drought grain yield qtls in rice -...

Drought grain yield QTLs in rice

Arvind Kumar

International Rice Research Institute,

Philippines

Fourth International Workshop

on

Next Generation Genomics and Integrated

Breeding for Crop Improvement

February 19-21, 2014

Major QTLs for grain yield under drought

• QTL identification program based on

grain yield per se

• Large effect QTLs in the background of

high yielding popular varieties

• Validate effect of identified QTLs in

different environments, different genetic

backgrounds

• Up to 2013, studied over 50 mapping

populations- 14 QTLs-17 publications- (QTL

identification: Bernier et al. 2007, Venuprasad et

al. 2009, Bernier et a. 2009, Venuprasad et al.

2009A, Venuprasad et al. 2009B, Vikram et al.

2011, Swamy et al. 2011, Dixit et al. 2012, Ghimire

et al. 2012, Vikram et al. 2012, Dixit et al., 2012,

Mishra et al. 2013, Yadaw et al. 2013, Swamy et

al. 2013, Dixit et al. 2014, Alvin et al. 2014., Nitika

et al. 2014.)

2013DS, IRRI

QTLs identified at IRRI

QTL Donor Recipient Ecosystem Chr Interval Reported by

qDTY1.1 Dhagad deshi Swarna Lowland 1 RM431-RM104 Ghimire et al. 2012

qDTY1.1 Dhagad deshi IR64 Lowland 1 RM104-RM12091 Ghimire et al. 2012

qDTY1.1 N22 Swarna Lowland 1 RM11943-RM12091 Vikram et al. 2011

qDTY1.1 N22 IR64 Lowland 1 RM11943-RM12091 Vikram et al. 2011

qDTY1.1 N22 MTU1010 Lowland 1 RM11943-RM12091 Vikram et al. 2011

qDTY1.1 Apo IR64 Upland 1 RM486-RM472 Venuprasad et al. 2012

qDTY1.1 Kali Aus IR64 Upland 1 RM488-RM315 Sandhu et al. 2014

qDTY1.1 Kali Aus MTU1010 Upland 1 RM259-RM315 Sandhu et al. 2014

QTL Donor Recipient Eco. Chr Interval Reported by

qDTY2.2 Aday Sel. IR64 Lowland 2 RM236/RM279 Swamy et al. 2013

qDTY2.2 Kali Aus MTU1010 Upland 2 RM211-RM263 Sandhu et al.2014

qDTY2.2 Kali Aus MTU1010 Lowland 2 RM211-233A Panalog et al. 2014

qDTY2.3 Kali Aus IR64 Upland 2 RM263-RM573 Sandhu et al. 2014

qDTY2.3 Kali Aus IR64 Lowland 2 RM573-RM250 Panalog et al. 2014

qDTY3.1 Apo Swarna Lowland 3 RM520-RM16030 Venuprasad et al. 2009

qDTY3.1 IR55419-04 TDK1 Lowland 3 RM168-RM468 Dixit et al. 2014

qDTY3.1 IR55419-04 TDK1 Upland 3 RM168-RM468 Dixit et al. 2014

qDTY3.2 Aday Sel. Sabitri Lowland 3 RM569-RM517 Yadav et al. 2013

qDTY3.2 N22 Swarna Lowland 3 RM60-RM22 Vikram et al. 2011

qDTY3.2 Moroberekan Swarna Lowland 3 id3000019-id3000946 Dixit et al. unpublished

qDTY3.2 Moroberekan Swarna Upland 3 id3000019-id3000946 Dixit et al. unpublished

qDTY4.1 Aday Sel. IR64 Lowland 4 RM551-RM16368 Swamy et al. 2013

qDTY6.1 Vandana IR72 Upland 6 RM589-RM204 Venuprasad et al. 2012b

qDTY6.1 Apo IR72 Upland 6 RM589-RM204 Venuprasad et al. 2012b

qDTY6.1 IR55419-04 TDK1 Lowland 6 RM586-RM217 Dixit et al. unpublished

qDTY6.1 IR55419-04 TDK1 Upland 6 RM586-RM217 Dixit et al. unpublished

qDTY6.2 IR55419-04 TDK1 Lowland 6 RM121-RM541 Dixit et al. unpublished

qDTY6.2 IR55419-04 TDK1 Upland 6 RM121-RM541 Dixit et al. unpublished

qDTY12.1 Way Rarem Vandana Upland 12 RM28048-RM28166 Bernier et al.2007

qDTY12.1 IR74371-46-1-1 Sabitri Lowland 12 RM28166-RM28199 Mishra et al. 2013

QTLs identified at IRRI

qDTY12.1 interactions with qDTY2.3

Eco-

system

qDTY12.1-qDTY2.3

Class mean

++ +- -+ -- Add.

USS-I 913 519 332 202 43.5

USS-II 533 428 242 200 16.7

UNS-I 3298 2991 3143 2851 5.2

UNS-II 3032 2533 2861 2703 9.3

Eco-

system

qDTY12.1-qDTY2.3

Add.

Class mean

++ +− −+ −−

LSS 1169 1012 1076 804 8

LMS 1542 1201 1429 1381 12.1

LMiS 2618 2566 2544 2498 1.1

Knowing more about QTLs Differential response of DTY2.2 & DTY4.1 under varying stress conditions

Upland Lowland Dixit et al., 2012

qDTY12. 1 works as a gene-complex of 10 genes

Of these, the transcription factor OsNAM is a major regulator

The 10 genes were identified as candidate genes based on:

1) Sequence and expression polymorphism

2) Co-localized targets of OsNAM

3) Relevant literature

The entire 1.7 Mb locus

was important as seen

through:

(A) SSR markers-based

fine-mapping

(B) Candidate gene-

based fine-mapping

Ajay Kohli, IRRI

- Transgenic plants overexpressing the WayRarem OsNAM

show similar phenotype as the NILs.

- However, the effect on yield was not as dramatic as in the

case of NILs.

- The need for additional co-localized minor genes and hence

the gene-complex (qDTY12.1 X qDTY2.3)

-P +P -P +P -P

+P

E1 E2 IR64 E2

Increased lateral roots Increased secondary branches Better Transpiration

Gene/mechanism study for other prominent QTLs under progress Ajay Kohli, IRRI

Facts or assumptions?

• Drought tolerant germplasm are

mostly tall in height

• Drought tolerant germplasm

mostly possess low yield potential

• Drought tolerant germplasm are

very early in duration

• Drought tolerant genotypes are

photosensitive

• Drought tolerant germplasm have

efficient root system

Effect of qDTY QTLs on undesirable traits

Most of the identified qDTY QTLs showed effect on one or the other

undesirable traits - tall plant height, very early maturity, reduced

yield under normal irrigated situation

qDTY1.1 showed effect on tall plant height and earliness

qDTY3.2 showed effect on very early maturity

qDTY3.1 showed effect on reduced yield under irrigated situation

qDTY6.2 showed effect on tall plant height

Pleiotropy vs Linkage

RM431

RRM11943

sd1

RM12023

qDTY1.1: pleiotropy vs linkage

The effect on grain yield under

drought predicted to be either

pleiotropic effect of Sd1 gene

itself or linkage between

qDTY1.1 with sd1

qDTY1.1 - strong association

with plant height explaining

50% of phenotypic variations

(Vikram et al. 2011).

sd1

qDTY1.1 effect in dwarf

population with sd1

allele fixed confirmed

DTY1.1

Similar to qDTY1.1, presence of IR55419-04 allele at three marker loci

(RM3, RM541 and RM275) at qDTY6.2 locus led to an increase in plant

height, Apo allele at three marker loci (RM520, RM416 and RM16030

respectively) within qDTY3.1 led to a reduction in grain yield under normal

condition, presence of Vandna allele at qDTY3.2 locus at three marker loci

RM7332, RM523 and RM545 led to a very high reduction in DTF

A BC1F3 derived population developed for IR55419-04/ TDK1 (365 lines),

a BC1F4 derived population of Apo/Swarna (490 lines), a F3 derived

population of Vandna/Way Rarem (242 lines) and was used to understand

the linkage in qDTY6.2, qDTY3.1, and qDTY3.2 regions respectively.

Linkage of other qDTY QTLs

A B C

DTY3.1- decrease in

yield, NS

DTY6.2 Increase in

height under NS, S

DTY3.2- Decrease in

DTF under NS

Designation Stress Non stress

DTF PHT GY DTF PHT GY

A IR 91659:41-95-5-B 90 72 3079 94 84 4530

IR 91659:54-36-9-B 92 68 3299 96 82 5027

IR 91659:41-95-6-B 86 69 3123 96 81 4487

Swarna 102 63 561 96 84 4312

qDTY1.1 LSD0.05 3 6 771 3 5 1246

B IR 90266-B-491-1 83 92 1750 74 109 5750

IR 90266-B-155-1 86 96 1637 73 113 5740

IR 90266-B-53-1 84 102 1947 70 116 5672

TDK1 99 73 173 74 111 5985

qDTY6.2 LSD0.05 4 10 714 8 14 1578

C IR81896-B-B-309 98 82 1928 92 138 5174

IR81896-B-B-481 98 76 929 95 127 5592

IR81896-B-B-305 102 85 808 94 130 6717

Swarna 54 0 101 126 4965

qDTY3.1 LSD0.05 7 24 664 6 11 2200

D

qDTY3.2

IR 79971-B-102-B 79 84 920 83 110 3547

IR 79971-B-421-B 84 79 756 84 110 3156

IR 79971-B-86-B 68 76 847 73 101 3311

Vandana 64 73 617 63 94 2180

LSD0.05 5 10 241 3 12 782

Drought tolerant lines free from linkage drag

Group1

Group2

Group3

Group 4

Group 5

Traditional, modern and drought tolerant varieties

grouping for DTY QTL alleles

Drought tolerant alleles in modern varieties

Synteny and comparative map of QTLs in rice and maize

DTY1.1 region in rice – Maize 3, wheat 4B, barley 6H

DTY3.1 region in rice – Maize 1

M. Swamy et al. 2011

QTLs introgression programs

Recipient Env. QTLs Present status

Vandana Upland qDTY12.1 Under evaluation,Jharkhand

IR64 Lowland qDTY2.2, qDTY4.1

AICRIP completed in India,

Identified for release in

Nepal, under evaluation in

Bangladesh, Indonesia,

Myanmar

Swarna sub1 Lowland qDTY1.1, qDTY2.1,qDTY3.1 BC3F5

TDK1sub1 Lowland qDTY3.1, qDTY6.1,qDTY6.2 BC3F3

Sabitri Lowland qDTY2.2, qDTY12.1 BC2F2

Anjali Upland qDTY12.1, qDTY3.1 BC2F4

Sambha Mahsuri Lowland qDTY2.2, qDTY4.1 BC2F4

IR64 sub1 Lowland

qDTY1.1, qDTY3.1,

qDTY2.2, qDTY12.1 BC2F3

MR219 Lowland qDTY2.2, qDTY3.1, DTY12.1 BC2F4

MRQ74 Lowland qDTY2.2, qDTY3.1, DTY12.1 BC2F4

BR11 sub1 Lowland qDTY3.1, qDTY1.1, qDTY2.1 BC1F1

MTU1010 Lowland qDTY3.1, qDTY6.1, qDTY6.2 BC2F4

Vandana IR90020:22-283-B-4-B

Genotypes

Upland severe stress Upland non- stress

GY DTF PHT BIO HI GY DTF PHT BIO HI

IR 84984-83-15-481-B 693 64 75 4160 0.17 2525 62 79 9584 0.29

IR 84984-21-19-78-B 478 66 74 3333 0.13 2996 65 89 10769 0.31

IR 90020:22-283-B-1-B 604 66 79 4160 0.14 3039 66 85 11610 0.29

IR 90020:22-283-B-4-B 515 67 77 4133 0.21 2245 68 84 7579 0.27

Vandana 27 70 79 2080 0.09 2127 68 91 10498 0.34

Apo 0.1 NF 57 226.7 0 2127 80 101 NA NA

SED 240 4 8 2151 0.13 813 5 8 3781 0.09

H 78.6 61.1 35.5 23.7 28.6 54.1 88.7 75.7 44.8 67.2

Vandana drought:qDTY12.1

IR 84984-83-

15-481-B Vandana

Hazaribagh, India

Rainout shelter,

WS2011

Yield advantage

across locations in

India

IR64 drought: qDTY2.2, qDTY4.1

IR64 IR64 drought

IR64 drought IR64

IR64 drought IR64

ENTRY

Rajsh

ahi

Nepal

ganj RPR HYD SS

HYD

MS HZB Rewa

IR64 NIL 1525 3472 3956 1684 3800 1604 3731

IR 64 980 1597 2662 660 3085 958 2503

SED 156 170 285 939 600 422 909

+ QTL - QTL

-500

0

500

1000

1500

2000

2500

3000

3500

0.0 5.0 10.0 15.0

IR 64

ir87729-69-b-b-b

ir87728-102-b-b

ir 87707-446-b-b-b

ir 87707-182-b-b-b

ir87707-445-b-b-b

ir87705-444-b

ir 87705-83-12-b

ir87705-14-11-b

IR87706-215-b-b-b

Aday sel

Parent 2007

RVA test: similar cooking

quality

0

100

200

300

400

500

HZ

B

CB

T

PS

A

DR

R

IR 64 (RP)

IR 87707-445-B-B-B

IR 87707-446-B-B-B

Yield advantage over IR64

IR81896-B-195 X Swarna(WS2009)

(DTY2.1and DTY3.1)

BC2 X Sub1Swarna(DS2010)

BC3 X Sub1Swarna (WS2010)

BC4F1 (DS2011)

BC4F2 (WS2011)

BC4F3 (DS2012)

Fore ground selection

Background selection





Select homozygote's


Flood+drought:qDTY1.1, qDTY2.1 and qDTY3.1 in Swarna Sub1

BC3 (DTY2.1 and DTY3.1) X BC3(DTY1.1) (WS2010)

BC4F1(DS2011)

BC4F2 (WS2011)

BC4F3 (DS2012)

Pyramiding three QTLs

Pyramiding two QTLs


Drought screening

Select homozygote's

Drought screening

Swarna sub 1 Swarna sub1

lLs with DTY

QTLs

QTLs Chr Interval R2 Additive

effect Donor

DTY1.1 1 RM11943-RM12091 14 30 N22

DTY2.1 2 RM327-RM262 16 12.5 Apo

DTY3.1 3 RM520-RM16030 30 25 Apo

Major effect drought grain yield QTLs in Swarna



Swarna sub1

lLs with DTY

QTLs

Drought + Submergence Swarna: India 2013 DS

Entry DTF-C HT-C GY-D Submergence

IR96321-1686-199-B 106 68 2055 Tolerant

IR96321-315-325-B 109 64 2610 Tolerant

IR96321-1447-561-B 110 68 2438 Tolerant

Swarna 116 53 551 Susceptible

Swarna sub1 118 51 401 Tolerant

Designation DTF-C HT-C GY-D

IR94313:19-36-3-4-2-B 92 90 3474

IR94313:18-4-1-4-1-B 89 83 2852

IR94314-20-2-2-B 100 77 2834

IR88287-600-1-B-B-1-3-B 107 80 2508

IR94314-20-5-2-B 95 78 2767

IR94314-20-11-2-B 111 76 3055

IR94391-856-1-2-B 95 90 2741

Swarna 112 64 557

Swarna Sub1 110 61 456

LSD0.05 16 11 1230

Non-Swarna type drought tolerant lines: India, 2013DS

Sambha Mahsuri drought: qDTY2.2, qDTY4.1: IRRI 2013DS

Line DTF-C HT-C GYKGPHA-D

IR99742-1-39-4-63 82 90 2063

IR99742-2-23-7-17 79 79 1979

IR99742-1-33-3-229 96 93 1814

IR99742-1-14-2-87 76 78 1753

IR99742-1-39-4-147 84 78 1649

IR99742-1-14-2-53 79 88 1582

IR99742-1-33-3-228 90 80 1559

IR99742-2-23-7-135 80 72 1447

IR99742-1-61-6-10 81 84 1368

IR99742-1-39-4-83 80 91 1352

IR99742-1-33-3-158 79 86 1340

Sambha Mahsuri 100 88 0

LSD0.05 970

MR219, MRQ 74 drought: qDTY2.2, qDTY3.1, qDTY12.1

DESIGNATION QTL

GRAIN YIELD

(kg ha-1)

PLANT

HEIGHT

(cm)

DAYS TO

FLOWERING

(days) DS

NS

DS

NS

DS

NS

MR219 - 0 6212 68 92 - 90

IR 99784-255-91 qDTY2.2 , qDTY3.1 1983 6381 71 90 85 83

IR 99784-156-95 qDTY2.2 ,qDTY3.1 2017 6456 72 91 88 79

IR 99784-255-55 qDTY2.2 ,qDTY12.1 2034 7657 71 95 86 82

IR 99784-255-49 qDTY3.1 , qDTY12.1 2248 6353 73 94 87 79

IR 99784-255-78 qDTY2.2 , qDTY3.1 2314 5851 74 91 85 77

Trial Mean 854 6751 71 95 94 85

Nora, IRRI

MRQ74 - 1087 4293 66 84 95 90

IR 98010-126-821 qDTY2.2 1724 5270 72 88 95 83

IR 98010-126-77 qDTY3.1 , qDTY12.1 1862 4733 69 83 94 89

IR 99616-44-145 qDTY3.1 , qDTY12.1 2171 4471 65 78 82 80

IR 99616-44-103 qDTY3.1 , qDTY12.1 2172 5405 67 82 92 81

IR 98008-103-445 qDTY2.2 , qDTY12.1 2526 5123 71 89 85 81

Trial Mean 799 4487 68 84 98 94

qDTYA X R1

F1

(300)

qDTYB X R1 qDTYC X R1

X X R1 F1

(300) F1

(300)

F1

(1000) FS, RS, BS

BC1F1

(500) FS, RS, BS X

F1

(2000) FS, RS, BS

F2

(6000-12000)

F3

(with varying combinations of QTLs for drought screening)

BC1F2

(1000)

BC1F3

(with qDTYC for test of QTL effect)

BC1F2

(1000)

F3

(with qDTYA and qDTYB for test of QTL effect)

FS, RS, BS

FS, RS, BS FS, RS, BS

MAB for DTY QTLs in any background

• Larger BCnF2, BCnF3 populations to: break the undesirable linkages, select for

plant type, GY under irrigated and drought situations, capture positive

interactions between different QTLs as well as QTLs and background and to

carry appropriate breeding modifications

• Proper association between genotype and phenotype through standardized

drought phenotyping. Phenotyping more complex for combining multiple traits.

0

500

1000

1500

2000

2500

3000

Vand

na

IR6

4

Sam

bha M

ah

su

ri

Sw

arn

a

Gra

in y

ield

(kg

/ha)

recipient parent

NIL

DTY12.1 DTY2.2 + DTY4.1 DTY1.1+DTY3.1+DTY2.1

Is rice different from other cereals?: GY under drought

0.00

10.00

20.00

30.00

40.00

50.00

60.00

70.00

80.00

90.00

QTL3.2

QTL2.3

QTL2.1

QTL6.1

QTL12.1

QTL3.1

QTL1.1

QTL1.1

QTL4.3

QTL8.1

QTL4.2

QTL1.2

QTL4.1

DTY QTLs

% o

f dro

ug

ht

pan

el li

nes

with

diff

eren

t DT

Y Q

TL

s

Fig 4. Frequency of DTY QTLs in drought panel lines

Upland grown still under continuous drought Carry DT alleles

Rice

Lowland grown mostly with ample water Lost many DT alleles

Partners

Bangladesh

BRRI, Gazipur

RRS, Rajshahi

India

AAU, Anand

BAU, Ranchi

BF, Hyderabad

CRRI, Cuttack

CRURRS, Hazaribag

DRR, Hyderabad

ICAR-NEH, Tripura

IGAU, Raipur

JNKVV, Jabalpur

NDUAT, Faizabad

OUAT, Bhubaneshwar

TNAU, Coimbatore

UAS, Bangalore

Nepal

NRRP, Hardinath

RARS, Nepalganj

RARS, Tarharra

Philippines – PhilRice

Laos – NAFRI

Mozambique-IIAM, Chokwe

Tanzania –DASRC, Morogoro

Malaysia – UKM and MARDI

RDA, Korea

Devgen

Donors

Bill and Melinda Gates Foundation

Generation Challenge program

Asian Development Bank

DBT, India

Devgen/Syngenta

RDA, Korea

BMZ, Germany

At IRRI

Shalabh Dixit , Nitika Sandhu

Nora, Anshuman Singh, A. Palong

B.P.M. Swamy, Prashant Vikram

Ajay Kohli

Amelia Henry

V. Ramaiah, Jerome Bernier

Gary Atlin

drought grain yield qtls in rice -...

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