New efforts to enhance the yield potential of rice through GRiSP

Parminder S. Virk

IRRI Rice Seminar Series

Current position Senior Scientist II

Education and training M.Sc. & Ph.D.

Punjab Agricultural University, Ludhiana, India

Work experience Senior Scientist, Plant Breeding, IRRI, 2004-2010

Irrigated Rice Breeder, IRRI, 2001-2004

Affiliate Scientist, IRRI, 1999-2001

Research Fellow, University of Birmingham, UK, 1985-1999

Research Fellow, PAU, 1984-1985

Research highlights 21 rice varieties released in the Philippines, China, India, Indonesia,

Cambodia

1 book and 46 research papers published in peer reviewed journals

Best publication award (1983), C.I.S.I., India.

Best paper award (2002), Crop Science Society , Philippines.

Best paper award (2006), Animal nutrition association of India.

CGIAR Outstanding Support Team Award (2009)

GRiSPGRiSP

IRRI Thursday Seminar14 April 2011

Havener Auditorium

New efforts to increase the yield potential of rice through GRiSP

Parminder S. VirkPBGB

GRiSPGRiSP

300

350

400

450

500

550

600

1991

1993

1995

1997

1999

2001

2003

2005

2007

2009

2011

2013

2015

2017

2019

2021

2023

2025

2027

2029

2031

2033

2035

Asia Africa Americas Rest of World

Million tons milled rice

Additional rice needed:116 million tons by 2035

2010 global rice production

GRiSP (2010)

GRiSPGRiSP How can we increase rice production?How can we increase rice production?

FarmFarmareaarea

2010

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

GRiSPGRiSPHow can we increase rice production?How can we increase rice production?

CloseCloseyield yield gapgap

RaiseRaiseyield yield

potentialpotential

PreventPreventyieldyielderosionerosion

FarmFarmYieldYield

(65%)(65%)

10 t/ha10 t/ha

GRiSPGRiSP

Use of sd1 dwarfing gene increased yield potential of irrigated rice (tropics) from 4-5 t ha-1 to 10 t ha-1

Cross Variety InstituteDee-Geo-Woo-Gen x Tsai-yuan-chung (1949)

TN-1 (1956) Taichung, Taiwan

Ai-zai-zhan x Guang-chung 13 Guang-chang-ai (1959)

Mainland China

Dee-Geo-Woo-Gen x Peta (1962) IR8 (1966) IRRI

GRiSPGRiSP

Yield potential is defined as the yield of a variety when grown in environments to which it is most suited; with nutrients and water non-limiting; and with pests, diseases, weeds, and other stresses effectively controlled (Evans 1993).

GRiSPGRiSPGreen 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%

GRiSPGRiSP

Program 2 Program 2 Sustaining productivity in Sustaining productivity in

intensive riceintensive rice--based based systems: rice and the systems: rice and the

environmentenvironment

High Yield Potential Group at IRRIBBouman,DBrar, RBuresh, ADobermann, NKobayashi,

TLafarge, SPeng, FXie, PVirk ++

2007

GRiSPGRiSP

0

200

400

600

800

1000

1200Jan 0

5

Apr 05

July 0

5

Oct 05

Jan 0

6

Apr 06

July 0

6

Oct 06

Jan 0

7

Apr 07

July 0

7

Oct 07

Jan 0

8

Apr 08

July 0

8

Oct 08

Jan 0

9

Apr 09

July 0

9

Oct 09

Jan 1

0

Apr 10

July 1

0

Oct 10

US

$/t

on

Thai 5%

Viet 5%

Thai 100%

Parboiled

Price VolatilityThai 5% vs other major grades

Expect greater price volatility and frequent spikes in the future (S Mohanty)

GRiSPGRiSP

IRRI DG in India (9 April, 2011):

“Agricultural investments must be doubled in the next two decades to maintain food security.”

“As the future poses more challenges governments and the scientific community need to focus on new strategies to raise food production.”

GRiSPGRiSP

GRiSPGRiSP

PL 2.4. Improved rice varieties for intensive production systems

PL 2.5. Hybrid rice for the public and private sectors

Theme 2: Accelerating the development, delivery, and adoption of improved rice varieties

GRiSPGRiSP

Ecology Current YPRequired

YP

% 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%

GRiSPGRiSP

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 (DS) in tropics 15.9 t ha-1 (Yoshida, 1981)

Realistic PY is 12.5 t ha-1

Potential Yield: the maximum yield predicted by a computer model for a variety growing without stress (Sheehy, 2001).

GRiSPGRiSP

Hybrid rice yields 15-20% more than Inbreds

There is potential to increase yield beyond 10 t ha-1

GRiSPGRiSP

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

GRiSPGRiSP

Enhance C3 photosynthesis (RUE),

Increase:

Biomass (HI > 0.5),

Sink strength traits,

Grain filling and

Lodging resistance

Key target traits to enhance yield potential

GRiSPGRiSP

1. Genomic approaches to accumulate yield potential traits/loci

GRiSPGRiSP

• Plant architecture• Large panicle size• Grain size and weight• Grain Filling• Lodging resistance

1.1 Pyramid genes for yield component traits using MAS

GRiSPGRiSP

GRiSPGRiSP

GRiSPGRiSP

Ashikari et al 2005 (Science 309:741-745)

Gn1

GRiSPGRiSPNature Genetics 40, 1370 - 1374 (2008) Published online: 28 September 2008 | doi:10.1038/ng.220

Control of rice grain-filling and yield by a gene with a potential signature of domesticationErtao Wang1,2, et al

GIF1 (GRAIN INCOMPLETE FILLING 1) gene encodes a cell-wall invertase required for carbon partitioning

GRiSPGRiSP

SCM2

GRiSPGRiSP

GRiSPGRiSP

Xing and Zhang (2010)

GRiSPGRiSP

GRiSPGRiSP

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)

GRiSPGRiSP

1.2 Accumulate QTLs controlling yield potential traits using Marker Aided Recurrent Selection (MARS) and and Genomic Selection (GS)

GRiSPGRiSP Marker Aided Recurrent Selection (MARS)

Eathington et al (2007)

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

GRiSPGRiSP

GRiSPGRiSP 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

GRiSPGRiSP

10,000 GeneBank accessionsCultivated + close wild relatives

Rice SNP Consortium1M Affymetrix genotyping chip

BGI de novosequencing 200 @ 50X depth

1000 @ 10-20X depthrest @ 5-10X depth

H Leung

Molecular Marker Resource for MARS/GS

GRiSPGRiSPSNP 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

GRiSPGRiSP1.3 Exploit yield enhancing loci from wild spp

Susan McCouch (2011)

GRiSPGRiSP

1.4 Increase hybrid seed yield:

Exploit germplasm with high outcrossing traits

Hybrid Rice

GRiSPGRiSP

Modify the floral structure (monoeciouness)

Luziola spp

GRiSPGRiSP

1.5 Enhance the level of heterosis:

• Exploit germplasm diversity

• Two-line system

• Identify heterotic gene blocks

GRiSPGRiSP 2. Crop modeling

Eco-physiological model to:

(1)Identify traits responsible for high yield and yield reliability, and explore their effects under different agro-climatic environments and temporal scales (2)Characterize environments to define the nature and frequency of challenges in the target population of environments (TPE) and (3)Relate QTL/genetic information to quantifiable traits and analyze their effects on yield.

B. Bouman, Tao Li

GRiSPGRiSP

3. Breeding for Physiological traits to improve yield potential

GRiSPGRiSP Wheat Yield Consortium1-3 March 2011, CIMMYT, Obregon

Reynolds et al (2010)

GRiSPGRiSP

Improve Source Sink balance

PRE-ANTHESIS SOURCE TRAITS

Biomass at Anthesis, Vegetative Stage, Booting Stage(Use spectral reflectance approaches)

PRE ANTHESIS SINK TRAITS

Spike mass & spike index

PHENELOGY TRAITSRelative spike growth duration (RSG) & Relative grain filling duration (RGF)

POST ANTHESIS ASSIMILATION RATE

Canopy temperature during grain filling

GRiSPGRiSP

Increase photosynthetic capacity and efficiency

Germplasm screening using HTP measurements of photosynthesis and modeling.

Rubisco amountRubisco propertiesVariation in Rubisco activase

Reynolds et al (2010)

GRiSPGRiSP

Explore natural variation:

Relationship between Rubisco and Rubisco-activase sequence variation and photosynthetic capacity

Heat shock proteins

ROS (reactive oxygen species) scavenging enzymes

A. Kohli

GRiSPGRiSP

Panicle architecture and grain filling

GRiSPGRiSPMulti-Environment Testing (MET)

� PhilRice CES, Muñoz, Nueva Ecija. � PhilRice CVES, San Mateo, Isabela� PhilRice, RTR, Agusan del Norte� IRRI, Los Baños, Laguna

NARES capacity to conduct the MET trials

Irrigated

Drought/

Flood Prone Salinity Aerobic TotalYear 1 /2

5 44 2 15

Year 2 /3 17 14 16 10 57

Year 3 /4 26 20 25 19 90

GRiSPGRiSPPhenotyping Workshop, Montpellier, March 28-30, 2011

Micheal Dingkuhn and colleagues at CIRAD, IRD, INRA

GRiSPGRiSP

GRiSPGRiSP

GRiSPGRiSP

Validate relationship between phenotypes determined by HTP and conventional methods

Identify HTP phenotyping applicable to breeding; establish genetic correlation, proxy for agronomic traits

H. Leung

GRiSPGRiSP

To better meet market demands and thus also improve commercialization and adoption of our breeding materials.

Develop breeding products that are better adapted to key market segments (consumer preferences and cropping environments).

Alignment of breeding programs according to key market segments

Alice LaborteSam Mohanty Andy Nelson Melissa Fitzgerald

GRiSPGRiSP High Yield Potential Team at IRRI

Parminder Virk Mike Thomson

Fangming Xie Guoyou Ye

Fulin Qiu

Zhao Xiangqian

Rebecca Laza (Crop

Physiologist IRS to be recruited)

GRiSPGRiSP Yield Potential (YP):A very tough nut to

crack!

YP

GRiSPGRiSP

However it is doable

GRiSPGRiSP

What Next?

August 22-26, 2011

GRiSP Yield potential workshop and GRiSP Latin America annual review and work planning for 2012, CIAT, Cali

GRiSPGRiSP Thank you for listening

GRiSPGRiSP Irrigated Rice & Hybridization Teams

Varoy Pamplona, Benny Romena, Julius Borgonia, Virgilio Angeles, Tony Evangelista, Mario Garcia, Louie Caracuel, Freddie Perez, Arsenio Morales, Nestor Ramos

Nelie Delos Reyes

GRiSPGRiSP

Dr. Fangming XieSenior Scientist, Hybrid Rice

Dr. Fulin QiuScientist, Hybrid Rice

Marino ReyesResearch Technician II

Reynaldo Dela CuevaResearch Technician III

Manny EsguerraAssistant Scientist, Hybrid Rice

Hybrid Rice Breeding Team

GRiSPGRiSP

Liberty AlmazanFinbarr Horgan Rayuel Quintana

Host Plant Resistance Teams

Entomology

Casiana Vera Cruz Isabelita Oña Jaleel Acedo

Pathology

I. Choi, C. Lantican, J. Domingo, P. Cabauatan, E. Coloquio, E. Baguioso, R. Cabunagan

Virology

GRiSPGRiSP Crop Physiology TeamCrop Physiology Team

Shaobing PengShaobing PengShaobing PengShaobing Peng Romeo VisperasRomeo VisperasRomeo VisperasRomeo Visperas Ma. Rebecca LazaMa. Rebecca LazaMa. Rebecca LazaMa. Rebecca Laza Anicio MacahiaAnicio MacahiaAnicio MacahiaAnicio Macahia Maximo PelagioMaximo PelagioMaximo PelagioMaximo Pelagio Eduardo TandangEduardo TandangEduardo TandangEduardo Tandang

Wide Hybridization Team

KK JenaD. Brar

GRiSPGRiSPInformatics Support Team

Guoyou YeBartolome, VioletaGulles, AlaineMorantte, Rose Imee ZhellaCañeda, AlexanderTabada, Ma. Luisa

Grain Quality Screening Team

Fitzgerald et al

GRiSPGRiSPInformatics Support Team

Guoyou YeBartolome, VioletaGulles, AlaineMorantte, Rose Imee ZhellaCañeda, AlexanderTabada, Ma. Luisa

Grain Quality Screening Team

Fitzgerald et al