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Marker-assisted Breeding to Improve Grain Yield Under Drought

ARVIND KUMAR
Current position: Senior Scientist 1, Plant Breeder Drought, Aerobic Rice

Education & Training:


Ph.D. 2002: Plant Breeding and Genetics, Indira Ghandi Krishi Vishwavidyalaya (IGKV)-ICGEB, India Plant Breeding and Genetics, IGKV, Raipur, India

M.Sc. 1992:

B.Sc. 1989:

Agriculture IGVK, Raipur, India

Work experience: Jan 19, 2010 present : Jan 19, 2007 Jan 18, 2010: July 1, 2006 - Jan 18, 2007 : Oct 30,2004 - Jun 30, 2006 : Jan 25, 1995 - Oct 29, 2004 : Nov 4, 1992 - Jan 24, 1995 :

Senior Scientist I, PBGB, IRRI Senior Scientist, PBGB, IRRI Senior Scientist, IGKV, India Post Doc Fellow, IRRI Scientist/Senior Scientist, IGKV Research Associate, IGKV

Research highlights: Varieties developed/ germplasm registered: 21 Genes/QTLs identified : 15 (7 genes for gall midge resist., 8 QTLs for DT) Book Chapters : 19 Manuscripts in peer reviewed journals : 76 Thesis Advisor : Post Doctoral: 5; Ph.D.: 7; M.S.: 5
Awards: 1. Young Scientist Award 96-97 from Madhya Pradesh Council of Science & Technology, India 2. Best Scientist Award of IGKV, Raipur for year 2002

Marker Assisted Breeding to Improve Grain Yield Under Drought

Arvind Kumar September 06, 2012

GSR
Afrida Abu Hassan

Conclusions from last seminar March 03, 2011


Conventional breeding approaches provide lines with 0.8-1.2 t ha-1 yield advantage under drought Breeding lines released in few countries

Increased water uptake- not always due to root depth, lateral roots and/or root hairs play important role also
Major drought yield QTLs are true and effective Effect of individual QTLs 300-500 kg ha-1, requires pyramiding of three QTLs to get 1.2 ton or more yield advantage Major QTLs with effect in the multiple improved genetic background exists, need to put in more efforts to identify something like sub 1 Vandana, Way Rarem, IR64 improved for yield under drought. DTY QTLs introgression in Swarna, Swarna sub 1 under progress As we move to deliver molecular breeding products in project driven research, efficient testing facility at IRRI required

Varieties released- conventional breeding


Name Designation Days to Maturity 110 115 110 110 110 110 110 Plant height (cm) 104 100 104 108 108 101 104 Country, release year, situation Philippines 2009, RL, UP Nepal 2009, RL India 2010, RL, UP Bangladesh 2011 , RL Nepal 2011, RL Nepal 2011, RL Nepal 2011, RL

Sahod Ulan 1 Hardinath 1 Sahbhagi dhan BRRI dhan 56 Sookha dhan 3 Sookha dhan 1 Sookha dhan 2

IR74371-54-1-1 IR80411-B-49-1-1 IR74371-70-1-1 IR74371-70-1-1 IR74371-70-1-1 IR74371-46-1-1 IR74371-54-1-1

Katihan 1 Sahod Ulan 3


Sahod Ulan 5 Sahod Ulan 6 Sahod Ulan 8 Inpago LIPI Go 1 Inpago LIPI Go 2

IR79913-B-176-B-4 IR81412-B-B-82-1
IR81023-B-116-1-2 IR72667-16-1-B-B-3 IR74963-262-5-1-3-3 IR79971-B-191-B-B IR79971-B-227-B-B

105 120
115 115 125 110 113

90 107
130 100 100 115 114

Philippines 2011, UP Philippines 2011, RL


Philippines 2011 , RL Philippines 2011, RL Philippines 2011 , RL Indonesia 2011 UP Indonesia 2011 UP

Why MAB for drought tolerance?


2.500
NON STRESS index values of top 20 entries tested from 2005-2007

3.500 3.000 2.500

2.000

MOD STRESS index values of top 20 entries tested from 2005-2007

1.500
NON STRESS index values of top 20 entries tested from 2008-2010

2.000 1.500 1.000

1.000

MOD STRESS index values of top 20 entries tested from 2008-2010

0.500

0.500 0.000
1 2 3 4 5 6 7 8 9 1011121314151617181920

0.000

1 2 3 4 5 6 7 8 9 1011121314151617181920

3.500 3.000

SEVERE STRESS index values of top 20 entries tested from 2005-2007

2.500
2.000 1.500 1.000 0.500 0.000
SEVERE STRESS index values of top 20 entries tested from 2008-2010

1 2 3 4 5 6 7 8 9 1011121314151617181920

Why MAB for drought tolerance?


Traditional donors- N22, Aday Sel, Moroberekan, Way Rarem, Dular are not good combiners Increasing GY by crossing two high yielding diverse improved lines did not provide further yield increase under drought MAB to provide unique opportunity to bring together large effect regions from different donors and get incremental yield increase under drought Consistent QTLs work effectively across stress levels MAB with large effect QTLs provide an opportunity to combine drought tolerance with other stresses/traits Once QTLs pyramided in improved background, MAB to other background becomes easy

Why rice is a suitable case for MAB for GY under drought?


In different crops Many QTL reported with high QTL x environment interaction QTL x genetic background interaction No QTL reported to work irrespective of ecosystem Many criticism from people working on other crops where large effect QTLs not detected In rice at IRRI Many QTLs reported with Consistent effect in different environments

Consistent effect in different genetic backgrounds


Consistent effect in different ecosystems Products developed with increased GY

Major effect QTLs for grain yield under drought


Variety Vandana QTL qDTY12.1 Donor Way Rarem Ecosystem Upland Additive effect 47 Phenotypic variance (R2) 33

IR64

qDTY1.1
qDTY2.2 qDTY4.1 qDTY9.1

N22
Adaysel Adaysel Adaysel

Lowland
Lowland Lowland Lowland

24
14 6 29

17
6 11 19

qDTY10.1
Swarna qDTY1.1 qDTY1.1 qDTY2.1 qDTY3.1 Sabitri qDTY12.1 qDTY3.2 Samba Mahsuri TDK1 qDTY11.1 qDTY3.1 qDTY6.1 qDTY6.2 MTU1010 BR11 qDTY1.1 qDTY3.1

Adaysel
N22 Dhagaddeshi Apo Apo IR74371-46-1-1 IR77298-5-6-18 IR55419-04 IR55419-04 IR55419-04 IR55419-04 N22 Apo

Lowland
Lowland Lowland Lowland Lowland Lowland Lowland Lowland Lowland Lowland Lowland Lowland Lowland

18
29 25 23 30 25 16 32 10 12 16 16 27

17
13 32 7 27 47 19 14 7 9 10 13 25

Large effect drought QTLs qDTY1.1, qDTY2.3, qDTY3.1, qDTY3.2, qDTY12.1 shows effect against Different drought susceptible recipient varieties Different environments Across both lowland and upland ecosystem

No guarantee if MAB is not carried by an experienced drought breeder as many minor modifications are needed during the process of MAB

qDTY1.1 effect across ecosystem, environments & backgrounds


Population CT9993-5-10-1M/IR62266-42-6-2 Additive effect* 20.6 Ecosystem Lowland Location Raipur, India Reference
Kumar et al. 2007

Apo/IR64 Apo/IR72
IR64*2/Azucena Vandana/IR64 Vandana/IR72

52.2 63.6
36.2 25.6 63.4

Upland Upland
Upland Upland Upland

IRRI IRRI
IRRI IRRI IRRI

Venuprasad et al. 2011 Venuprasad et al. 2011


Venuprasad et al. 2011 Venuprasad et al. 2011 Venuprasad et al. 2011

N22/IR64
N22/MTU1010 Dhagaddeshi/Swarna Dhagaddeshi/IR64

24.3
16.1 24.9 8.3

Lowland
Lowland Lowland Lowland

IRRI
IRRI IRRI IRRI

Vikram et al. 2011


Vikram et al. 2011 Ghimire et al. 2012 Ghimire et al. 2012

* Maximum additive effect as the % of trial mean

Prashant, IRRI

qDTY3.1 : Major and consistent QTL in Swarna and BR11


QTLs
DTY3.1 DTY3.1

Chr
3 3

Interval
RM520-RM16030 RM15935-RM520

R2
30 20

Additive effect 25 22

Donor
Apo Apo

Recipient
Swarna BR11

Apo x Swarna

Apo x BR11

Swamy, IRRI

Introgression of major effect drought grain yield QTLs DTY3.1 and DTY12.1 Anjali
IR81896-B-195 ( DTY3.1) F1 X Anjali (WS2010) Fore ground selection QTLs DTY3.1 BC1 X Sub1Swarna (DS2011) Fore ground selection DTY 12.1 Chr 3 12 X Anjali (DS2010) Fore ground selection

Major effect drought grain yield QTLs


Interval RM520-RM16030 RM28048-RM28166 R2 30 36 Additive effect 25 47 Donor Apo Way Rarem

BC2F1 (WS2011)

Fore ground selection Selection of homozygote for DTY3.1

BC2F2 (DS2012)

IR 84984-83-15-18-B-B-93 X Anjali (DS2010) Fore ground selection ( DTY12.1) F1 X Anjali (WS2010) Fore ground selection

BC1 X Sub1Swarna (DS2011) Fore ground selection

Anjali lLs with DTY12.1 , 12DAS

BC2F1 (DTY3.1)

BC2F1 (DTY12.1) (WS2011)

Fore ground selection


Fore ground selection BC3F1 Selection of BC2F2 (DS2012) homozygote for DTY 12.1 Selection of homozygote for DTY3.1 and DTY12.1 Anjali lLs with DTY3.1 12DAS

BC3F2 (WS2012)

Selected homozygotes with DTY3.1, DTY12.1 and their combinations will be tested under drought DS2013

Swamy, IRRI

Effect of qDTY12.1 in upland and lowland conditions

Upland
Additive effect of QTL as % of trial mean

Lowland

Trial mean grain yield (kgha-1)

Vandana/ Way Rarem


Bernier et al. 2007, 2009

IR74371-46-1-1/ Sabitri
Mishra et al. 2012, BMC Genetics (Revision)

qDTY2.3, qDTY3.2 were also detected to show effect in Vandana/Way Rarem in upland

Moroberekan: a donor that has eluded Breeders: Moroberekan/ 3* Swarna


Around 2000 SNP markers surveyed for polymorphism. 191 markers run on a population of 361 BC2F3 derived lines Traits measured: grain yield, plant height and DTF over 2 seasons under lowland stress (severe and moderate) and non- stress conditions in DS 2011 and DS 2012 3 QTLs detected for grain yield under stress 13 QTLs detected for grain yield under non- stress which showed effect across both seasons
Moroberekan X 3* Swarna

BC2F2 population screened for blast tolerance 361BC2F3 derived lines tolerant to blast for mapping yield QTLs under stress and non- stress

Drought Tolerant NILs

Drought tolerant BILs with similar/ superior grain quality

QTLs for grain yield under drought stress and non- stress conditions

At present 381 single plant selections from the population being screened in India
A subset of 100 lines being screened at IRRI under aerobic conditions
S. Dixit, IRRI

QTLs for grain yield under drought stress: Moro/3*Swarna

QTL qDTY2.2 qDTY2.3 qDTY3.2 qDTY12.2 qDTY12.1 qDTY12.3

Chr

Interval

2 id2001301-id2003908 2 id2011110-id2012785 3 id3000757-id3002606 12 id12000292-id12002057 12 id12005302-id12007081 12 id12007577-ud12001525

Severe Stress Add LOD R2 id2002229 18.8 60.4 4.7 5.8 k_9 112.8 33.9 8.8 10.6 id3000757 5.1 43.4 10.8 12.9 ud12000118 11.0 55.1 4.0 5.0 id12005428 61.7 id12007988 89.0 31.0 5.2 6.4 Peak Position

Moderate stress Combined Add LOD R2 Add LOD R2 10.6 4.1 10.6 5.6 7.2 3.8 5.1 19.0 9.7 7.0 18.8 12.5 25.4 3.9 4.8 12.1 4.1 11.7 14.9 4.9 5.1

S. Dixit, IRRI

IR64 drought tolerant NILs under upland drought


DTF NS 77 75 DTF S 89 HT NS 72 HT S 69 64 GY Kg/ha NS 2844 GY Kg/ha S 576

ENT DESIGNATION 1 2 IR 87707-446-B-B-B IR 87707-445-B-B-B

90 IR64 77

2800 471 IR64+DTY QTLs

3
4 5 6 7 8

IR 87707-182-B-B-B
IR 87707-118-B-B-B IR 87729-69-B-B-B IR 87706-215-B-B-B IR 87705-44-4-B-B IR 87705-14-11-B-B

78
83 80 80 78 78

89
93 95 90 95 90

69
82 80 61 81 61

59
74 56 51 50 61

2863
1209 2073 1506 1861 2180

451
102 97 174 113 439

9
10 11

IR 87705-83-12-B-B
IR 87728-102-B-B-B IR64

83
86 83

95
95 90

69
76 77

54
54 65

1920
1542

114
54

IR 1383 64 96

* 500 Kg yield advantage over IR64 under upland drought

Has this been an easy job?


Year 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 Total Lowland Population RIL RIL RIL BIL RIL BIL RIL BIL RIL RIL BIL RIL BIL RIL BIL RIL BIL No. 5 2 4 1 3 1 4 2 8 5 9 9 3 3 11 6 11 87 Upland Populations No.

RIL
RIL

4
8

BIL RIL, BIL BIL BIL

6 1, 1 2 2

RIL BIL

1 4 29

No second example of such a massive effort to identify QTLs The efforts resolved many misgivings about drought yield QTLs

Efficient, cost effective strategy: BSA for identifying consistent QTLs


N22 IR64 BH BL N22 IR64 BH BL

QTL identification in multiple populations simultaneously


RM431

Dhagaddeshi

Dhagaddeshi

Swarna

Swarna

Identify few markers in BSA


BH BL

BH

BL

BSA with adjoining markers of the identified one


Validation of BSA results
Consistent Drought Grain Yield QTLs Identified via BSA

RM11943

RM431

ADVANTAGES of BSA

Cost effective
Can be applied with expensive marker systems like SNP (Becker et al. 2011-Plos One) RNA can be pooled for microarray (Kadam et al. 2012)

qDTY1.1; qDTY2.2; qDTY3.1; qDTY3.2; qDTY4.1; qDTY6.1; qDTY12.1

Vikram et al. 2012, FCR

What is within DTY QTLs?


Regions that increase yield under drought Regions that increases yield under irrigated situation Regions that increases yield under dry direct seeded aerobic situation (DS flooded?)

Regions that increases plant height


Regions that decreases days to flowering

Regions that might have a negative effect on GY

Elimination of linkage drag


qDTY1.1 was linked with plant height; Linkage needed to be broken prior to application of the QTL
FG N22 Swarna BC3F1 Selected 21 F1s X ~ 3000 BC3F2 217 dwarf plants FG FG +QTL & recombinants FG Selection for Swarna plant type Single plants with QTL ~ 180 BC3F3 X Ratooned, split planted 2 Plants segregating for qDTY1.1 Generating QTL lines Screened plants with Swarna grain type Breaking linkage

X Selfing of recombinants Screened for GY under drought

Phenotypic selection

Background genotyping Being Screened at IRRI under ROS Plants with clear background Phenotypically and genotypically Background selection

Being Screened in India under ROS

FIELD SCREENING AT MULTIPLE LOCATIONS

Drought screening

Vikram, Prashant

MAB for drought tolerance


Identify two to three major QTLs with high effect in the background of popular high yielding varieties.

Introgression and pyramiding of identified QTLs for Maintenance breeding improve popular high yielding varieties- Vandana, IR64, Swarna, Sabitri, TDK 1 keeping the other traits intact Forward breeding- From segregating BC2F2 population select lines with high yield irrespective of background clearance, and traits different from the recipient variety Develop near isogenic lines in improved background with different QTL combinations for basic as well as applied research

Marker assisted Breeding Strategy for high grain yield under drought
Mega varieties Swarna, IR64, MTU1010, TDK, Vandana Sabitri, Sambha Mahsuri
F1 F2

Drought tolerant land races N22, Dhagad Desi,

Mega varieties Saro5, IR64 MTU1010, Nerica lines

Land races & wild species

Apo, Dular, Adaysel Kalis Aus, Aus 226, Wayrarem

x
F1 BC1F1 BC2F1 BC2F2 BC2F3

Adaysel, IRGC81994, IRGC105775 Advanced Back Cross mapping population

Recombinant Inbred mapping Population

F3 F3:4 F3:5 (300-400)

QTLs identified for high grain under drought using BSA/ WG Consistent and major effect QTLs selected for MAS in each recipient background

BC2F4 (300 -400 )

qDTY1.1, qDTY2.1, qDTY3.1,qDTY12.1, qDTY6.1, qDTY11.1

qDTY2.2, qDTY4.1qDTY9.1, qDTY10.1

Pyramiding of 3 major QTLs


Fore ground and back ground genotyping

Lines with QTLs and combinations identified from the mapping populations and Intercrossed/back crossed to recipient parents BC1F1(500)/ BC2F1 ( 1000) / BC3F1(1500-2000) lines with all the QTLs Selected

Selection of BC3F2 (4000-5000) homozygous lines and background genotyping (To break DTF and HT linkages)

Lines with single QTLs Lines with two QTLs


lines with different QTL combinations

Lines with all the QTLs

Selection of QTL lines based on DTF and HT

Screening under managed drought stress and non-stress (IRRI) Phenotyping Selected best lines evaluated for grain quality and Other parameters Best lines evaluated in target environments of the respective variety

High yielding Forward Breeding Lines

Multi-location evaluation

Best lines released for cultivation by Farmers

IR 64 introgression lines with DTY QTLs: AB QTL approach

+ QTL Parents- 2007

- QTL

IR64

IR64+DTY QTLs

Introgressions under drought- 2010

DTY introgressed line

IR 64

Similar to IR64 grain quality traits of introgressed lines

Product - 2011

IR64 QTLs lines under non-stress and stress

+ QTL line

Non-Stress IR64 2011 DS, IRRI

+ QTL line Drought Stress IR64 2011DS, IRRI

IR64 QTL lines under testing in WS2011, WS2012 at 14 locations in India under AICRIP program; Nepal (03), Bangladesh (01), Philippines (01),

IR 64 + QTLs lines performance at IRRI


Line QTLs DF (NS) DS11 83 82 PH (NS) DS11 91 95 GY GY (NS) (S) DS10 DS11 DS10 DS11 4312 6308 2011 1943 6232 1041 1879 GS (%) 94.4 92.6

IR 87729-69-B-B-B IR 87728-491-B-B

DTY9.1, DTY2.1, DTY10.1, DTY4.1 DTY9.1, DTY2.1, DTY4.1

IR 87707-186-B-B-B DTY2.1, DTY10.1, DTY4.1


IR 87707-446-B-B-B IR 87707-445-B-B-B IR 87728-162-B-B IR 87705-83-12-B IR 87705-80-15-B IR64 LSD0.05 DTY2.1, DTY4.1 DTY2.1, DTY4.1 DTY9.1, DTY2.1 DTY2.1, DTY10.1 DTY10.1, DTY4.1

78
80 77 84 80 81 80 3

99
98 96 94 95 89 96 7

4550
3752 5045 4796 3850 2987

6103
4388 5844 6115 5526 5516 5435 1053

2068
2556 2555 1147 1916 2074 636

2632
3000 3023 1636 2270 2151 1442 690

96.9
97.0 96.9 92.4 95.0 94.6

Swamy and Helal, IRRI

Improved drought tolerant IR64 lines under lowland drought in target environments
Grain yield (kg ha-1) Rajshahi Entry IR87707445-B-B IR87707446-B-B IR87707182-B-B IR64 LSD NS 4167 4521 4312 3379 240 DS 1525 1933 1508 980 156 Nepalganj NS 5990 6302 6510 4297 324 DS 3472 2847 2778 1597 170 Raipur NS 5084 5771 5646 4083 434 DS 3956 3614 3419 2662 285 Hyderabad 1 NS 5672 5634 6047 5699 186 DS 1684 1813 1383 660 939 Hyderabad 2 NS 5672 5634 6047 5699 186 DS 3800 4057 3604 3085 600 Hazaribagh NS 5690 5711 4453 5612 475 DS 1604 1229 1500 958 422 NS 4100 4911 4513 3586 920 Rewa DS 3731 3899 3509 2503 909

* 500 to 1500 Kg yield advantage over IR64 under lowland drought

Swamy, 2012

IR64 drought tolerant NILs under upland drought: IRRI


ENT NO DESIGNATION 1 2 IR 87707-446-B-B-B IR 87707-445-B-B-B DTF NS 77 75 DTF S 89 HT NS 72 HT S 69 64 GY Kg/ha NS 2844 GY Kg/ha S 576

90 IR64 77

2800 471 IR64+DTY QTLs

3
4 5 6 7 8

IR 87707-182-B-B-B
IR 87707-118-B-B-B IR 87729-69-B-B-B IR 87706-215-B-B-B IR 87705-44-4-B-B IR 87705-14-11-B-B

78
83 80 80 78 78

89
93 95 90 95 90

69
82 80 61 81 61

59
74 56 51 50 61

2863
1209 2073 1506 1861 2180

451
102 97 174 113 439

9
10 11

IR 87705-83-12-B-B
IR 87728-102-B-B-B IR64

83
86 83

95
95 90

69
76 77

54
54 65

1920
1542

114
54

IR 1383 64 96

* 500 Kg yield advantage over IR64 under upland drought

Performance of IR64 QTL lines under drought

IR 87707-445-B-B-B

IR 87707-182-B-B-B

IR64

CRURRS, Hazaribag, India 2011 WS

Similar RVA and cooking quality traits for IR64 & IR64 NILs
ENTRY IR 87706-215-B-B-B IR 87705-14-11-B IR 87705-83-12-B IR 87707-445-B-B-B IR 87728-102-B-B IR 87707-446-B-B-B IR 87705-444-B IR 87729-69-B-B-B IR 87707-182-B-B-B IR64
3500 3000 2500 2000 1500 1000 500 0 0.0 -500 2.0 4.0 6.0 8.0 10.0 12.0 14.0

Peak 1 Trough 1 Breakdown Final Visc Setback Peak Time Pasting Temp Retro

2932 2845 2793 2689 2627 2828 2778 2681 2646 2799

1356 1405 1348 1521 1311 1561 1433 1288 1404 1462

1576 1440 1445 1168 1316 1267 1345 1393 1242 1337

2840 2750 2633 2868 2620 2938 2798 2631 2793 2825

-92 -95 -160 179 -7 110 20 -50 147 26

5.6 5.67 5.67 5.87 5.67 5.87 5.73 5.67 5.73 5.8

78.4 78.25 78.3 79 79.05 79.1 78.4 78.4 78.25 79.85

1484 1345 1285 1347 1309 1377 1365 1343 1389 1363

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

NILs Moro/3* Swarna: AB QTL, SNP, maintenance breeding: 2009-2012


GY (Severe) IR 91648-B-85-B 2032 IR 91648-B-285-B 1403 IR 91648-B-319-B IR 91648-B-73-B IR 91648-B-192-B IR 91648-B-240-B
SWARNA MOROBEREKAN

LINE

Stress GY (Moderate) 3141 2566 3389 3438 3025 3017 2326 717

Non stress GY (Combined) 2613 1979 2124 2398 1832 2336 1211 384 GYC 5118 6496 4418 5474 4569 4499 4282 1701 DTFC 86 88 91 91 86 81 99 95

Grain type Similarity HTC % Swarna Class to Swarna 98 90 Yes Medium 96 90 No Medium 93 95 93 83 91 120 91 92 93 95 No Yes Yes Yes Medium Medium Medium Medium

819 1372 689 1775 86 88

S. Dixit, IRRI

NILs Moro/3* Swarna: AB QTL, SNP, Forward breeding


Stress LINE IR91648-B-89-B IR 91648-B-101-B IR 91648-B-55-B IR 91648-B-139-B IR 91648-B-105-B IR 91648-B-131-B IR 91648-B-146-B IR 91648-B-151-B IR 91648-B-74-B IR 91648-B-54-B IR 91648-B-210-B IR 91648-B-95-B IR 91648-B-347-B SWARNA MOROBEREKAN GY (Severe) 1743 947 1845 999 762 1090 1635 566 934 1352 1240 1887 749 86 88 GY (Moderate) 3169 2956 2168 2481 3218 2536 2542 3068 3497 2856 2387 2729 3098 2326 717 GY (Combined) 2448 1967 2013 1755 1956 1799 2060 1814 2219 2125 1864 2315 1945 1211 384 GY 6811 5171 5514 4447 5461 5267 4304 5698 4643 5410 4409 4467 5040 4282 1701 Non stress DTF 90 87 89 85 88 89 86 87 89 87 94 82 91 99 95 HT 94 90 93 89 95 98 95 98 99 94 97 91 97 91 120 Grain type % Similarity to Swarna Class Swarna 35 44 45 85 85 86 87 87 87 87 88 89 89 No No No No No No No Yes No Yes Yes No No Long Medium Long Medium Medium Medium Medium Medium Medium Medium Medium Medium Medium

S. Dixit, IRRI

QTLs for grain yield under non- stress

QTL qDTY2.1 qDTY3.3 qDTY4.2 qDTY4.3 qDTY6.3 qDTY6.2 qDTY8.2 qDTY8.3 qDTY9.2 qDTY9.3 qDTY11.2 qDTY12.3

Chr

Markers

Peak

Position

2 id2004861- id2007213 id2006621 54.8 3 id3010094-ud3001370 id3010740 95.1 4 id4001205- ud4000437 id4001882 63.4 4 id4003690-id4005389 id4004461 137.4 6 id6006336- id6007759 id6007312 44.6 6 id6010515- id6012967 id6011613 72.6 8 id8001604- id8002632 id8002098 30.1 8 id8006885- id8007977 id8006997 100.1 9 id9002357- id9003188 id9002721 37.7 9 id9004727- id9007259 id9004727 65.7 11 id11009197- id11011285 id11009456 102.9 12 id12006515- id12007988 id12007081 85.0

Non stress 2011 Add LOD R2 37.7 9.3 11.2 32.4 7.8 9.5 22.3 7.4 9.0 32.0 6.1 7.5 28.2 9.9 11.9 22.6 10.1 12.1 12.1 12.2 14.4 43.7 7.4 9.0 35.9 7.8 9.5 25.7 13.1 15.4 30.6 10.4 12.5 29.9 5.2 6.5

Non stress 2012 Add LOD R2 33.5 6.3 7.8 26.8 7.2 8.8 15.8 5.0 6.2 26.7 7.4 9.1 20.2 8.9 10.8 16.0 6.7 8.3 5.9 5.7 7.1 32.2 4.5 5.6 30.7 5.4 6.8 16.5 5.2 6.5 26.0 6.7 8.3 19.5 4.5 5.6

Combined Add LOD R2 35.7 10.6 12.8 29.8 10.2 12.2 19.2 8.3 10.1 29.5 8.2 10.0 24.5 13.0 15.4 19.5 10.7 12.8 9.2 12.3 14.6 38.3 8.0 9.8 33.4 8.8 10.8 21.4 12.3 14.6 28.4 11.8 14.1 25.0 6.6 8.2 S. Dixit, IRRI

High yielding BILs with QTLs affecting yield under non- stress
Line IR91648-B-7-B QTLs qDTY2.1, qDTY3.3, qDTY4.2, qDTY4.3, qDTY6.3, qDTY6.2, qDTY8.2, qDTY8.3, qDTY9.2, qDTY9.3, qDTY11.2, qDTY12.3 qDTY2.1, qDTY3.3, qDTY4.2, qDTY4.3, qDTY6.3, qDTY6.2, qDTY8.2, qDTY8.3, qDTY9.2, qDTY9.3, qDTY11.2, qDTY12.3 qDTY3.3, qDTY6.3, qDTY6.2, qDTY8.2, qDTY9.3, qDTY11.2, qDTY12.3 qDTY6.3, qDTY6.2, qDTY8.2, qDTY8.3, qDTY9.3, qDTY8.2 qDTY9.3 qDTY6.2 qDTY3.3, qDTY4.2, qDTY4.3, qDTY6.3, qDTY6.2, qDTY8.2, qDTY8.3, qDTY9.3, qDTY11.2, qDTY12.3 qDTY3.3, qDTY6.3, qDTY8.3, qDTY9.3, qDTY11.2, qDTY12.3 qDTY2.1, qDTY3.3, qDTY4.2, qDTY4.3, qDTY6.3, qDTY6.2, qDTY8.2, qDTY8.3, qDTY9.3, qDTY11.2, qDTY12.3 qDTY8.2, qDTY9.3,

Grain Yield DS2011 DS2012 Combined


9458 7690 8577

DTF 81

HT % Swarna 120 72

IR91648-B-13-B IR91648-B-20-B IR91648-B-22-B IR91648-B-32-B IR91648-B-150-B IR91648-B-57-B IR91648-B-59-B IR91648-B-76-B IR91648-B-89-B IR91648-B-251-B MOROBEREKAN SWARNA

7161 7009 7909 7230 6237 6025 6323 6395 7020 7321 2234 4552

6434 6085 5518 4840 4826 5114 5341 4613 6592 4349 1171 4012

6792 6553 6714 6034 5529 5566 5835 5511 6811 5845 1701 4282

81 83 85 92 93 82 85 85 90 92 95 99

118 103 116 118 94 102 104 100 94 119 120 91

71 47 34 67 67 34 40 53 35 67

-B

-B

-B

-B

Development of Vandana NILs with qDTY12.1: MAB

Way Rarem

Vandana

Apo

IR90020:22-283-B-4-B

Dixit et al. 2012, TAG

Performance of Vandana NILs at IRRI and in India


Upland severe stress Designation IR84984-83-15-481-B IR90020:22-283-B-1-B IR90020:22-283-B-4-B GY 693 604 515 DTF 64 66 67 PHT 75 79 77 BIO 4160 4160 4133 HI 0.17 0.14 0.21 Upland non- stress GY 2525 3039 2245 DTF 62 66 68 PHT 79 85 84

Way Rarem
Vandana Apo

0
27 0.1

NF
70 NF

60
79 57

2667
2080 2267

0.01
0.09 0

1660
2127 2127

87
68 80

100
91 101

Designation IR84984-83-15-481-B IR90019:22-283-B VANDANA WAY RAREM

DTF 78 78 81 90

PHT 116 107 105 115

GY- C 5670 5208 4348 4649

GY-D 2343 2410 1799 868

DTF 61 60 60 90

GY-D 1687 1580 1327 100

IR84894-83-15-481-B

Vandana

S. Dixit, IRRI; NP Mandal, CRURRS

Pyramiding of major effect drought grain yield QTLs DTY1.1, DTY2.1 and DTY3.1 in Swarna Sub1:MAB
Pyramiding two QTLs
IR81896-B-195 X Swarna(WS2009) Fore ground selection Background selection (DTY2.1and DTY3.1) Fore ground selection Background selection

Major effect drought grain yield QTLs in Swarna


QTLs Chr Interval R2 Additive effect Donor

DTY1.1
DTY2.1 DTY3.1

1
2 3

RM11943-RM12091
RM327-RM262 RM520-RM16030

14
16 30

30
12.5 25

N22
Apo Apo

BC2 X Sub1Swarna(DS2010)

BC3 X Sub1Swarna (WS2010)

Fore ground selection Background selection

BC4F1 (DS2011)

Fore ground selection Background selection

BC4F2 (WS2011)

Select homozygote's Background selection

BC4F3 (DS2012)

Drought screening

Pyramiding three QTLs


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

BC4F1(DS2011) Fore ground selection

BC4F2 (WS2011)

Select homozygote's

Swarna sub1 lLs with DTY QTLs

Swarna sub 1

Swarna sub1 lLs with DTY QTLs

BC4F3 (DS2012)

Drought screening

Swamy, IRRI, 2012

Performance of Swarna Sub1 two QTL:MAB


Designation IR 94391-131-358-19 IR 94391-131-245-2 IR 94391-131-722-2 IR 94391-131-455-19 IR 94391-131-165-2 IR 94391-131-605-20 IR 94391-131-344-1 IR 94391-131-42-2 IR 94391-131-713-1 DTF 88 88 88 88 88 88 88 85 88 HT 103 89 94 101 84 89 93 84 89 GYS 5237 4839 4450 3994 3975 3896 3887 3823 3784 GYNS 7421 7101 10675 8500 6947 7586 7374 7365 6840
QTLs DTY3.1 DTY3.1 DTY3.1 DTY3.1 DTY3.1 DTY3.1 DTY3.1 DTY3.1 DTY3.1 DTY2.1 DTY2.1 DTY2.1 DTY2.1 DTY2.1 DTY2.1 Sub1 h . s1 s1 s1 . s1 s1 s

IR 94391-131-605-17
IR 94391-131-120-2 IR 94391-131-74-9 IR 94391-131-358-16 IR 94391-131-161-13 Swarna Sub1 Swarna

88
88 85 88 88 92 92

90
83 87 106 86 90 90

3731
3716 3714 3695 3686 2558 2120

6115
6582 6479 7907 6683 5207 4435

DTY3.1
DTY3.1 DTY3.1 DTY3.1 DTY3.1

DTY2.1
DTY2.1 DTY2.1 DTY2.1 DTY2.1

.
h h h s

Performance of Swarna Sub1 three QTL lines: MAB


Designation IR96321-558-206 DTF HT GY S 4919 DTY1.1 QTLs DTY3.1 DTY2.1
ART5

s1

IR96321-1080-91
IR96321-327-107 IR96321-327-210 IR96321-1099-154

90
90

103
93

4479
4202 4022 3948

DTY1.1
DTY1.1 DTY1.1 DTY1.1

DTY3.1
DTY3.1 DTY3.1 DTY3.1

DTY2.1
DTY2.1 DTY2.1 DTY2.1

s
h s h

IR96321-1080-278
IR96321-967-412 IR96321-967-105 IR96321-1099-44 IR96321-967-57 IR96321-558-209 IR96321-1393-58 IR96321-678-240 IR96321-315-374

86
86 82 90 82 90 89

121
139 136 94 138 89 90

3939
3918 3909 3891 3885 3876 3855 3845 3836

DTY1.1
DTY1.1 DTY1.1 DTY1.1 DTY1.1 DTY1.1 DTY1.1 DTY1.1 DTY1.1

DTY3.1
DTY3.1 DTY3.1 DTY3.1 DTY3.1 DTY3.1 DTY3.1 DTY3.1 DTY3.1

DTY2.1
DTY2.1 DTY2.1 DTY2.1 DTY2.1 DTY2.1 DTY2.1 DTY2.1 DTY2.1

s
h s1 s1 s s1 s s s1

Apo
Swarna

76
96

115
92

2078
1896

Performance of Swarna ILs early: under drought


2012 Designation IR94313:16-22-2-3-2 IR94313:2-1-1-5-1 IR88286-136-B-B-B-2-1 DTF-NS 75 75 81 HTAVE-NS 103 91 110 GY-NS 3841 4699 4404 GY-S 5777 5465 5428

IR94391-564-1-3
IR94391-707-1-1 IR94314-20-11-2 IR94313:1-9-2-1-1

75
75 78 78

102
100 93 107

3429
4238 5186 5767

5392
5343 5188 5059

IR94391-755-1-2
IR94313:16-37-1-3-4 IR94313:2-1-1-4-2 IR94314-20-9-3 IR94313:1-9-2-8-1 IR94313:18-4-1-5-2 IR94391-587-1-3 Apo Swarna Sub1

78
78 75 81 81 81 75 78 87

85
111 93 80 118 82 93 111 87

4098
3863 4634 5458 3895 4473 3662 6284 4789

5018
4989 4909 4868 4865 4863 4849 4263 1695

Swarna

91

88

4475

1895

Performance of Swarna ILs medium: under drought


Designation
IR94313:8-1-5-5-2 IR94313:19-36-1-7-1 IR94313:16-32-1-9-3 IR94313:8-1-3-9-3 IR94313:8-1-1-6-1 IR94313:16-32-3-2-1 IR94313:19-36-3-6-2 IR94313:12-32-1-2-1

DTF-NS
81 90 81 85 85 81 90 85

HTAVE-NS
89 95 99 95 97 93 102 93

GY-NS
6511 6464 6559 5967 7321 6478 10047 6783

GY -S
5817 5557 5354 5335 5271 5210 5093 5048

IR94313:19-7-1-4-1
IR88286-582-1-B-B-4-3 IR94313:8-1-1-4-1 IR94313:16-32-1-2-3

90
92 85 81

90
113 98 97

6544
10821 5055 4234

5029
4913 4898 4897

IR94391-303-1-1
Swarna Swarnasub1 Apo

85
95 93 78

101
92 95 110

10808
4867 5530 5574

4877
3048 3205 3386

*1500 -2000 Kg yield advantage over Swarna and Swarna Sub1

Swamy, IRRI

MAB to improve GY under drought of MRQ74, MR219


MRQ74 X IR77298-14-1-2-10 (qDTY2.2)

MRQ74
X IR84984-83-15-18-B (qDTY12.1)

MRQ74
X IR81896-B-B-195 (qDTY3.1)

Foreground genotyping for qDTY2.2 F1 (145) X F1 (142)

Foreground genotyping for qDTY12.1

Foreground genotyping for qDTY2.2 & qDTY12.1


388 (Total) 18 (foreground genotyping)

Foreground genotyping for qDTY3.1 X F1 (53) Foreground genotyping for qDTY2.2, qDTY 3.1 & qDTY12.1,

F1 (18)

743 (Total)

21(foreground genotyping) 10 (PH, background genotyping)

F1 (10)

MRQ74 Foreground genotyping for qDTY2.2, qDTY 3.1 & qDTY12.1, Recombinant & Full background genotyping

878 (Total)

35 (foreground genotyping)

10 (PH, background genotyping)

BC1F1 (10) X Foreground genotyping for qDTY2.2, qDTY 3.1 & qDTY12.1, Recombinant & Full background genotyping

Wet Season 2012

BC1F2 (5000) X Foreground genotyping for qDTY2.2, qDTY 3.1 & qDTY12.1, (homozygous condition), Recombinant & Full background genotyping, Selecting lines with different +qDTY combinations and -qDTY BC1F3 Field Screening (Dry season 2013)

Forward breeding
Currently at this stage

Nora, IRRI- UKM, Malaysia

Pyramiding qDTY3.2 and qDTY12.1 in Sabitri


IR74371-46-1-1 X Sabitri IR77298-5-6-18 X Sabitri

qDTY12.1 mapped and effect tested

BC1F5 [5]

BC1F5 [5]

qDTY3.2 mapped and effect tested

Plants segregating for qDTY12.1 and qDTY3.2 identified, background genotyped

F1 [300]

Sabitri

Plants segregating for qDTY12.1 and qDTY3.2 with clearest background to be identified and back crossed to Sabitri

BC1F1 [1000]
Plants with qDTY12.1 and qDTY3.2 with clearest background to be identified and seeds multiplied

Plants segregating for qDTY12.1 and qDTY3.2 with clearest background identified and selfed

F2 [1000] BC1F2 [1000]

Plants with qDTY12.1 and qDTY3.2 with clearest background to be identified

F3 [1000]
Seed multiplication and drought screening

BC1F3
Seed multiplication and drought screening

Shalabh and Prashant, IRRI

Wild species derived mapping population development


SL No 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 Female Parentage MTU 1010/IRGC 81994 MTU 1010/IRGC 105757 MTU 1010/IRGC 106109 MTU 1010/IRGC 106283 MTU 1010/IRGC 106285 Saro 5/IRGC 81994 Saro 5/IRGC 105757 Saro 5/IRGC 106109 Saro 5/IRGC 106283 Saro 5/IRGC 106285 NericaL-14/IRGC 105757 Nerica-L-14/IRGC 106277 Nerica-L-14/IRGC 106285 Nerica-L-31/IRGC 104639 Nerica-L-31/IRGC 106277 Nerica-L-5/IRGC 106109 Nerica-L-7/IRGC 106283 Nerica-L-8/IRGC 106285 Male Parent MTU1010 MTU1010 MTU1010 MTU1010 MTU1010 Saro 5 Saro 5 Saro 5 Saro 5 Saro 5 NericaL-14 NericaL-14 NericaL-14 Nerica-L-31 Nerica-L-31 Nerica-L-5 Nerica-L-7 Nerica-L-8

Mapping strategy
Development of Advanced Back Cross mapping population (BC2F2) Genotyping BC2F2 population Phenotyping BC2F3 and BC2F4 populations Identification novel major effect QTLs Introgression of QTLs in the recipient backgrounds

Swamy, IRRI

What we still do not know How the different combinations of QTLs work together in different genetic backgrounds In case of IR64, two QTL combinations with qDTY2.2 and qDTY4.1 were the best yielders

The identified QTLs have shown effect under drought in lowland and upland situations as well as for yield under normal situation, indicating their possible role in improving yield in puddled irrigated situation, dry direct seeded aerobic and dry direct seeded flooded situation (better water uptake, nutrient uptake ?)
Need to know the involved trait?

NILs for different QTLs in IR64 background


Line
IR87729-69-B-B-B IR87728-491-B-B IR87707-186-B-B-B IR87707-359-B-B-B IR87707-446-B-B-B IR87707-445-B-B-B IR87728-162-B-B IR87705-83-12-B IR87705-80-15-B IR87705-72-12-B IR87705-6-8-B IR87728-395-B-B IR99261:12-13 IR99619:342-1 IR96301:140-10 IR99619:143-7 IR 96296-35-11 IR99261:33-17 IR99261:78-25 IR 96296-113-16 IR99619:333-8 IR 96296-112-10

QTL Combinations
qDTY9.1, qDTY2.2, qDTY10.1, qDTY4.1 qDTY9.1, qDTY2.2, qDTY4.1 qDTY2.2, qDTY10.1, qDTY4.1 qDTY2.2, qDTY10.1, qDTY4.1 qDTY2.2, qDTY4.1 qDTY2.2, qDTY4.1 qDTY9.1, qDTY2.2 qDTY2.2, qDTY10.1 qDTY10.1, qDTY4.1 qDTY2.2 qDTY4.1 qDTY9.1 qDTY12.1 qDTY2.2 qDTY1.2 (S) qDTY1.1+ qDTY1.2 qDTY12.1+qDTY2.3 (P) qDTY12.1+qDTY3.2 (P) qDTY12.1 (P)+qDTY3.2 (P) qDTY12.1 +qDTY3.2 (S)+qDTY2.3 qDTY1.1+ qDTY1.2 +qDTY2.2 qDTY12.1 +qDTY3.2 (S)+qDTY2.3(S)

Background
IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64 IR64
BPM. Swamy, IRRI

NILs for different QTLs in IR64 background


Line
F1 Plants (S) F1 Plants (S) F1 Plants (S) F1 Plants (S) F1 Plants (S) F1 Plants (S) F1 Plants (S) F1 Plants (S) F1 Plants (S) F1 Plants (S) F1 Plants (S) F1 Plants (S) F1 Plants (S) F1 Plants (S) F1 Plants (S) F1 Plants (S) F1 Plants (S)

QTL Combinations
qDTY1.1 qDTY2.2 qDTY2.3 qDTY3.2 qDTY12.1 qDTY2.3+qDTY2.3 qDTY2.2 +qDTY12.1 qDTY1.2+qDTY12.1 qDTY1.1+qDTY12.1 qDTY2.2 +qDTY2.3+qDTY12.1 qDTY1.1+ qDTY1.2 +qDTY2.2 qDTY1.1+ qDTY1.2 +qDTY2.3 qDTY1.1+ qDTY1.2 +qDTY12.1 qDTY1.1+ qDTY1.2 +qDTY12.1+qDTY2.2 qDTY1.1+ qDTY1.2 +qDTY2.2+qDTY2.3 qDTY1.1+ qDTY1.2 +qDTY12.1+qDTY2.3 qDTY2.2 +qDTY2.3+qDTY3.2+qDTY12.1

Background
IR64 Sub1 IR64 Sub1 IR64 Sub1 IR64 Sub1 IR64 Sub1 IR64 Sub1 IR64 Sub1 IR64 Sub1 IR64 Sub1 IR64 Sub1 IR64 Sub1 IR64 Sub1 IR64 Sub1 IR64 Sub1 IR64 Sub1 IR64 Sub1 IR64 Sub1

F1 Plants (S)

qDTY1.1+ qDTY1.2 +qDTY2.2+qDTY2.3+qDTY12.1

IR64 Sub1
(S): Segregating (P): Partial introgression
S. Dixit, IRRI

NILs for QTLs in Swarna and Swarna Sub 1 background


Line IR 96321-678-508 IR96321-558-209 IR 96321-678-271 IR96321-315-60 IR 96321-1626-132 IR 96321-1393-244 IR 96321-1393-367 IR964391-131-358-19 IR 96321-647-73 IR96321-678-240 IR 96322-34-332 IR 964391-131-242-2 IR 96321-1080-29 IR964391-131-624-1 Combinations qDTY1.1, qDTY3.1, qDTY2.1 qDTY1.1, qDTY3.1, qDTY2.1 qDTY1.1, qDTY3.1 qDTY1.1, qDTY3.1 qDTY1.1, qDTY2.1 qDTY1.1, qDTY2.1 qDTY3.1, qDTY2.1 qDTY3.1, qDTY2.1 qDTY1.1 qDTY1.1 qDTY2.1 qDTY2.1 qDTY3.1 qDTY3.1 Background Swarna Sub1 Swarna Sub1 Swarna Sub1 Swarna Sub1 Swarna Sub1 Swarna Sub1 Swarna Sub1 Swarna Sub1

Line IR 91659:41-59-1 IR 91659:41-59-3 IR 91659:41-95-11 IR 91659:41-95-12 IR 91659:41-95-14 IR 91659:41-95-15 IR 91659:41-95-3 IR 91659:41-95-4

QTL combination qDTY1.1 + qDTY3.2 qDTY1.1 + qDTY3.2 qDTY1.1 + qDTY3.2 qDTY1.1 + qDTY3.2 qDTY1.1 + qDTY3.2 qDTY1.1 + qDTY3.2 qDTY1.1 + qDTY3.2 qDTY1.1 + qDTY3.2 qDTY1.1 + qDTY3.2 qDTY1.1 + qDTY3.2 qDTY1.1 + qDTY3.2 qDTY1.1 + qDTY3.2 qDTY1.1 + qDTY3.2

Background Swarna Swarna Swarna Swarna Swarna Swarna Swarna Swarna Swarna Swarna Swarna Swarna Swarna

Swarna Sub1

IR 91659:41-95-9
Swarna Sub1 Swarna Sub1 Swarna Sub1 Swarna Sub1 Swarna Sub1

IR 91659:54-36-3 IR 91659:54-36-4 IR 91659:54-36-6 IR 91659:54-36-8

BPM. Swamy, IRRI

P. Vikram, IRRI

NILs for DTYQTL Developed NILs shall help to Understand physiological and molecular mechanism involved with each QTL

Know the combinations of QTLs highly likely to provide higher grain yield under drought Facilitate MAB in different background without any undesirable linkage drag

Characterize individual QTLs/QTL combinations for their effect in different severity of stresses
Characterize different regions for severity of stress they are prone to.

Breeding for drought tolerance in rice An over view


Selections based on secondary yield traits QTL mapping for physiological and secondary traits under drought MAS for QTLs of secondary traits
Managed field drought screening standardized Selection for GY under drought qDTY12.1 identified Questions on consistency of large effect QTLs MAS for large effect QTLs initiated
Additional

2000-2004

2005-2008

2009 - 2013

large effect QTLs identified QTL pyramiding in popular rice mega varieties Fine mapping QTLs and candidate gene analysis MAS products successfully developed and tested in TPE Identification of novel QTLs from land races and wild species Marker aided recurrent selection (MARS) initiated

MARS and GWS fully implemented for better genetic gain Wild species derived QTLs used in MAS 2014 beyond QTLs pyramided and tested in hybrid parental backgrounds Genetic stocks developed, characterized, best combination of QTLs SNP chip developed, drought QTLs combined with other traits

Fast track MAB using SNP platforms


Construction of the chip with consistent DTY-QTLs

Application in Marker Assisted Breeding


qDTY1.1

DTY-QTL Recipient donors background DTY1.1 R X DTY3.1 R DTY3.2 R DTY6.1 R DTY12.1 R DTY2.3 R

qDTY3.1

Large number of F2s genotyped in few days

qDTY3.2 qDTY6.1 qDTY12.1

F2
Lines with QTL homozygote selected

Combining QTLs 1.5 year

Generation advancement, genotyping , Seed multiplication

Drought screening at multiple locations 1 year

1 year

MAB Product

Why we did not clone the drought genes?


Many initial challenges- QTLs real?, effect of individual QTL? led us to focus on identification and effect confirmation of more than one QTL First priority product development Initial involvement with with gene cloning, we would have limited ourselves to qDTY12.1 There are better people available to do this

Collaborating within and outside IRRI on three qDTY1.1,qDTY3.1 and qDTY12.1

Conclusions
At least six QTLs- qDTY1.1, qDTY2.2 qDTY2.3, qDTY3.1, qDTY3.2, qDTY6.1 and qDTY12.1 have shown effect in more than one genetic backgrounds and across both lowland and upland ecosystem.
Their use in MAB have successfully shown yield increase of Vandana, IR64, Swarna, Swarna sub1 under drought. There are indications that these QTLs provide yield increase under normal situation, aerobic situation and can be useful to increase yield under dry direct seeded flooded situation. We do not know the best QTL combination for different backgrounds. Understanding the physiological and molecular mechanism of individual QTLs on NILs will help us to streamline this and make MAB easy. Developing SNP chip for these QTLs/QTLs combinations can help to make MAB quick, easy and help to integrate these QTLs into market segmentation breeding program of IRRI to combine with other traits.

Partners
Bangladesh BRRI, Gazipur RRS, Rajshahi India BAU, Sabour BAU, Ranchi BF, Hyderabad CRRI, Cuttack CRURRS, Hazaribag DRR, Hyderabad ICAR-NEH, Tripura ICAR, Patna 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

Donors

Rockefeller Foundation Bill and Melinda Gates Foundation Generation Challenge program Asian Development Bank DBT, India Devgen RDA, Korea GIZ, Germany Univ. Kebangsaan Malaysia, Bangi MARDI, Malaysia

Thank you very much for your kind attention and time

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