GRM 2013: Dissemination and Community of Practice for newly developed drought tolerant QTLs pyramided lines and Detecting and fine mapping QTLs with major effects on rice yield under

Arvind Kumar

Dissemination and Community of Practice for

newly developed drought tolerant QTLs pyramided lines

G4011.04

Detecting and fine mapping QTLs with major effects on rice yield under drought stress for

deployment via marker aided breeding G3007.05

Outlines

• Major QTLs for grain yield under drought in background of high yielding popular varieties

• Marker assisted introgression and pyramiding of QTLs in popular varieties Vandna, IR64, Sambha Mahsuri, Swarna

• Is rice different from other cereals for gains in yield under drought?

• Products, partners, capacity building

• Conclusions

Major QTLs for grain yield under drought • Efforts initiated in 2002-03

• Based on grain yield per se

• To identify 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 (17 publications just on QTL identification: Bernier et al. 2007, Venuprasad et al. 2009, Bernier et a. 2009, Venuprasad et al. 2009A, Venuprasad et al. 2009B, Vikram t 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. Sub, Alvin et al. Subm., Nitika et al. Subm.)

2013DS, IRRI

QTLs Donors Backgrounds Ecosystems

qDTY1.1 N22, Dhagaddeshi, Apo, CT9993-

10-1-M, Kali Aus, Basmati 334 Swarna, IR64, MTU1010 Lowland, Upland qDTY2.1 Apo, AUS 276 Swarna, MTU1010 Lowland

qDTY2.2 Aday sel, Kali Aus MTU1010, IR64, Sambha Mahsuri Lowland, Upland

qDTY2.3 N22, IR74371-46-1-1 IR64, Sabitri Upland, Lowland qDTY3.1 Apo, IR55419-04 Swarna, TDK 1 Lowland

qDTY3.2 N22, IR772978-5-6-18, IR74371-

46-1-1, Moroberekan Swarna, Sabitri Lowland, Upland

qDTY4.1 Aday Sel IR64, Sambha Mahsuri Lowland qDTY6.1 Apo, Vandna, IR55419-04 Swarna, IR72, TDK 1 Upland, Lowland qDTY6.2 IR55419-04 TDK 1 Lowland qDTY8.1 Basmati 334 Swarna Lowland qDTY9.1 Aday sel IR64 Lowland

qDTY10.1 N22, Aday sel, Basmati 334 IR64, MTU1010, Swarna Lowland qDTY11.1 IR55419-04 Sambha Mahsuri Lowland qDTY12.1 Way Rarem, IR74371-46-1-1 Vandna, Sabitri Upland, Lowland

QTLs for GY under drought identified at IRRI

Major QTLs: grain yield under drought in rice Over all picture on QTL study:

• Fourteen QTLs identified • Nine QTLs: showed effect against two or more genetic backgrounds.

• Six : showed effect in both lowland and upland ecosystem

• Six QTLs: showed effect against two or more genetic backgrounds as

well as in both lowland and upland ecosystems

In the background of popular high yielding variety:

• 5 QTLs: qDTY1.1, qDTY2.1,qDTY3.1, qDTY3.2 and qDTY8.1 in Swarna; • 4 QTLs: qDTY2.2, qDTY4.1, qDTY9.1, qDTY10.1, qDTY1.1, qDTY2.3 in IR64; • 2 QTLs: qDTY12.1, qDTY3.1 in Sabitri; • 3 QTLs: qDTY2.1, qDTY1.1, and qDTY10.1 in MTU1010; • 3 QTLs: qDTY11.1, qDTY2.2, qDTY2.3 in Sambha Mahsuri; • 3 QTLs: qDTY3.1, qDTY6.1,, qDTY6.2 in TDK 1;

Way Rarem 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

Apo

qDTY12.1introgressed in Vandna

DESIGNATION DTF-C DTF-D GY- C GY-D

IR 84984-83-15-110-B 62 80 5249 2099

IR 84984-83-15-481-B 61 78 5670 2343

IR 84984-83-15-862-B 62 79 4932 2146 IR 90019:17-159-B 60 78 4775 2268 IR 90019:22-283-B 60 78 5208 2410 VANDNA 60 81 4348 1799 WAY RAREM 90 90 4649 868 MEAN 64 81 4976 1998 LSD0.05 2 2 284 922

Vandna NIL lines yield in India

Vandna NILs are under testing in state trials in Jharkhand for possible release in 2015.

Vandna IR 84984-83-15-481-B

Hazaribag, India, 2011 WS

First case of yield increase of a drought tolerant cultivar

Increase in yield 9-30% in irrigated condition; 16-33% in moderate drought; 1670 - 2466% in severe drought

qDTY2.2, qDTY4.1 introgressed in IR64

IR64 + QTL line Drought Stress 2011DS, IRRI

Non-Stress 2011 DS, IRRI

+ QTL line IR64

IR64 QTL lines tested at 14 locations in India under AICRIP program; Nepal (03), Bangladesh (01) and are in the process of being released as varieties in India, Nepal and Bangladesh

IR64 QTL line with qDTY2.2, qDTY4.1 under drought at IRRI: 2013DS

ENTRY Rajsh

ahi Nepal ganj Raipur

Hydera bad SS

Hydera bad MS

Hazari bag Rewa

IR87707-445-B-B 1525 3472 3956 1684 3800 1604 3731 IR87707-446-B-B 1933 2847 3614 1813 4057 1229 3899 IR87707-182-B-B 1508 2778 3419 1383 3604 1500 3509

IR 64 980 1597 2662 660 3085 958 2503 Trial mean 1269 2871 3413 1339 3636 1323 3410

LSD0.05 312 340 570 1878 1200 844 1818

IR64 QTLs lines yield: India, Nepal, Bangladesh 2012WS

ENTRY Rajshahi Nepalganj Raipur Rewa Faizabad IR87707-446-B-B 4167 5990 5084 4100 5439 IR87707-445-B-B 4521 6302 5771 4911 6199 IR87707-182-B-B 4312 5078 5646 4513 6141 IR 64 3379 4297 4083 3586 4291 Trial mean 4011 5687 4694 3962 5323 LSD0.05 480 648 868 1840 528

GY under drought

GY under irrigated situation

Irrigated control -14-46% increase; Mild drought – 16-23% increase, Moderate drought- 28-117% increase; Severe drought – 53-155% increase Likely to be released in India, Nepal in 2013-14, Bangladesh 2015

IR64 IR 87707-445-B-B-B

IR 87707-182-B-B-B

CRURRS, Hazaribag, India 2011 WS

Performance of IR64 QTL lines under drought

qDTY2.2, qDTY4.1 introgressed in Sambha Mahsuri: 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

Chr QTL Additive Effect Trait Donor 11 q DTY11.1 15% Yield -S IR55419-04 3 and 6 qDTY3.1 , q DTY6.1 35% Yield -S IR55419-04 3 qBl3.1 - Blast IR55419-04

MARS: Improving yield under drought and blast resistance

Second cycle of recurrent selection

Total samples: 7013, Samba Mahsuri grain type: 38, slender, longer than Samba Mahsuri: 1045. 850 introgression lines with QTLs fixed, in different combinations and having grain quality similar to Samba Mahsuri, high grain weight selected

First cycle of recurrent selection

LIKE SAMBA MAHSURI

SAMBA MAHSURI

LONGER, SLENDER THAN SAMBA MAHSURI

qDTY12.1, qDTY2.3, qDTY3.2 introgressed in IR64: Earlier shown effect in upland in Vandna in upland

ENTRY DTF -C HT -C GY-C GY-D IR99621-78-25 73 83 5460 3047 IR99621-33-1 76 123 6352 2947 IR99621-33-17 76 84 5605 2939 IR99621-33-11 77 124 5473 2929 IR99621-33-19 78 88 5864 2809 IR99621-33-15 78 127 5479 2743 IR99621-115-17 77 135 5231 2582 IR99621-115-26 78 127 6758 2527 IR64 79 87 4846 1607 LSD0.05 3 8 1556 801 H 75.7 97.6 70.1 76.2

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

IR 74371-70-1-1:Sahbhagi dhan, BRRI dhan 56, Sookha dhan 3

• A variety of 105-110 days duration, high yielding, good grain quality variety • Developed through conventional breeding • Possess root plasticity trait • Suitable to cultivation under both dry direct seeded upland or lowland as well as transplanted lowland situations- Need to provide such variety for planting flexibility to farmers • Provides yield advantage of 0.8-1.2 t/ha over currently grown varieties: IRRI, India, famers field in India, Nepal and Bangladesh

Identified RF-GCP:-FS022 Released:G3007.05 Dissemination:G4011.04

0

500

1000

1500

2000

2500

3000

Vand

na

IR64

Sam

bha

Mah

suri

Swar

na

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?: response to GY under drought

• Yield increase under drought to the tune of 0.5- 2.0 t/ha • Grown in diverse conditions- upland-lowland-deepwater • Rice grown in uplands have conserved regions for better response under drought. Rice is uniquely placed to move the alleles from upland to lowland to obtain high yield advantage under drought

Products, partners, capacity building • Sahbhagi dhan, a drought tolerant variety in India, Bangladesh, Nepal

• Major QTLs for GY under drought

• Improved Vandna with 0.5 t/ha increased yield under drought

• Improved IR64 with 0.8 -1.2 t/ha increased yield under drought

• Improved Sambha Mahsuri with 1.0 -1.5 t/ha improved yield under drought

• Two Ph.D. Scholars, NARS partners trained, 02 rainout shelters to partners

• Linkage with scientific community

Conclusions

• Major QTLs for Grain yield under drought with effect in multiple high yielding genetic background, diverse- upland, lowland ecosystems identified in rice. • Identified QTLs introgressed and pyramided in popular rice varieties of South Asia- Vandna, IR64, Sambha Mahsuri, Swarna. Introgression in 5 other varieties in progress • Introgressed QTLs effect higher than predicted in QTL analysis. Effect also observed in irrigated situation not detected in QTL study, could also result from selection of positive interactions/ effect of QTLs in background of improved varieties with less linkage drags • Large effect QTLs, MAS + practical breeding, larger population size, linkage breakage/positive use of existing linkage, standardized managed drought screening key to success

Thank you very much for your kind attention

Thanks to GCP for all support over years, hope it continues