; the first planned set of activities involved extension of the existing collaborative arrangement with the Thai Government Department of Fisheries (DoF) and the Asian Institute of Technology Aqua Outreach Programme (AOP) in order to prepare a field research team and plan for field activities. The second stage was participatory action research field work which involved invitations to collaborate being extended to four formal groups and one informal group of hatchery operators in two Provinces of Northeast Thailand. Research facilitated by the research team used a range of participatory methods for identification and prioritisation issues, analysis, action planning, monitoring and evaluation. Actions were supported by the project logistically and financially. The exploratory approach to project planning meant that monitoring processes was as important as monitoring specific indicators. The output of the first set of activities was a formal agreement to collaborate however the strength of the collaboration was indicated by the low level of commitment shown by the DoF and AOP representatives in planning and team building. The lack of commitment had important implications for impact and sustainability of the research. Greater attention to the partnership process was an important lesson. Four of the hatchery operators’ groups approached accepted the invitation to collaborate with the project. This collaboration resulted in a range of knowledge outcomes, the development of social relations horizontally within the hatchery groups and vertically to include individuals from service providing agencies in the local administration. Participatory evaluation by participants and the DoF partners was positive. Evaluation of the project indicated that the approach was; appropriate in terms of the needs of primary stakeholders, the requirements of the donor and the circumstances under which it was carried out; effective in achieving knowledge outcomes that contributed to gains in livelihood assets for participants but ineffective in influencing the policies, institutions and processes that would have ensured sustainable impact from the collaboration as a result of the shortcomings in the institutional partnership arrangements; efficient in terms of resource use to obtain outputs and also in emergence of lessons to inform future practice.