Role of Biotechnology in

Sustainable Rice Production

Dr. R.M. Sundaram
Principal Scientist (Biotechnology)
ICAR-Indian Institute of Rice Research
(ICAR-IIRR) Hyderabad
E-mail: rms_28@rediffmail.com

Rice - Indian perspective

Staple food for two thirds of the population

contributing 20-25% of GDP

Coverage ~44 m.ha (22% of cropped area)

2234 calories/person/day from rice (ie., ~30%)

Current production ~ 104 Mt

Demand ~ 130 Mt by 2025 AD and ~ 150 Mt by 2050 AD

How can we meet this demand?

Scope for biotechnological interventions in rice

improvement.
Conventional breeding responsible for progress
witnessed in green revolution era
But, can conventional breeding alone can be helpful to
meet future rice production targets? NO
A paradigm shift witness in breeding methodologies
New paradigm: Application of biotechnological tools for
rice improvement
Biotechnology can be helpful to
(i) increase productivity levels beyond yield barriers and

(ii) to sustain productivity over the coming years

through reduction of pest and disease incidence and
under reduced agro-inputs

Biotechnology can be helpful in enhancing breeding

efficiency through
i. Transfer of economically important traits/genes across species
and genera into the rice gene pool (i.e., broadening the genetic
base)
ii. Precise manipulation of target trait without any disruption
(or with minimal disruption) to non-target sites of the genome
(i.e., increasing the efficiency of selection)
iii. Shortening the breeding cycle considerably

Molecular breeding: Application of biotechnological tools in

breeding process

Biotechnological tools of relevance to rice improvement

DNA marker technology

Genetic Engineering
Genomics

A judicious, pragmatic application of these tools can be helpful to

avoid anticipated food shortages in future and enhance the food and
nutritional security of our country

Application of DNA markers technology

for rice improvement

DNA markers: Definition

A marker is a signpost linked to the trait/gene of interest and
is co-inherited along with the trait.
DNA
markers

- Gene of interest
Marker polymorphism = Trait / gene polymorphism
Presence of specific allele of marker = Presence of specific allele of target gene

Application of DNA markers

Seed purity testing
Varietal fingerprinting and patenting
Tagging, mapping and pyramiding major
genes for pest and disease resistance
Pyramiding QTLs of agronomic importance like Yield,
abiotic stress tolerance etc.
Map based cloning
Testing of GMOs and GMO products through PCR based
markers

Pyramiding multiple resistance genes in a single cultivar

Marker assisted breeding can reduce the time taken

for breeding significantly
Traditional breeding

marker assisted breeding

10,000 breeding
lines

10,000 breeding
lines
500
Field testing

100

Seed increase

20

-----Year 1-----

500

-----Year2----

20

----Year3--------Year4----

Commercial launch
Of 4 or 5 varieties

----Year5----

Molecular
Marker analysis

Field testing
Seed increase

Commercial launch
Of 4 or 5 varieties

Focus areas MAS program at ICAR-IIRR

Breeding for Biotic stress resistance (bacterial blight, blast, gall
midge, BPH and RTV resistance; elite varieties and Basmati
cultivars)
Application of molecular markers for hybrid rice improvement
- Seed purity assessment
- Fertility restoration
- Wide compatibility
- Introgression of biotic stress resistance gene(s) and quality

Identification and introgression of yield QTLs from wild relatives and

landraces of rice

Tagging and mapping grain quality traits

Marker-assisted introgression of biotic

stress resistance genes in rice

Rice

Bacterial blight

Gall midge

Blast

Marker assisted introgression of bacterial blight (BB)

resistance genes into Samba Mahsuri (BPT 5204)
Samba Mahsuri

High yield

Premium grain quality

Highly susceptible to BB

Markers used for Foreground and Background selection

1
RM6340
RM428

3
RM3340
RM485
RM110
RM279

RM60

RM551

xa5
RM231

5
RM335

RM7029
RG556

RM413
RM13

RM261
RM490
RM583
RM24

7
RM508
RM589
RM204
RM402
RM7488

RM174

8
RM295
RM481

RM163

RM541
RM3628

RM316
RM524

11

RM346
RM3859

xa13

RM332
RM247
RM491

RM6051
RM25
RM72
RM331
RM339
RG136

RM18
RM478

RM434
RM242
RM107

Xa21
RM271
RM269
RM304

RM215

RM246

RM497
RM250

RM178
RM340

RM411
RM212

RM248

RM6070
RM5545
RM458
RM264

RM280
RM7324
RM186

RM482
RM207

RM442
RM85

Foreground selection: 3 markers

Background selection: ~ 90 SSR markers

RM536
pTA248

RM287
RM229
RM5961

RM511
RM5590
RM463

RM294A
RM206

RM5919
RM5473
RM470

12

RM7545
RM244

RM5556

RM7
RM119

RM337
RM407
RM3309

RM320

RM169

RM324
RM561

10

RM591

RM17

Foreground selection of BC1F1 progeny for target trait

Selection for Xa21

44/145

Selection for xa13

Selection for xa5

23/44

11/23

Background selection of foreground selected BC1F1

plants using parental polymorphic SSR markers
SS SM 1

2 3 4

7 8

9 10 11
RM19

RM201

SS = SS1113; SM = Samba Mahsuri; 1 to 11 = BC1F1 lines

Screening of gene-pyramid lines of Samba Mahsuri against a

hypervirulent bacterial blight (BB) isolate (PNT8585)

Samba
Mahsuri
-Highly
susceptible
to BB

3-gene pyramid
lines (Xa21, xa13
and xa5) of
Samba Mahsuri
showing BB
resistance

Improved Pusa Basmati 1

Backcross mediated transfer of two bacterial blight

resistance genes from IRBB 55 to Pusa Basmati 1
Pusa Basmati 1

(Xa13 Xa13 xa21 xa21)

F1

IRBB 55
(xa13 xa13 Xa21 Xa21)

Pusa Basmati 1
MAS for BB resistance and
Phenotypic selection for
Basmati
and other characteristics

BC1F4 Generation
Joseph et al. 2004, Mol. Breed. 13: 377387

Grain quality features of Bacterial blight resistant Basmati

Breeding for bacterial blight resistance

A new bacterial blight resistance gene, Xa33 has been identified from Oryza
nivara (Acc. IRGC105710) and introgressed into Samba Mahsuri

Samba Mahsuri with Xa33 possessing bacterial blight

resistance and good grain type

Natarajkumar et al. 2010 Rice Genetics Newsletter 25: 54-56

Natarajkumar et al. 2011, Phytopathology (under revision)

Biotic stress resistance

Achievements: Blast resistance
10 novel resistance alleles of Pi54 and Pi-2 along with
their native promoters isolated and characterized
Functional marker developed for Pi54 and new set of
markers developed for Pi2
Pyramiding of Pi1, Pi2 and Pi54 in the genetic
background of Swarna and Imp. S. Mahsuri completed
Achievements: Gall midge resistance
Major gall midge resistance genes Gm1, Gm2, tagged
and fine-mapped on Chr. 9 and 4 respectively.
gm3 and Gm8 tagged and mapped on Chr. 4 and 8,
respectively
The gene combinations Gm1 + Xa21 and Gm4 + xa13
introgressed into Samba Mahsuri through MAS

Marker-assisted introgression
of yield enhancing QTLs from
wild rice into elite varieties and
parental lines

Major yield enhancing QTLs, yld2.1 and yld8.2

identified from O. rufipogon

Ref: Marri et al. BMC Genet (2005) 6: 33

Fine-mapping of yld2.1

Ref: Swamy and Sarla (2008) Biotech Adv. 26: 106-120

Increased grain number in KMR3-IL50

with yld2.1 subQTL3-4

Swarna introgression lines containing yield QTL

from O. nivara

Swarna

Swarna ILs

Genetic Engineering

Genetic Engineering: a potential alternative!

The possibility of introgression of alien genes into the host

plant genome across the barrier.

The gene can be derived from practically any organism

Handling single or few trait with perfection

What is Transgenic (GM) crop?

A crop plant, which has been artificially inserted with

a gene or genes (not acquiring them through
pollination), is termed as transgenic or geneticaly
modified (GM) crop.

There are two major DNA delivery methods plants:

Agrobacterium

Gene Gun

Genetic Engineering: a potential option for

Rice Improvement .
Among different breeding options, genetic engineering opens a
window of hope for rice improvement, particularly for some of
the recalcitrant traits, which cannot be improved through
conventional breeding or MAS.
Several Recalcitrant traits in rice: Tolerance to stem borer, leaf folder,
sheath blight, Nutritional improvement, NUE, Abiotic stresses, Herbicide
resistance

GE
A window of opportunity

Applications of GE in crop/rice improvement

Biotic stress resistance
o Resistance to insect pests
o Resistance to diseases
Abiotic stress tolerance
o Drought, salinity, low /high temperature, low soil
Nitrogen
Herbicide tolerance
o Complementary herbicide system
Development of value added products
o Improving vitamin content
o Improving protein quantity and quality
o Increasing starch, zinc and iron content
Enhancing photosynthetic efficiency of rice
o C3
C4 rice
33

Engineering rice for insect resistance

Insects causing damage

Yellow stem borer (Scirpophaga incertulas)

Striped stem borer (Chilo suppressalis)
Brown plant hopper (Nilaparvata lugens)
Leaf folder (Cnaphlocrasis medinalis)

Transgenes deployed:
Insecticidal proteins of B. thuringiensis

cryIA(b) (Fujimoto et al., 1993)

cry1A(b) (Datta et al., 1996)
cry1A(c) (Nayak et al., 1997)
cry1Ab/Ac (Cheng et al., 1998)

Protease inhibitors
Snowdrop lectin (Foissac et al., 2000,
Nagadhara et al., 2003)

Vegetative insecticidal proteins of Bt

vip (Estruch et al, 1996)

Disease resistance
Fungal

Bacterial

R. solani
Sheath blight
Yield Loss of 20-50% and even
upto 70% in severe conditions

Though chemical control is

effective, it is costly and not safe
for the environment..
Candidate Genes:
Chitinases
1,3-glucanases
Antifungal peptides

Bacterial blight caused by Xoo

10-30% yield loss

Chemical control methods not

available..
Candidate Gene:
Xa21, a dominant gene identified
from Oryza longistaminata is
known confers excellent
resistance to most races of BB

Disease resistance (Viral)

Viral Disease:
Rice tungro virus
Rice hoja blanca virus
Irregular incidence but
severe damage
No chemical control
Candidate Genes:
Coat protein gene
Replicase gene
RNAi based viral
silencing

Herbicide tolerance

Tolerance/resistance to herbicides could be

achieved through:
altering the level and sensitivity of the
target enzyme to the herbicide
introducing the gene that can detoxify
the herbicide in the plant. e.g.:
Transgenic rice plants resistant to high
doses of glufosinate under green house
conditions were produced by
constitutive expression of the bar gene
Various stages of evaluation by Pvt.
Companies in India

Transgenes available
bar gene (Basta
resistance)
CP4EPSPS
(Glyphosate
resistance)

Abiotic stresses: A major threat to rice production in India

Soil problems

Salinity

Changing climate

Drought

Conventional breeding: only limited success..

38

Genes at hand: Abiotic stress tolerance

The first group (functional proteins)
includes proteins that function
directly in stress tolerance (e.g. LEA,
Trehalose biosynthesis proteins etc.)
The second group (regulatory
proteins) consists of genes associated
with signal transduction and
expression that have indirect role in
stress response (e.g. DREB, Protein
kinases etc.)

Field testing of transgenic rice with high Nitrogen Use Efficiency (MAHYCO & Arcadia)

Transgenic

Candidate gene: Alanine amino transferase

Non-transgenic

Nutritional improvement
Nutritional quality of rice grains can be altered using genes cloned
from different plants, bacteria & animal species.
Golden rice
Iron rich rice (Ferretin)
Rice with high zinc (transporter)

High lysine rice

Back cross derived lines of Swarna

Swarna

Golden Swarna

Homozygous lines available for evaluation..

Improved S. Mahsuri

Golden Imp. S. Mahsuri

BC1F2 homozygous lines

Development of Ferretin rich GM rice: An opportunity to

increase iron content in rice endosperm

Sst I
nos

Bam HI
ferritin

GluB-1

Sst I
nos

Hind III

35S

bar

g7

Bam HI Kpn I
ferritin

Glo-P

Ferretin rice

Non GM rice
Sst I
nos

Bam HI Kpn I
ferritin

Pro-P

Mitigating climate change risks through C4 rice

Scope for increasing yield and abiotic stress tolerance
By converting the photosynthetic system in rice (i.e. C3 system) to
the more efficient, supercharged C4 system used by maize.
C4 Rice Consortium
The C4 Rice Consortium was formed in order to handle the diverse
range of scientists needed to make the C4 rice project a viable
endeavour. The consortium contributes extensively to the development
of C4 rice, under the leadership of IRRI, by providing appropriate levels
of expertise and, where suitable, personnel and resources.

46

Transgenic Research in Public & Private

Sectors (Trait-wise)
Traits

Crops

Insect resistance

Blackgram, brinjal, cabbage, cauliflower, chickpea,

cotton, maize, pigeon pea, potato, rice, tobacco,
tomato, wheat

Disease resistance

Blackgram, brinjal, chickpea, coffee, rice, tomato

Herbicide tolerance

Blackgram, cotton, mustard, rice

Abiotic Stress
tolerance

Mustard, rice

Nutritional
enhancement

Mustard, potato, rice

Edible vaccines

Muskmelon, tomato

Fruit ripening

Banana, potato, tomato

Out of 50 crops where GM research is actively pursued in India

, 40 are food crops

Transgenic crops under development and field trial

S.No.

Crop

Organization

Transgene

Rice

NRCPB/IARI, New Delhi,

DRR, Hyderabad, Osmania University,
TNAU, MKU, MAHYCO, Metahelix, Bayer
Biosciences, DKC, Calcutta University, BASF

cry1B-cry1Aa fusion gene, Cry1Ac,

Cry1Aa3, Cry1Abc, gna lectin,
Herbicide tolerance SPT (male
sterility/fertility), Golden rice,
Ferretin rice, Productivity traits

NRCPB/IARI, New Delhi

cry1Aa and cry1Aabc

Sungro Seeds Ltd, New Delhi

cry1Ac

Mahyco, Mumbai

cry1Ac

Cabbage

M/s. Nunhems India Pvt. Ltd., Gurgaon

cry1Ba and cry1Ca

Castor

Directorate of Oilseeds Research,

Hyderabad

cry1Aa and cry1Ec

Sungro Seeds Ltd, New Delhi,

cry1Ac, cry1Ba and cry1Ca

M/s. Nunhems India Pvt. Ltd., Gurgaon

cry1Ac, cry1Ba and cry1Ca

3
4
5

Brinjal

Cauliflower

Corn

Monsanto, Mumbai

cry1Ab gene (Mon 810 event)

Groundnut

ICRISAT, Hyderabad

chitinase gene from rice(Rchit)

Okra

Mahyco, Mumbai

cry1Ac, cry2Ab

Potato

Central Potato Research Institute (CPRI),

Shimla

RB gene derived from Solanum

bulbocastanum

Rice Genomics
An opportunity to uncover
the unknown from rice
genome and to manipulate
them

Rice Genomics

Structural genomics

Functional genomics

Deciphering (reading) the

complete genome sequence
of rice (~389 Mb)

Understanding the
function of each and every
rice gene (~30,000 genes)

Accomplished recently
(2005) through International
collaboration IRGSP
Sequencing done in
Nipponbare

Utilization of genes and

gene specific markers for
rice improvement

India, a key partner to IRGSP

Profile of Rice Genome

Genome Size
: ~389 Mb
No. of genes
: ~30,000
Chromosomes(n) : 12
SSR markers
: ~20,000
Includes several Retrotransposons
eg. Copia Gypsy, Tos17
Various types of transposable
elements
eg. En/spm
CACTA- like
Marimer like
Mites

International Rice genome sequencing Initiative

Comparative genome mapping: Genes discovered in rice

helpful to identify syntenic genes in related cereals

Rice

Maize

Barley

Rice Improvement
through biotechnology

Farmers fields

Policy and IPR

issues

Pre-breeding
stage
DNA
technology

Marker
assisted
selection

Transgenic
technology

Genomics

Gene
discovery

The way forward..

A judicious, pragmatic application of molecular markers, transgenic

technology and genomic tools can result in tangible genetic
improvement of rice and lead us towards a second green revolution.
But isolated efforts by molecular biologist alone cannot help

Involvement of Geneticist/breeder is necessary at each step

Targeting towards second green revolution