Innovations%20in%20Agriculture:%20Genomics%20for%20Better%20Agri-Productivity%20%20Dr%20Shahana%20Urooj%20Kazmi%20Dean%20 - PowerPoint PPT Presentation

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Innovations%20in%20Agriculture:%20Genomics%20for%20Better%20Agri-Productivity%20%20Dr%20Shahana%20Urooj%20Kazmi%20Dean%20

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Nutritional Genomics ... The term 'nutritional genomics' is used to describe work at the interface of plant biochemistry, genomics, and human nutrition. ... – PowerPoint PPT presentation

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Title: Innovations%20in%20Agriculture:%20Genomics%20for%20Better%20Agri-Productivity%20%20Dr%20Shahana%20Urooj%20Kazmi%20Dean%20


1
Innovations in AgricultureGenomics for Better
Agri-Productivity Dr Shahana Urooj KazmiDean
Faculty of Science and Professor of
Microbiology and ImmunologyUniversity of
Karachi(F-Member Animal Sciences )_Pakistan
Agricultural Research Council Islamabad
2
Nutrigenomicsfor 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.

3
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.

4
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.

5
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.

6
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.

7
PARC Research Establishments
8
National Agricultural Research CentreIslamabad
9
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, gt 30 small ruminant
    breeds
  • Fifth largest milk producing country

10
Sub-Sectoral Contribution to Agricultural GDP -
2006-07
Source Economic Survey of Pakistan 2006-07
11
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 gt 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)

12
LIVESTOCK PRODUCTS
  • Milk 33.230 million tons
  • Beef 1.237 million tons
  • Mutton 0.827 million tons
  • Poultry meat 0.514 million tons
  • Eggs 9.618 billions
  • Wool 41.2 thousand tons
  • Hair 25.0 thousand tons
  • Skins and hides 57.6 million nos.
  • Economic Survey (2006-07)

13
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)

14
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)
15
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)
16
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)
17
Improved Cattle Breeding Through Embryo
Transfer Technique with Doubling of Milk Yield
per Animal per Year
18
Research Priorities for Better Future of
Livestock
19
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

20
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.

21
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 bio-security
    issues and disease epidemics.

22
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.

23
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

24
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.

25
NATIONAL INSTITUTE FOR GENOMICS AND ADVANCED
BIOTECHNOLOGY (NIGAB)
26
  • PROJECT OBJECTIVES
  • Molecular evaluation of crops, microbes and
    food animals for improving productivity.
  • QTL mapping in selected plants and food
    animals.
  • Development of genetic linkage/fine genome maps
    for important traits and marker-assisted
    breeding.
  • Development of gene based therapeutics, vaccines
    and diagnostics for food animals.
  • Characterization of important genes of crops,
    animals and microbes and their exploitation
    through functional genomics.
  • Identification of SNPs/DNA mutation for disease
    management in animals and plants.
  • Data management and development of
    bio- informatics tools.

27
QUANTIFIABLE/MONITORABLE TARGETS
Activity Quantifiable/Monitor able Targets/Indicators
1 Molecular evaluation and QTL analysis of stress responsive genes in selected animals, crops and microbes Quantification of genetic diversity and QTLs identification for biotic (disease, insect etc.) and abiotic (drought, salt, temperature) stresses in major crops. In case of domesticated 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 targetted genes/SNPs/mutation of significance in animals, plants and microbes SNPs and their association with disease resistance / susceptibility and drug efficacy in animals will be investigated. In case of microbes, gene mutation in avian influenza virus, FMD virus will be studied in field isolates, 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 techniques PCR, RT-PCR, and NA-sequence based diagnostics will be developed against 4 selected animal diseases and would be made available for public or private institutional usage.
28
4 DNA fingerprinting of traditional and improved cultivars of different and animals (cattle, poultry, fish etc) and crops (wheat, rice, etc) DNA pattern and profiles of various crop cultivars and animal breeds would be available for identification and utilization in breeding programme
5 Development of transgenic plants (wheat, rice, etc, for disease, insect, drought and salt tolerance. Genetically modified plants of given crops resistant to various stresses will be made available.
6 Development of DNA based vaccines against selected animal diseases Genetically modified against at least 2 major food animal diseases (FMDV, Av influenza) will be made available for public or private sector usage.
7 Organize seminars/ workshops/ conferences/training courses 10 training Workshops/ seminars/ conferences to be conducted
29
  • PROJECT OUTPUTS
  • Molecular evaluation of major crops and animal
    species
  • Identification transformation of disease
    resistance and stress responsive genes.
  • Elucidation of genetic diversity in local food
    animals such as chicken and buffalo.
  • Identification of genes affecting milk
    production and disease resistance.
  • Availability of genetically modified plants
    resistant to stresses (drought, salt, temperature
    etc).

30
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.
  • Availability of gene based therapeutic molecules
    for animal treatment.
  • 9. Data base regarding gene sequencing from
    plants, animals and microbes.

31
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.

32
  • 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.

33
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.

34
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.

35
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.

36
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.

37
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.

38
  • 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.

39
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.

40
Nutrigenomics
  • Results from molecular and genetic
    epidemiological studies indicate that dietary
    unbalance can alter genenutrient 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.

41
TASK
  • We can meet this challenge by using innovative
    methodologies ,comprehensive analyses of
    nutrientgenotype 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.

42
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

43
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.

44
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.

45
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 whole-genome databases. Comparison
    of an individual's geno-type 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.

46
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 ---

47
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 dis-ease
    with pharmaceuticals.

48
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.

49
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.

50
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.

51
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.

52
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.

53
  • THANK YOU VERY MUCH
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