GRiSP

Using genomic approaches to increase rices yield potential

Parminder S. Virk Exit Seminar

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Million tons milled rice
600

550

Additional rice needed: 116 million tons by 2035

500

450

400

2010 global rice production

350

300

91

93

95

97

99

01

03

05

07

09

11

13

15

17

19

21

23

25

27

29

31

33 20

19

19

19

19

19

20

20

20

20

20

20

20

20

20

20

20

20

20

20

20

20

Asia

Africa

Americas

Rest of World

GRiSP (2010)

20

35

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PHILIPPINE RICE NEEDS

2010 Palay production 15.77 M mt
7 Million Tons Additional Rice Needed by 2035

Production,Consumption (milled, in '000 tons)

24,000

20,000

16,000

Consumption
12,000

Production
8,000

4,000

1960

1963

1966

1969

1972

1975

1978

1981

1984

1987

1990

1993

1996

1999

2002

2005

2008

2011

2014

2017

2020

2023

2026

2029

2032

Historical Data: USDA; Demand Projections: Our own estimates

Sam Mohanty

2035

GRiSP How can we increase rice production?

2010

Farm area

Additional Area needed: 41 m ha to produce additional 176 m tons by 2035

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How can we increase rice production?

10 t/ha

Farm Yield
(65%)
Close yield gap Raise Prevent yield yield potential erosion

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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)

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Average yield (t ha-1)

Green Revolution Slows World Rice Yield (1961-2010) Data Source: FAO
Average yearly increase over previous 10 years (kg ha-1)

5.0

200

4.0

160

3.0

2.0

120 Investment in productivity research 80 dropped from 2.2% to < 0.8%

1.0

40

0.0 1955 1965 1975 1985 Year 1995 2005

0 2015

Courtesy P. Quick

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Target Yield Potential (YP)

(to produce additional 176 m tons of rice by 2035) Required % Current YP YP t ha-1 increase t ha-1 in YP 10 8 12.3 16.97 23% 112%

Ecology Irrigated alone Rainfed alone Irrigated + Rainfed

10 8

11.3 10.1

13% 26%

Yield gap: Irrigated=35%; Rainfed= 55%

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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

RCF g DW Pot. Yield MJ-1 t ha-1 2.20 10 2.64 12 3.30 15 The key is to enhance RCF/RUE RCF= Radiation Conversion Factor RUE= Radiation Use Efficiency

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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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Key target traits to enhance yield potential

Enhance C3 photosynthesis (RUE),

Increase:
Biomass (HI > 0.5), Sink strength traits, Grain filling and Lodging resistance

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

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Simulation models predicted that a

25% increase in yield potential was

possible by modification in the plant type for certain traits

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Strategies for increasing the yield potential

Redesign the ideotype of semidwarf 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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Salient Features of proposed NPT

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

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The 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

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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).

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Improved NPT lines IR77186-122-2-23 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.

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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.

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Screening for Zn deficiency tolerance and grain Zn

Grain yield (kg ha-1) Experiment station (moderately Zn deficient) 6444a Farmers field (severely Zn deficient site) 6544a

Genotype name NSIC222

IR64
IR68144 IR83668 IR85800 IR83317AC-25 IR91152AC

3600de
4566c 3149e 4291cd 5621b 2325f

4306bc
4448bc 3775cd 3286cde 5642ab 40f

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
Brown rice Zn concentration

IR83317AC-124
IR91143AC IR64196 IR75862

3845cde
3265e 4286cd Not Planted

3456cde
1686ef Not planted 2309de

25 20
(mg kg-1 )

Water-sprayed control Foliar Zn sprayed at 50% heading

15 10 5 0 Experiment station Farmers field

Foliar Zn application (@ 4 kg Zn ha-1 ) at heading significantly increased brown rice grain Zn, indicating phloem mobilization

Courtesy: Impa & Sarah

Performance of NSIC Rc 222 in GRiSP Challenging environments (Bicol)1

Courtesy: Eileen Garcia

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Performance of NSIC Rc 222 in Challenging environments (Bicol) 2

Courtesy: Eileen Garcia

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

Courtesy: Eileen Garcia

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NSIC Rc 222
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)
NSIC Rc 222 Mestiso 7

6.1 t ha-1
6.1 t ha-1 (Rank 3) 5.7 t ha-1 (Rank 13)

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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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Pyramid genes for yield component traits using MAS

Plant architecture Large panicle size Grain size and weight Grain Filling

Lodging resistance

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Traits Large panicle Grain size, shape, quality Grain number

Yield related functional genes

Genes OsSPL14 OsSPL16/ GW8 Gn1a Functional Protein Squamosa Promoter Binding protein-like 14 Squamosa Promoter Binding protein-like 16 Cytokinin oxydase/dehydrogenase Chromosome location 8 8 1

Strong and thick culm

Grain yield, Heading

SCM2/APO1
Ghd7

F-box protein ortholog of Arabidopsis

CCT domain protein

6
7

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Yield related functional genescontinued

Genes Functional Protein Chromosom e location 5 5 2 3

Traits

Grain size and grain weight (grain filling)

GS5

Serine carboxypeptidase

GW5
GW2 GS3

Nuclear protein
Ring-type E3 ubiquitin ligase Putative trasmembrane like protein

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Grain Filling

Sugar Phosphate Synthase (SPS) and Sucrose Transporter Genes

12 SPS and 5 transporter genes

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Gene
Gn1a GW2 Gs3 GS5 GW5 SCM2 Ghd7 OsSPL14 OsSPL16

Position (bp) Chr

5,270,103 8,146,286 17,369,402 3,423,243 5,342,545 27,484,483 9,186,690 25,280,969 26,501,167 1 2 3 5 5 6 7 8 8

7 cM

5 cM

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Mutants in general produce too severe phenotype (growth retardation, morphological abnormalities, sterility) to introduce directly in Crop Improvement Tillering

MONOCULM (MOC1), OsTB1/FC1 (Fine Culm 1), OsTB1, D88 (D14) D3, D10, HTD1, HTD2, D27

Regulation of panicle development

Rate of spikelet formation
Apo1, SP1 (short panicle)

LAX1(lax panicle), SPA/MOC1-3 (small panicle), fzp (frizzy panicle)

Duration of panicle differentiation

RCN1 and RCN2 (rice TERMINAL FLOWER)

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Accumulate QTLs controlling yield potential traits using Marker Aided Recurrent Selection (MARS)

and Genomic Selection (GS)

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Marker Aided Recurrent Selection (MARS)

Selection for several QTLs relies on index (genetic values) computed for each individual based on its haplotype at target QTLs

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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!

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Molecular Marker Resource for MARS/GS

Rice SNP Consortium 1M Affymetrix genotyping chip

200 @ 50X depth 1000 @ 10-20X depth rest @ 5-10X depth

BGI de novo sequencing

10,000 GeneBank accessions Cultivated + close wild relatives

H Leung

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Multidisciplinary teams

Eathington et al (2007)

SNP genotyping workflow at IRRI

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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

BeadXpress 384-plex
NanoDrop 8000 Aurora Versa mini liquid handler

DNA normalization: DNA samples checked on a NanoDrop and normalized using an automated system

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

Data storage & analysis: Automated marker scoring

BB

M. Thomson

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Unknowns!
Interactions between different genes Compensation between traits Pleiotropy with other agronomic traits

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Some thoughts
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 Baos 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

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Acknowledgements
Gurdev Khush Darshan Brar Gerard Barry Tony Evangelista Nelie Delos Reyes Benny Romena Jaesal Ison Vit Lopena Raul Boncodin Varoy Pamplona Members of Irrigated, Golden rice and H+ teams PBGB and IRRI family Collaborating colleagues in IRRI, ARIs and several NARES partners

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Visit us in Hyderabad (ICRISAT)

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Thank you for listening