IRRI Rice Seminar Series

Parminder S. Virk
Current position Senior Scientist II

Education and training

M.Sc. & Ph.D. Punjab Agricultural University, Ludhiana, India 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 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)

Work experience

Research highlights

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New efforts to increase the yield potential of rice through GRiSP

Parminder S. Virk PBGB

IRRI Thursday Seminar
14 April 2011 Havener Auditorium

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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

19 91 19 93 19 95 19 97 19 99 20 01 20 03 20 05 20 07 20 09 20 11 20 13 20 15 20 17 20 19 20 21 20 23 20 25 20 27 20 29 20 31 20 33 20 35

Asia

Africa

Americas

Rest of World

GRiSP (2010)

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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 yield potential Prevent yield 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 Cross
Dee-Geo-Woo-Gen x Tsai-yuanchung (1949) Ai-zai-zhan x Guang-chung 13 Dee-Geo-Woo-Gen x Peta (1962)

Variety
TN-1 (1956) Guang-chang-ai (1959) IR8 (1966)

Institute
Taichung, Taiwan Mainland China IRRI

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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).

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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

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

40

120

1.0

0.0 1955 1965 1975 1985 Year 1995 2005

0 2015

Courtesy P. Quick

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2007 Program 2 Sustaining productivity in intensive rice-based systems: rice and the environment

High Yield Potential Group at IRRI BBouman,DBrar, RBuresh, ADobermann, NKobayashi, TLafarge, SPeng, FXie, PVirk ++

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US$/ton 1000 1200 200 400 600 800

J an 05 A pr 05 J uly 05 O c t 05 J an 06 A pr 06 J uly 06 O c t 06 J an 07 A pr 07 J uly 07 O c t 07 J an 08 A pr 08 J uly 08 O c t 08 J an 09 A pr 09 J uly 09 O c t 09 J an 10 A pr 10 J uly 10 O c t 10

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

0
Viet 5% Thai 5% Parboiled Thai 100%

Price Volatility Thai 5% vs other major grades

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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.

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GRiSP Theme 2: Accelerating the development, delivery, and adoption of improved rice varieties PL 2.4. Improved rice varieties for intensive production systems PL 2.5. Hybrid rice for the public and private sectors

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Target Yield Potential (YP)

(to produce additional 176 m tons of rice by 2035)

Ecology Irrigated alone Rainfed alone Irrigated + Rainfed

% Required increase Current YP YP in YP 10 8 10 8 12.3 16.97 11.3 10.1 23% 112% 13% 26%

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

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Potential rice grain yield (DS) in tropics 15.9 t ha-1 (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

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

The key is to enhance RCF/RUE

RCF= Radiation Conversion Factor RUE= Radiation Use Efficiency

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Hybrid rice yields 15-20% more than Inbreds

There is potential to increase yield beyond 10 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

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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

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1. Genomic approaches to accumulate yield potential traits/loci

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1.1 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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Gn1

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

GRiSP Published online: 28 September 2008 | doi:10.1038/ng.220

Nature Genetics 40, 1370 - 1374 (2008)

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

GIF1 (GRAIN
INCOMPLETE FILLING 1)

gene encodes a cellwall invertase required for carbon partitioning

GRiSP SCM2

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Xing and Zhang (2010)

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GRiSP 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

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

Rate of spikelet formation

Apo1, SP1 (short panicle)

Duration of panicle differentiation

RCN1 and RCN2 (rice TERMINAL FLOWER)

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

Eathington et al (2007)

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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

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Molecular Marker Resource for MARS/GS

Rice SNP Consortium 1M Affymetrix genotyping chip

BGI de novo sequencing

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

10,000 GeneBank accessions Cultivated + close wild relatives

H Leung

GRiSP Preparation: Leaf Tissue

punch samples in 96-well plates freeze-dried and ground into a powder

SNP genotyping workflow at IRRI

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

GRiSP 1.3 Exploit yield enhancing loci from wild spp

Susan McCouch (2011)

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Hybrid Rice
1.4 Increase hybrid seed yield:
Exploit germplasm with high outcrossing traits

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Modify the floral structure (monoeciouness)

Luziola spp

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1.5 Enhance the level of heterosis:

Exploit germplasm diversity Two-line system Identify heterotic gene blocks

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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

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3. Breeding for Physiological traits to improve yield potential

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Wheat Yield Consortium 1-3 March 2011, CIMMYT, Obregon

Reynolds et al (2010)

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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 TRAITS Relative spike growth duration (RSG) & Relative grain filling duration (RGF) POST ANTHESIS ASSIMILATION RATE Canopy temperature during grain filling

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Increase photosynthetic capacity and efficiency

Germplasm screening using HTP measurements of photosynthesis and modeling. Rubisco amount Rubisco properties Variation in Rubisco activase

Reynolds et al (2010)

GRiSP Explore natural variation: Relationship between Rubisco and Rubiscoactivase sequence variation and photosynthetic capacity Heat shock proteins ROS (reactive oxygen species) scavenging enzymes

A. Kohli

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Panicle architecture and grain filling

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Multi-Environment Testing (MET)

PhilRice CES, Muoz, Nueva Ecija. PhilRice CVES, San Mateo, Isabela PhilRice, RTR, Agusan del Norte IRRI, Los Baos, Laguna

NARES capacity to conduct the MET trials

Drought/ Irrigated Aerobic
Year 1 /2 Year 2 /3 Year 3 /4

5 17 26

4 14 20

Flood Prone 4 16 25

Salinity 2 10 19

Total 15
57 90

Phenotyping Workshop, Montpellier, March 28-30, 2011 GRiSP

Micheal Dingkuhn and colleagues at CIRAD, IRD, INRA

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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

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Alignment of breeding programs according to key market segments

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).

Sam Mohanty

Andy Nelson

Alice Laborte

Melissa Fitzgerald

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High Yield Potential Team at IRRI

Parminder Virk Mike Thomson

Fangming Xie

Guoyou Ye

Fulin Qiu

Rebecca Laza (Crop Physiologist IRS to be recruited)

Zhao Xiangqian

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Yield Potential (YP): A very tough nut to

crack!

YP

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However it is doable

GRiSP What Next? August 22-26, 2011 GRiSP Yield potential workshop and GRiSP Latin America annual review and work planning for 2012, CIAT, Cali

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Thank you for listening

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Irrigated Rice & Hybridization Teams

Nelie Delos Reyes

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

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Hybrid Rice Breeding Team

Dr. Fangming Xie

Senior Scientist, Hybrid Rice

Dr. Fulin Qiu

Scientist, Hybrid Rice

Manny Esguerra
Assistant Scientist, Hybrid Rice

Reynaldo Dela Cueva

Research Technician III

Marino Reyes
Research Technician II

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Host Plant Resistance Teams

Entomology

Finbarr Horgan

Liberty Almazan

Rayuel Quintana

Pathology
Casiana Vera Cruz Isabelita Oa
Jaleel Acedo

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

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Crop Physiology Team

Shaobing Peng

Romeo Visperas

Ma. Rebecca Laza

Anicio Macahia

Maximo Pelagio

Eduardo Tandang

Wide Hybridization Team

D. Brar

KK Jena

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Informatics Support Team

Guoyou Ye Bartolome, Violeta Gulles, Alaine Morantte, Rose Imee Zhella Caeda, Alexander Tabada, Ma. Luisa Grain Quality Screening Team
Fitzgerald et al

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Informatics Support Team

Guoyou Ye Bartolome, Violeta Gulles, Alaine Morantte, Rose Imee Zhella Caeda, Alexander Tabada, Ma. Luisa

Grain Quality Screening Team

Fitzgerald et al