Transcript Nutritional Genomics Manipulating Plant Micronutrients to

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.
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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
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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
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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
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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
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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
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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)
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Preparedness for Bird Flu at National
and Regional Level (SAARC)
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Developed State of Art
Diagnostic Tools
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Effective Surveillance
& Monitoring System
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Network Covers whole
Pakistan (12 Labs)
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Includes Domestic and
Commercial Poultry,
Wild & Migratory Birds
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H5N1 in the Country
(yes)
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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
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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.
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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.
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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
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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.
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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
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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
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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
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1) DNA based characterization of germplasm of important
crops, genome of microbial pathogens and food animals .
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2) Development of genetic linkage/fine genome maps for
important traits of interest, and marker-assisted breeding.
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3) Development of gene-based veterinary therapeutics,
drugs, vaccines & diagnostics.
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4) Discovery of important genes of crop, animal and
microbes and their exploitation through functional
genomics.
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5) Data management and development of Bioinformatics.
Outreach & Training.
Challenges
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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
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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.
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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
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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
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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.
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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
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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
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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
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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.
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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
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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
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1) include a highly comprehensive set of metabolite
measurements (a profile) by multiparallel analyses,
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2) measure the metabolic profile of indi-viduals over
time rather than simply in the fasted state, and
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3) integrate these metabolic profiles with genomic,
expression, and proteomic databases.
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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
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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
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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
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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.
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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
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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.
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THANK
YOU VERY MUCH