eChapters

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

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

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.

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

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.

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

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

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

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

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

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

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

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

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.

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 20^th century and in the 21^st 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 20^th 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

The contribution of agrochemicals in improving food security and human health cannot be undermined. They are, however, like a double-edged weapon; their indiscriminate use could result in a serious threat to the sustainability of the agricultural production system and human health. Though their long-term effects on environment and human health are yet to be fully understood, the short-term adverse effects of their indiscriminate use became apparent soon after their invention during the World War II. Many insect pests have developed resistance to chemical pesticides, and a number of beneficial insects that are natural enemies of the pests have disappeared. Realizing these threats, the scientific community has been proactive and developed safer alternatives using flora and fauna as substitutes for chemical pesticides. These alternatives are claimed to be as effective as chemical pesticides. Experimental evidences indicate that these provide effective protection against pests when used in conjunction with other methods of pest control, including chemical pesticides. The strategy is often referred to as Integrated Pest Management (IPM). Since the adoption of IPM as a cardinal principle of plant protection in 1985, India has devised and implemented many IPM programmes encompassing research, extension and education with the objective to reduce the use of chemical pesticides, improve farm profitability, conserve environment and reduce adverse effect of pesticides on human health. Their effect is revealed in considerable reduction in pesticide-use, particularly during 1990s. The purpose of this paper is to provide a perspective on the IPM with emphasis on food security and safety.

Variation is inherent in almost all biological populations. In any science, research work, that is, the study and explanation of development changes in a phenomenon can be theoretical as well as experimental. Thus, in order to have solution to a problem the need arises to collect relevant information (called data) their analysis and interpretation through appropriate statistical tools. Statistical analyses help the biologists to draw appropriate conclusions. For instance, in Integrated Pest Management (IPM) the entomologists are primarily concerned with the estimation of insect-pest population, its distribution pattern over time and space, its relationship/fluctuation in population with the prevailing weather parameters and ultimately its control measure through the judicious use of chemicals, biological control agents and resistant varieties etc. There are two broad modes of collection of data:

Introduction

Impact of WTO or Globalization of Indian agrarian sector claims to extend benefit of trade even to widely spread villages. In India, a sizeable number of rural masses are self-employed and able to produce what is needed just for their livelihood. They cannot be brought into market exchange relationship. So, there is every possibility of their being deprived of expected benefits. Globalization, rather, will widen the disparity between who are associated with market and who are not. Developed countries seem to have held globalization as a powerful weapon in their hands. They are stressing on opening up of national boundaries for movement of their goods and capital to developing countries but they are putting lot of restrictions on technology and labour movement, which can be far more beneficial to developing countries.

The World Trade Organization (WTO) is an international organization designed to supervise and liberalize international trade. It was established on 1^st January 2005 and is responsible for making and enforcing rules for trade between nations. WTO marks a major change in global trade rules. As an organization, it replaces the General Agreement on Tariffs and Trade (GATT), which had been in existence since 1947. The Eighth Round of Multilateral Trade Negotiations under GATT, which started in Uruguay in 1986, was concluded in 1994, leading to the creation of WTO as the new permanent international trade organization. The role of WTO is much more extensive than that of GATT, which dealt with trade in goods. Apart from goods, the two other broad areas that WTO covers are services and intellectual property, which previously belonged to the domestic domain. Accordingly, WTO administers not only the Multilateral Trade Agreements (MTAs) in goods but also the General Agreement on Trade in Services (GATS) and the Agreement on Trade Related Aspects of Intellectual Property Rights (TRIPS), which came into existence with WTO. All the agreements annexed to the Agreement establishing the WTO were signed as part of a package deal. Member countries did not have the option of choosing some and rejecting others. Another important difference with the erstwhile GATT is that WTO has a stronger compliance mechanism than did GATT-a member’s failure to meet the obligations can invoke retaliation across agreements and sectors.

Introduction

Plant protection in India is mainly based on use of pesticidal chemicals. Chemical control is one of the effective and quicker methods in reducing pest population where farmer gets spectacular results within a short time. However, indiscriminate use of pesticides results in a series of problems in the agricultural ecosystem mainly the development of resistance in insects to insecticides, resurgence of treated population, environmental contamination and residue hazards. Destruction of natural enemies of insect-pests, expenses on pesticides etc. contributed to a new way of thinking concerning pest control practices i.e. integrated approach of pest control. IPM was first proposed by Stern and his collegues for integration of biological and chemical control measures. This is not altogether a new concept; it was practiced before the advent of modern chemicals. The date of sowing the crop were carefully studied to ensure that crop was not being planted when it would encounter severe pest problems, cultural practices such as ploughing after harvest, timely weed control, well timed irrigation and reduced use of fertilizers all contributed to reduce pest population. Most of these methods were curtailed when modern pesticides become available it was thought that these chemicals alone could control pests, but now we know that this is not possible and a single method of approach in pest control is not feasible. An integrated approach of pest management (IPM) was devised on the principles of managing the pest rather than eradicating them. IPM is a broad ecological approach for managing pest problem encompassing available methods and techniques such as cultural, biological, mechanical and chemical in a compatible manner to reduce and maintain the pest problem below the economic injury level.