Nutritional Genomics Manipulating Plant Micronutrients to Improve ...

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5 Δεκ 2012 (πριν από 4 χρόνια και 6 μήνες)

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Innovations in Agriculture:

Genomics for Better Agri
-
Productivity




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.

Thatta

Mansehra

D.I.Khan

Bahawalpur

Umerkot

Kaghan

Tandojam

Faisalabad

PARC (9)

NARC

AZRC

SARC

NSCRI

NTRI

KARINA


AZRIs

1

1

3

1

1

1

1

7



TTIs


Muzaffarabad

Gilgit

PARC Research

Establishments

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

Source: Economic Survey of Pakistan: 2006
-
07

Minor Crops
12%
Forestry
3%
Fisheries
1%
Major Crops
35%
Livestock
49%
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



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)









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 bio
-
security 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 bio
-

informatics tools.

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
.

QUANTIFIABLE/MONITORABLE TARGETS

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

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).


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.

PROJECT OUTPUTS contd..

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 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.

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 dis
-
ease 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