Genomic Resources for

Molecular Plant Breeding

A. K. Singh Division of Genetics

IARI, New Delhi

Plant genome sequencingSpecies and genotype Genome

size (Mb)Ploidy Sequencing

strategyCov erage Refs

Finished genome sequences (2)

Arabidopsis (cv. Columbia)

125 Diploid BAC-by-BAC ∼15× AGI, 2000

Rice (cv. Nipponbare) 389 Diploid BAC-by-BAC 10× IRGSP, 2005

Improv ed High quality draft genome sequences (7)

Sorghum (cv. BTx623), Grapev ine (cv. PN40024), Brachypodium (line Bd21), Soybean (cv. Williams 82),

Poplar (cv. Nisqually-1), Maize (cv. B73), Cucumber (IL 9930)

High quality draft genome sequences (7)

Rice (cv. Nipponbare, 93-11), Grapev ine (cv. ENTAV 115), Papa ya (Scv. unUp), Peach (cv. Lov ell), Apple

(cv. Golden delicious)

Standard draft genome sequences (11)

Pigeonpea (cv. Asha), Me dicago (cv. Jemalong A17 ), Maize (cv. Palomero Toluqueno), Lotus (cv.

Mi yakoj ima MG20), Castor (cv. Hale), Potato (DM1-3-516 R44), Cassav a (cv. AM560-2), Toma to (cv.Esculentum x pennellii), Chinese cabbage (cv. Chiifu-401-42), A. lyrata

Genome sequencing underway (15)

Rapeseed, Brassica oleracea, B. rapa (cv. B3), Sweet orange (cv. Ridge pineapple), Oil palm (cv. Tenerax dura), Eucalypltus (cv. BRASUZ1), Gossypium raimondii, Jatropha, Tobacco (cv. Hicks broadleaf),

Foxtail millet (cv. Yugu1), Potato (RH89-039-16), Cowpea, Maize (cv. Mo17), Bread wheat (cv. Chinesespring)

‘Omic’ resources in plants

Mochida and Shinozaki (2010) Plant Cell Physiol, 51:497-523

TIPS (2005)

Translating potential of genetic resources into with genomic resources

Abe et al (2012) Nat. Biotech. http://www.nature.com/doifinder/10.1038/nbt.2095

Mutmap – Utilizing mutagenesis and NGS for mapping traits

Basmati rice in India

Rice

Total rice area - 44 mha

Total rice production – 100 mt

Basmati rice

Total Basmati rice area - 2.0 mha

Basmati rice production - 4.0 mt

Forex earning- 11,000 Crores

Traditional Basmati Varieties

Tall

Prone to lodging

Photoperiod sensitive

Poor yield

Beginning of Basmati Breeding

(1966)

TKM 6 IR 8

TN1 Basmati 370

Pusa 2-21

Sabarmati

Ratna

Surinam 81-8-25 Pusa 70 Pusa 33

Pusa 140 IR 22

Pusa 150 Karnal Local

Pusa Basmati – 1

(Pusa 615)

Improved Sabarmati

Pusa Basmati 1 – First Semi-dwarf High

Yielding Basmati Rice Variety (1989)

Improved rice varieties developed at IARI

19892001

2001

2001

2003

2004

100

110

120

130

140

150

160

170

Taraori

Basmati

Pusa Basmati

1

Pusa

Sugandh 2

Pusa RH 10

(Hybrid)

0

1

2

3

4

5

6

7

Du

ratio

n (

da

ys)

Yie

ld (

t/h

a)

Higher yields with short duration cultivars

0

2000

4000

6000

8000

10000

12000

1990-91 1995-96 2000-01 2005-06 2006-07 2007-08 2008-09 2009-10 2010-2011

294

850

2148

30302792

4344

8000

1088910582

Value (Rs. in Crores)

Value of Basmati rice

($ 2.17 billion)

($ 5.6 million)

1. Bacterial blight

Challenges for Molecular Breeding

2. Blast

3. Hopper

Brown Plant Hopper damage can be really serious

Bacterial blight Blast

BPH Hopper BurnFalse Smut

37 genes 83 genes

21 genes

Sheath Blight

12 QTLs

Genes/ QTLs mapped for

biotic stress resistance in rice

Pusa Basmati1

Farmers’ Participatory Seed Production

Improved PB 1(Pusa 1460)

Pusa 1460: Improved Pusa Basmati 1

Empowering Farmers to Fight Blight

Pusa1460+blast (Pi54)+ SB(qSHB) (Submitted AOB Plants)

Pusa1460

Pusa1608-1

Pusa1608-2

Pusa1608-3

Pusa1608-4

Pusa1608

Designation Parentage KLBC

(mm)

KLAC

(mm)

ER Aroma

Pusa 1475-1 PB-1/IRBB60//P1302 8.4 18.6 2.21 2

Pusa 1475-2 PB-1/IRBB60//P1302 8.5 18.6 2.18 3

Pusa 1560-1 P1463/P1460 8.4 18.0 2.14 2

Pusa 1560-2 P1463/P1460 8.6 18.3 2.12 2

Pusa 1560-3 P1463/P1460 9.2 21.0 2.28 2

Pusa 1560-4 P1463/P1460 7.8 18.5 2.37 2

Pusa 1560-5 P1463/P1460 8.5 19.3 2.27 2

Pusa 1560-6 P1463/P1460 8.1 18.8 2.32 2

Pusa Basmati 1121 8.3 18.0 2.16 2

Pusa 1460: An Enhanced Germplasm

with BB Resistance for Basmati Breeding

Field view of advanced breeding lines

P1560-5P1475-1PB 1121P1485-1P1551-1P1560-6

M P1460 PB1 SPS

xa13 with xa13prom

Xa21 with pTA248

M P1460 PB1 SPS

500bp

500bp

1000bp

250bp

MAS - An Integral Part of Basmati Breeding program

Pusa RH 10

MAS for xa13 and Xa21

C101A51

Tetep

PRR78

Donors

Recipient

180bp

160bp

M P1 P2 1 5

Piz-5

Pi54

180bp

160bp

M P1 P2 1 5

Rf1

M P1 P2 1 5

180bp160bp

NILs Nominated in AVT1-BT

Pusa1609Pusa1601

Pusa Sugandh 5

BB Res.: xa13 + Xa21 Blast Res.: Pi54 + Piz-5

Genomics assisted breeding for improving

fruit quality in tomato

Barone et al (2009) Curr. Genomics, 10(1): 1–9

Genetic Enhancement: Development of NILs for major

blast resistance genes in the background of Pusa Basmati 1

S. No. Gene (s) No. of NILs

1. Pi-1 10

2. Pi-kh 20

3. Pita 20

4. Pi1+ Pikh 20

5. Pi1+Pita 10

6. Pita+Pikh 20

7. Pi-1+ Pita+Pikh 15

8. Pi5 20

9. Pi9 20

10. Pib 10

11. Piz-5 20

This is the first set of NILs carrying major blast resistance genes in the of a

Basmati background to be utilized in functional genomics

Besides the potential for release as improved variety, they will be useful donors

for Basmati breeding

Pusa Basmati 1

Pi-9

PB1/IRBL9-W (Pi-9 – AP5930)

Pi-b

PB1/IRBLb-B (Pi-b – RM 208)

M R D 1 2 3 4 5 6 7 8 9 10

M R D 1 2 3 4 5 6 7 8 9 10

Pusa Basmati 1+ Pi9

(Fjellstrom et al., 2006)

Validation of markers linked to gene of interest

Pusa1401/Pusa1602(PRR78+Piz5)//Pusa1401*4

P1: 160bp, P2: 180bp

M P1 P2 1 2 3 4 5 6 7 8 9 10

AP5930

M 1 2 3 4 5 M 1 2 3 4 5

AP5930

(0.6 cM)

AP4007

(1.55 cM)

Lane M- 50 bp ladder, 1- PB1, 2- IRBLZ5-CA, 3- C101A51, 4- PRR78, 5- Pusa 1460

(Fjellstrom et al., 2006)

AP5930 more closer to the gene Piz-5 but?

Validation of markers linked to gene of interest

Isogenic lines of PB1carrying major blast resistance gene(s)

Stress Gene Donor Parent LG Marker

BB

xa13

P1460

8 xa13-prom

Xa21 11 pTA248

Blast

Piz-5 P1602 6 AP5930

Pi54 P1603 11 RM206

BPH

Bph-3

Rathu Heenathi6 RM589

Bph-17 4 RM5953

Bph-18 IR65482 12 RM6217

4 BP-20-2Bph-20

IR71033Bph-21 12 B121

MAS for development of multiple biotic stress

resistance in Basmati rice varieties

MAS for transferring Saltol locus in PB 1121

PB1121 is cultivated in 64% of area (0.94/1.5 mha)

under Basmati rice in Haryana and Punjab

Pusa Basmati 1121 is sensitive to salinity

PB1121FL478BC3 F1:2 Seeds

Molecular marker based

development of heterotic

pools in rice

Source: BC Viraktamath, DRR

Diversity in rice germplasm

Karjat-1

84

IR-5

45

JAYATHI

Kharvela

KHARAVDA

PRATAPRASI

JAYA

Gauta

mSamle

shw

ari

Pantdhan19

HU

R-4

-3

Chandra

hasini

PN

R381Ja

ldiD

han6

Heera

4015

jogeshP

NR

519

Him

alaya

2

Rat

na

HU

R-3

022

MTU

7029

Sw

arna

Hal

dim

uri

AD

T37

ASD18

ADT39Him

alay

a1

Pan

tdha

n18

Him

alay

a799

RP24

21

Him

alay

a221

6

CSR36

CSR13

UPRVS-2

003-

26

Ras

kand

am

PR60

0R

AU

3061

Kud

rat3

HU

R-1

05

HU

R-2

00-5

7-1

Kan

akC

R-2

46-1

6Pun

jabM

ehak

1

PM

K-1

HU

BR

-2-1

UR

VA

SH

IM

TU

4870

Dee

pti

Sag

arsd

amba

sidh

anta Ran

chan

Jagb

hand

u

MA

S10

9

IR50

CR

2340

-7

Pus

a20

5A

DT45

ND

R97

ND

118

ND

R118

Kesa

va

UP

RI-

2003-4

6

UP

RI-

2003-4

5

Pantd

han12

Pantd

han10

SK

R126

IRB

B54

MA

S946-1

MA

S0-9

46

MR

-220

MR

-219

SO

NA

KH

AU

KH

AN

DA

GIR

I

Shiv

a

SU

RE

ND

RA

Gaja

pati

Manasw

ini

SU

KH

ALA

SH

AT

AB

DI

KE

SH

AV

Hem

aG

auri

Day

a

Sah

ib14

0IR77

384-

12-3

5-3-

6-7-

BIR

7738

4-12

-35-

3-6-

7-2-

B

HK

R12

0C

R24

99P

RA

CH

I

NA

RE

ND

RA

US

AR

DH

AN

IIIN

AR

EN

DR

AU

SA

RD

HA

NII

SU

PE

RR

ICE

-2N

DR

9830

3144

ND

R80

02

ON

-1

Sw

arna

muk

hi

SK

AU

220

IR70

AD

T42

Mah

anad

iIn

drav

ati

CR

-100

9R

IL-4

5Ram

acha

ndi

Shy

amal

aS

EB

AT

IP

R11

5P

AU

201

RIL

-10

PR

116

Pus

a134

2P

R10

6P

R12

0B

L-14

2R

R85

85A

JAY

CR

2461

-9IR

BB

21

Sitw

adha

n

MI4

8

Pok

ali

PR

118

PU

SA

44

Sar

joo-

52MTU

3626

prab

at

IR-8

IR-2

0AR

S36

Bha

drak

ali

Sne

haP

R11

1IR

BB

-3 IRB

B1

IRB

B-5

IRBB

14

IRBB

13IR

BB55

IRBB4

HKR

-55

IRBB60

IRBB-5

9IR

24

IRBB-8

IRBB10

PC19IR

BB-211

IRBB-2

08

IRBB-7

Govind

P1447

-00-

5-1-

P1325

xAJA

Y-

P-1447

Inta

nHPR2143

HPR2083PUSABASM

ATI1

PUSA-1401

PS-2

P1460Awns

:0.1206

MUSKAN

PantSugandhDhan17

TYPE-3P1463-02-1-1

P1306Gonrrabhog

IRBB-203

BL-245

IR-348

DHMAS-70G-164-29

Sukaradhan1

PR114

PR113Sadabahar

Poornima

Abhaya

PrasadBaraniDeep

Pantdhan11Bameshwari

Himalaya741

IR66ADT-36

MAS25IR-64pusa169

PantDhan4

MTU1010

MAS26RAU3002Rajendrabasmati

JGL-3828HKR-200-57-1

OYR128

NDR2026

OYR69PUSA33

IMPROVEDSABARMATI

NDR3026-331R

CR-2496UPRI-2003-24

JD-13CN-1268-7

C22UPLRI7Hazaridhan

NDR359Narendra359Pantdhan16VLDhan221VOH-PCR-3110

SELECTEDSABARMATISHARBATIADTYAGI-2

SHARBATIADTYAGI-1

VOH-PCR-3114NDR9830312CR-2363-26

ADT43KasturiIndirasonaADT38

KalanamakHPR2082PLA1100MTU1064Amara

SARATHIIC-258220SurekhaOrugulluSahbhagidhanB6144-MR-6-0-0

JGL-11727BirupaRNRM7JGL-3844Varalu

TKM-9NILAGIRIErramallaluPothanaC1268-7-10

MTU2077krishnaveni

MTU2067ChaitanyaMTU5249Vajram

MTU5293Pratibha

UpharSantephap

kantiNDR8015NDR8011

AbhiskekMTU1001Vijetha

JhulhatPDKV-chinoor2

MTU1061Indra

Joymati

MTU1075Pushyami

BPT5204

KarmaMahsuri

Jeeragasambha

Malviyadhan

MAHALAKSHMI

HUR-36

Sonamahsuri

WGL14

SambhaMahsuri

Rambha

UPRI-2003-15

NirriVandana

HPr2104

CO-37

IR-78908

PUSA6B

25A

Pantsankardhan3

Pusa6AHMT-2-PURE-

PRR78

PRH-10PS-5PS-3

IRBLB-BIRBLB-5-M

RR-393-R

PantSankarDhan1

ChandanaC

O39

C101PKTAC

C.N

O.-19

Nipponbare

C101A51-Piz-5-

Piz-5

C101LAC

AC

C.N

O-18

C102PK

TAC

C.N

O.-20

A57-115-4

Ril-249

Oryzica-1

RIL-29 P

-1280-SAF-06

HARYANABASM

ATI1

HKR-288

Jyoti

Sum

ati

PANTS

UG

ANDHDHAN-15

PantD

han15

VLT

-6VL7-3

Maham

aya

KrautiV

LT-2

ASD16

WG

L-23

985

Kav

ya

WG

L321

00

CSR10

Man

ika

CR24

94

LALI

THAG

IRI

Kon

ark

Lala

tIR

36

Kar

jat-1

IR72

Dud

huaD

han

Pan

tdha

n6

HPR

1068

Meh

erK

alin

ga-II

Red

trin

aini

PN

R-1

62

Kal

inga-

IB

hanj

a

Ana

nga

Bhubana

Sty

aP

arija

tB

hoi

Div

yaC

N-1

793

PA

TH

AR

A

kesh

ari

Ghante

swari

Badam

iA

nnpurn

a

Vik

asJK

201

Manhar

SU

BH

AD

RA

KA

LY

AN

I1K

aM

LE

SH

CR

143-2

-2H

KR

-26

CS

R27

PR

108

FL-

478

Raj

aVae

llu

shan

kar

IR46

30C

SR

23

TO

MP

HA

KH

AU

Tap

asw

ani

PH

UN

CH

I

LEIM

AP

HO

RE

TE

TE

P

CR

2364

-25

ND

R98

3013

5D

hara

Hee

raP

1490

-03-

HE

IBA

O

Pal

amD

Han

957

Chi

na98

8S

KA

U23

CH

45 SR

1

SK

AU

5

SK

AU

27

SK

AU

382

VL-

88-9

7-1-

7

VLK

39

Him

dhan

RR

222-

1A

njal

i

Vire

ndra

Err

amai

lerr

Ana

nda

Van

prab

ha

UD

YA

GIR

I

SA

MA

UTH

A

Kal

yani

-II

Kal

inga

-III

Vl-7

626

TKM

-6

RR

166-

645

DO

BE

EJA

-2

DO

BE

EJA

-1

JR50

3

IC-2

4819

9

Kal

inga

463

DA

OS

EW

1-A

C25

SE

WD

AE

NG

KH

AO

PON

GK

RA

ISE

WM

AEJA

N

KHAO

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AO

TRI8

4091

78

KHAO

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Sala

mpi

kit

PMK-

2DH

OU

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IC-1

143

1NRC

779

KHAR

AMUN

GA

Bela

IC-8

6318

IC-2

4820

9Rosom

Chang

a

Vl-95-

6-3-

9-4

VL16Sing

huva

male

t

JR35

3

MUNNA

UPRI-2003-1

8

Lakhansh

aljhalda

Tripur

aMed

icina

lrice

KHAODAENKRAI

KALAJE

ERA307

BHUMANNAGAU

BHUMANSAN

TaiPei3

09

K429Naggardhan

IRBLZ5-C

A

IRBLB-B K332Bhirgudhan1

CNA4130

CAN4136

IRAT240IR

EM950

CNA4125DV-85IR

BL9-W

96718-CG20-

96717-CG14-

SATTIMADHUMATI

sirim

ula

Kalika

ti

KETAIJOHA

IC-2

127

DomSiahCHIM

BALATEBASM

ATI

4006

Highlya

rom

atic

SONASAL-sm

allGra

in-or

igina

l

Pimpu

dibas

a

CRRIA4002

Karpura

kranti

DhanaPrasa

d

Khosaka

ni

Kalajeera

Thakurbhog

NDR6237

NDR6138

CR-2361

NDR9437

Mahisugandha

CR-2362

CN-1789NDKN-3327

CRRIBLACKAROMA

THAK-1GSR-2-1-46

CN-1791CN-1790

NanuLajakulibadan

A4010Tulsiphoola

BHANTAPHOOL

Thakurasuna

DhusaraHeerakaniBadsahbhogGangaballChinikaminiISGR-21-39NDR6232Pusa1176

BindliPusa1174NeelabattiHassanseraiSAHPASANDPusa1173

PunjabBasmati2

HBC-19CSR30Basmati386SuperBasmati

SB-3000T23

SeondBasmatiNAGINA12Basmati379

VOH-PCR-3139IC-1089

VOH-PCR-3113Basmati370

RanbirBasmatiNDR625

VOH-PCR-3119CR-2407

SaanwalBasmatiBasmati564HKR-39

PUSABASMATI-1121P-1301P1460-awnless-

SAF-1221-83BJ-1Aditya

PANIKASirhati1

Lalmati Boro-II

VL-9891

LALANKANDA

VL-10091

KATAKTARA

BasmatiSATHI34-36AUS257AUS157

DULAR

Bada-BALA-N-22

Goalmalati

Peelibadam

BROWNGORAJhumkhasa

IRAT144 NapangKonkoiLunishree

IndiraSugandhDhan-1

ZANGBHUMAN

JaldubiPhourelAmubi

Phourelakuppi

Phoungang

PheCharao

Phougak

PhourelTujombi

PhourelPhoudongba

NapiPhou

Langphou

ChinishakkarA4007

Acharmati

Jaiphulla

RiceEarly

OYC183A400

PDKV-chinoor7HMT1

TilakchandanChinoor

A4023

A4019

Dubraj

0.05

Dendrogram depicting genetic relationship among the 566 rice genotypes

Genetic diversity among 566 genotypes

based on 40 SSR markers

Grouping of genotypes according to flowering time

Pan

tdha

n16

P14

90-0

3-U

PR

I-20

03-4

6

UP

RI-

2003

-24N

DR

3026

-331

R

Haz

arid

han

Vl-7

626

PU

SA

33N

DR

8015

Joym

ati

Abh

iske

k

Kar

maM

ahsu

riJe

erag

asam

bha

HU

R-3

6

PM

K-2

DH

OU

BI

PM

K-1

Jyot

i

UR

VA

SH

IC

R23

64-2

5si

dhan

ta

Pan

tdha

n19

Seb

athi

Bho

i JAY

AG

auta

mSam

lesh

war

i

Stya

Divya

ASD18

Redtrinain

i

PNR-162

PNR381

ADT37

HUR-4-3Chandra

hasini

JGL-3844

AnjaliCSR10

Pathara

Bhubana

Bhanja DayaKharavela

Karavada

PratapUDYAGIRI

JAYATHI

RatnaHUR-3022

SURENDRA

GajapatiKwshav

IR36SUKHALAShtabdiKasturiBirupaOrugulluIC-258220PothanaErramallaluC1268-7-10

VaraluVLT-6VL7-3

MahamayaSonakhauPusa205

Leimphore

PunjabMehak1

Pantdhan12Pantdhan10

SKR126

UPRI-2003-45MAS25IR64

MAS26

MTU

1010

MAS946-1

Sahib140OYR

128

NDR2026PU

SA6B

Pusa6A

Pantsankardhan3

HKR

-26

CS

R27

PR

120B

L-142

PR

106

PR

114P

R113

Sitw

adhan

Pokali

PU

SA

44

MT

U3626prabat

IR8 IR

BB

-211IR

BB

-208

PR

115P

AU

201R

IL-10P

R116 C

R2461-9

AJA

YIR

BB

21A

RS

36AD

T38H

KR

120C

R2494

IRB

B-5

IRB

B14

IRB

B13

IRBB55

IRBB4

HKR

-55Tetep

IRBB-8

IRBB10

IR24IRBB60

IRBB-59

IRBB-3Tapaswani

Swarnamukhi

PLA1100

ManharTKM-6

JR353

AC25Vl-95-6-3-9-4

UPRI-2003-18

Peelibadam

BROWNGORAKatakTara

BasmatiSATHI34-36AUS257Bada-BALA-JhumkhasaN-22Goalmalati

LalanKandaVL-9891VL-10091

BJ-1Aditya

OYC183Kamlesh

CR143-2-2HPR2143

HPR2083 Prasad

Vikas

VL-88-97-1-7

China988

Salampikit

HARYANABASMATI1

SeondBasmati

Sahpasand

DomSiah

CHIMBALATEBASMATI

HassanseraiSB-3000

SaanwalBasmati

Basmati564CR-2407 PS-2

P1463-02-1-1

CNA4130

CAN4136

IRAT240IREM950

DV-85

TaiPei309

TripuraMedicinalrice

IRBL9-W

96718-CG

20-

IRBB-203

Chandana

VOH-PC

R-3110

SelectedSabarmati

VO

H-P

CR

-3114

IR78908

HPr2104

PS-5

PS

-3 PR

R78

B6144-M

R-6-0-0

0.05 Mid early flowering group (91 to 110 days)

WGL14

SambhaMahsuriBPT5204Malviyadhan

HUR-36JeeragasambhaSonamahsuri

NDR8011

ZANGBHUMAN

Hema

RR166-645

KHAO-KEO-4

T23

IC-2127

SuperBasmati

VOH-PCR-3113

NAGINA12

Basmati370

RanbirBasmati

NDR625

SONASAL-sm

allGrain-original

GSR-2-1-46 Pusa1174

BHUM

ANNAG

AU

HKR

-39

KHARAM

UNG

A

TOM

PHAKH

AUPHUNCHI

LangphouRajaVaellu

Oryzica-1 M

R-220

MR-219

Nirri

HMT1RAU3002

Rajendrabasmati

ManaswiniDHMAS-70G-164-29

WGL32100

WGL-23985

CN-1793Lalat

IndirasonaCSR13

RR8585IR4630

CSR23

IMPROVEDSABARMATI

HaldimuriCN-1268-7

C22UPRVS-2003-26

PR600

RAU3061

Kudrat3H

UR-105

Pusa1342P1460Awns

:0.1767

MUSKAN

PUSABASMATI-1121

TYPE-3

JGL-3828

HKR-200-57-1

IndiraSugandhDhan-1

Kanak

CR-246-16

Sagarsdamba

0.05 Late flowering group

(121-135 days)

MTU5249Vajra

m

MTU2067Chaita

nya

MTU1001Vijeth

a

JhulhatPDKV-chinoor2

MTU1061Indra

UPRVS-2003-26KalanamakRamachandiCSR36

Meher

Bameshwari

NDR9830135

CN-1793

PUSA33ADT39

UPRI-2003-24

PUSABASMATI1

PUSA-1401

Inta

n

Sirhati1 PANIK

A

PunjabBasmati2

Basm

ati386 H

BC-1

9

CSR

30

VO

H-P

CR

-313

9

Pus

a117

3

CN

-179

0C

hini

kam

ini

ISG

R-2

1-39

CR

-236

2

CN

-178

9

CN

-179

1N

DR

6237

NDR6138

CR-2361

NDR9437

Mahisugandha

NDKN-3327

CRRIBLACKAROMA

A4010

DhanaPrasad

Bindli

NDR6232

UPRI-2003-18

Singhuvamalet

Lakhanshaljhalda

Jaiphulla

ChinishakkarDOBEEJA-1Acharmati

TilakchandanChinoorDubrajJaldubi

UPLRI7TKM-6

NDR9830312

IR70

ADT42

JagbhanduNDR

98303144

ND

R8002

ON

-1 SU

PE

RR

ICE

-2

PR

AC

HI

UP

RI-2003-46

UP

RI-2003-45

UR

VA

SHI

MTU

4870Deepti

MTU

1075Pushyami

Ram

bha

MAH

ALAKSHM

I

Uphar Santephap

UPRI-2003-15

0.05 Very late flowering group

(>135 days)

PantDhan4IR66

UPRI-2003-15CO-37

Sahbhagidhan

Mahanadi

Indravati

SKAU220

NARENDRAUSARDHANIII

NARENDRAUSARDHANIINarendra359

OYR69

Kona

rk

IR77

384-

12-3

5-3-

6-7-

2-B

Pant

Suga

ndhD

han1

7

MUS

KAN

KHAO

DAEN

KRAI

BHUM

ANSA

N

Pusa

1176

SAF-12

21-8

3

Gonrrabhog

P1447-00-5-1-P

1325xAJAY-

P-1447

Poornima

ADT43

Sitwadhan

PR118Sarjoo-52Bhadrakali

Gauri

Ananga

KHAO-KHAOVLT-2

JR503

Shya

mala

Kavy

a

JGL-

1172

7

Pant

dhan

18 NDR9

7

Sum

ati

PANTSUGAN

DHDHAN-15

PantDhan15

ShivaHUR-200-57-1

CR2499CR2364-25

0.05

Medium flowering group

(111-120 days)

SKAU5SKAU27VLK39HimdhanVirendra

SKAU23

PalamDHan957CH45

SR1

RASI

Gajapati

Kalinga-IStya

Parijat

Ananga

Kalinga-II

shankarJK201

Karjat-184

JR353

CO

39

C10

1PKT

ACC

.NO

.-19

Piz-

5

C10

1LAC

ACC

.NO

-18

C10

2PK

TAC

C.N

O.-2

0

A57-

115-

4

ASD

16BL

-245

Lalm

ati

DU

LAR

IRBL

Z5-C

A

IRBL

B-B

Nag

gard

han

Bhirg

udha

n1CNA41

25

Vanda

na

Varal

u

TKM-9ADT-3

6

RIL-29

ADT43

Sneha

IRBLB-BIRBLB-5-M

PC19

GovindIRBB1

Lalithagiri

Karjat-1IR72HPR1068SadabaharGhanteswariBadami

keshariJyoti

JaldiDhan6

Heera

UPLRI7

Vanprabha

Samoutha

Kalyani-II

Kalinga-III

jogesh

PR108FL-478

ADT45

SUBH

ADR

AKALYAN

I1

RIL-45

Pantdhan11H

imalaya741

ADT38 VLD

han221

JD-13

Sukaradhan1BaraniDeep

MAS109

IR50 Kandagiri

ND118

PoornimaHimalaya1

Kalinga463

Himalaya2

Himalaya799

Himalaya2216

0.05

Early flowering group (<90 days)

Number of alleles 376G.D. range 0.05 to 1Average G.D. 0.50

Number of alleles 352G.D. range 0.025 to 1

Average G.D. 0.55

Number of alleles 250G.D. range 0.10 to 0.97

Average G.D. 0.55

Number of alleles 260G.D. range 0.032 to 1

Average G.D. 0.60

Number of alleles 286G.D. range 0.10 to 0.95

Average G.D. 0.63

38.29%

3.26% 4.25%

34.78%

4.25%

13.83%

0

5

10

15

20

25

30

35

40

45

Allele-132bp Allele-135bp Allele-141bp Allele-144bp Allele-147bp Allele-150bp

Series1

Allelic frequency at RM 6100 marker locus in 94 additional genotypes

Classification of 94 Genotypes Based on

Restorer Linked Marker RM6100

• In additional set of genotypes, 48.61% possessing known restorer type

(144 or 150 bp) alleles and 38.29 % possessing known maintainer type

(132bp) allele

• Ratio of maintainer and restorer in additional set of 94 rice genotypes

is near about same as previously found ratio in 472 genotypes

Sonasal Pusa Basmati 1121

QTL mapping for grain

dimension traits

Variation for grain characteristics in RILs

Sonasal

PB 1121

QTLs for grain Dimension Traits

Chromosome 3

Chromosome 3

Trait QTL ID Chr. Marker Interval Allele

ER elr10-1 10 RM244-RM5304 Pusa 1121

AC amy6-1 6 RM217 – RM3 Pusa 1342

ASV asv6-1 6 RM217 – RM3 Pusa 1121

Aroma

aro3-1 3 RM5474-RM282

Pusa 1121aro4-1 4 RM5633-RM273

aro8-1 8 RM44-RM42

aro8-2 8 RM223-RM80

Validation of BADH2 gene based marker

( NKSDEL) in aromatic/non-aromatic genotypes

M 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27

M 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53

Aromatic varieties: 82 bp Non-aromatic varieties: 90 bp

Efficacy: 100 %, Highly efficient compared to markers developed

by Bradbury et al(2005)

100 bp

100 bp

QTL mapped for Grain dimension & Quality Traits

using RILs from Cross Pusa 1342 X Pusa 1121

Trait QTL ID Chr Marker Interval Allele

Grain LengthGrl1-1 1 RM431-RM104

Pusa 1121grl2-1 2 RM154-RM233A

grl7-1 7 RM11-RM505

Grain widthgrb7-1 7 RM11-RM505

Pusa 1342

grb7-2 7 RM505-RM336

L/B ratio

lbr1-1 1 RM431-RM104

Pusa 1121lbr2-1 2 RM154-RM233A

lbr7-1 7 RM11-RM505

lbr7-2 7 RM505-RM336

QTLs for Cooking Quality

Trait QTL ID Chr. Marker Interval Allele

ER elr10-1 10 RM244-RM5304 Pusa 1121

AC amy6-1 6 RM217 – RM3 Pusa 1342

ASV asv6-1 6 RM217 – RM3 Pusa 1121

Aroma

aro3-1 3 RM5474-RM282

Pusa 1121aro4-1 4 RM5633-RM273

aro8-1 8 RM44-RM42

aro8-2 8 RM223-RM80

Validation of BADH2 gene based marker

( NKSDEL) in aromatic/non-aromatic genotypes

M 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27

M 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53

Aromatic varieties: 82 bp Non-aromatic varieties: 90 bp

Efficacy: 100 %, Highly efficient compared to markers developed

by Bradbury et al(2005)

100 bp

100 bp

Mapping of Yield and Yield Related

QTLs using Recombinant Inbred Line

Population in Rice (Oryza sativa L.)

Materials and mapping strategy

Pusa1266 X Jaya RILpopulation (310) for QTLmapping

Locations: NewDelhi, Karnal, Aduthurai

Traits: yield and yield relatedtraits (12)

Markers: RMseries, RGNMS, HvSSR andgene-based(1063)

Germplasm lines (120) forvalidation of marker-QTLassociation

Frequency distribution of 12 traits at New Delhi

80 90 100 110 120

0

10

20

30

40

50

60

70

Jaya

Pusa 1266

Number o

f RIL's

Days to 50% flowering 80 90 100 110 120 130 140

0

10

20

30

40

50

60

70

80

Jaya

Pusa 1266

Number o

f RIL's

Plant height

20 21 22 23 24 25 26 27 28 29 30 31 32 33

0

10

20

30

40

50

60

70

Jaya

Pusa 1266

Number o

f RIL's

Panicle length

6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

0

10

20

30

40

50

60

Jaya

Pusa 1266

Number

of RIL's

Number of panicles per plant20 30 40 50 60 70 80

0

10

20

30

40

50

60

70

80

Jaya

Pusa 1266

Number o

f RIL's

Flag leaf length

1.6 1.8 2.0 2.2 2.4 2.6 2.8 3.0 3.2 3.4

0

10

20

30

40

50

60

70Jaya

Pusa 1266

Number

of RIL's

Flag leaf width

200 250 300 350 400 450 500

0

5

10

15

20

25

30

35

40Jaya

Pusa 1266

Number o

f RIL's

Total spikelets per panicle

50 100 150 200 250 300 350

0

10

20

30

40

50

Jaya

Pusa 1266

Number o

f RIL's

Filled grains per panicle

20 40 60 80 100

0

10

20

30

40

50

60

70

80

Jaya

Pusa 1266

Number o

f RIL's

Percent sterility

14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31

0

10

20

30

40

50

Jaya

Pusa 1266

Number o

f RIL's

1000 grain weight

10 20 30 40 50 60

0

10

20

30

40

50

60

Jaya

Pusa 1266

Number o

f RIL's

Grain yield per plant8 9 10 11 12 13 14 15 16 17 18 19 20 21

0

10

20

30

40

50

60

Jaya

Pusa 1266Number o

f RIL's

Spikelet setting density

50% f lowering Plant Height Panicle Length

Panicles/plant Flag Leaf Length Flag Leaf Width

Spikelets/Panicle Filled Grains/Panicle % Sterility

1000-Grain Weight Grain Yield/Plant Spikelet Setting Density

Map of Pusa1266 X Jaya RIL population

Marker interval: 19.64cMMap Length: 2023.1 cM

Tree View of RIL Population

Graphical representation of QTLs identified for all traits

Trait wise Number of QTLs Identified

S. No. Trait Number of QTLs

1. Days to 50% flowering 7

2. Plant height 16

3. Panicle length 13

4. Panicles/plant 4

5. Flag leaf length 15

6. Flag leaf width 9

7. Spikelet/panicle 12

8. Filled grains /panicle 10

9. Per cent sterility 6

10. 1000-grain weight 17

11. Grain yield/plant 9

12. Spikelet setting density 10

Total QTLs: 128 Novel QTLs: 51

QTL mapping for Grain Chalkiness

Jaya Pusa 1266

Introgression Breeding for

Development of Golden Rice :

Current Status

Funded by the Department of Biotechnology, GOI under ISCB

Rice in the Asian Diet

565

836

1547

1918

1419

870

756

1467

627

745

905

1527

866922

996894

1086

1645

16710992102

1210089

173847659

1497686149197155

8457127

Worl

dA

sia

Bangla

desh

Mya

nmar

Cam

bodia

Chin

a

India

Indon

esia

Japan

Kore

a, DPR

Kore

a, Rep

.

Laos

Mal

aysia

Nep

al

Pakista

n

Philippin

es

Sri L

anka

Thai

land

Vie

t Nam

Supply/Cap/Y: Kg

Cal/Cap/Day: Number

Total Calories/cap/day = ~2000 – ~3000

Rice contributes ~30-~75% of the Calories

Carotenoid Biosynthesis Pathway

GR-2 Events

S. No. Line Carotenoid Content

(g/g)

1. SGR2E1 11.4

2. SGR2G1 12.8

3. SGR2L1 13.8

4. SGR2R1 19.7

5. SGR2T1 23.0

6. SGR2W1 25.4

Genetic Background: Kaybonnet

( Seed Received in February (2006)

Flanking markers for background selection on carrier chromosome

Physical location of transgene in different events

GR2R1 GR2L1

Ch. 1

(186.6)

Transgene RM 472

RM 265

RM 486

RM 315

RM 431RM 104

RM 165

RM 529

(153.5)

(171.6)

(155.9)

(165.3)

(178.3)

(189.6)

Transgene

RM 123

RM 250 RM 425

RM 166

RM 482

RM 207

RM 266 RM 495

Ch. 2

(186.4)

(170.1)(166.0)

(183.0)

(187.5)

(191.2)

(192.2)(194.6)

(153.9)

(158.6)

GR2E1

Transgene

RM 347

RM 411RM 156

RM 18

RM 503

RM 135

RM 504RM 49

Ch. 3

(134.1)

(127.9)(125.7)

(131.5)

(157.3)

(161.1)

GR2T1

Ch. 3

GR2W1

Ch. 10

Transgene RM 473D

RM 554RM 563

RM 338

RM 156

RM 411RM 16RM 347

(113.2)

(100.6)(89.00)

(108.4)

(125.7)

(127.9)

(131.5)

Transgene

GR2G1

Ch. 5

RM 536

RM 87

RM 274

RM480

RM 334

(132.7)

(129.2)

(126.6)

(130.6)

(141.8)

Transgene

RM 271

RM 184RM 596

RM 625

RM 269

RM 258

RM 304RM 294A

(59.40)

(58.30)(54.70)

(58.30)

(69.60)

(70.80)

(73.00)(87.10)

MABB for transfer of pro-vitamin A trait in Swarna

KaybonnetSwarna

BC1F1

BC2F3

BC2F4

MA

S fo

r pro

vitam

in A

gen

es

BC2F2

F1 Season II

Season III

Season IV

Season V

Season VI

Season VII

X

BC2F1

Ph

en

oty

pic a

nd b

ack

gro

un

d

sele

ction

usin

g S

SR

mark

ers

Homo. Hemi. Null

P1 &P2 P1 & P2 P2 & P3P2 & P3

K S 1 8

Event Specific PCR for Zygosity Analysis

Back cross derived lines in Swarna background

Swarna Golden Swarna

Hybrid Breeding in Rice

Hybrid Rice for sustainable food security

Comparison China India

Total area under rice 30 m ha 44 m ha

Area under hybrids 16 m ha 1.4 m ha

% coverage under hybrids 53.33 2.82

Average yield of hybrid rice 7 t/ha 6 t/ha

Average yield advantage >20% 15-20%

60 million additional people fed in China through increased

productivity from hybrid rice

In India, 47 hybrids released so far

Projected coverage by 2000 was 2 m. ha but current coverage is

only 1.2 m.ha.

World’s first super fine grain

aromatic rice hybrid

115 days seed to seed maturity

Highly aromatic, long

slender, non- chalky grains with

ER 1.8 after cooking

Duration : 115 days

Average yield : 75 q/ha

Paddy price : Rs. 1800/q

Gross return : Rs. 1,35,00/ha

Cultivation cost : Rs. 20,000/ha

Net Return : Rs. 1,15,000/ha

Transfer of Technology: Pusa RH 10 Model

Jakhoda, Bahadurgarh, Haryana,

Sardar Rajpal Singh, Kheri Walon Ka Dera, Haryana

IARI-IFSSA partnership: A PPP model

Advanta Farm in Hyderabad

China India

RiceTec,USA

Molecular mapping and validation of fertility

restorer gene, Rf1

M – Marker lane; A – Maintainer line; R – restorer line ; Lane 1- 48 Indicates F2 lines

150 bp

M A R 1 48

RM258

M A R 1 48

150 bp

RM6100

cM RM258

Rf

7.0

RM6100

4.3

Chr. 10

Arrow indicates the contaminant ( B line)

Testing Genetic Purity of PRH-10 Hybrid Seed Lot

M A R1 47 M

RM 258

GOT of PusaRH10 from different companies

Goldie Aatash KDL810

IARI Annapurna JKRHH10

Fingerprinting, IPR and Genetic Purity Analysis

Challenges and opportunities

Validation of markers

Selection - Molecular markers vs phenotype

Population size – still a critical factor in isolating

desirable recombinants

Optimising novel techniques, revisiting strategies

for mapping and MAS

Our Team and CollaboratorsT. Mohapatra, N. K. Singh, T. R. Sharma, UD Singh, S. Chander, S.S.

Atwal, R. Seth, M. Nagarajan, K. K. Vinod, S. Gopala Krishnan, PK

Bhowmick, K.V. Prabhu

Technical Staff

Sudesh Kumar

Devinder Singh

M. Ravindran

Supporting Staff

Jagdish

Paramasivam

Sunil (DPL)

Mentors

Prof. E.A Siddiq

Dr. F. U. Zaman

Dr. V.P. Singh

Director, IARI

Thank You