FULL-LENGTH RESEARCH ARTICLE

Screening Protocols in Breeding for Drought Tolerance in Rice

S. B. Verulkar • S. K. Verma

Received: 30 December 2012 / Accepted: 2 January 2014 / Published online: 21 February 2014

� NAAS (National Academy of Agricultural Sciences) 2014

Abstract Drought tolerance in rice is a complex trait collectively determined by numerous component traits. These traits

are governed by many genes with huge environmental interactions, with low heritability, and thus are difficult to inves-

tigate. In this context, it is important to define the drought tolerance from practical point of view and design a screening

protocol accordingly. The grain yield under defined stress conditions in comparison with normal condition is used to assess

the ‘drought tolerance’. The new tools of phenomics are now available mainly for genomic studies and high-throughput

screening. The protocols for imposing stress at different stages and intensity for different breeding populations are

elaborated.

Keywords Rice � Drought � Screening protocol

Introduction

One of the major limitations for slow progress in breeding

for drought tolerance is lack of standard screening method

for large number of genotypes [19, 36]. This is mainly

because of incomplete understanding of the mechanisms of

drought resistance; the importance of phenology and

potential yield as components of yield under limited water

that override the effectiveness of drought resistance char-

acteristics; large genotype-by-environment interaction for

yield, causing inconsistency in yield performance in dif-

ferent environments [19]; and the different types of drought

in terms of stage and intensity as well as its unpredictable

nature.

It is desirable to start the drought comparative pheno-

typic screening of breeding material at a very early step of

test lines along with both susceptible and resistant lines,

which would allow a precise monitoring of the applied

drought stress level and a competitive advantage of the test

material versus the promising breeding lines. Secondly, the

performance of the line should be assessed under both

stress and normal irrigation in order to unravel any yield

penalty in optimal conditions while identifying the best

lines under drought stress. Both the genetic background

and the biophysical environments where the lines are

grown and evaluated will have large impacts on gene

expression and plant performance [16].

It is highly unlikely that universal ‘drought tolerance’

traits and screening methodology may be identified. Any

putative drought-tolerant secondary trait is unlikely to be

important across all water-deficit scenarios. A drought trait

that might offer substantial benefit in one weather scenario

of developing drought, e.g., early closure of stomata, might

well result in a negative response in another scenario [30].

One important point to note here is that many of the

observed responses to drought in plants obey Le Chatelier’s

Principle (when subject to a perturbation, a system tends to

respond in such a way as to minimize the effect of the

perturbation). For example, drought responses such as

stomatal closure, leaf rolling, enhanced root growth,

enhanced ABA production, and so on act to minimize

water deficits. It follows that in any particular case, one of

these responses could indicate particular sensitivity to

S. B. Verulkar (&) � S. K. Verma

Department of Genetics and Plant Breeding, Indira Gandhi

Krishi Vishwavidyalaya, Raipur 492 012, CG, India

e-mail: satishverulkar@gmail.com

123

Agric Res (March 2014) 3(1):32–40

DOI 10.1007/s40003-014-0094-x

drought or may indicate a highly responsive drought tol-

erance mechanism. It is often difficult or impossible to

distinguish these two, and this must be remembered when

choosing indicators of drought stress.

Characters for Screening

To decide the character for screening, it is important to

define the drought tolerance from practical point of view and

design a screening protocol accordingly! From a breeder’s

and off-course farmers’ point of view, it is important to

select genotypes able to optimize water harvest and water

use efficiency while maximizing grain yield under water

stress condition. Therefore, the term ‘drought tolerance’

relates to final grain yield rather than to the capacity of the

plant to survive in water-limited conditions [33]. However, if

the drought tolerance is defined in terms of final yield under

stress conditions, it becomes very complex, influenced by

almost unlimited number of factors some controllable and

uncontrollable, predictable and unpredictable factors,

genetically difficult to understand and manipulate; therefore,

grain yield is not a trait of choice in the areas of genomics.

Plant phenomics offers new technologies to understand

dynamic nature of drought, plant development, and its

physiological response in understanding gene function.

These high-throughput and high-resolution phenotyping

tools are being developed and will be great help in providing

robust phenotypic markers for basic as well as applied

aspects [4, 13]. Scientists often try to split up the overall

tolerance in individual components such as root system, leaf

water potential, osmotic adjustment, relative water content,

and biomass accumulation, but these secondary traits are

also often difficult to measure using routine and conven-

tional tools; with the advent of high-throughput pheomics

tools, these traits have recently gained more attention and

scientists [12, 18, 25, 26, 32] assume that these traits are

more correlated and heritable than the grain yield. The grain

yield under stress conditions has been reported to be less

heritable, being a complex quantitative character reducing

its selection efficiency [5, 8, 11, 29]. However, the secondary

traits have not been successfully used in breeding program.

In the recent years, broad-sense heritability for yield under

stress conditions has been reported to be similar to that of

non-stress conditions [1, 2, 6, 21, 22, 34]. Recently the

effective selection for grain yield under stress condition has

been reported [20, 34, 35]. Therefore, from breeding point of

view, grain-yield-based selection criteria would be better

than any other secondary traits. However, a more rational

approach would depends on specific experiment purposes,

and availability of high-throughput precise phenotyping

facility different traits as listed in Table 1 can be considered.

The most robust and integrative selection criteria are

biomass accumulation and yield performance. Grain yield

under defined stress condition should be the primary cri-

terion for selection. One may want to assess the impact of

water deficit on plant growth, and non-destructive mea-

surements could be the preferred methodology. Parameters

such as plant phenology, canopy growth, and temperature

measurements with imagery, leaf rolling, tillering ability,

and spikelet fertility are relatively simple parameters to be

measured for a large number of events and plants. A cor-

rect assessment would require two cycles of screening. As

already mentioned, it is essential to include both suscep-

tible and resistant cultivars during the early screening since

the application of the drought treatment and re-watering

decision would require a visual inspection of well-known

cultivars. These reference cultivars are the key controls for

a linkage of improved lines by gene technology with

breeding [16].

Dry Season Versus Wet Season Screening

Screening in dry season, rainout shelters, and drained upper

paddies can be controlled more effectively, but their pre-

dicted performance under natural drought stress is not

known [19, 34]. Particularly in dry season, temperature is

very high, humidity is very low, wind velocity is high, and

sunlight is very intense; so under these conditions, water

stress is often imposed rapidly and confounded with other

stresses as well and therefore is not a good option. Wet

season would be more appropriate. But during wet season,

screening for vegetative stage drought is often is not pos-

sible; so for this stage, it would be advisable to screen the

material during the summer season. The typical advantage

of vegetative stage screening is that this is not affected by

the maturity period of different varieties, which is a serious

problem under reproductive stage screening. If you look at

the rainfall distribution at Raipur during wet season of

2011, it is apparent the seedling stage and reproductive

stage drought can be effectively managed under wet season

with agronomic manipulations. Pandey [24] observed that

in Eastern India terminal stage drought is the most frequent

type and severely affects yield. Fukai [10] and Ouk [23]

reported categorically that the free water level from

3 weeks before anthesis until maturity is closely related to

grain yield in rainfed lowland.

Intensity of Drought

The spatial and temporal information on water availability

at the sub-ecosystem level indicates the highly unpredict-

able nature of drought stress in terms of stage, duration,

Agric Res (March 2014) 3(1):32–40 33

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and intensity. Screening methodology cannot be designed

for large number of different intensities, but the ideal

would be the level of intensity, which can discriminate the

tolerance and susceptibility. Different parameters can be

employed for this purpose. Performance of check entries

for leaf rolling, RWC, osmotic potential, yield under stress

compared to under non-stress which can be interpreted in

terms of drought intensity index (DII) [27] etc. would be

the best criteria, which can be supplemented effectively by

physical means like soil moisture content which itself can

be measured by gravimetric method, neutron probes, ten-

siometers etc. The managed water stress protocol should

result ideally the DII between 0.5 and 0.7 with quite

consistent results over years. This level of stress is required

to clearly discriminate between drought-tolerant and sus-

ceptible genotypes. Most breeding program screening for

drought tolerance fails to impose sufficiently severe stress

in their trials and thus is not able to accurately select

drought-tolerant lines [20].

This level of intensity can be developed with proper

selection of field, water, and agronomic management.

Selection of field: The important features for the selection

of field includes its soil type—the soil type should pref-

erably by sandy loam with less water-holding capacity so

that as soon as the rain stops, soil do not retain water for

long and stress is induced rapidly. The field should be high

Table 1 Secondary traits related to drought tolerance

S. no. Trait Proposed function

Root traits

1. Deeper thicker roots To explore a greater soil volume from deeper soil layers

2. Greater root volume More extraction of water from soil

3. Root fresh weight Proportionate to extraction of water from soil

4. Root dry weight Proportionate to extraction of water from soil

5. Root pulling resistance Deeper and greater root anchorage in soil for better water and nutrient

absorption

6. Root anatomical features (number of xylem vessels) Vertical movement of water

7. Root anatomical features (presence of aerenchyma,

sclerenchyma, etc.)

Barrier for transverse movement of water

8. Greater root penetration ability To extract water from deeper layers below hard pan

Shoot traits

9. Osmotic adjustment To allow turgor maintenance at low plant water potential

10. Membrane stability Allows leaves to continue functioning at high temperature

11. Leaf rolling Reduced transpiration

12. Leaf relative water content Indicates the maintenance of favorable plant water status

13. Water use efficiency Indicates greater carbon gain per unit of water lost by transpiration

14. Proline content For osmotic adjustment

15. Higher sugar content For osmotic adjustment

16. Canopy temperature Maintenance of transpiration and metabolism

17. Spikelet fertility Maintenance of normal metabolic activities

18. Harvest index Maintenance of normal partitioning of photosynthate

19. Biological yield Maintenance of normal growth and metabolic activities

20. Grain yield Maintenance of normal growth and metabolic activities

21. Delay in flowering Low-water potential for exertion of panicle

22. Carbon isotope discrimination Measure of transpiration efficiency

23. Recovery after re-watering Restoration of normal metabolism

24. Stay green Continued photosynthesis

25. Stomata frequency and closure Control and reduced transpiration

26. Leaf drying Reduced photosynthetic area

27. Epicuticular wax Reduced non-transpirational loss of water

28. Transpiration rate (under stress condition) Relates to water absorption and metabolic activities

29. Photosynthetic rate (under stress condition) Also relates to water absorption and metabolic activities

34 Agric Res (March 2014) 3(1):32–40

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on the topo-sequence so that runoff from other field does

not reach screening field and drainage would be very

effective. The next important point in selection of field is

its uniformity, which we usually do not consider. Now-a-

days, the field can be laser leveled. The uniformity of field

can be assessed by uniformity trials or more practically by

growing tolerant and susceptible lines uniformly spread

over the entire field and observing its performance. A

simple measurement of parching water at 10 points spread

across field of 40 9 50 m gives a good idea of uniform

depletion of water (Fig. 1). Soil mapping can be done for

this purpose, which gives a good idea about homogeneity/

heterogeneity of experimental field (Fig. 2). Agronomic

management can be effectively employed for proper

coincidence of exposure of most susceptible stage of crop

(mainly PI) with most expected dry spell. Most commonly

delay in sowing by 20–25 days exposes the reproductive

stage to the severe water stress at the end of mono-modal

monsoon usually expected in Central India (Fig. 3).

Seedling Stage Drought Screening

For seedling stage drought screening, the experiment can

be conducted in field/nursery. The method of establishment

should preferable be direct line sowing. The experiment

should be conducted in alpha lattice with four replications

to get better results. A raised bed prepared like nursery is

shown in Fig. 4. After sowing, irrigate the nursery once

and then do not irrigate for imposition of stress. Preferably

conduct this experiment under rainout shelter.

Observations to be Recorded

Score the seedling mortality when IR 20 or other suscep-

tible check exhibits mortality or

Score days required for mortality (more number of

days—more tolerant)

Seedling height, seedling vigor, seedling biomass, leaf

temperature, etc., can be recorded.

The advantage of seedling stage drought screening is

that it takes less time, required small area (which can be

more uniform), more number of replications possible, and

unaffected by maturity period, but the major disadvantage

is that it may not correlate with adult plant reaction to

stress. Using this protocol, number of genotypes like

Dagaddeshi were identified to be tolerant at seedling stage

(which is also tolerant at adult plant stage), including lines

such as Swarna and IR 64 (which are susceptible at adult

stage).

Vegetative Stage Drought Screening

For vegetative stage drought screening, the experiment

should be conducted in field during summer/dry season.

Prepare the field well and preferably level the field with

laser leveler. The method of establishment should prefer-

able be direct line sowing. The fertilizer dose should be as

per normal recommendation for rainfed trial. The experi-

ment should be conducted in alpha lattice with four repli-

cations to get better results. Experiment can be laid out as

shown in Fig. 1. Red line—IR 20/IR 64 (one line), green

Line—Annada/Moroberican (one line), black line—test

entries (two lines each). The row length should be mini-

mum 2 m.

Imposition of Stress

Stage of crop—maximum tillering stage (*50 days of

sowing for mid–early duration genotypes). First, com-

pletely irrigate the field on 45th day of sowing and drain

the paddy uniformly. When the IR 20/IR 64 exhibits leaf

rolling of score 9 (fully rolled looks like onion leaf), start

taking observations. Measure the soil moisture content at

Field Layout:

Fig. 1 Vegetative stage/reproductive stage drought screening. Open

circle hole for recording parching water level (this should be about 1 m

deep), red line IR 20/IR 64 (one line), green line Annada/Moroberican

(one line), black line test entries (two lines each). Row length—2 m.

(Color figure online)

Agric Res (March 2014) 3(1):32–40 35

123

depth of 30 cm (probably the best method is gravimetric

method or any other method can be used). Also record the

tensiometer reading which off-course with regard to soil

type should be in the range of *50 kPa.

Observations to be Recorded

1. Canopy temperature—by infrared thermometer (cooler

canopy indicates tolerance)

2. Leaf rolling (scored between 12 and 2 pm)—more

rolling indicates more susceptibility

3. Relative water content (RWC)—higher RWC indicates

more tolerance

4. Other traits such as osmotic adjustment, membrane

stability, proline content, sugar content, carbon isotope

discrimination, recovery after re-watering, stomata

frequency and closure, epicuticular wax, transpiration

rate, and photosynthetic rate can be recorded. Always

compare these traits with genotypes under well-

irrigated condition to derive a logical conclusion.

The stress can be released by irrigating the field when

[50 % genotypes exhibits wilting symptoms. Short list the

lines based on these observations and then record other

physiological traits.

The major advantage of vegetative stage stress is that

screening is not seriously affected with the maturity dura-

tion of crop; however, the stress at this stage usually does

not affect the grain yield seriously as compared to repro-

ductive stage drought condition.

Fig. 2 Soil mapping based on electrical conductivity

Fig. 3 Daily rainfall during wet season 2011

36 Agric Res (March 2014) 3(1):32–40

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Rainfed Trials

Assessment of genotypes under rainfed condition has tre-

mendous practical advantage, where we can simulate the

farmers’ situation. In this situation, one can expect drought

stress at any stage, and therefore, the final yield may be an

outcome of one or more stress period, as well as problems of

fertilizer applications. Some points for considerations:

• Select an appropriate field (consider the points explained

above)

• Preferably go for dry direct seeding

• Grow susceptible and tolerant checks at regular interval

• The test entry should be planted with at least three rows

with 2 m length

• Keep minimum of three replications

• Conduct the trials using alpha lattice design

• Keep the paddy field open all the time with proper

drainage so that the rainwater does not stand in the field

• Record the observations whenever the drought spell

occur, but be sure that susceptible genotype is exhib-

iting good drought symptoms.

• For the quantification of drought, various soil parameters

such as parching water level, soil moisture content, and

tensiometer reading can be taken along with plant traits

such as leaf rolling, RWC, and leaf osmotic potential etc.

• Apart from secondary traits, importantly record the

grain yield under rainfed situation and compare the

yield under normal irrigated condition.

• The DII can be calculated DII = (1 - Xs/Xi) [27].

Where Xs is the mean yield under rainfed condition,

and Xi is mean yield under irrigated condition. Assume

trial to be successful only when DII is more than 0.5.

• Higher grain yield under stress can be taken as a

criterion for drought tolerance.

• Drought susceptibility index (DSI) for each genotype

can be calculated by formula DSI = (1 - Ys/Yi)/DII

[9], where Ys is the yield of a genotype under stress

condition, and Yi is the yield under irrigated condition.

• Other secondary traits such as leaf rolling, leaf senes-

cence, stomatal conductance, RWC, osmotic potential,

spectral reflectance, canopy temperature, growth pattern,

and membrane stability can be recorded. For most of

these traits, high-throughput phenotyping facilities can

be established. These secondary traits along with grain

yield give an excellent idea about the genotypes reaction

to stress.

• Root pulling resistance (at maximum tillering stage) can

be recorded under normal conditions. This trait is a

destructive indirect measurement of root architecture,

gives a very good idea about constitutive root develop-

ment, and correlates significantly with yield under stress

condition.

The major advantage of this type of stress imposition is

that throughout the life cycle, usually the probability of

stress at least once is very high, and to a great extent, this

situation usually simulates the conditions of rainfed

Side view

Areal view:

Fig. 4 Seedling stage drought screening. Red line IR 20/IR 64 (one line), purple line Annada/Moroberican (one line), green line test entries (two

lines each). Row length—50 cm, plant-to-plant spacing 5–7 cm. (Color figure online)

Agric Res (March 2014) 3(1):32–40 37

123

ecosystem, and therefore, the screening under rainfed con-

dition is of great practical significance. However, under this

condition, the intensity of stress and imposition of stress at

fixed crop stage are not controllable, and often the result of

1 year is not repeatable.

Reproductive Stage Drought

In Eastern India, reproductive stage drought is one of the

major factors limiting grain yield, mainly because of mono-

modal distribution of rainfall (Fig. 3), which ceases at about

first or second week of September. For this situation, keep all

the other things common with rainfed trial, with following

modifications:

• Sowing can be delayed by 20–25 days

• Keep the field irrigated to about 50 days of sowing or

till maximum tillering stage and then drain the water.

• Then record the grain yield under stress and compare

with yield under irrigated condition and with known

susceptible and tolerant lines.

• Other secondary traits such as partitioning of dry

matter, photosynthetic activity, and spikelet fertility can

be recorded.

This protocol is extremely useful in imposition of severe

stress at reproductive stage, which is highly sensitive stage of

rice crop, and results in significant reduction in grain yield.

We have been following this protocol since last more than

10 years, and invariably in all the years, we could impose the

stress ranging from 0.4 to 0.6 DII every year. This protocol

can be effectively followed for early and mid-duration

genotypes only.

Screening of High Value Early Generation Segregating

Populations

For population size of about 1,000, the early generation

material (e.g., BC1F1, BC2F1, F2), which cannot be repli-

cated or evaluated under stress and non-stress conditions,

this method is very useful. Even this can be a better approach

for expression analysis under different sets of conditions.

The points are the following:

• Sown the seed in petri dish after treatment with

fungicide (Bavistin)

• Transfer the germinated seed in wooden boxes filled

with soil.

• After 12–13 days of sowing, transplant the seedlings in

a very well-leveled, puddled, and fertile soil (high soil

fertility level will induce early and more tillering).

• Follow alternative wetting and drying, which usually

results in more tillering.

• Put two labels in each plant.

• Up-root the plants at about 42–45 days of sowing and

separate the tillers vertically in such a way that each

tiller has root system.

• Transplant one tiller under normal condition and one

under stress condition.

• By this way, single plant can be evaluated under two

sets of conditions!

This method if combined with high-throughput pheno-

typing facility will be of great utility for genomic studies.

Vegetative cloning in rice has been reported long back by

Dr. Richaria and is very much successful with almost

100 % survival and normal growth of cloned plants.

High-Throughput Phenomic Platform

Furbank and Tester [13] described phenomics as the study of

plant growth, performance, and composition. A number of

forward phenomics and reverse phenomics tools are now

available, which can now be readily used for high-through-

put automated low-resolution measurements on large num-

ber of genotypes followed by higher-resolution lower-

throughput measurements with the limited number of

genotypes. Further, these physiological traits can be dis-

sected to biochemical or biophysical process leading to the

identification of gene(s). Some of the phenomics tools

includes carbon isotope discrimination (CID), an indirect

measurement of transpiration efficiency [7, 28], infrared

thermography for measuring stomatal conductance under

water stress [31], which indicate clear differences in differ-

ent genotypes, or simply the canopy temperature can be

measured with infrared thermometer or gun. The other

phenomics tools include chlorophyll fluorescence analysis

using pulse amplitude-modulated fluorometry [3] along with

digital growth analysis from projected leaf area. Another

optical technique associated with chlorophyll fluorescence is

leaf spectroscopy using radiometric or imaging sensors to

calculate various indices such as normalized difference

vegetation index (NDVI) [17] and photosynthetic reflective

index (PRI) [14], related with crop stress. Simple digital

imaging in visible wavelength region in real time from dif-

ferent angles simultaneously gives an idea of growth pattern

and water use efficiency [15]. Such tools (with their own

limitations and assumptions) are now becoming popular and

can overcome the issues related to phenotyping.

Conclusions

The major emphasis in these protocols has been given to

the grain yield as selection criterion, and drought tolerance

38 Agric Res (March 2014) 3(1):32–40

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has been defined in terms of comparative yield of a

genotype in stress and non-stress conditions. Depending on

the most prevalent stress in the region, stage and intensity

of drought can be managed. Apart from grain yield, based

on the objectives, facilities, and resource availability, dif-

ferent criteria for drought tolerance can be used to evaluate

the genotypes under field conditions under target popula-

tion of environment. Using the aforementioned protocol, a

rice variety ‘Indira Barani Dhan-1’ has been developed and

released for the rainfed area of this region.

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