Breeding new flood-tolerant rice varieties
description
Transcript of 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
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PART II: Current activities
PART III: Future directions
Flooding
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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
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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.
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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
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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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
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~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!