Sustainable aquaculture and aquatic resources management

Proceedings of the Expert Consultation on Genetic Erosion Risk Analysis for Shrimp Diseases in Asia

Published: 27/1/2014 | 3177 views

Shrimp aquaculture in tropical regions is facing a disease-induced catastrophe of lost production.  It is estimated that more than 40% of tropical shrimp production is lost to disease annually. The devastating impacts of disease on lost incomes, livelihoods, increased operational costs, trade restrictions and loss of consumer confidence has been a subject of many consultations and policy dialogues.  Discussions of disease crisis have to date been largely focused on identification of pathogens, guidelines and standards for disease detection and surveillance, regulations to limit trans-boundary movement of animals, and adoption of better management practices. 

There is reason to believe that current broodstock management practices may induce genetic erosion that increases susceptibility to disease and vulnerability to epizootics:

  1. Broodstock management as it is currently conducted in SE Asia, particularly by secondary and small-scale hatcheries, is likely to cause rapid accumulation of inbreeding and loss of genetic diversity ("genetic erosion") at farm level;
  2. Inbreeding increases susceptibility to diseases and lowers the threshold for the outbreak of epidemics. This effect may be especially strong in shrimps;
  3. Separately from its correlation with inbreeding, declining genetic diversity also increases the incidence of epizootics (the monoculture effect) and impedes the ability to adapt to stressful environments and changing climate;
  4. These epidemiological effects of climate stress and inbreeding are likely to be multiplicative;
  5. The possible role of genetic erosion in the incidence and prevalence of diseases and epizootics are not included in current discussions of the disease problem in tropical aquaculture.

The basic tenet for this Expert Consultation is that an important aggravating factor in the disease crisis is an agro-economic system that locks shrimp breeders, hatcheries and farmers into behaviour that induces high levels of inbreeding.  If inbreeding does increase the severity and frequency of epidemics, this disease crisis will only get worse over vast areas of Asia, Central and South America, Africa and the Middle East until  it is addressed.

This Expert Consultation was organized in conjunction with the annual meeting of the NACA Aquatic Animal Health Advisory Group (NACA-AG) to take advantage of the physical presence and expertise of a small group of world renowned Aquatic Animal Health experts from several national and international institutions. The list of participants and workshop agenda are presented in Annexes 1 and 2.  This consultation is perhaps the first of its kind to bring together a balanced group of experts from diverse fields – epidemiology, microbiology, disease diagnostics & surveillance, aquaculture genetics, fish breeding, and evolutionary biology – to take a fresh, in-depth, and wider perspective on the possible interaction between genetic side-effects of broodstock management and the looming threat of aquatic animal diseases, in particular the contemporary shrimp disease crisis. 

Part 1: Manual on Application of Molecular Tools in Aquaculture and Inland Fisheries Management

Published: 9/3/2007 | 8821 views
PART I: Conceptual basis of population genetic approaches

The aim of this manual is to provide a comprehensive practical tool for the generation and analysis of genetic data for subsequent application in aquatic resources management in relation to genetic stock identification in inland fisheries and aquaculture.

The material only covers general background on genetics in relation to aquaculture and fisheries resource management, the techniques and relevant methods of data analysis that are commonly used to address questions relating to genetic resource characterisation and population genetic analyses. No attempt is made to include applications of genetic improvement techniques e.g. selective breeding or producing genetically modified organisms (GMOs). The manual includes two stand-alone parts:

Part 1 : Conceptual basis of population genetic approaches: will provide a basic foundation on genetics in general, and concepts of population genetics. Issues on the choices of molecular markers and project design are also discussed.

Part 2 : Laboratory protocols, data management and analysis: will provide step-by-step protocols of the most commonly used molecular genetic techniques utilised in population genetics and systematic studies. In addition, a brief discussion and explanation of how these data are managed and analysed is also included.

This manual is expected to enable NACA member country personnel to be trained to undertake molecular genetic studies in their own institutions, and as such is aimed at middle and higher level technical grades. The manual can also provide useful teaching material for specialised advanced level university courses in the region and postgraduate students. The manual has gone through two development/improvement stages. The initial material was tested at a regional workshop and at the second stage feedback from participants was used to improve the contents.

Please note that Part II of this manual is also available for download.

Part 2: Manual on Application of Molecular Tools in Aquaculture and Inland Fisheries Management

Published: 9/3/2007 | 6020 views
PART 2: Laboratory protocols and data analysis

This is the second part of the manual, ?Application of molecular genetic techniques in aquaculture and inland fisheries management?. The major aim of this part of the manual is to provide step-by-step laboratory protocols and methodologies for data analysis, and a guideline to design a population genetic study.

The scope covers most commonly used techniques for screening genetic variation, general background on the methodologies for estimation of important parameters in population genetic studies for different forms of molecular genetic markers. Part 2 includes three sections:

Section I - Molecular markers - an overview: will provide an overview of common molecular markers used in population genetic studies.

Section I - Laboratory protocols: will provide step-by-step protocols of commonly used molecular genetic techniques.

Section III - Data analysis and project design: will deal with aspects of data management such as data analysis, interpretation and presentation, and a guideline to design a population genetic studies.

Please note that Part 1 of the manual is also available for download.

Inbreeding and brood stock management

Published: 15/11/2006 | 5580 views
This manual, written for extension workers, aquaculturists, and those who work with natural resource management programmes, primarily deals with the problems caused by unwanted inbreeding in cultured fish populations and describes management techniques that can be used to prevent or minimize inbreeding. The manual also describes how inbreeding can be used to improve captive populations of fish. The manual contains chapters on: basic genetics and the genetics of inbreeding; how to determine individual inbreeding values when pedigrees are known; how to determine the average inbreeding value in a population when pedigrees are not known; genetic drift, which is random changes in gene frequency; how inbreeding programmes can be used to improve cultured populations of food fish; how to prevent inbreeding depression and loss of genetic variance in farmed populations; and recommendations on how to manage cultured populations of fish to prevent unwanted inbreeding and genetic drift from depressing productivity, profits, and survival. One of the most important aspects of managing a closed population of fish at a fish farm or fish culture station is the management of the population's effective breeding number, because inbreeding is inversely related to the effective breeding number. Techniques to determine and manage the effective breeding number are described, and recommended minimum effective breeding numbers are provided for a variety of farm sizes and fish culture goals. A number of culture techniques can affect inbreeding, and ways to modify them so there is minimal impact on inbreeding are discussed. Finally, ways to minimize inbreeding during selective breeding programmes are described. This manual, written for extension workers, aquaculturists, and those who work with natural resource management programmes, primarily deals with the problems caused by unwanted inbreeding in cultured fish populations and describes management techniques that can be used to prevent or minimize inbreeding. The manual also describes how inbreeding can be used to improve captive populations of fish. The manual contains chapters on: basic genetics and the genetics of inbreeding; how to determine individual inbreeding values when pedigrees are known; how to determine the average inbreeding value in a population when pedigrees are not known; genetic drift, which is random changes in gene frequency; how inbreeding programmes can be used to improve cultured populations of food fish; how to prevent inbreeding depression and loss of genetic variance in farmed populations; and recommendations on how to manage cultured populations of fish to prevent unwanted inbreeding and genetic drift from depressing productivity, profits, and survival. One of the most important aspects of managing a closed population of fish at a fish farm or fish culture station is the management of the population's effective breeding number, because inbreeding is inversely related to the effective breeding number. Techniques to determine and manage the effective breeding number are described, and recommended minimum effective breeding numbers are provided for a variety of farm sizes and fish culture goals. A number of culture techniques can affect inbreeding, and ways to modify them so there is minimal impact on inbreeding are discussed. Finally, ways to minimize inbreeding during selective breeding programmes are described.

Comparative assessment of the environmental costs of aquaculture and other food production sectors

Published: 16/4/2008 | 2928 views

Bartley, D.M.; Brugere, C.; Soto, D.; Gerber, P.; Harvey, B. (eds). Comparative assessment of the environmental costs of aquaculture and other food production sectors: methods for meaningful comparisons. FAO/WFT Expert Workshop. 24-28 April 2006, Vancouver, Canada. FAO Fisheries Proceedings. No. 10. Rome, FAO. 2007. This document represents the report of the FAO/WFT workshop, Comparative Environmental Costs of Aquaculture and Other Food Production Sectors, convened in Vancouver, British Columbia, 24-28 April, 2006.


The global food production sector is growing. In many areas farming systems are intensifying. This rapid growth has in some cases caused environmental damage. This document include an introduction and 12 review papers describing methods for such comparisons as well as the deliberations of their authors, a group of nineteen international experts on environmental economics, energy accounting, material and environmental flows analysis, aquaculture, agriculture and international development. Experts concluded that comparisons can be useful for addressing local development and zoning concerns, global issues of sustainability and trade and consumer preferences for inexpensive food produced in an environmentally sustainable manner. In order to be useful, however, methods to assess environmental costs should be scientifically based, comparable across different sectors, expandable to different scales, inclusive of externalities, practical to implement and easily understood by managers and policy-makers. Aquaculture in many locations and conditions is or could be much more environment friendly than other food sectors.

Guidelines for genetic management and conservation of mahseer

Published: 12/11/2007 | 3566 views
This document presents:

1. Current status on genetic diversity of empurau and semah in Sarawak, Malaysia; including taxonomic status;

2. A management guideline based on genetic data.

The mahseer species, Tor tambroides and T. douronensis, are often referred to as empurau and semah, respectively in Sarawak, Malaysia. The two species are indigenous to the State with an aquaculture potential and of conservational value. Empurau and semah are well sought after due to high market value as well as being attractive sport fish. Semah is considered the State Fish of Sarawak, and juveniles of both species are also increasingly sought after by the aquarium industry (Ng, 2004). Semah are found in most major river systems of Sarawak, while empurau are restricted to some rivers, and both species often inhabit upper reaches of the headwaters. They also occur in Peninsular Malaysia and are distributed throughout southeast Asia from Indonesia to southern China (Kottelat et al., 1993, Roberts, 1999, Zhou and Cui, 1996).

Many anthropogenic activities, including the recent developments in watersheds within the natural distribution of empurau and semah, as well as increased fishing pressure have led to depletion of their natural stocks. As such there is an urgent need to replenish such depleted stock as well as reducing pressure that affects the well being of natural populations of empurau and semah.

The Government of Sarawak, recognizing the importance of these two species, made an attempt to evaluate their aquaculture potential, including captive breeding using long-term pond-reared broodstock, commencing in the 1990s. However, limited success was achieved until the period 2002-2004 through an international collaboration, where researchers from Australia and Sarawak were able to breed both species using hormone induction techniques, popularly referred to as hypophysation, on long-term, pond-reared broodstock. Success in artificial propagation of empurau and semah would bring about significant developments in term of aquaculture and conservation. On the one hand, fish produced from aquaculture can be used to replenish the wild stocks ? the practice often known as stock enhancement, and on the other hand, fishing for food fish will also be reduced due to the availability of cultured fish.

However, it is important to note that aquaculture and stock enhancement could be counter-productive if genetic aspects of broodstock management are not taken into account or broodstock are not properly managed. Detrimental genetic impacts of poorly or inappropriately managed fish breeding programs for both aquaculture and stock enhancement have well documented over the last two decades (Waples, 1991). When fish are removed from the natural environment and placed in a cultured environment and domesticated, random genetic drift and domestication effects (new and greatly different selective forces act upon fish in the domestic environment compared to the natural environment) alter the gene frequencies and reduce genetic variation. Domestication reduces genetic variability in fish through both selective processes and random genetic drift. Such fish once released in to the natural waters could have potential impacts on altering or diluting natural gene pools, and such events have been documented for many species.

Hybridization between closely related species can have a detrimental affect on natural gene pools. Interspecific hybridization among other mahseer elsewhere has been reported. Because of the high level of morphological similarity between empurau and semah there is risk that inadvertent mixing of the two species, especially during breeding, may lead to hybridization. Therefore hybridization is an important threat to the genetic integrity of both species.

In order to avoid the above mentioned potential problems, it is crucial that a genetic management plan be developed with the aim to warrant the long-term maintenance of genetic diversity of cultured stocks, as well as to minimize potential adverse effects on the genetic integrity of the wild populations through proper stock enhancement practices. Surveys on current status of genetic variability of empurau and semah are reported herein, and the results from which are used as baseline data for development of a genetic management plan.

Further, this document represents the first example in Asia of a comprehensive genetic management plan that was developed at the inception of industry development and commercialization, and that takes into account both commercial aquaculture of fish species as well as the conservation and management of wild populations. As such it is imperative that the State Government of Sarawak publicises this exemplary event and brings it to the notice of the rest of Malaysia.

Glossary of biotechnology and genetic engineering

Published: 15/11/2006 | 3285 views
Biotechnology is a general term used in a very broad field of study. According to the Convention on Biological Diversity, biotechnology means:

Quote:

"any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use."



Interpreted in this broad sense, the definition covers many of the tools and techniques that are commonplace today in agriculture and food production. If interpreted in a narrow sense, the definition considers only the "new" DNA, molecular biology and reproductive technology.

The swiftness of change in the sector means that terminology is constantly evolving and yesterday's buzzword is today's jargon and might be tomorrow's mainstream term. The rate of evolution of terminology has been such that it has been very difficult to remain abreast of current usages.

The idea for such a collection of terminology associated with the rapidly expanding fields related to or deriving from biotechnology and genetic engineering, was stimulated by the difficulty of communicating effectively in discussions at intergovernmental level. On various occasions, simple differences of interpretation of terminology have threatened to de-rail negotiations of international importance.

There are numerous publications addressing the terminology of narrow disciplinary areas, but FAO was unable to find a single list that attempted to cover the broad swath of disciplines and applications germane to its mandate and competence. Hence this Glossary.

It tries to provide a consolidated, comprehensive and yet accessible list of terms and acronyms that are used regularly in biotechnology sensu lato and in the very broad area commonly dubbed "genetic engineering," with all the associated problems of usage of originally discrete technical terms in a general context by a mass media that does not discriminate, or in a legal context that requires very exact definitions.

This Glossary is an attempt to present an up-to-date list of terms currently in use in biotechnology, genetic engineering and closely allied fields. It is intended to provide a convenient reference source for researchers, students and technicians. The Glossary should also be of particular value to those whose native language is not English.

The Glossary has been prepared in response to an expressed need. Many of the terms listed in this volume are otherwise found only in published papers and books. The terms included have been selected by examination of books, dictionaries, journals and abstracts dealing entirely or in part with biotechnology or allied fields.

In addition, an attempt has been made to include terms from applied biotechnology that are important for FAO's intergovernmental activities and especially in the areas of plant and animal genetic resources, food quality and plant protection.

This publication is available in English, French, Spanish and Arabic.

Useful publications on Genetics and Biodiversity

Published: 5/1/2005 | 3055 views
Dear colleagues,

NACA as a regional organisation dedicated to aquaculture development and sustainable aquatic resources management has recognised the importance of genetics in the long-term sustainability of all development activities and its relevance to maintaining biodiversity. In addition to the ?Genes and Fish? column in Aquaculture Asia - the quarterly magazine of NACA, this special page is developed with a hope to deliver some recently published information relating to biodiversity and genetics of fisheries and aquaculture. These publications are complied by conducting a literature search on AFSA, the Web of Science and Cambridge Scientific Abstract databases. Please contribute to make this page more informative by sending your own related publications.

Dr. Thuy Nguyen
NACA
P.O. Box 1040, Kasetsart Post Office, Bangkok 10903, Thailand
Tel: 66-2-561 1728 (Ext 120);
Fax: 66-2-561 1727

International mechanisms for the control and responsible use of alien species in aquatic ecosystems

Published: 15/11/2006 | 2279 views
The use of alien species is a proven means to increase production and value from aquatic ecosystems. In the Mekong/Lanchang Basin, alien species such as tilapia (Oreochromis spp.) play an important role in providing cheap and readily available protein to rural and poor sectors. However, alien species are now recognized as one of the most significant threats to aquatic biodiversity. Members of FAO and signatories to the Convention on Biological Diversity have obligated themselves to manage and control alien species that may adversely impact ecosystems. There are a range of international mechanisms that have been established to assist countries in meeting international obligations and responsibilities. The coverage of these international instruments, the signatory countries and the degree to which they are implemented varies throughout the world. Implementation is often difficult due to lack of awareness at national level of responsibilities under the respective instruments, problems with enforcement, and lack of basic information and capacity to undertake risk assessment. Several steps are necessary for effective use and control of alien species, but one of the most important was identified to be following codes of practice similar to that developed by the International Council for the Exploration of the Sea. The development and use of indigenous species are options to the use of alien species. However, indigenous species have not received the same amount of attention, research, development and use as many alien species. Regional coordination of policies and practices on alien species is needed for effective national management. National policies need to be in place and the population needs to be aware of issues before countries can implement international mechanisms. Thus, regional coordination and national policy development are necessary actions that should go hand in hand in order to facilitate implementation of broader international agreements.

Biodiversity and Conservation - a hypertext book

Published: 6/9/2006 | 4295 views
BIODIVERSITY and CONSERVATION

A Hypertext Book by Peter J. Bryant

This hypertext book deals with the problems of trying to preserve biological diversity on the earth. It discusses the history of life on earth, the reasons for depletion and extinction of animals and plants at various times including the present, the reasons for being concerned about these losses, and what can be done to preserve some of what is left.

The book was written by Peter J. Bryant (pjbryant@uci.edu) School of Biological Sciences, University of California, Irvine, USA and are being used as resource material for Bio 65, Biological Conservation (on UCI campus and online). It is also being used in Biol 215 Conservation Biology at Northwest Indian College, Bellingham, Washington.

To access the full content of the book please follow the link http://www.dbc.uci.edu/~sustain/bio65/Titlpage.htm

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