Rice Seminar Series

Bert Collard
Current position: Scientist II (breeder)
Since March 2011

Education and training

PhD in Agricultural Science (1998 2002 ) - University of Melbourne, VIC, Australia Bachelor of Science (Honours) (1993 1997) - University of Melbourne, VIC, Australia

Work experience
Durum wheat breeder (2009-2011) - Department of Primary Industries NSW Research Scientist (2008) - Department of Primary Industries VIC Research Scientist (2006-2007) - Queensland Department of Primary Industries Postdoctoral Research Fellow (2005-2006) - PBGB, IRRI Postdoctoral Research Fellow (2003-2004) - University of Southern Queensland Research 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 Collard IRRI

PART I: Past achievements PART II: Current activities

PART III: Future directions

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Flooding

Types of flooding
1. Crop establishment (anaerobic germination) 2. Flash-flooding (short duration ~2 weeks) 3. Medium deep water (Stagnant, slow rise)

FR13A

Sub1 is major QTL for submergence tolerance

0 OPQ1 600 OPN4 1200 OPAB16 850 10 LOD score 20 30 40

Sub-1(t)

C1232 RZ698

OPS14 900
RG553 R1016 RZ206 50cM

OPH7 950
RZ422

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

100cM C985

RG570 150cM RG451 RZ404

Xu KN & Mackill DJ (1996). Mol. Breeding 2: 219-224.

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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

Swarna (India)

BR11 (Bangladesh)

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. ...

Normal Borlaug

1957

...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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DNA markers improve efficiency of backcrossing

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CONVENTIONAL BACKCROSSING
x P1 P2 VARIETY DONOR P1 x F1
P1 x BC1 P1 x BC2

~6 YEARS

Select target gene. Discard ~50% BC1 Visually select BC1 progeny that closely resemble variety

P1 x BC3
P1 x BC4

P1 x BC5
P1 x BC6
Repeat process until at least BC6
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BC6F2

MARKER ASSISTED BACKCROSSING

x P1 P2 VARIETY DONOR P1 x F1
MAS

3 - 4 YEARS

P1 x BC1
MAS

P1 x BC2
MAS

P1 x BC3
MAS

BC3Fn fixed lines

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CONVENTIONAL BACKCROSSING
Unwanted donor chromosome segments
1 2 3 4 5 6 7 8 9
SUB1

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11

12

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MARKER ASSISTED BACKCROSSING

High level of precision
1 2 3 4 5 6 7 8 9
SUB1

10

11

12

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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

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Short video

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Name Swarna-Sub1 IR64-Sub1 Samba MahsuriSub1 TDK 1-Sub1 BR11-Sub1 CR1009-Sub1 Ciherang-Sub1 PSBRc18-Sub1

Year developed 2006 2007 2007 2007 2007 2007 2009 2009

Country India, Bangladesh, Nepal All Asia India, Bangladesh, Nepal Laos Bangladesh India Indonesia, Bangladesh Philippines

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

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The price of Sub1 fame

Frequent seed requests and visitors!

Allan Salabsabin INGER

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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

Umesh Singh IRRI, STRASA South Asia Project 25 Co-ordinator

IRRI Submergence group

BR11-Sub1 Pavel Iftekharaudaula

Ciherang-Sub1 Nurul Hidayatun

Varoy

Septi

PSB Rc18-Sub1 Darlene Sanchez

Eloi

Estoy

Freddie
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PART II: Current activities

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Sub1 variety enhancements in progress

Country Nepal Variety Sabitri-Sub1 Stage BC2F2/ BC1F3 BC2F1/ BC1F2 Target date 2014 2014-2015 Philippines* PSBRc82-Sub1 (*PhilRice collaboration)

Pakistan

IR6-Sub1 Super Basmati-Sub1

BC2F1

2014-2015

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New SNP genotyping platforms

Illumina BeadXpress 384 SNPs

Fluidigm EP 24, 48 or 96 SNPs with flexible assays

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Improving disease resistance

Bacterial leaf blight

606)

Collaboration with Dr. Nollie Vera-Cruz

Marker assisted pyramiding of 5 genes: SUB1 + Xa4 + xa5 + xa13 + Xa21

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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

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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

Swarna-Sub1

Sub1 has no affect on tolerance 3 varieties with Sub1 + stagnant flooding tolerance:
Sacobia (Philippines, 1997); Schwe Pyi Tan (Myanmar, 2005)

Indonesia (2008)

Popoul (Cambodia 1999)

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Limited knowledge on stagnant flooding tolerance

Correlation with plant height = 0.17 (NS) Correlation with elongation ability = 0.69 (P<0.001)
Dr. Yoichi Kato (CESD)

Breeders eyes:
Tillering R2 = 0.12 Maturity R2 = 0.39
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Dr. S.R. Das (OUAT)

Promising elite lines with Sub1 + stagnant flooding tolerance

IRRI 154 (NSIC Rc222)

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Forward breeding
>200,000 PLANTS
n = 1,000/ pop. x 50 crosses/ season

F2
SUBMERGENCE

<10,000 PLANTS

F3
SUBMERGENCE

~8,000 lines
3000-4000 lines

F4 F5

Selection for intermediate height + yield + yield components

BACTERIAL BLIGHT

BACTERIAL BLIGHT

1000 lines ~400

F6

Quality

Yield, SUBMERGENCE, Blast, BPH, GLH

OBSERVATION YIELD TRIAL (OYT)

Yield under NORMAL + STAGNANT FLOODING

MAS
80
ADVANCED YIELD TRIALS (AYT)
Yield under NORMAL + STAGNANT FLOODING
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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
n = 10 30 per season
Eastern Indian Rainfed Lowland Shuttle breeding network (CRRI)

BEST ELITE LINES

INGER
Flood prone nurseries

IRRI multienvironment testing (MET)

OVERSEAS PARTNERS
Observational or replicated yield trials

NEW VARIETIES
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BRRI

South Asian Breeding Network

EIRLSBN

NEPAL BRRI

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

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New QTLs

PSB Rc18 (IRRI 105)

PSB Rc18 Sub1

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Stagnant flooding
Research needs: 1. Set of elite breeding lines 2. Phenotyping methods 3. Germplasm evaluation 4. Physiological trait characterization 5. Molecular genetic information

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Stagnant flooding

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Germplasm screening
New sources of submergence tolerance

Elite germplasm for stagnant flooding tolerance

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Improved routine phenotyping

SES

Precision phenotyping

Submergence screening

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Submergence computer model

DAY 1

DAY 7

SAMPLE #1
Input: Water temp. pH Dissolved O2 EC Turbidity

DAY 10 DAY 12 DAY 14 DAY 15

SAMPLE #2 SAMPLE #3

OUTPUT #1: Drain water now. 85% survival tolerant check OUTPUT #2: 10% yield loss for 55 Swarna-Sub1

DAY 16
DAY 17

DAY 18

Precision phenotyping - digital image analysis

16.8%

40.7%

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

Multiple stress tolerances

Submergence + drought tolerance Submergence + salinity tolerance

IRRI 119

IR10F388

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Priorities and constraints

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

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Towards a rainfed breeding program

SUB1 automatically built into all new varieties

Flood tolerance

Salinity

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Disease & insect resistance

Drought

Eero Nissila, Head PBGB

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FLOOD TOLERANCE TRAIT DEVELOPMENT TEAM

ABIOTIC STRESS SCREENING

MOLECULAR BREEDING

PHYSIOLOGY + AGRONOMY

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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

Thank you!

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
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