Improving the Phenotypic Expression of Rice Genotypes: Reasons to Rethink

Selection Practices and ‘Intensification’ for Rice Production Systems

Norman Uphoff, Cornell University, USA; Vasilia Fasoula, University of Georgia, USA; Anas Iswandi, Institut Pertanian Bogor (IPB), Indonesia; Amir Kassam, University of Reading, UK (presenter); and A.K. Thakur,

Directorate of Water Management, ICAR, India

2014 International Rice Congress, BangkokSection C02, Panel E: Improved varieties for

intensive production systems

‘Intensification’ has different meanings --The role of rice breeding will differ according to

the way that ‘intensification’ is understood

The most common idea of intensification -- coming from Green Revolution experience --

depends on increasing material inputs used with new rice varieties bred to be responsive to

the application of more inorganic fertilizers,more water, and agrochemical protection

Question: Will this strategy be sufficient? World rice production needs to double by 2050

(Ray et al., 2013)

Country paddy yields (t ha-1), 1959-2011, 3-year averages from FAO and USAID statistics (IRRI, 2014)

The gains from this paradigm have been decelerating as it encounters diminishing returns. We need to exploit more fully

the genetic potentials that we have and/or can improve.

Countries* 

1959-61 

1969-71 

1979-81 

1989-91 1999-2000 

2009-11Total % increase

Bangladesh 1.67 1.70 1.89 2.59 3.77 4.20 151%Brazil 1.69 1.34 1.46 2.14 3.25 4.53 176%China 2.03 3.30 4.28 5.62 6.32 6.60 225%India 1.53 1.67 1.86 2.62 3.01 3.30 116%Indonesia 1.93 2.38 3.53 4.33 4.38 4.36 126%Myanmar 1.65 1.71 2.45 2.85 3.14 3.29 100%Pakistan 1.36 2.24 2.41 2.32 2.95 3.28 141%Philippines 1.21 1.65 2.23 2.79 3.10 3.64 200%Thailand 1.65 1.93 1.85 2.10 2.60 2.83   71%Vietnam 1.94 2.07 2.15 3.18 4.25 5.44 180%Average yield 1.67 2.01 2.41 2.99 3.57 4.15 149%% increase over the decade 

  1960s 20.4%

1970s 19.4%

1980s 23.2%

1990s 19.3%

2000s 16.2%

 

*Producing 85% of the world’s rice

SRI is a different kind of intensification, depending mostly on mental inputs

(knowledge) and different methods for managing plants, soil, water and nutrients

SRI’s highest yields have come with improved varieties

(tho it also helps unimproved varieties produce more) •Using less inorganic fertilizer, to the extent that

organic materials are available and provided,• Less water, by 30-50%, because no flooding, and

•Less need for agrochemical protection

More production with lower costs per hectare gives farmers more profitability

Additional benefits from this kind of agroecologically-grounded intensification:

More resistance to biotic and abiotic stresses:•Drought-resistance – tolerate water stress•Less lodging from wind and rain of storms•Tolerance of more extreme temperatures

•Resistance to damage from pests and diseasesAll are important for dealing with climate change;

also SRI makes net reductions in GHG emissions

Plus shortening of the crop cycle, by 5-15 days, andhigher milling outturn (>10%) because of

fewer unfilled grains and less breakageSo: more rice per unit time and per bag of paddy

Resistance to both biotic and abiotic stresses in East Java, Indonesia: adjacent fields hit by both brown planthopper (BPH) and by storm damage – the field on left was grown

with standard practices, while the field on right is organic SRI

Modern improved variety

(Ciherang) – no yield

Traditional aromatic variety

(Sintanur)- 8 t/ha

How are such effects possible? By eliciting different, more productive, more resilient

phenotypes from given genotypes

Modification of management practices for rice plants, soil, water and nutrients leads to

changes in plant morphology and physiology and at same time to changes in the soil environment: Pay more attention to E in equation: P = ƒ G + E + GxE

•Get larger, deeper, healthier root systems, and•More abundant, diverse and active soil biota --

living around, on, and even inside the plantsBoth contribute to better plant phenotypes

Effects of inoculation with Rhizobium leguminosarum bv. trifolii E11 on root architecture of two rice varieties: (a) Rootlets per plant; (b) Cumulative root length (mm); (c) Root surface area (cm2);

(d) Root biovolume (cm3). Y. G. Yanni et al., Australian Journal of Plant Physiology, 28, 845–870 (2001)

Indeed, there are positive interactions between microbial populations and roots’ growth

Root systems support soil microbes, and v.v.

NEPAL: Farmer with a rice plant

grown from a single seed

with SRI methods

in Morang district

LIBERIA: Farmer with rice plants ofsame variety

and age: usualmethods on left, and SRI methods on

right in GrandGedee country

INDIA: Farmer with rice plants ofsame variety

and age: usualmethods on

right, and SRI methods on left, grown in Punjab state

CUBA: Two plants of the same age (52 DAS) and same variety (VN 2084) -- different phenotypes from the same genotype

SRI

0

50

100

150

200

250

300

IH H FH MR WR YRStage

Org

an d

ry w

eigh

t(g/

hill)

I H H FH MR WR YR

CK Yellow leafand sheath

Panicle

Leaf

Sheath

Stem

47.9% 34.7%

CHINA: Research done at China National Rice Research Instituteby Dr. Tao Longxing, 2004 – same variety, different phenotypes

IRAQ: Pairs of trials at Al-Mishkhab Rice Research Station, Najaf, 2007, comparing varieties with SRI management (on left) and RMP (on right)

INDONESIA: Stump of a rice plant

(modern variety: Ciherang cv) grown from a single seedusing SRI methods

-- with 223 tillers and massive root growth

Panda’an, E. Java, 2009

Data from comparative evaluations of SRI effects on the physiology and morphology of rice plants, conducted 2005-10 at ICAR’s Directorate of Water

Management in Bhubaneswar, India

The variety planted was Surendra (IET-12815), 130-135 days, usual yield 3.5-5.0 t ha-1 (DRD, 2006)

Published by Thakur et al. in Exper. Agric. (2010), Paddy & Water Envir. (2011), Plant & Soil (2013)

SRI practices and RMP were taken from the respective websites of SRI-Rice (Cornell) and the Central Rice Research Institute (Cuttack)

Table 1: Effects of rice management practices on morphological characteristics of roots, tillers, leaves, and canopy

 

ParametersManagement practices Increase 

with SRISRI RMP LSD.05

Root growth parameters below-groundRoot depth (cm) 33.5 20.6 3.5   63%Root dry weight  (g hill-1) 12.3 5.8 1.3 112%Root dry weight (g m-2) 306.9 291.8 NS     5%Root volume (ml hill-1) 53.6 19.1 4.9 111%Root volume (ml m-2) 1340.0 955.0 180.1   40%Root length (cm hill-1) 9402.5 4111.9 712.4 129%Root density (cm-2) 2.7 1.2 0.2 125%

Tillers, leaves and canopy structures above-groundPlant height (cm) 124.2 101.4 8.1     22%Tiller number hill-1 18.3 8.9 3.5 106%Tiller number (m-2) 450.1 441.2 NS      2%Leaf number (hill-1) 79.8 35.6 15.8 124%Leaf number (m-2) 1997.6 1766.5 229.4   13%Leaf length (cm) 65.25 48.14 6.09   35%Leaf widtha (cm) 1.82 1.34 0.21   35%Leaf area index (LAI) 3.95 2.60 0.28   52%Canopy angle ( ° ) 33.1 17.8 3.6   86%

Table 2: Effects of rice management practices on root functions, physiological performance, N-uptake in rice

ParametersManagement practice Increase 

with SRISRI RMP LSD.05

Amount of exudates (g hill-1) 7.61 2.46 1.45 209%

Amount of exudates per m2 (g m-2) 190.25 122.95 39.72   55%

Exudation rate per hill (g hill-1 h-1) 0.32 0.10 0.06 220%

Exudation rate per m2 (g m-2 h-1) 7.93 5.12 1.66   55%

Mean leaf elongation rate (cm day-1) 5.97 4.45 0.21   36%

Chlorophyll a (mg g-1FW) 2.35  1.68  0.14   40%

Chlorophyll b (mg g-1FW) 1.02  0.90  0.07   13%

Total chlorophyll (mg g-1FW) 3.37  2.58  0.11   30%

Chlorophyll a/b ratio 2.32  1.90  0.29   22%

Fv/Fm ratio 0.796  0.708  0.017   13%

Φ PS II 0.603  0.486  0.020   24%

Transpiration (m mol m-2 s-1) 6.41  7.59  0.27   19%

Leaf temperature (°C) 34.48  33.09  NS     4%

Net photosynthetic rate (μ mol m-2 s-1) 23.15  12.23  1.64   89%

N-uptake (kg N ha-1) 77.4 51.0 8.6   52%

Table 3: Effects of rice management practices on yield-contributing characteristics,

grain yield, straw weight, and harvest index Parameters

Management practice Increase with SRISRI RMP LSD.05

Panicle number hill-1 (ave.) 16.9 6.9 3.5 145%Panicles (m-2) 439.5 355.2 61.6   24%Panicle length (cm) (ave.) 22.5 18.7 2.3   20%Number of spikelets panicle-1 151.6 107.9 12.9   40%Filled spikelets (%) 89.6 79.3 5.1   13%1000-grain weight (g) 24.7 24.0 0.2     3%Grain yield (t ha-1) 6.51* 4.40* 0.26   48%Straw weight (t ha-1) 7.28 9.17 1.19 -21%Harvest index 0.47 0.32 0.04 47%* ICAR’s Directorate of Rice Research reports this variety’s yield as 3.5-5.0 t ha-1

Figure 1: Changes in crop growth rate (CGR) during the vegetative stage of rice grown with SRI and RMP practices Black circles = SRI management, and open circles = RMP

Vertical bars represent SEm ± (n=6)

0

10

20

30

40

50

60

30-40 40-50 50-60 60-70

Period (Days after germination)

CG

R (

g m

-2 d

ay-1

)

Figure 2: Changes in light interception by the canopy during vegetative stage in rice grown with SRI practices and RMP

Black circles = SRI management, and open circles = RMPVertical bars represent SEm ± (n=6)

0

20

40

60

80

100

12 25 30 40 50 60 70

Days after seed germination

Ligh

t Int

erce

ptio

n (%

)

Root Morphology and Physiology of Rice Plants Cultivated under System of Rice Intensification (SRI)Nurul Hidayati, Triadiati and Iswandi Anas, IPB, Indonesia

(Poster IRC2014-0616)Culti-vation method

Root aeren-chyma

(%)

Stem aeren-chyma area (µm2)

Total stem aerenchyma area (µm2/ circumfer-

ence)

Conven-tional

70.9b 53,597b 1,491,835b

SRI 45.1a 30,939a 83,5966a

Cultivation method

Number of root hairs per mm2

Conventional 510.41b

SRI 816.50a

Conventional SRI

Rice physiology at vegetative, flowering, grain-filling, maturity phasesOrange lines = SRI; brown lines = conventional management.

Comparative research at IPB in Indonesia (Poster IRC2014-0595)

WHAT IS THE SYSTEM OF RICE INTENSIFICATION?

Simple Principles and Practices:1. Undertake early, quick and healthy plant establishment, minimizing transplant shock by careful treatment of the plants’ roots2. Reduce competition among plants through wider spacing within and between hills3. Improve the structure and functioning of the soil with organic matter amendments4. Maintain an aerobic soil environment for plant growth through reduced or controlled water applications & active soil aeration (aka weeding)

WHAT IMPLICATIONS FOR PLANT BREEDING?

• Selection of plants for breeding improved lines should focus on the phenotypical expression of individual plants, not on group averages

• Plants being evaluated should be growing with wide spacing, so their potentials for great production are not diminished by others’ competition

• This means that ‘honeycomb selection designs’ are best suited to identifying ‘champions’ (Fasoulas and Fasoula, 1997), able to screen large numbers of lines

Fig. 3. This replicated D-31 honeycomb design evaluates the plants of 31 sibling lines, grown in 26 rows with 23 plants per row. Each plant is in the center of a complete moving replicate, shown for two random plants of line

no.11 (gray circles). Plant Yield Index (PYI) measures plant yield devoid of confounding effects of soil heterogeneity. Stability Index (SI) measures the stability of each sibling line by taking account of soil heterogeneity through

formation of the triangular grid that allocates plants uniformly across the whole field. The grid shown here is for plants of line no. 11.

This strategy deals with a genetic relationship that confounds conventional plant breeding strategies

• Genes for productivity are inversely related to genes for competition (Fasoula, Euphytica, 1990; Fasoula & Fasoula, Plant Breeding Review, 1997; Field Crops Research, 2002)

• Selection of ‘champions’ growing within dense populations -- where genes for competition are expressed -- will favor strong competitors/ weak yielders over their opposites

• The aim of breeding should be to select density-neutral best producers, with all plants in a population producing at their maximum

• This strategy, coincidentally, matches SRI’s

COSTS OF PRODUCTION: TNAU study, Tamiraparani command area (N=100); cost reduction with SRI system over conventional system = Rs. 2,369/ha (11 %); labor input reduced by 8% (Thiyiagarajan, 2004 World Rice Research Congress)

Practices

Tractor hours @

Rs.150/hr

Bullock pair @

Rs.200/hr

Men’s labour @ Rs.40/day

Women’s labour @ Rs.40/day

Cost/ha (Rs.)

Con SRI Con SRI Con SRI Con SRI Con SRI

Nursery preparation

1 - - - 6 3 0.5 5.5 2,110 681

Main field preparation

7.5 7.5 2 2 12 12 - - 2,005 2,005

Manures & fertilizers

- - - - 7 7 10 10 7,254 7,254

Transplanting - - - - 5 5 55 75 2,400 3,200

Weeding - - - - - 38 80 - 3,200 1,520

Irrigation - - - - 7.5 6 - - 300 240

Plant protection - - - - 2 2 2 2 660 660

Harvesting 1 1 - - 12.5 12.5 75 75 3,500 3,500

Total 9.5 8.5 2 2 52 85.5 222.5 167.5 21,429 19,060

Microbial populations in rice rhizosphereTamil Nadu Agricultural University research

Micro-organisms

Standard mgmt

SRI mgmt

Difference

Total bacteria 88 x 106 105 x 106 1.2x

Azospirillum 8 x 105 31 x 105 3.9x

Azotobacter 39 x 103 66 x 103 1.7x

Phospho-bacteria

33 x 103 59 x 103 1.8x

T. M. Thiyagarajan, WRRC presentation, Tsukuba, Japan, 2004

Total bacteria Total diazotrophs

Microbial populations in rice crops’ rhizosphere soil under conventional crop management (red) and SRI management (yellow) at different

stages: active tillering, panicle initiation, and flowering. Units are √ transformed values of population/gram of dry soil (data from IPB)

Phosphobacteria \ Azotobacter0

10

20

30

40

Dehydrogenase activity (μg TPF) Urease activity (μg NH4-N))

Microbial activity in rice crops’ rhizosphere soil under conventional crop management (red) and SRI management (yellow) at different

stages: active tillering, panicle initiation, and flowering. Units are √ transformed values of population/gram of dry soil per 24 h

Acid phosphate activity (μg p-Nitrophenol) \

Nitrogenase activity (nano mol C2H4)

These results suggest the importance of

studying and understanding the

contributions that are made by microbes

living around, on and in plants =

symbiotic endophytes, which are

major components of the

plant-soil microbiome

“Ascending Migration of Endophytic Rhizobia, from Roots and Leaves, inside Rice Plants and Assessment of

Benefits to Rice Growth Physiology” Feng Chi et al., Applied and Envir. Microbiology 71: 7271-7278 (2005)

Rhizo-bium strain

Total plant root

vol/pot (cm3) ± SE

Shoot dry wt/pot

(g) ± SE

Net photosyn-thesis rate

(µmol of CO2 m-2 s-1) ± SE

Water utilization efficiency

± SE

Grain yield/pot

(g) ± SE

Ac-ORS 571

210 ± 36A

63 ± 2A

16.42 ± 1.39A

3.63± 0.17BC

86 ± 5A

Sm-1021 180 ± 26A

67 ± 5A

14.99 ± 1.64B

4.02 ± 0.19AB

86± 4A

Sm-1002 168 ± 8AAB

52 ± 4BC

13.70 ± 0.73B

4.15 ± 0.32A

61± 4B

R1-2370 175 ± 23A

61 ± 8AB

13.85 ± 0.38B

3.36 ± 0.41C

64± 9B

Mh-93 193 ± 16A

67 ± 4A

13.86 ± 0.76B

3.18 ± 0.25CD

77 ± 5A

Control 130 ± 10B

47 ± 6C

10.23 ± 1.03C

2.77 ± 0.69D

51 ± 4C

“Proteomic analysis of rice seedlings infected by Sinorhizobium meliloti 1021”

Feng Chi et al., Proteomics 10: 1861-1874 (2010)

Data are based on the average linear root and shoot growth of three symbiotic (dashed line) and three non-symbiotic (solid line) plants.

Arrows indicate the times when root hair development started.

Ratio of root and shoot growth in symbiotic and non-symbiotic rice plants -- seeds were inoculated

with the fungus Fusarium culmorum vs. controlsR. J. Rodriguez et al., ‘Symbiotic regulation of plant growth,

development and reproduction” Communicative and Integrative Biology, 2:3 (2009).

Growth of nonsymbiotic (on left) and symbiotic (on right) rice seedlings. On the growth of endophyte (F. culmorum) and plant inoculation procedures,

see Rodriguez et al., Communicative and Integrative Biology, 2:3 (2009).

More productive phenotypes also can give higher water-use efficiency as measured by the ratio of photosynthesis to transpiration

For each 1 millimol of water lost by transpiration:3.6 micromols of CO2 are fixed in SRI plants,

1.6 micromols of CO2 are fixed in RMP plants

This becomes more important with climate change and as water becomes a scarcer factor of production

“An assessment of physiological effects of the System of Rice Intensification (SRI) compared with recommended rice cultivation

practices in India,” A.K. Thakur, N. Uphoff and E. AntonyExperimental Agriculture, 46(1), 77-98 (2010)

Economics, environmental vulnerabilities, and climate change effects will require a

different kind of agriculture in 21st century.We need to REBIOLOGIZE AGRICULTURE

Fortunately, opportunities for a paradigm shiftare available; but they will require significant

changes in our crop and soil sciences

Work in microbiology, crop physiology, soil ecology, and esp. epigenetics needs to become more central

to agricultural research and development

THANK YOU

Web page: http://sri.ciifad.cornell.edu/ Email: ntu1@cornell.edu [NTU-one]