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

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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

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Use of sd1 dwarfing gene

increased yield potential of

irrigated rice (tropics)from

4-5 t ha-1 to 10 t ha-1

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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%

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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%

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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

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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

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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

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• 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.

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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

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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

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Courtesy: Eileen Garcia

Performance of NSIC Rc 222 in Challenging environments (Bicol)…3

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“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

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Genomic approaches to accumulate yield potential traits/loci

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Hypothesis

Functional genes controlling yield related traits when pyramided into an elite line using MAS should increase yield potential of rice

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• Plant architecture

• Large panicle size

• Grain size and weight

• Grain Filling

• Lodging resistance

Pyramid genes for yield component traits using MAS

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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

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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

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Unknowns!

Interactions between different genes

Compensation between traits

Pleiotropy with other agronomic traits

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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

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GRiSP Thank you for listening