Preface   The idea of compiling the book was conceived while conducting National workshops on ‘Bioinformatics and Statistics in Aquaculture Research at the Bioinformatics center of Central Institute of Freshwater Aquaculture, Kausalyaganga during past ten years. During the workshops the course content in the form of lecture, hands on training and demonstration of various aspects of Internet, CD-ROM search, data analysis using statistical and bioinformatics soft wares, web page & database development and many other frontier areas of science and technology were covered. Many participants expressed their keen interest in the emerging areas aquaculture and expressed for a book which will cater to the need of understanding the basics of computers, communications and micro electronics, analytical tools and techniques. The book is on out growth of the workshops. The book is an effort to compile and document the latest trend and technologies especially ICT application in fisheries and aquaculture besides statistics and economics. The book spread over broadly in three sections like Bioinformatics, Statistics and Economics. Each section consists of a number of chapters. Bioinformatics section covers computational aspect of genomics and microarray data using latest tools and techniques apart from fundamental issues of carp, prawn and ornamental fish breeding, culture and management. Chapters on probiotics, immunology, cryo-conservation and disease that are included in this section are new and of paramount importance. Chapters like non-evasive methods of fish freshness determination by electronic olfaction, fisheries data mart, nano-technology, mapping fisheries research in India are altogether new approaches in fisheries and aquaculture research in Indian context. The statistics section covers chapters on application of designs of experiment, sample survey, biometrical techniques, quantitative genetics and selective breeding techniques that are noteworthy. Economics section is embodied with interesting chapters like quantitative techniques in econometric analysis and impact assessment in addition to fundamental computational aspects of economic indicators along with illustrated examples. Chapters on estimation of technical efficiency, project evaluation, IPR issues and fisheries legislation and policy in India are new introductions. The endeavour could not have been materialized without the active support in terms of contributing articles by the dedicated subject matter specialists, professionals from various National Institutes of repute like DBT, IASRI, C-DAC, CIBA, NBFGR, B.C.K.V.V, KIITS, IGAU, CRIDA, NAARM, NCAP, CARI, WTCER, OUAT, RRL, MANAGE, ILS, CIFRI, CIFA, ZCU-VI, KVIC, Essar, China, Purdue University USA, IMS Engineering College, Utkal, Jadavpur and Delhi University. All out support, guidance, suggestion and encouragements from Dr. M.K. Bhan, Secretary, DBT and Dr. T.Madhan Mohan, Advisor, DBT are thankfully acknowledged. We express our gratitude to Dr. S.Ayyappan, DDG (Fy.), ICAR for constant encouragement and guidance at all stages of the programme.

Need of Bioinformatics Bioinformatics, an emerging area offering a fundamental tool to the scientific community, to speed up the research, application and commercialization of biotechnology. In fact the best thing, which has happened towards the end of the 20th century and in the 21st century, is the marriage between biotechnologists and information technologists leading to the growth and development of this field. India took a lead as early as in the 1980s but more precisely from 1986 onwards by establishing a strong base of Bioinformatics with the necessary infrastructure. As a result one has seen major breakthroughs in biology and the growth of biotechnology has been phenomenal in the last decade, especially with the most outstanding technological breakthrough of the 20th century wherein the draft human genome sequence was completed in 2000 and now the genetic code is completely sequenced. This has provided the worlds scientific community information on the vast sequence and structure of the Genomes, the crystal structures and there is an increasing dependence on computational approaches. Biotechnology has emerged as a front-line area with vital significance in unraveling secrets of life, particularly in the studies of new biology and biotechnology. The genomic revolution has underscored the central role of Bioinformatics in understanding the very basic of life processes.

Introduction In this era of international competitiveness of knowledge economy, there is an emergent need for identifying new knowledge streams likely to emerge for mapping the directions for transition of knowledge from industry to information technology. National Knowledge Commission, Government of India has undertaken a survey of agricultural sector for exploring and discovering the dynamic role of innovation of knowledge for growth and competitiveness and recommended for ascertaining the role of the Governmental factors as innovation enablers in development of Indian economy (Anon, 2006). The knowledge network and development of knowledge infrastructure in the field of information and communication technology lead for knowledge generation, knowledge transfer and it’s preservation as intellectual property right which will support for adoption of effective knowledge management practices and provide guidelines for envisioning the policy makers to formulate appropriate plans in the filed of research and development.

Introduction The biological information that are being generated by research in modern biology worldwide is so huge that it is not possible to manage through conventional file keeping or simple computing. Secondly, analysis of these data certainly needs specific interfaces, software and management facilities. Therefore, such requirements to store, analyze and manage the biological information/data in an appropriate way has led to the origin of a new branch of science called “Bioinformatics”. Here, emphasis will be given on the disciplines of research mostly from which generation of data is made. Broadly, they can be classified as follows.

Introduction Nucleotide and protein sequences construct the core of Bioiformatics. These biological sequences form complex and very large datasets. Various Statistical techniques have been used for analysis and extraction of precise information form small as well as large biological datasets. Evolution and natural selection makes biological sequences redundant and statistically biased. Once the mechanisms involved in such biases have been characterized, their analysis and systematic investigation become valuable tools for use in predicting the properties of other biological sequences. This biased nature results in relative codon usage value among the synonymous codons or Relative Synonymous Codon Usage (RSCU) value. Codon usage variation within a single genome can be an important source of information about gene expression levels and events of horizontal gene transfer (Medigue et al., 1991). The analysis of codon usage patterns can be traced back to when first molecular sequence databases were being colleted (Grantham et al., 1981). In order to evaluate the codon and amino acid usage variation, multivariate analysis options like Correspondence Analysis, Principal Component Analysis, Cluster Analysis, Factor Analysis, Multidimensional Scaling and Eigenanalysis Ordination are available (Morrison et al., 1994). It is well established that codon usage by its nature is multivariate. These methods provide a low dimensional point representation of genes, where the proximity of gene specific points indicates (CoA) a similar codon usage of associated genes. Correspondence Analysis is an exploratory graphical approach that requires contingency tables and generates results in the form of tables, scattered plots and graphs. CoA can identify the major sources of variation in the dataset. The output from a CoA can be used to evaluate other aspects of genes, such as base composition, expressivity, aromaticity and location on the genome (Thiouse et al. 1997).

Introduction Recent advances in bioinformatics such as microarray analysis are bringing about a revolution in our understanding of the molecular mechanisms underlying normal and dysfunctional biological processes. With the help of microarray technologies, biologists are currently capable of observing the abundance of transcripts from tens of thousands genes in biological samples, enabling the exploration of the dynamics of transcription and interaction between genes on a genome-wide scale. With the accumulation of gene expression dataset, the challenging task of all microarray experiments is how to extract meaningful and trustworthy information out of thousands of genes that do not contribute in the designed experiments. To achieve this goal, many rigorous mathematical tools and computational software were introduced to the field, like statistical techniques for data normalization, clustering algorithms, class prediction methods, ANOVA, and gene-gene interaction studies. Microarray technology has been used widely in various areas of agriculture and allied field. Application of statistics in microarray is limited particularly in experiments involving fishes. In this chapter it is attempted to present various statistical methods applied to accessory microarray experiments with illustrated example of fish microarray data.

Introduction The United Nations’ Food and Agricultural Organisation reported that global aquaculture is increasing by 11 percent per year and is the world’s fastest growing food-producing sector. More than 38 million people are employed in aquaculture and associated industries worldwide, and 131 aquatic species are currently being commercially cultured. In 2002, Asia led the world in the aquaculture production, with about 12.4 million tonnes, while Europe and America together produced 1.2 million tonnes. Among the Asian countries, India ranks second in aquaculture and third in capture fisheries. Freshwater aquaculture in India is mainly based on Indian major carps (Labeo rohita, Catla catla and Cirrhinus mrigala) with an annual production of 1.8 million tonnes, and exotic carps, which together contribute to over 87% of the total aquaculture production of 2.2 million tonnes. Disease problems represent important constraint to the aquaculture industry. The need to control endemic diseases imposes severe year-on-year costs on producers. The advances made in the development of vaccines for diseases of Indian major carps are very meager.

Introduction Fish production in aquaculture has increased dramatically over the last 20 years with an increment of 9-10% per year over the last decade. Microbial disease problems are prevalent in aquaculture as in any other intensive animal or plant production sector. Vaccines are used as disease prevention and can be very effective, however, they do not work at all developmental stages of fish or in all species. Therefore, antibiotics play a major role in control of fish bacterial diseases, although serious concerns have been raised with respect to development of antibiotic resistance and its transfer to human pathogenic bacteria. Also, new EU regulations call for specific license for antibiotic use in aquaculture and this is too costly even for fish farmers. The urgent need for development and application of non-antibiotic disease control measures has led to research in probiotic organisms. Probiotics are “live microorganisms which when administered in adequate amount, confer a health benefit on the host (FAO/WHO 2001)” and the principle is most widely known from the belief that ingestion of high numbers of lactic acid bacteria (fermented foods) can control human pathogenic organisms in the intestine. Fish pathogenic agents, however, can invade via skin and gills and probiotic organisms may therefore be as efficient if applied to the outer environment of the fish.

Introduction Brood stock management is an essential component of fish farming since the success of aquaculture industry mainly depends on quality of brood stock in order to ensure the production of top quality offspring. Their health condition is also important from culture point of view, which in turn increases the fish production. Unfortunately, in India, less attention is given to the brood stock management during non-breeding seasons. The pond aquaculture is also becoming over utilized due to high stocking beyond the carrying capacity, addition of huge quantities of chemicals, drugs, fertilizers and supplementary feeds etc. Physical injury due to rough handling, temperature fluctuations, extremes in oxygen levels can also work in a cumulative way and produce stress and make the fish susceptible to variety of diseases. Environmental deterioration, which occurs due to dumping of pesticides and chemicals alongwith metabolic waste products, left out feed materials and organic load of the pond bottom regularly come in contact with certain vital organs and tissues of fish. All such factors can cause deterioration of fish health and magnify the risk of outbreak of diseases. Disease outbreaks are one of the stumbling blocks in the development of aquaculture industry affecting both the economic development and socio-economic revenue from this sector. Today, there is no availability of exact figure on loss due to diseases in fish farming. The phenomenon is more common in carp Industry, and mortalities due to disease outbreaks cause major management problems and economic loss every year.

Introduction Indian major carps viz. Catla catla, Labeo rohita and Cirrhinus mrigala are the fast growing, consumer preferred and the stay component species in Indian pond aquaculture system. These carps breed spontaneously in natural water viz. river and bundh type tanks where fluviatile condition prevails (Hora, 1945; David 1959; Quasim and Qayyam, 1962; Natarajan, 1971). Above three species under culture condition attain sexual maturity but do not spawn in confined water (Chaudhuri, 1960; Chaudhuri and Singh, 1984). Khan and Jhingran (1975) in their review described several factors viz. temperature, run off water, photoperiod, turbidity and water depth that are playing important roles in initiating natural spawning in ‘bundhs’ and rivers. They further described that no single factor can be considered responsible for spawning separately. The act spawning involves a chain of interrelated conditions as prerequisite to spawn. Monsoon, flood forms the spawning ground and initiates natural spawning. Although fish bred in its natural environment, it was difficult to understand why some species do not breed in confined water where as other species in the same environment breed somoto. The initial attempt to induce breed IMC (mrigal) was made during 1937. Khan (1938) was able to induce ovulation in Cirrhinus mrigala by administration of mammalian pituitary extract but eggs were not fertilized. No remarkable success on induced breeding of Indian major carps was made till 1957. Indian major carps were induced to breed for the first time on 10th July, 1957 by the injection of aqueous carp pituitary extract at Govt. Fish Farm, Angul of Orissa state by the scientific team from pond culture substation, Cuttack (Chaudhuri and Alikunhi 1957). Eversince 1957, the induced breeding of carps have been tried by many permutation and combination, addition and alteration of inducing agents.

Introduction Majority of the commercially important freshwater prawns belongs to the genus Macrobrachium of family Palaemonidae. Among the commercially important freshwater prawns of India the most important cultivable species at present is the giant freshwater prawn Macrobrachium rosenbergii due to its superior cultivable attributes such as fast growth rate, large size, wide range of salinity tolerance, hardiness and compatibly to grow with carps. The species enjoys good consumer preference and domestic as well as export market demand. Freshwater prawns are cultured in freshwater or low saline brackish water (salinity <10 ppt) and can be cultured either alone (monoculture) or in combination with fishes such as carps, tilapia and milkfish (polyculture). Freshwater prawn culture can be carried out in earthen ponds, cement cisterns, in pens or in cages. However, most of the operations are being carried out in earthen ponds.

Introduction Global diversity in domestic animals and aquatic organisms is considered to be under threat worldwide. Worldwide 11 % birds, 25 % mammals and 34 % of fish species are threatened (Lovell-Badge, 2001; Vemuganti and Balasubramanian, 2002) and aquatic ecosystem is becoming more vulnerable to disasters due to run off from agriculture and industrial sources, oil spills or sudden environmental changes leading to total elimination of stocks from different ecosystems. The multifarious human activities in open waters have threatened the fish diversity all round the world. Fish worldwide are in crisis. The effective population sizes in fish hatcheries are getting smaller and smaller that causes loss to farmers worldwide. The World Resources Institute has reported that nearly 70 percent of the world’s marine fish stocks are over fished or are being fished at their biological limit. Apart from fish, across all live stock species there is a shrinking pool of genetic diversity. For instance, the effective population size for all dairy cattle breeds is less than 60 animals. To preserve the gene pool of unique populations by protecting them from extinction, loss of genetic variability (inbreeding) and dilution due to inter breeding with unrelated populations (hybridization) gene banks or germplasm repository can play a vital role. Germplasm repositories in fisheries could be used for: 1) restoration of threatened species, 2) brood stock improvement through genetic modification of a targeted population, and 4) information and technology development including gene pool database management.

The term ‘Ecology’ deals with the study of organisms from all sources and their interaction with surrounding environments. The aim of ecology is, therefore, to understand and also to explain the relationships of all organisms to their environment. In this respect, the duty of the ecologist is to study a particular environment, estimate the population of each species, recognize the communities, and determine their activities and their interactions with both related species, the rest of the community, and their environment. Macroecological studies always initiate by defining the species composition and then proceed to draw certain conclusions on the role of these species in the ecosystem. On the other hand microbial, especially bacterial classical taxonomy (based on isolation techniques and determination of morphology and in vitro biochemical characteristics of isolates) for determination of each species of aquatic bacteria is almost impossible, except in a few cases. Consequently, the microbial ecologist has to depend upon certain methods that can measure the biomass or activity of a very large conglomerate of coexisting microbial taxa in an aquatic environment. Probably, this has caused the very slow development of microbial ecology concepts and application of a general ecological theory to the microbial ecology.

Introduction Ornamental fish keeping in aquarium has emerged as the second most popular hobby next to photography. As these fishes usually are kept in aquarium, they are popularly known as ‘Aquarium Fishes’. These beautiful fishes form an important commercial component of aquaculture, providing for aesthetic requirements and upkeep of the environment. At present the market for ornamental fish in the world for public aquaria is less than 1% and over 99% of the market is still confined to hobbyist. In India the hobby of ornamental fish keeping is nearly 70 years old. The brilliant, flamboyant color and exotic appearance of fish appeal almost for every one, children and aged alike. According to psychiatrists, placing aquaria with ornamental fishes in the patient’s house could treat certain type of mentally disordered problems. The relatively minimum requirement of space or attention compared to other pet animals is the reason of growing interest in keeping aquaria all over.

Introduction Activities to promote and monitor the growth of aquaculture inherently have a spatial component, because of the variations among biophysical and socio-economic characteristics from location to location. Biophysical characteristics may include water quality, soil type and climate. Socio-economic characteristics in aquaculture development may include administrative regulations, competing resource uses, market conditions, infrastructure support, and availability of technical expertise. Geographical Information Systems (GIS) provides the spatial information needed for decision-makers who evaluate such biophysical and socioeconomic characteristics as part of aquaculture planning efforts more effectively and timely (Kapetsky and Travaglia, 1995). GIS is potentially a powerful tool for assisting this class of decision-makers, and is already being effectively used for such purposes in some places (Carswell, 1998; Arnold et al., 2000) where advanced capabilities in terms of infrastructure and trained personnel exists. Nath et al. (2000) discussed various applications of GIS in aquaculture. In general spatial information technologies are being effectively used for sustainable management of aquaculture and inland fisheries. Some potential applications are as follows:

Introduction India is an agrarian society where 70% of the population depends on agriculture, animal husbandry and fisheries. Fishery is an important sector, its planning and development largely depends on a sound and reliable data and information on resource, production, marketing and distribution. Generating reliable information basically needs identification, conceptualization, classification and sound scientific techniques for collection, compilation and analysis of data. Geographical Information System emerged as an efficient tool to access, organize, update and analyse the information and to utilize it in an optimal way. A proper computer based information system is the need of day to organize such complex data in order to draw reliable conclusions which may help in drawing action programmes. This multidimensional nature of information on topography, physico-chemical parameters, socio-economics and fish production data can only be handled and processed by Geographical Information System (GIS).

Introduction The major potential areas for inland aquaculture have already been explored in India. Additional production can only be achieved through successful manipulation of available resources that influence the productivity of various aquaculture systems. This can be achieved through maintenance of adequate levels of nutrients in the pond environment. Pond management in fish culture is mainly concerned with fertilization requirements and strategies with better management practices (BMP) of pond soil and water quality. BMP could be achieved through adoption of advanced technology, computer based diognostic/decision tools, software packages for quick, accurate, authetic data management.

Introduction Of the five human sensory perceptions, the feelings of sight, hearing and touch have been simulated by artificial sensors quite successfully. Electronic eyes (digital cameras), electronic ears (microphones) and touch sensitive electronic devices are quite common nowadays. In comparison to these devices, the perception of smell and taste are relatively unexplored. Sensing of smell and taste is full of uncertainty and the prevalent technology is at its infancy. Electronic noses for smell and electronic tongues for taste or a combination of both have vast prospects in the field of standardization of quality of food and agro products. In India, proper use of these instruments can revolutionize the quality of the food and agro products, thereby increase the export worthiness of these products. In this article, we have tried to discuss applicability various electronic olfaction technologies like electronic nose and electronic tongue for fish freshness determination. A report on an experiment with electronic nose on fish samples has been presented.

Nanotechnology: The Next Big Thing is Really Small Nanotechnology can be considered as a brainchild of Richard Feynman, as the conceptual underpinings of nanotechnologies were first laid out in 1959 in his historical lecture, ‘ There is plenty of room at the bottom’. The term ‘nanotechnology’ was not used until 1974, when a researcher, Norio Taniguchi, at the University of Tokyo, Japan, used it to refer to the ability to engineer materials precisely at the nanometer level. The prefix ‘nano’ is derived from the Greek word ‘drawf’. One nanometer (nm) is equal to one billionth of a meter or about the width of six carbon atoms or ten water molecules. A human hair is approximately 80,000 nm wide and a red blood cell is approximately 7000 nm wide1. Nanotechnology can be defined as the science and engineering involved in the design, synthesis, characterization and application of materials and devices whose smallest functional organization in at least one dimension is on the nanometer scale or one billionth of a meter2-5. It is a multidisciplinary field, which covers a vast, and diverse array of devices derived from Engineering, Physics, Chemistry and Biology and the cumulative efforts of all the disciplines is necessary for any significant outcome.

Introduction Technologies and tools that have developed in the recent information technology revolution can play a very vital role in overcoming most of the present problems related to agriculture and rural development. In order to achieve the goal of an economically sound and stable society through environmentally friendly systems of agricultural production, it is imperative to have a comprehensive data storage system. This will not only help in providing systematic and periodic information to the planners, decision-makers and developmental agencies, but also help to manage our limited natural resources efficiently. The development of a data warehouse is one of the recent tools in the field of information technology that can fulfill the demands of the information that is required in the field of agriculture research, management and education

Introduction The development of DNA technology over the last few decades has led to generation of huge amount of data from plant and animal genome. The main sources of markers are mitochondrial DNA (mt DNA), minisatellites, micro satellites and anonymous nuclear sequences assayed using highly specific PCR primers or by using the RAPD technique. A major contribution comes from molecular markers used for analyzing genetic variations. There has been the infusion of computers, softwares and online databases into the daily activities of many molecular geneticists. The identification of abundant, highly variable loci, detectable by a wide variety of techniques has led to a revolution in the way researcher view and analyses levels of variation. We will here discuss about current computer programs in this area to characterize the DNA profiles and data analysis for intra and inter population structure, phylogenetic inference and parentage determination.

Introduction In this computer age software plays a vital role in speeding up the research activity. Software and databases help in storage, processing and accessing large volumes of information. Software helps to retrieve right information at the right time at the right place for the right purpose. The time of researchers is very precious. Instead of spending it in monotonous and tedious tasks, it could be used more effectively for new findings. With the advent of computer and its softwares, this problem could be overcome to a considerable extent. Software is a set of instructions given to the computer to perform certain tasks. In this era of information technology, its essential to apply different softwares to speed up the research activity. It is therefore, utmost importance to have information about the different software already developed in the area of fisheries/aquaculture worldwide. Almost all the routine tasks which the scientists or the farmers are doing, could be automated in the areas like financial & economic analysis, development planning and project appraisal, facility design, management planning and production forecasting, facility construction, management decision support and record keeping, disease diagnosis and treatment, environmental regulation and aquaculture databases. FAO, World Fish Centre and other International Research Organisations have contributed software and database development in the area of aquaculture (Anon, 1999; ICLARM, 1998; FAO, 1999; Erist, 1998). In India also initiative to develop software and database has been taken up. Preliminary report on the availability of fishery related software and databases are available (Roy, 2000). In this communication, an attempt has been made to list softwares and databases that may be used in fisheries and aquaculture research and development/activities.

Introduction Improvements in Information and Communication technology are revolutionizing the way people access information. These new technologies are helping to improve communication, disseminate information and facilitate sharing of knowledge and skills. Zijp (1994) notes, Information Technology is making both public and private sector agricultural information systems more accessible and more rapid in transmission. The increase in electronic information and communication technologies and in particular networked information is the most notable change to affect the working practices of information professionals in recent years. Digital technologies have led to the emergence of wide-area connectivity through the Internet, making information on agriculture available worldwide and on-demand. Information technology and electronic networking particularly can strengthen organizations by improving their knowledge base and ability to share information and experiences with partners in the field. Electronic networking not only helps in the exchange of the growing volume of information but also brings people together in partnerships and facilitates a joint programme of action on common themes.

Introduction Fish and the aquaculture products contribute a significant amount of animal protein to the diet of the people worldwide. Being highly nutritive they serve as valuable food supplement in diets lacking essential vitamins and minerals. Besides its role of food security, fish is a source of income for millions of people around the World. Though the trade is not prominent at Global level, in some countries its contribution to foreign currency earning is vital to the National Economy. India has a coastline measuring 7500 km and important aquaculture country in the World. Being the home for more than 10% of the global fish biodiversity, the country ranks third in the World in the total fish production with an annual fish production of about 6.4 million tones. Constituting over the 1% of the GDP, fisheries contributes to 5.3% of the agricultural GDP. The estimated foreign earning for the year 2006 was US$ 1365 million.

Introduction We shall discuss in this section some of the fundamental Statistical Tests that may be applied in the field of research in Aquaculture. Introduction to tests of hypothesis, test procedures and the concept of decision making are also covered here. At the outset, stages of research process and different formulae are briefly enlisted, for a quick reference by the young researchers. Later, a detail discussion is made on various fundamental statistical tests, including one-way and two-way ANOVA. Research Methodology What is Research A good researcher should first feel/realize the importance/relevance of the research, he is undertaking. It should be quite convincingly clear to him particularly on the issue of “why” such research.

Introduction A careful compilation and scrutiny of data of aquaculture variables is essential for appropriate statistical analysis and meaningful statistical inference and interpretation of results. In nature, many aquaculture variables are inter-related with each other and the changes in variables would often depend on different variables which are either correlated or independent. In some cases, the variables could also be intra-related over a period of time. For statistical analysis of data of aquaculture variables comprising of different physical growth variables like fish weight, body mass, length and bio-chemical growth variables like muscle protein, lipid, glycogen, protease etc. and variables like pond size, water and its quality, the environmental parameters, type of feed, chemicals used etc., appropriate statistical procedures of correlation and regression could be explored for statistical analysis, testing and interpretation of results. Different statistical procedures are used for analysis of aquaculture data with the objective of making an assessment of

Introduction In almost all biological studies, it will be impossible to account for every individual in a population. Therefore, it is necessary to examine a sub-group of the total population and extrapolate from this to the whole population. The process by which the sub-group of the population is selected is sampling. Nearly, all statistical tests make a fundamental assumption that sampling of individual will be at random from all the individuals that could possibly be sampled. It is very important that timing is taken into account either by sampling strategy or by later analysis. Most population will be affected by season, time of day and local weather conditions. What is considered here is the problem faced by an ecologist working in the field and trying to design a suitable sampling strategy. The use of the very powerful statistical technique; analysis of variance (ANOVA) is more common in the situation of a controlled experiment, where, we are analyzing the effects of different levels of a treatment (e.g. feed, fertilizer, temperature etc.) on some measured aspect of population, Then, to get a true estimate of the effect of the treatment, experimental design will be of paramount importance.

Introduction The method of obtaining the data for each and every unit belonging to the population or universe, which is the aggregate of all units of a given type under consideration, is known as complete enumeration survey or complete census. Examples of units are family, a period of time such as an hour, day, fishing village, fishing household, fishing establishment, fishing boat, fish landing centres etc. The type of unit to be considered would depend on the purpose of the view. The population may be finite or infinite. It is obvious that for any statistical investigation complete enumeration of the population is rather impracticable. For example, if we want to have an idea of the total catch of fish (monthly) in India, we will have to enumerate all the fishers who catch fish in the country, which is rather a very difficult task. If the population is infinite, complete enumeration is not possible. In addition, if the units are destroyed in the course of inspection, 100% inspection though possible, is not at all desirable. However, even if the population is finite or the inspection is not destructive, complete enumeration is not taken because it is time-consuming, expensive, and as well as it needs a large amount of resources in terms of trained personnel.

The need for better analytical tools to analyze the data in aquaculture leads to major developments in statistics. These tools play a significant role in the analysis and interpretation of data. Improvement in carp culture through genetic techniques is the only alternative for increasing the carp production and its quality when area of pond is fixed. For better hybrids or efficient strains for higher production it is essential to collect the data on the genetic diversity among the different carp species on the basis of traits. Therefore, sound statistical procedures are needed in the design of experiments as well as in the analysis of the data. This involves, the use of variability studies and the use of multivariate statistical techniques like correlations, path coefficients, D2 analysis and other classificatory analysis.

Introduction India possesses rich fish germplasm resources, accounting for about one-tenth of the 20,000 and odd species of fish known in the world. The Ganga network of rivers in the North, the Brahmaputra and the Mahanadi in the East, the Sutlej, the Narmada & the Tapti in the West and, the Godavari, the Krishna and the Cauvery in the South are very rich sources, harbouring bulk of the important fish fauna. (Jhingran, 1982). The major carps of India which are also referred to as Gangetic carps are the most important among the commercial fish species and form the major component of the aquaculture system in the country (Jhingran, 1982). Since the last two to two and a half decades, there was a steady progress in carp farming in India due to the availability of seed of the major carps and the development of different packages of culture technologies (Chaudhuri et al. 1975).

Introduction Information Technology (IT) is a relatively-recent gift of Science and Technology for the mankind, revolutionising even the basic perception of people. It is a boon to the ever-growing complexities of life in each sphere. Be it simple household chores to the complex and humanly impossible task of advanced space research, Bioinformatics is the application of Information Technology in the field of bio- or life-sciences. The advantages from this fusion of two sciences are many. Bioinformatics in particular, and information technology revolution in general have been a grace to today’s biological researchers, particularly the groups involved in experiments at micro level, be it microorganisms (such as bacteria) of microbiologists or macromolecules (of micro/nano size, such as DNA/RNA) of geneticists/molecular biologists or the nanotechnologists. For example, computer software package IMPAC (Interactive Modeling Package for Carbohydrates) has its applications in the modeling of 3-D structure of carbohydrates. MYCIN is another package popular amongst medical doctors for diagnosis of bacteriological diseases and to prescribe treatments.

Introduction Data collection, compilation and analysis of Aquaculture data has a major role to play in Aquaculture research. The time spent in collecting, compiling, analysing statistical data and taking appropriate timely action creates a gap in aquaculture. Therefore timely action is very much essential. This gap can be reduced by taking help of computers in collection, compilation and analysis of statistical data which will save time as well as manpower and will help in taking appropriate action in appropriate time. Electronic spreadsheet has a major role to play in this context even if the user is having little or no programming knowledge. The most widely used office automation package is one of the components which consists of spreadsheet application, in which accounting, balance sheet calculations, statistical data analysis, graphical presentations, etc. are possible with few key strokes and mouse operation only. EXCEL has several capabilities which include opening of a workbook; entering and editing data; building formulas to calculate values; managing list of data; formatting data; creating a chart; saving a workbook; opening and saving files from other spreadsheets; linking documents from other spreadsheets, data analysis, etc.

Introduction Fish is a renewable natural resource. It is a significant part of the domestic food supply which amount of foreign exchange. Export of fish and fish products has expanded very significantly. Fish earns increasing farming is an important component of India’s rural economy. Inland fisheries including rivers and ponds produce about 35 to 40 percent of the total fish harvest of the country. Fresh water aquaculture belongs to the unorganised traditional sector, which consists of many socio economically weak fishermen and small-scale fish farming units that use traditional methods of fish culture. Fish farming faces dual problem of conservation and development. Conservation may be defined as an approach to resource management that seeks to leave fish resources relatively untouched. Development on the other hand amounts to the use and modification of fish resources. It may involve transformation of fish resources. It is considered as a renewable resources because with proper management it can be made to yield direct services indefinitely into the future. But its renewability does not imply that it is free from pressing problem of over exploitation and total depletion.

Introduction Quantification of costs and revenues is necessary to evaluate farm performance in aquaculture at experimental station level. Such calculations aided by economic engineering methods can help in determining the most appropriate package of technologies for different categories of farmers in different geographical locations. The method described below is based on the works of T.V.R. Pillay (Aquaculture: Principles and Practices). The computation of capital cost (initial cost), annual operating cost (variable cost plus fixed cost), and gross revenue (income) shows the performance of aquaculture farms. In this chapter an attempt has been made to illustrate the above mentioned useful fundamental economic indicators along with the computational procedure of assessment of economic feasibility of aquacultural projects which is very important for any entrepreneur.

Introduction In view of the existence of productive agro-climatic and soil-morphological conditions, a dynamic estuarine river system and unique network of productive brackishwater aquaculture has emerged in the coastal states of India. It is immensely suitable for the shrimp/shrimp+fish culture providing high valued export quality shrimp. The Indian contribution of world shrimp export is at 6% (Katiha et al., 2003). Unfortunately, investment in shrimp farming has slowed down (Hempel, 2000) in recent years due to lack of interest among the entrepreneurs. Therefore, it is pertinent to work out and compare the economic feasibility of various shrimp farming system. Studies on cost and return for shrimp production are scanty, therefore, in depth analysis with identification of bottlenecks, yield gaps and constraints is the need of hour. It may lead to harness the potential for shrimp farming through inculcating entrepreneurs’ interest. This may also help the financial institutions for reconsidering loan procedure and further investment in this enterprise. Considering, over one third of national potential area for the enterprise and its sustainability over past decade, the study mainly concentrates on shrimp farming in the state of West Bengal.

Introduction Aquaculture resources in India is vast in the form of ponds and tanks of 2.35 million ha, reservoirs of 3.15 million ha, oxbow lakes and derelict waters of 1.3 million ha and brakishwaters of 1.24 million ha. At present, the total fish production is 6.4 mmt. Out of which inland fish production is 3.4 mmt. The total aquaculture production of 2.47 million tonnes that constitutes 4.2% of global production was valued at US$ 2.9 billion (FAO, 2006). Ponds and tanks are the prime resources for aquaculture, however only about 0.8 – 0.9 million ha is used for aquaculture currently. Recently, National Fisheries Development Board with huge budget provision has been established to improve production, processing, storage, distribution and marketing of fisheries products (Anon, 2006 a, 2006 b). During 10th and 11th plan periods higher fish production targets have been kept evisiging a growth of about 8 percent from inland sector.

Introduction Market intelligence is a basic requirement for attaining global trade competitiveness in agriculture and allied sectors. In a free market economy, a commodity’s current price and expected future price have consequences on its future supply as the entrepreneur’s production plans are accordingly changed. Additionally market intelligence on non-price issues like changes in consumer perceptions, traceability and quality related issues of HACCP is also equally important. This can guide the farmers in deciding the quality and the quantity of a commodity to be produced for particular target market/market segment. Market analysis and quantity that is likely to be in demand and price forecasts for fish are important to producers for rational production planning and for processors/exporters for taking right marketing decisions. Domestic and international input suppliers, bankers, insurers and policy analysts need market intelligence to estimate the requirements of fishers at macro-level for their advance planning.

Introduction Project evaluation aims at analysing research and development projects, or activities or ideas, for any or all of the following purposes: Getting an overall understanding of the project.  Making priorities among a set of projects.  Taking a decision about whether or not to proceed with a project.  Monitoring projects, eg. by following up the parameters analyzed when the project was selected.  Terminating projects and evaluating the results obtained.

Need for Impact Assessment Fisheries Research is an economic activity. Like any other investment propositions, resource allocation to Fisheries Research needs to be justified. The society or the donors are always interested to know what happened to the money invested in Fisheries Research. It is important to document the returns and/or benefits accrued from the research investment. Objective assessment of research investment helps in making decision and allocating resources in high returns research portfolio. It also helps to know which research areas and programs benefit the poor and regions. In the paradigm shift, the donors are seeking evidences on impact of past funding as a basis for future financial support. Systematic impact assessment forms the basis for efficient resource allocation in alternative research programs competing for financial support. Research programs demonstrate better historical performance, in terms of benefits generated for the society, and are rated higher for attracting required research resources. Impact assessment studies are also getting more prominence as the international environment is rapidly changing due to many emerging complex problems. Socioeconomic and environmental problems, like poverty, international trade, degradation of natural resources, are growing fast and the donors are looking for the research programs, which can overcome these challenges. Therefore, systematic impact assessment studies would form a strong base for higher research funding to overcome many regional, national and global problems.

Introduction The floodplain wetlands or beels are used as multiple use and multiple users system. The large numbers of the stakeholders participate in the beels both within fisheries and across other sectors like forestry, animal husbandry, agriculture, flood control etc. (Sugunan & Sinha 2001, Ramsar Convention Secretariat 2004). The different set of stakeholders constitutes a diverse set of interests, goals and priorities for the fisheries. Therefore, under the present context, the fisheries managers face an extremely complex situation in governing fisheries of the wetlands. Such complexities lead to sub-optimal or unwise use of the wetlands. There is growing concern over the depletion of resources, poor quality of aquatic environment, poor potential realization, poor fisheries management, inequities, conflicts, over exploitation etc of the beels (CIFRI 2000, Pomeroy & William 1994, Welcomme & Bartley 1998). These issues are the outcome of the complex fisheries exploitation system and research efforts are being made to find suitable management regimes to address such issues. The evaluation of outcomes, identification of the shortcomings and understanding decision making process have been an important researchable areas (Pomeroy & William 1994, ICLARM & NSC 1998). Evaluation of a system should include depiction of its goals or objectives and an assessment of how well they are met as well as obstacles faced in meeting them. Accordingly, it is important to identify the management context of the beel fisheries management viz., the formal goals of a fishery management regime; the formal or informal goals of the various actors within it; the processes by which goals are identified and contested; processes through which they are linked to other aspects of the regime- including knowledge production and the implementation of action measures (ICES 2000). Therefore, it is imperative to understand the objectives, decision making process and criteria for evaluation of the fisheries management of the wetlands as a step towards further research in designing effective management regimes. The paper attempts to delineate the system in the simplistic way as well as review the relevant literature to map the objectives, decision making arrangements and evaluation criteria for assessing the fisheries management regimes of the beels. The present paper has been made based on the experience and understanding developed in the context of the beel fisheries management of Assam.

Introduction Linear programming (LP) is one of the most widely applied operation research techniques and owes its popularity to George Dantzig’s simplex method (Danzig 1963). It is an important field of optimization for several reasons. Many practical problems in operation research can be expressed as linear programming problems. Linear programming is heavily used in microeconomics and business management, either to maximize the income or minimize the costs of a production scheme. Some examples are food blending, inventory management, portfolio and finance management, resource allocation for human and machine resources, planning advertisement campaign etc. In our economy, there are limited resources at our disposal. Our problem is to make such use of these resources to yield maximum quantity of production or to minimize the cost of production. Therefore, there arises the question of Linear Programming that is defined as a mathematical method of calculating the least cost combination of the factors of production, when there are many possible alternative combinations available to an enterprise.

Introduction A little information when shared can go a long way. Information patented can elevate India to great heights. Property (tangible) is associated with physical objects: house, land, etc., while intellectual property (intangible) includes Patents, Trade secrets, Copyrights, and Trademarks. Intellectual property rights (IPR) are legal rights which result from intellectual activity in industrial, scientific, literary, and artistic fields. Intellectual property protection (IPP) is right to protect intellectual property. Various types of IPR are:

Introduction S tates/organizations/agencies with statuary powers constitute Legislation, which are directly or indirectly related to their basic needs, smooth functioning of targeted system and to facilitate the safe survival of present as well as future generations of human being under jurisdiction. Legislation is a Latin word and customary that include all law constituted or in the process of constitution by empowered statuary houses/persons/group of people. Such Law has been categorized as Bill, Act, Rules and Regulations etc. Policy is a multipurpose dynamic tool, which activates different levels of administrative mechanism to perform various assignments systematically according to legislation systems. It includes collection of important information and statistics along with usefulness and validity of prevailing system of law. It brings required changes based on authentic and evaluated proper information. Legislation and policy and appropriate administrative mechanism are linked to each other in circular sequence. Constitution of legal documents and its success is totally linked with administrative mechanism presumed to implement it. Basically administrative mechanism for implementation of legislation and policy is the responsibility of state/government. To devise a good administrative mechanism to implement legislation successfully, is a complicated, dynamic and multidimensional process system which ensure the balance functioning of the different components with automatic feedback of the targeted output and effectiveness of the legislation system in place.