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Innovations in Agriculture: Genomics for Better AgriProductivity Dr Shahana Urooj Kazmi Dean – Faculty of Science and Professor of Microbiology and Immunology University of Karachi (F-Member Animal Sciences ) _Pakistan Agricultural Research Council Islamabad Nutrigenomics for Better Health The nutritional health and well-being of humans is entirely dependent on plant foods either directly or indirectly when plants are consumed by animals. Plant foods provide almost all essential vitamins and minerals / micronutrients and a number of other health- promoting phytochemicals which are very often low in staple crops, research is under way to understand and manipulate synthesis of micronutrients in order to improve crop nutritional quality. Genomics for Productivity Genetic and biotechnology products are providing innovative solutions to the crucial global problems. Advances in molecular genetics, agricultural and veterinary sciences and related biotechnology fields are leading to the development of novel drugs, recombinant vaccines, diagnostics, GM crops, removal of harmful pollutants from the environment, safe food-chain production and increasing world food supply. Genomics-- Genomics and proteomics are two very important expanding fields expected to lead to the development of additional gene-base therapeutics, drugs, new generation of vaccines, diagnostic tests for the detection of genetic conditions, providing means of identifying and characterizing disease specific proteins as well as proteomics that play important role in growth, reproduction and metabolism of animals, microbes and plants. Nutrigenomics Nutrigenomics is the study of how constituents of the diet interact with genes, and their products, to alter phenotype and, conversely, how genes and their products metabolize these constituents into nutrients, antinutrients, and bioactive compounds. Nutritional Genomics Genome sequencing projects are providing novel approaches for identifying plant biosynthetic genes of nutritional importance. The term "nutritional genomics" is used to describe work at the interface of plant biochemistry, genomics, and human nutrition. PARC Research Establishments Gilgit Kaghan Mansehra Muzaffarabad D.I.Khan Faisalabad PARC Bahawalpur Umerkot Tandojam Thatta (9) NARC AZRC AZRIs SARC NSCRI NTRI KARINA TTIs 1 1 3 1 1 1 1 7 National Agricultural Research Centre Islamabad Role of Livestock Livestock plays an important role in the economy of Pakistan and in the rural socio-economic system 30-40% of income of more than 35 million rural population comes from livestock production activities The livestock sector contributed 50% of the agriculture value added and 11% to National GDP in 2006-07 Eight percent of total exports derived from livestock and livestock products Pakistan possesses some of the finest dairy breeds like Nili-Ravi and Kundi buffaloes, and Red Sindhi & Sahiwal cattle, > 30 small ruminant breeds Fifth largest milk producing country Sub-Sectoral Contribution to Agricultural GDP - 2006-07 Fisheries 1% Livestock 49% Forestry 3% Major Crops 35% Minor Crops 12% Source: Economic Survey of Pakistan: 2006-07 LIVESTOCK IN NATIONAL ECONOMY Agriculture in Pak GDP 22.0 % Livestock in Pak GDP 10.4 % Share in agri GDP 49.1 % Livestock in export 8.5 % (935 m US$) Dependent population > 6.5 m families Provides raw material for industry Social security for rural poor Security against crop failure in rainfed areas Growth rates 1990s 4.5% 2000-2007 3.2 % Economic Survey (2006-07) LIVESTOCK PRODUCTS Milk Beef Mutton Poultry meat Eggs Wool Hair Skins and hides nos. 33.230 million tons 1.237 million tons 0.827 million tons 0.514 million tons 9.618 billions 41.2 thousand tons 25.0 thousand tons 57.6 million Economic Survey (2006-07) Challenges Facing Livestock Poor genetic & reproductive efficiency Epidemics of infectious diseases Lack of organized marketing Small holders’ production system Shortage (by 30%) of feed resources in quantity & quality Unavailability of credit to the livestock farmers (11% of agricultural credit) Preparedness for Bird Flu at National and Regional Level (SAARC) Developed State of Art Diagnostic Tools Effective Surveillance & Monitoring System Network Covers whole Pakistan (12 Labs) Includes Domestic and Commercial Poultry, Wild & Migratory Birds H5N1 in the Country (yes) Poultry Pathogen (H7 & H9) Bird Flu virus (AI type A) Genetic Improvement of Indigenous Cow (Dhanni) w/ Exotic Jersey Bull Yielded Crossbreds upto 2 to 3 Times Increase in Milk Production (From 3 to 8.5 lit/day) Exotic Rambouillet sheep of USA when cross-bred with Waghani Sheep of Malakand & Kaghan- valley sheep with doubling of quantity of wool of superior quality (from 0.8 kg to 2 kg & fiber diameter 30 to 23 µ per shearing per animal) Improved Cattle Breeding Through Embryo Transfer Technique with Doubling of Milk Yield per Animal per Year Research Priorities for Better Future of Livestock Breeding & Genetics Characterization & sustainable management of animal genetic resources for meeting future needs of food and agriculture. Development of genetic improvement programs for indigenous livestock & poultry breeds Development of breed inventories and population trends for assessment of breed status. Develop advanced molecular genetic techniques for detection of QTLs for economically important traits Development of indigenous chicken breeds for backyard poultry Development of growth curves for different dairy and meat breeds of livestock Development of recording and breeding models for various livestock breeds Improving Feed Resources and Technologies Improved fodder production & preservation. Improving nutritional quality of existing feed/fodder resources & agro-industrial wastes. Economical calf and heifer rearing for different production systems. Research & Biotechnological interventions in relation to animal nutrition. Animal Health Development of efficient and innovative methods for diagnosis of livestock and fish diseases. Development of techniques for production of vaccines to control important livestock & poultry diseases such as, FMD, PPR, AI, ND, IBD, HS, Brucellosis, Infectious Mastitis, CCPP, etc. using genomics, proteomics and other techniques. Studies on antiviral activity of indigenous plants. Epidemiology and control of emerging and re-emerging infections/diseases in livestock. Animals and farm bio-safety and biosecurity issues and disease epidemics. Animal Reproduction Improvement of cryo-preservation techniques of buffalo and cattle semen and embryo. Research in oestrus detection and control of seasonal infertility in buffaloes. Biotechnological interventions in animal reproduction. Livestock Product Technology Studies on improvement of quality of livestock products Studies on development of value added products Establishment of starter culture bank of fermented dairy products Research in human bio-safety issues in animal origin food chain Fisheries and Aquaculture Development of improved aquaculture system for high value fish & shell fish species like carps, trout, catfish, snake head, prawn, crabs & shrimps Development of genetically enhanced fish for aquaculture system & production of superior germplasm. Development of least cost feed for intensive fish culture Research on Immunology & infectious diseases of fish. Effe3cts of pollution on fish & fisheries. Marine & inland resource assessment & their management with specific reference to mangrove forests, mahaseer, Hilsa (palla) and tuna fishes. Establishment of data base on fish & fisheries outlook. NATIONAL INSTITUTE FOR GENOMICS AND ADVANCED BIOTECHNOLOGY (NIGAB) PROJECT OBJECTIVES 1. Molecular evaluation of crops, microbes and food animals for improving productivity. 2. QTL mapping in selected plants and food animals. 3. Development of genetic linkage/fine genome maps for important traits and marker-assisted breeding. 4. Development of gene based therapeutics, vaccines and diagnostics for food animals. 5. Characterization of important genes of crops, animals and microbes and their exploitation through functional genomics. 6. Identification of SNPs/DNA mutation for disease management in animals and plants. 7. Data management and development of bioinformatics tools. QUANTIFIABLE/MONITORABLE TARGETS Activity Quantifiable/Monitor able Targets/Indicators 1 Molecular evaluation and QTL Quantification of genetic diversity and QTLs identification analysis of stress responsive genes in for biotic (disease, insect etc.) and abiotic (drought, salt, temperature) stresses in major crops. In case of domesticated selected animals, crops and microbes animals (including livestock, poultry and fish), disease specific markers as well as growth enhancing markers will be identified for exploitation/ genetic manipulation. 2 Identification and characterization of SNPs and their association with disease resistance / targetted genes/SNPs/mutation of susceptibility and drug efficacy in animals will be significance in animals, plants and investigated. In case of microbes, gene mutation in avian influenza virus, FMD virus will be studied in field isolates, microbes for developing new vaccines. In case of plants, gene/s responsive to growth/production, disease tolerance, insect/parasite , drought, salt, will be identified and their expression will be monitored accordingly. 3 Development of molecular diagnostic PCR, RT-PCR, and NA-sequence based diagnostics will be developed against 4 selected animal diseases and would be techniques made available for public or private institutional usage. 4 DNA fingerprinting of traditional DNA pattern and profiles of various crop cultivars and and improved cultivars of animal breeds would be available for identification different and animals (cattle, and utilization in breeding programme poultry, fish etc) and crops (wheat, rice, etc) 5 Development of transgenic plants Genetically modified plants of given crops resistant to (wheat, rice, etc, for disease, various stresses will be made available. insect, drought and salt tolerance. 6 Development of DNA based Genetically modified against at least 2 major food vaccines against selected animal animal diseases (FMDV, Av influenza) will be made diseases available for public or private sector usage. 7 Organize seminars/ workshops/ conferences/training courses 10 training Workshops/ seminars/ conferences to be conducted PROJECT OUTPUTS 1. Molecular evaluation of major crops and animal species 2. Identification & transformation of disease resistance and stress responsive genes. 3. Elucidation of genetic diversity in local food animals such as chicken and buffalo. 4. Identification of genes affecting milk production and disease resistance. 5. Availability of genetically modified plants resistant to stresses (drought, salt, temperature etc). PROJECT OUTPUTS contd.. 6. Gene based diagnostic techniques will be made available for animal health improvement. 7. Genetically modified vaccines available against avian influenza and foot and mouth disease. 8. Availability of gene based therapeutic molecules for animal treatment. 9. Data base regarding gene sequencing from plants, animals and microbes. Biotechnology -- Genetic and biotechnology products are providing innovative solutions to the crucial global problems. Advances in molecular genetics, agricultural and veterinary sciences and related biotechnology fields are leading to the development of novel drugs, recombinant vaccines, diagnostics, GM crops, removal of harmful pollutants from the environment, safe food-chain production and increasing world food supply. Genomics and proteomics are two very important expanding fields expected to lead to the development of additional gene-base therapeutics, drugs, new generation of vaccines, diagnostic tests for the detection of genetic conditions, providing means of identifying and characterizing disease specific proteins as well as proteomics that play important role in growth, reproduction and metabolism of animals, microbes and plants. NIGAB The ultimate goal of initiating genomic studies is to understand the structure and function of every gene in an organism. With the intent of exploiting this knowledge for the betterment of society, efforts will be made to focus on plant species, food animal species and microbes important to agriculture, and livestock. NIGAB The present project will result in discovering new genes; function of the genes; structural and genomic organization of the genes; DNA markers for different traits of interest etc which will play a pivotal role in developing new crop varieties, and animal breeds, development of new drugs, generation of new knowledge and development of human resource. This increased emphasis on the genome will radically change fundamental agriculture & livestock research along with the environment in the country. Objectives: NIGAB 1) DNA based characterization of germplasm of important crops, genome of microbial pathogens and food animals . 2) Development of genetic linkage/fine genome maps for important traits of interest, and marker-assisted breeding. 3) Development of gene-based veterinary therapeutics, drugs, vaccines & diagnostics. 4) Discovery of important genes of crop, animal and microbes and their exploitation through functional genomics. 5) Data management and development of Bioinformatics. Outreach & Training. Challenges Major challenges in the 21st Century are increased food and fiber production, a cleaner environment, and renewable energy resources. A greater understanding of the organization and function of different genomes is essential, if agriculture in Pakistan is to be successful in meeting the growing needs for food, feed and a source of industrial raw materials as Pakistan moves towards an "agri-based" economy. Challenges The study of genomes, also called genomics, consists of mapping, sequencing, and analyzing genomes to determine the function of genes in plants, microbes and animals. Efforts to study genomes of different crop plants, i.e. Arabidopsis (USA); rice (India China and Japan; cotton (USA); maize (USA) etc., have started very actively during the last five years. Under these projects, a team of molecular, quantitative and evolutionary geneticists and bioinformatics experts has been assembled to build up investments in plant genomics to develop the novel high-throughput genetic mapping technologies and resources needed to meet the future challenges. Information and knowledge gained through genomics would be utilized to improve the useful traits of plants through genetic engineering and molecular breeding strategies. Similarly, in case of food animal genomics, linkage and comparative maps for all livestock species have been made available to the public, through international collaborations and efforts. The recent and ongoing development of whole genome sequence maps of chickens, honeybee, dog, and cattle species is a major step forward. SNP based maps now being developed from the chicken and cattle genome sequencing projects in USA and elsewhere, will be of enormous value in evaluating genetic diversity, fine mapping of QTL and development of DNA-based animal identification systems. Nutritional Genomics Genome sequencing projects are providing novel approaches for identifying plant biosynthetic genes of nutritional importance. The term "nutritional genomics" is used to describe work at the interface of plant biochemistry, genomics, and human nutrition. Nutrigenomics Results from molecular and genetic epidemiological studies indicate that dietary unbalance can alter gene–nutrient interactions in ways that increase the risk of developing chronic disease. The interplay of human genetic variation and environmental factors will make identifying causative genes and nutrients a formidable, but not intractable, challenge. TASK We can meet this challenge by using innovative methodologies ,comprehensive analyses of nutrient–genotype interactions involving large and diverse populations. For this we need to stimulate discourse and collaboration among nutrigenomic researchers and stakeholders, a process that will lead to an increase in global health and wellness by reducing health disparities in developed and developing countries. Genomics and Metabolomics as Markers for the Interaction of Diet and Health Foods are not purified compounds acting on single molecular targets, but complex mixtures of molecules that modulate many biochemical pathways simultaneously. Diet affects the probability of developing various diseases. Nevertheless, specific recommendations for individual diets are not simple. Recommending nutrient intakes above and beyond those needed to provide adequacy requires scientific knowledge and regulatory scrutiny to ensure the efficacy and safety even of essential nutrients Genomics and Metabolomics as Markers for the Interaction of Diet and Health Designing a diet to improve metabolic health is a bold and ambitious goal. It is possible to design foods that will alter metabolism, but what change will make everyone who is otherwise healthy even healthier? Changing one aspect of metabolism to lower the risk of one disease does not improve overall health if it comes at the expense of disrupting another aspect of metabolism that increases the risk of another disease. Pharmacogenomic Differences An individualized system for metabolic assessment needed to establish the efficacy and safety of nutrients such as amino acids or fatty acids when these are designed to be consumed at levels providing improved metabolic health. The need to document the lack of an adverse effect of a food or drug on physiology necessitates a global, i.e. metabolomic approach. Individual Metabolism should guide agriculture for improved health and nutrition Genomics and bioinformatics have the vast potential to identify genes that cause disease by investigating wholegenome databases. Comparison of an individual's genotype with a genomic database will allow the prescription of drugs to be tailored to an individual's genotype. This same bioinfor-matic approach, applied to the study of human metabolites, has the potential to identify and validate targets to improve person-alized nutritional health and thus serve to define the added value for the next generation of foods and crops. Individual Metabolism and agriculture Advances in high-throughput analytical chemistry and computing technologies make the creation of a vast database of metabolites possible for several subsets of metabolites, including lipids and organic acids. In creating integrative databases of metabolites for bioinformatic investigation, the current concept of measuring single biomark-ers must be expanded to 3 dimensions – that is --- Individual Metabolism agriculture 1) include a highly comprehensive set of metabolite measurements (a profile) by multiparallel analyses, 2) measure the metabolic profile of indi-viduals over time rather than simply in the fasted state, and 3) integrate these metabolic profiles with genomic, expression, and proteomic databases. Application of the knowledge of indi-vidual metabolism will revolutionize the ability of nutrition to deliver health benefits through food in the same way that knowl-edge of genomics will revolutionize individual treatment of disease with pharmaceuticals. Genomics and Biotechnology Molecular Biotechnology, accelerated by genomics, will create wealth for both producers and consumers by reducing the cost and increasing the quality of food. Famine and malnutrition in the poorest countries may be alleviated by applying genomics or other tools of biotechnology to improving subsistence crops. The Rationale for Biotechnology The new wealth of the developing world has made possible the transition to a meat-based diet, with a consequent expansion in the demand for grain. The demand for food is expected to grow with population increase which will double over the next 45 years . Worldwide production acreage probably will not change, although in some areas there will be decline because of urbanization and environmental degradation. Molecular Biotechnology The ability to make large, qualitative or quantitative improvements by using transgenic methods provides the rationale for biotechnology in agriculture. Genomics is vital to this ability because it can greatly accelerate the discovery of genes for transformation and enhanced productivity. The next generation of improved traits will include disease resistance, hybrid seeds and grain quality. These traits may be conferred by multiple genes whose products cause major changes in cell physiology. Stacking multiple traits into a single cultivar will be a challenge. Genomic Databases Creating an EST (expressed sequence tags) DNA database of our major crops should be the top priority for agricultural plant genomics. In contrast, complete genome sequencing is currently only practical for microbes with small genomes, with the exception of a few large, international efforts to sequence the yeast, human, nematode, fruit fly, and mouse-ear cress genomes. The sequence of the latter, also known as Arabidopsis thaliana, will be invaluable for both science and the development of agricultural products. Contributing to the timely completion of the Arabidopsis sequencing project should be the second-highest priority for agricultural plant genomics. Genomics Genomics will accelerate the application of gene technology to agriculture , will enhance food security, by increasing productivity, and food safety, by eliminating mycotoxins and improving economic indicators. significantly increases the value of seeds and agricultural products adding wealth to the customers, company owners, employees, and citizens of the nations in which genetic supply companies operate, and to both producing and importing nations whose food costs consequently are decreased. THANK YOU VERY MUCH