Breeding new flood-tolerant rice varieties

Bert Collard

Rice Seminar Series

Current position: Scientist II (breeder)Since March 2011

Education and trainingPhD in Agricultural Science (1998 – 2002 ) - University of Melbourne, VIC,

AustraliaBachelor of Science (Honours) (1993 – 1997) - University of Melbourne, VIC,

Australia

Work experienceDurum wheat breeder (2009-2011) - Department of Primary Industries NSWResearch Scientist (2008) - Department of Primary Industries VICResearch Scientist (2006-2007) - Queensland Department of Primary IndustriesPostdoctoral Research Fellow (2005-2006) - PBGB, IRRIPostdoctoral Research Fellow (2003-2004) - University of Southern QueenslandResearch Assistant (2000-2002) - RMIT University, VIC

Research highlights• Senior durum wheat breeder/ program leader for Australian Durum wheat

breeding program• >10 years experience in molecular genetics research for disease

resistance, abiotic stress tolerances and quality traits in bread wheat, chickpea, barley, sorghum and rice

• Experience in DNA marker validation research within Australian Wheat and Barley Molecular Marker Program

• Working with Dave Mackill at IRRI (2005-2006) in marker-assisted backcrossing program for Sub1 and abiotic stress tolerances

IRRI claim to fame:• Rice breeding course co-ordinator• Highest water bill by research staff in PBGB (or even IRRI ?)

Breeding new flood tolerant rice varieties

Bert CollardIRRI

PART I: Past achievements

4

PART II: Current activities

PART III: Future directions

Flooding

5

Types of flooding1. Crop establishment (anaerobic germination)

2. Flash-flooding (short duration ~2 weeks)

3. Medium deep water (Stagnant, slow rise)

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FR13A

7

Sub1 is major QTL for submergence tolerance

0 10 20 30 40

LOD score

50cM

100cM

150cM

OPN4

OPAB16

C1232

RZ698

OPS14RG553

R1016RZ206

RZ422

C985

RG570

RG451

RZ404

Sub-1(t)

1200

850

900

OPH7950

OPQ1600

~ 69% of the variation explained by a single QTL on chromosome 9: Sub1

Xu KN & Mackill DJ (1996). Mol. Breeding 2:

219-224.

8

9

Xu et al. (2006) Nature 442: 705-708

“Mega-varieties” of rice• extremely popular varieties which have higher yields

and farmers prefer• Problem: susceptible to abiotic stresses• Solution: use backcrossing strategy

BR11 (Bangladesh)

Swarna (India) IR64 (Asia)

“…there are many undesirable aspects associated with precipitous changes in varieties. Farmers are reluctant to rapidly shift their production from an old proven variety to an unknown new one. Their reluctance is based on their familiarity with the old variety which permits them to exploit to the maximum potential yielding ability. They know the best rates and dates of seeding of the old variety for their local conditions. ...

...The conventional backcross method .... [produces] new varieties which are phenotypically similar to the recurrent parent and is thereby readily received by both farmer and miller.”

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Normal Borlaug 1957

DNA markers improve efficiency of backcrossing

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CONVENTIONAL BACKCROSSINGx P2P1

DONORVARIETY

P1 x F1

P1 x BC1

P1 x BC2

P1 x BC3

P1 x BC4

P1 x BC5

P1 x BC6

BC6F2

• Select target gene. Discard ~50% BC1

• Visually select BC1 progeny that closely resemble variety

~6

YE

AR

S

Repeat process until at least BC6

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MAS

MARKER ASSISTED BACKCROSSINGx P2P1

DONORVARIETY

P1 x F1

P1 x BC1

P1 x BC2

P1 x BC3

BC3Fn fixed lines

3 -

4 Y

EA

RS MAS

MAS

MAS

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1 2 3 4 5 6 7 8 9 10 11 12

SUB1

CONVENTIONAL BACKCROSSING

Unwanted donor chromosome segments

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1 2 3 4 5 6 7 8 9 10 11 12

SUB1

MARKER ASSISTED BACKCROSSING

High level of precision

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C25 straight after de-submergence 2011 WS

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Swarna-Sub1 after submergence stress

1 week 2 weeks 3 weeks

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Submergence tolerance screening

Swarna Swarna Sub1 19

Short video

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Rigorous evaluation of Sub1 varieties lines for:• Submergence tolerance• Yield and agronomic traits• Grain quality

Rigorous evaluation of Sub1 varieties lines for:• Submergence tolerance• Yield and agronomic traits• Grain quality

Name Year developed Country

Swarna-Sub1 2006India, Bangladesh, Nepal

IR64-Sub1 2007 All Asia

Samba Mahsuri-Sub1 2007

India, Bangladesh, Nepal

TDK 1-Sub1 2007 LaosBR11-Sub1 2007 BangladeshCR1009-Sub1 2007 India

Ciherang-Sub1 2009 Indonesia, Bangladesh

PSBRc18-Sub1 2009 Philippines

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22

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The price of “Sub1 fame”• Frequent seed requests and visitors!

24Allan Salabsabin

INGER

Looking ahead

Promotion• Replace Swarna (approx. 5 M

ha area) with Swarna-Sub1• Take Swarna-Sub1 to

additional flood prone areas where Swarna cannot be cultivated

Tracking of diffusion of Swarna-Sub1 using

• GIS & Remote sensing• Seed production &

diffusion through formal & informal systems

• Ground survey

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Umesh SinghIRRI, STRASA

South Asia Project Co-ordinator

IRRI Submergence group

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BR11-Sub1“Pavel” Iftekharaudaula

Ciherang-Sub1Nurul Hidayatun

PSB Rc18-Sub1Darlene Sanchez

Eloi Estoy Freddie

Varoy Septi

PART II:Current activities

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Sub1 variety enhancements in progress

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Country Variety Stage Target date

Nepal Sabitri-Sub1 BC2F2/ BC1F3

2014

Philippines*(*PhilRice collaboration)

PSBRc82-Sub1 BC2F1/ BC1F2

2014-2015

Pakistan IR6-Sub1Super Basmati-Sub1

BC2F1 2014-2015

New SNP genotyping platforms

Illumina “BeadXpress”

384 SNPs

“Fluidigm EP”24, 48 or 96 SNPs with

flexible assays30

Improving disease resistanceBacterial leaf blight

Marker assisted pyramiding of 5 genes:

SUB1 + Xa4 + xa5 + xa13 + Xa21

606)

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Collaboration with Dr. Nollie Vera-Cruz

Developing Swarna-Sub1 with photoperiod sensitivity

• May overcome problems due to delays in flowering

• Used MABC for se1 (chr. 6)

• Field observations 2012 dry and wet season

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Screening of Sub1 in elite IRRI material

Expanded submergence screening facilities at IRRI

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Stagnant flooding

• Water depth: 50-60 cm for up to several months

• Yield losses: ~<60% • Common in South

(Eastern India, Bangladesh, Nepal) and SE Asia (Thailand, Cambodia) and parts of Africa

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Sub1 has NO effect on stagnant flooding tolerance

• Sub1 has no affect on tolerance

Swarna-Sub1

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“Sacobia” (Philippines, 1997); “Schwe Pyi Tan” (Myanmar, 2005)

“Popoul” (Cambodia 1999)

Indonesia (2008)

• 3 varieties with Sub1 + stagnant flooding tolerance:

Limited knowledge on stagnant flooding tolerance

• Correlation with plant height = 0.17 (NS)

• Correlation with elongation ability = 0.69 (P<0.001)

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Dr. Yoichi Kato (CESD)

Dr. S.R. Das (OUAT)

• Breeder’s eyes:– Tillering R2 = 0.12– Maturity R2 = 0.39

Promising elite lines with Sub1 + stagnant flooding tolerance

38IRRI 154(NSIC Rc222)

F2

F3

F4

F5

F6

OBSERVATION YIELD TRIAL (OYT)

ADVANCED YIELD TRIALS (AYT)

<10,000 PLANTS

>200,000 PLANTSn = 1,000/ pop. x 50 crosses/ season

~400

80

~8,000 lines

3000-4000 lines

1000 lines

MAS

Quality

SUBMERGENCE

SUBMERGENCE

BACTERIAL BLIGHT

Yield, SUBMERGENCE, Blast, BPH, GLH

Forward breeding

Yield under NORMAL + STAGNANT FLOODING

BACTERIAL BLIGHT

Selection for intermediate height + yield + yield components

39Yield under NORMAL

+ STAGNANT FLOODING

Promising material

• Selection for yield under SF stress

• Developed SUB1 + SFT lines outperforming both Sub1 varieties and checks

International collaboration is critical for developing new varieties

IRRI CORE BREEDING PROGRAM

INGER Flood prone nurseries

OVERSEAS PARTNERSObservational or replicated

yield trials

BEST ELITE LINES

IRRI multi-environment

testing (MET)

n = 10 – 30 per season

NEW VARIETIES

Eastern Indian Rainfed Lowland Shuttle breeding network (CRRI)

BRRI41

South Asian Breeding Network

BRRI

NEPAL

EIRLSBN

BRRI

PART III:Future directions

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Enhancing submergence tolerance

West Bengal 2011 WS

Several regions were affected by complete

submergence for 20 to 26 days

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Current level of tolerance

Swarna Swarna Sub1 45

New QTLs

PSB Rc18(IRRI 105)

PSB Rc18 Sub146

#1

Stagnant flooding

Research needs:1. Set of elite breeding lines2. Phenotyping methods3. Germplasm evaluation4. Physiological trait

characterization5. Molecular genetic

information

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#2

Stagnant flooding

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#2

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Germplasm screening

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#3New sources of submergence tolerance

Elite germplasm for stagnant flooding tolerance

Improved routine phenotyping

SES

#4

Precision phenotyping#4

Submergence screening

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DAY 1

DAY 7

DAY 10

DAY 14

DAY 15

DAY 16

DAY 17

DAY 18

DAY 12

SAMPLE #1

SAMPLE #2

SAMPLE #3

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Submergence computer model

Input:• Water temp.• pH• Dissolved O2• EC• Turbidity

OUTPUT #1:Drain water now.85% survival tolerant check

OUTPUT #2:10% yield loss for Swarna-Sub1

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Li et al. (2010) Field Crops Research 118: 221-227.

16.8% 40.7%

Precision phenotyping - digital image analysis

Multiple stress tolerances

Submergence + salinity tolerance

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Submergence + drought tolerance

IRRI 119 IR10F388

#5

Priorities and constraints

Dr. J.N. Reddy, Central Rice Research Institute (CRRI), Cuttack, Odisha

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Towards a rainfed breeding program

Disease & insect resistance

Salinity

Drought

Flood tolerance

SUB1 automatically built into all new varieties

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Eero Nissila, Head PBGB

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MOLECULAR BREEDING

PHYSIOLOGY + AGRONOMY

FLOOD TOLERANCE TRAIT DEVELOPMENT TEAM

ABIOTIC STRESS SCREENING $

Summary

1. Sub1 varieties have had a big impact in a short time

2. Currently developing new Sub1 varieties with multiple types of flooding tolerance

3. “Building” new rainfed varieties with multiple stress tolerances next priority

4. Sub1 will be a “default” gene for all breeding programs

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• Marlyn Rala

SUB Breeding team• Jerome Carandang• Julius “Jojo” Borgonia• Richard Daif• Richard Formaran

Lab Team• Jean Gonzaga• Eloi Suiton• Darlene Sanchez• Kashif Aslam Physiology (CESD)• Yoichi Kato• Ella Evangelista• Abdel Ismail

ES• Leigh Vial• Caling Balingbing

PBGB• Varoy Pamplona• Dr. S.R. Das• Endang Septiningsih• Glenn Gregorio• Allan Sallabsabin• Rafiq Islam

MMAL • Jade Dilla-Ermita• Mike Thomson

Pathology• Nollie Vera-Cruz• “Abe” Ona• Ruby Burgos

• Umesh Singh• Dave Mackill

Thank you!