Post on 28-Oct-2014
description
GRiSPUsing genomic approaches to increase rice’s yield potential
Parminder S. VirkExit Seminar
GRiSP
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Asia Africa Americas Rest of World
Million tons milled rice
Additional rice needed:116 million tons by 2035
2010 global rice production
GRiSP (2010)
GRiSP PHILIPPINE RICE NEEDSProduction,Consumption(milled, in '000 tons)
Production
Consumption
0
4,000
8,000
12,000
16,000
20,000
24,000
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7 Million Tons Additional Rice Needed by 2035
Historical Data: USDA; Demand Projections: Our own estimates Sam Mohanty
2010 Palay production 15.77 M mt
GRiSP How can we increase rice production?
Farmarea
2010
Additional Area needed: 41 m ha to produce additional 176 m tons by 2035
GRiSPHow can we increase rice production?
Closeyield gap
Raiseyield
potential
Preventyield
erosion
FarmYield
(65%)
10 t/ha
GRiSP
Use of sd1 dwarfing gene
increased yield potential of
irrigated rice (tropics)from
4-5 t ha-1 to 10 t ha-1
GRiSP
Yield Potential
Potential Yield: the maximum yield
predicted by a computer model for a
variety growing without stress
(Sheehy, 2001)
GRiSPGreen Revolution Slows
World Rice Yield (1961-2010)Data Source: FAO
Average yield (t ha-1) Average yearly increase overprevious 10 years (kg ha-1)
0.0
1.0
2.0
3.0
4.0
5.0
1955 1965 1975 1985 1995 2005 2015
Year
0
40
80
120
160
200
Courtesy P. Quick
Investment in productivity research dropped from 2.2% to < 0.8%
GRiSP
EcologyCurrent YP
t ha-1
Required YP t ha-1
% increase
in YP
Irrigated alone 10 12.3 23%
Rainfed alone 8 16.97 112%
Irrigated + Rainfed
10 11.3 13%8 10.1 26%
Target Yield Potential (YP)(to produce additional 176 m tons of rice by 2035)
Yield gap: Irrigated=35%; Rainfed= 55%
GRiSP
RCF g DW MJ-1
Pot. Yield t ha-1
2.20 102.64 123.30 15
The key is to enhance RCF/RUE
RCF= Radiation Conversion FactorRUE= Radiation Use Efficiency
Potential rice grain yield (PY) in the tropics is 15.9 t ha-1 in Dry season (Yoshida, 1981)
Realistic PY is 12.5 t ha-1
GRiSP
Yield Potential = Light interception x RUE x HI
Stay green
Low Specific Leaf Area (thicker leaves)
Compact plant architecture
Limited potential to increase HI
The key is to enhance RUE
GRiSP
Enhance C3 photosynthesis (RUE),
Increase:
Biomass (HI > 0.5),
Sink strength traits,
Grain filling and
Lodging resistance
Key target traits to enhance yield potential
GRiSP Scientists at IRRI in the late 1980s postulated that the plant type of indica HYVs varieties may limit the further improvement in their yield potential
Semi-dwarf indica varieties have:
• a large number of unproductive tillers • limited sink size• excessive leaf area that may cause mutual
shading and a reduction in canopy photosynthesis
GRiSP
Simulation models predicted that a
25% increase in yield potential was
possible by modification in the
plant type for certain traits
GRiSP Strategies for increasing the yield potential
Redesign the ideotype of semi-dwarf plant type (New Plant Type)
Semi-dwarf indica varieties have:• a large number of unproductive tillers • limit sink size• excessive leaf area that may cause
mutual shading and a reduction in canopy photosynthesis
GRiSP
• lower/moderate tillering capacity
• no unproductive tillers
• 200-250 grains per panicle
• 90-100 cm tall
• sturdy stems
• dark green, thick and erect leaves
• vigorous root system
• 100-130 growth duration
• multiple disease and insect resistance
• acceptable grain quality
Salient Features of proposed NPT
GRiSPThe original NPT lines
• possessed bold grains
• lacked disease (tungro) and insect
(BPH) resistance
• the preference in the tropics is for long
and slender grains
Therefore, for developing NPTs with wider
acceptability, the original NPTs were
crossed with elite indicas
GRiSP Three of the NPT lines have been released in the Yunnan province of China, with a yield of more than 13 tons ha-1at farmers’ fields.
IR64446-7-10-5 ‘Dianchao 1’ IR69097-AC2-1 ‘Dianchao 2’IR64446-7-10-5 ‘Dianchao 3’
GRiSP
Several NPT-IJ lines produced significantly
higher yield than the check variety, IR72.
During 2003 dry season, IR72967-12-2-3 was the
top yielder NPT-IJ line. It produced 10.2 t/ha,
which was significantly higher than the indica
check variety (9.2 t/ha).
GRiSP
Improved NPT lines ‘IR77186-122-2-2-3’ has been released as a national variety under the name ‘NSIC Rc 158 (Tubigan 12)’ in the Philippines during 2007.
NSIC Rc 158 – 36 ultimate landraces
This is probably the first example of an improved NPT line, originating from a cross between indica and tropical japonica, released as a variety in the Philippines.
GRiSP
Target traits for selection:
Plant height, Leaf and Panicle morphology, Grain size, Biomass production, and Grain filling percentage
Direct selection for yield per se was more effective in increasing grain yield than indirect selection for plant traits
Lines with ideal plant traits did not express higher yield under optimal crop management conditions.
GRiSP NSIC Rc 222
It has set a new bar for grain yield in the Philippines
• High grain yield 11.5 t ha-1 (USM, 2011WS)• Tolerance to major biotic stresses• Wider adaptability :
Rainfed Irrigated Stagnant flooding Low radiation etc.
GRiSP
Grain yield (kg ha-1)
Genotype name
Experiment station (moderately Zn deficient)
Farmers field(severely Zn deficient site)
NSIC222 6444a 6544a
IR64 3600de 4306bc
IR68144 4566c 4448bc
IR83668 3149e 3775cd
IR85800 4291cd 3286cde
IR83317AC-25 5621b 5642ab
IR91152AC 2325f 40f
IR83317AC-124 3845cde 3456cde
IR91143AC 3265e 1686ef
IR64196 4286cd Not planted
IR75862 Not Planted 2309de
Screening for Zn deficiency tolerance and grain Zn
NSIC Rc 222 was the top yielder at both sites, with no significant reduction in yield at severely Zn deficient site compared to moderately Zn deficient site
Foliar Zn application (@ 4 kg Zn ha-1 ) at heading significantly increased brown rice grain Zn, indicating phloem mobilization
0
5
10
15
20
25
Experimentstation
Farmers field
Bro
wn
rice
Zn
conc
entr
atio
n (m
g kg
-1)
Water-sprayed control
Foliar Zn sprayed at 50% heading
Courtesy: Impa & Sarah
GRiSPPerformance of NSIC Rc 222 in Challenging environments (Bicol)…1
Courtesy: Eileen Garcia
GRiSP
Courtesy: Eileen Garcia
Performance of NSIC Rc 222 in Challenging environments (Bicol) …2
GRiSP
Courtesy: Eileen Garcia
Performance of NSIC Rc 222 in Challenging environments (Bicol)…3
GRiSP
“Hybrid rice breeders are intimidated by the performance of Rc 222” Thelma Padolina
2011WS NCT trials (35 Hybrids)
P201031 (Pioneer) 6.5 t ha-1
PHDR0912 (Devgen) 6.1 t ha-1
NSIC Rc 222 6.1 t ha-1 (Rank 3)
Mestiso 7 5.7 t ha-1 (Rank 13)
NSIC Rc 222
GRiSP
Genomic approaches to accumulate yield potential traits/loci
GRiSP
Hypothesis
Functional genes controlling yield related traits when pyramided into an elite line using MAS should increase yield potential of rice
GRiSP
• Plant architecture
• Large panicle size
• Grain size and weight
• Grain Filling
• Lodging resistance
Pyramid genes for yield component traits using MAS
GRiSP
Traits Genes Functional Protein Chromosomelocation
Large panicle OsSPL14 Squamosa Promoter Binding protein-like 14
8
Grain size, shape, quality
OsSPL16/GW8
Squamosa Promoter Binding protein-like 16
8
Grain number Gn1a Cytokinin oxydase/dehydrogenase
1
Strong and thick culm
SCM2/APO1 F-box protein ortholog of Arabidopsis
6
Grain yield, Heading
Ghd7 CCT domain protein 7
Yield related functional genes
GRiSP
Traits Genes Functional Protein Chromosomelocation
Grain size and grain
weight (grain filling)
GS5
GW5
GW2
GS3
Serine carboxypeptidase
Nuclear protein
Ring-type E3 ubiquitin ligase
Putative trasmembrane like protein
5
5
2
3
Yield related functional genes…continued
GRiSP
Grain Filling
Sugar Phosphate Synthase (SPS) and Sucrose Transporter Genes
12 SPS and 5 transporter genes
GRiSP
Gene Position (bp) ChrGn1a 5,270,103 1GW2 8,146,286 2Gs3 17,369,402 3GS5 3,423,243 5GW5 5,342,545 5SCM2 27,484,483 6Ghd7 9,186,690 7OsSPL14 25,280,969 8OsSPL16 26,501,167 8
7 cM
5 cM
GRiSP
Mutants in general produce too severe phenotype (growth retardation, morphological abnormalities, sterility) to introduce directly in Crop Improvement
TilleringMONOCULM (MOC1), OsTB1/FC1 (Fine Culm 1), OsTB1, D88 (D14)
D3, D10, HTD1, HTD2, D27
Regulation of panicle developmentLAX1(lax panicle), SPA/MOC1-3 (small panicle), fzp (frizzy panicle)
Rate of spikelet formationApo1, SP1 (short panicle)
Duration of panicle differentiationRCN1 and RCN2 (rice TERMINAL FLOWER)
GRiSP
Accumulate QTLs controlling yield
potential traits using Marker
Aided Recurrent Selection (MARS)
and Genomic Selection (GS)
GRiSPMarker Aided Recurrent Selection (MARS)
Selection for several QTLs relies on
index (genetic values) computed for
each individual based on its haplotype at
target QTLs
GRiSP
GRiSP GWS/GS
• Gain in predictive ability due to GS ranged from 7.7 to 35.7% relative to pedigree model in wheat.
• 0.79 correlation between observed and predictive values in maize
Private sector has reported significant gains in yield following MARS/GS
Training set data quality and GXE!
GRiSP
10,000 GeneBank accessionsCultivated + close wild relatives
Rice SNP Consortium
1M Affymetrix genotyping chip
BGI de novo sequencing
200 @ 50X depth1000 @ 10-20X depthrest @ 5-10X depth
H Leung
Molecular Marker Resource for MARS/GS
GRiSP Multidisciplinary teams
Eathington et al (2007)
GRiSPSNP genotyping workflow at IRRI
Data storage & analysis: Automated marker scoring
Tissue Preparation: Leaf punch samples in 96-well plates freeze-dried and ground into a powder
DNA extraction: DNA is purified using an
automated magnetic bead system ($1/sample)
Thermo Scientific: Kingfisher Flex 96
DNA normalization: DNA samples checked on a
NanoDrop and normalized using an automated
system
NanoDrop 8000
Aurora Versa mini liquid
handler
SNP genotyping: BXP 96 x 384 SNPs ($24/sample)
Fluidigm 96 x 96 SNPs ($6/sample) and future 192
x 24 SNPs (<$1/sample)
Fluidigm 96.96 ,48.48 and 192.24 IFC
Dynamic Array system
AA
AB
BB
M. Thomson
BeadXpress 384-plex
GRiSP
Unknowns!
Interactions between different genes
Compensation between traits
Pleiotropy with other agronomic traits
GRiSP
Conventional Breeding will remain irreplaceable
Genomic approaches will complement traditional breeding
Phenomics will play a bigger role in future to support conventional breeding
Multi-environment Testing should be strengthened(Los Baños vs HY environments)
Probability of combining multiple traits is low hence large number of crosses and large population size will remain a key to success
Breeders should be amply supported with resources and multidisciplinary teams
Some thoughts
GRiSP Acknowledgements
Gurdev KhushDarshan BrarGerard Barry
Tony Evangelista Nelie Delos ReyesBenny Romena Jaesal IsonVit Lopena Raul BoncodinVaroy PamplonaMembers of Irrigated, Golden rice and H+ teamsPBGB and IRRI familyCollaborating colleagues in IRRI, ARIs and several NARES partners
GRiSP
Visit us in Hyderabad (ICRISAT)
GRiSP Thank you for listening