Stress and disease tolerance



Breeding for drought resistance in rice



  • Define the types of drought & functional definition of drought ‘resistance/tolerance’ (DR)

  • Describe considerations in designing a drought screening program

  • Describe the design & management of field drought experiments   







1. Introduction: Challenges of drought and water scarcity


Plant responses to drought stress are very complex as stress itself involves various climatic, soil and agronomic factors, frequently complicated by substantial variation in timing of occurrence, duration and intensity. The general complexity of drought is often aggravated under rainfed conditions in marginal areas by erratic and unpredictable rainfall, and by the occurrence of high temperatures, high levels of solar radiation, and poor soil characteristics. This high variability in the nature of drought stress and an insufficient understanding of its complexity, have made it difficult to identify specific physiological traits required for improved crop performance under drought, consequently limiting plant breeding efforts to enhance crop drought tolerance. It is highly probable that optimal drought-adaptation requires the combination of several morphological, physiological, and phenological processes, which depend on a multitude of genes and varies within each target environment.


In addition to its direct effects on yield, drought can also reduce the potential beneficial effects of improved crop management practices such as fertilizer application or pest and disease management. Given the increasing scarcity of water resources, and competition for them, irrigation is not a practical option for alleviating drought in most of the rainfed areas. Drought management strategies therefore need to focus on maximizing extraction of available soil moisture and the efficiency of its use in crop establishment, growth, biomass and grain yield. However, agronomic and genetic options that do not involve external inputs of irrigation can only partially alleviate drought effects, because yield will always be lower than what can be achieved with irrigation.


This lesson will discuss, from a physiological and breeding perspective, some of the current challenges and opportunities in genetic enhancement of drought resistance in rice and introduce some of the screening tools and methods.








2. What are the challenges in manipulating drought resistant (DR) genes?


  • Most physiological and metabolic processes are affected by water deficits: cell growth, stomatal regulation, photosynthesis, translocation, etc.

  • A very large number of genes up- or down- regulated by drought

  • A very high level of field spatial variation, which complicates phenotyping

  • Large genetic populations and replicates required

  • Even drought component traits are often complex and difficult to screen

  • Logistical challenges for dealing with a large number of genes even when identified





3. Characterization of the target environment and drought definition


Importance of timing, duration and intensity of stress occurrence.

Use historical climate series, crop simulation and water balance models to define the breeding target:  Germination, crop establishment, vegetative growth and tillering, flowering, grain filling.


The rice toposequence includes:

  • drought-prone upper fields that do not retain standing water

  • well-drained mid-toposequence fields, and

  • poorly drained lower fields in which water accumulates to depths of 1 m or more during the rainy season.


Drought is most severe in unbunded uplands and shallow, bunded fields at the top of the toposequence, but can also occur in the shallow rainfed lowlands.


Rice terraces Toposequence (Jharkhand, India)



The functional definition of ‘drought resistance’ should be based on yield stability under water deficits. Drought resistance/tolerance has to be researchable, breakable into simpler levels (e.g. floret sterility and ASI in maize, rooting effects vs. rooting pattern..), and should focus on heritable genetic variation, linked to yield.


Rice tends to be more sensitive to drought stress than other crops


Is rice more drought sensitive than other crops/cereals?

Rice has generally a lowland and semi-aquatic adaptation, a shallow compact root system (especially in lowlands).

Deep roots not always very efficient at water extraction.

Higher tissue sensitivity to water deficit?

High sensitivity of grain set to stress.

Very sensitive to timing of stress.



Know your target environment:

What type of stress is more frequent?


4. Drought screening environments


1. Artificially create stress in the "normal" growing season: avoids genotype x season problems, excluding water is costly/difficult (reproducibility).  But no control of stress occurrence (timing, severity and duration)


2. Manage water-deficits in a non-growing season: application of uniform, repeatable and controlled stress environment, possibility to maximize genetic component of the observed variation. BUT the extrapolation of results to ‘natural’ target environment can be difficult.


Drought screening experiment, using drip irrigation at IRRI upland station

(Dry season 2006)


The main objectives of a screening system should be:


(i) Focus on target environment and adaptation to major stress constraints


(ii) Minimize problems in detecting heritable differences in drought resistance (DR)


(iii) Yield under stress is as function of: yield potential, escape, and drought response, therefore the use drought-response index (DRI) can help to distinguish DR from escape and yield potential


(iv) Ultimately, DR should be viewed as the ability to maintain yield components in stress compared to non-stress: maintenance of grain number, grain size, biomass, yield, harvest index.


In addition, screening system should:


(i) differentiate among genotypes: degree of yield reduction (+ 50%), manage ‘escape’ effects, use period of max evapotranspiration (ET)demand, time initiation of stress carefully, adjust for differences in escape,


(ii) apply uniform stress (drought nursery approach): “uniform” soil water profile, uniform pre-stress crop growth, water application & water use,


(iii) be repeatable: with standard planting time and management procedures, initiate stress by phenological stage, stable water use environment, dedicated field facility, well-established management practices


Screening systems should also take into account the following parameters/criteria: variations in crop phenology and morphology, the growth stage at which stress occurs, the severity and duration of stress, the management options and levels (e.g. fertilizer applications), the plot size and experimental design, all potential interacting factors such as biotic and other abiotic stresses (e.g. temperature), crop quality and economic factors.







5. Control of field irrigation:






Surface / Furrow


3 x wk

Robust components

Efficient water use

Easy to measure

Inefficient water use

Requires land leveling

Hard to measure amount of water

Requires raised beds

Row spacing too wide for rice


3 x wk

Robust components

Efficient water use

Easy to measure

Uneven distribution pattern

same timing of stress for all entries

Large border areas needed

Leaks, blockages and wind



Differential irrigation/ plot

Efficient water use

Uniform application

Expense of components (filters etc)

Limits weed control options

Labor cost: check quality of irrigation








Develop screening methods that are simple and reproducible under the target environment conditions


6. What are the screening tools and methodologies?


  • Line-source irrigation

  • Rain-out shelters

  • Drained paddy (lowland)

  • Continuous intermittent stress (upland)


In order to identify sources of drought resistance it is necessary to develop screening methods that are simple and reproducible under the target environment conditions. Therefore, managing drought-screening nurseries requires a careful analysis of likely sources of non-genetic variation among plots, replications and repeated experiments, and establishing procedures for minimizing these factors.


Several field and laboratory screening methods have been used successfully to screen for drought resistance, including line-source sprinkler irrigation, rainout shelters, and measurement of drought susceptibility index (DSI).


The line-source sprinkler irrigation method creates a gradient of drought stress, and allows the evaluation of large numbers of genotypes at varying intensities of drought in a given environment. However, where response to applied water is linear, simpler stress/no stress techniques provide a more efficient, means of conducting preliminary evaluations.


Line-Source Drought screening experiment at IRRI upland station

(Dry season 2006)








7. What are the drought breeding strategies?


Both conventional and trait-based approaches have been used in breeding programs for drought tolerance. The empirical breeding approach is based on selection for yield and its components in a given drought environment. While such an approach has been partly successful, it requires large investments in land, labor, and capital to screen a large number of progenies plus the difficulty of sampling even a part of the expected range of variability in stress occurrence in the target environment. In addition, there is evidence of increasingly marginal returns from conventional breeding, suggesting a need to seek more efficient methods for genetic enhancement of drought tolerance.


On the other hand, the ability to associate drought adaptive responses with the expression of specific physiological mechanisms has the potential to help greatly in establishing screening protocols and permit better management of genotype × environment (G × E) interactions.


Recent research developments in biotechnology have revived interest in targeted drought tolerance breeding and use of new genomics tools to enhance crop drought resistance. Marker-assisted breeding is making possible the improvement of field crops, particularly for traits where phenotyping is only possible late in the season, is difficult, or is prohibitively expensive. As a complement to the recent rapid progress in genomics, a better understanding of physiological mechanisms of drought response will also contribute to the progress of genetic enhancement of crop drought tolerance.


It is now well accepted that the complexity of the drought syndrome can only be tackled with a holistic approach that integrates physiological dissection of crop drought avoidance and tolerance traits using molecular genetic tools such as MAS, microarrays and transgenic crops, with agronomic practices that lead to better conservation and utilization of soil moisture, and better matching of crop genotypes with the environment.





8. Crop Yield and plant water use


Generally, the response of plants to soil water deficits can be described as a sequence of three successive stages of soil dehydration (Fig. 1).


Stage I occurs at high soil moisture when water is still freely available from the soil and both stomatal conductance and water vapor loss are not limited by soil water availability. The transpiration rate during this stage is therefore determined by environmental conditions around the leaves.


Stage II starts when the rate of water uptake from the soil cannot match the potential transpiration rate. Stomatal conductance declines, limiting the transpiration rate to a rate similar to that of uptake of soil water, resulting in the maintenance of the water balance of the plant.


Finally, stage III begins when the stomata are no longer able to limit the transpiration to that water available from the soil even through stomatal conductance is at a minimum. At this time the plant must resort to other mechanisms of drought adaptation if the plant is to survive.



Virtually all major processes contributing to crop yield including leaf photosynthetic rate, leaf expansion and growth are inhibited late in stage I or in stage II of soil drying. The focus of stage III is survival and water conservation mechanisms which will allow the plant to endure under these severe conditions must be used if available. Plant survival is a critical trait in natural dry-land ecosystems, but for most agricultural situations, stage III often, but not always has little relevance to questions about increasing crop yield. Consequently, the amount of water available up to the end of stage II for all practical purposes determines the cumulative growth and yield on a particular soil. Recovery from stage III can only be of relevance to yield performance if water is added to the system while there is still sufficient time for growth. Therefore, options involving mechanisms to enhance crop survival, thus do not usually mean any increase in crop yield under severe drought stress conditions. Increased crop yields and water use efficiency generally require the optimization of the physiological processes involved in the critical early stages (mainly stage II) of plant response to soil dehydration.





9. Characterization of drought resistance traits


Several physiological, morphological and phenological traits/mechanisms have been associated with drought stress adaptation, either in stage-I, stage-II or stage III processes of soil drying including:


- Plant emergence characteristics/vigor

- Phenology/ Elasticity of development

- Nutrient acquisition/Uptake efficiency

- Water use efficiency

- Photosynthesis, Radiation Use Efficiency

- Carbon Isotope Discrimination (13C)

- Deep Root development

- Hormonal regulation (ABA, GA, Ethylene)

- Osmotic Adjustment/RWC

- Canopy temperature

- Staygreen/ Delayed senescence

- Grain number maintenance

- Grain fill duration and rate

- HI under Drought

- Yield and its components, Etc.


Despite many decades of research on ‘drought tolerance’ in several crops, little progress has been reported in terms of genetic enhancement of crop productivity under water-deficits environments. Breeders and crop physiologists need to work closely in testing the viability/validity of the trait-based approaches for drought tolerance. This has not happened to any great extent previously, but a few success stories have been recently reviewed (Richards, 2004).


Identification of simple to observe morphological and phenological traits, reflective of mechanisms and processes that confer drought tolerance is a priority activity in drought research. An appropriate screening trait for drought stress tolerance should fill the following criteria: (i) a strong link with higher or more stable grain yield in the target stress environment, (ii) a high level of heritability, and (iii) the expression of tolerance must be easily measurable, with adequate replication.





10. What are the integrated drought management options?


Drought management strategies, whether agronomic or genetic, need to focus on maximum extraction of available soil moisture and its most efficient use in crop establishment, maximum crop growth, and for increasing biomass and seed yield. In order to plan crop yield improvement programs for a given target drought-prone area the following steps are essential:

  • Characterize the major patterns of drought stress and their frequency of occurrence in the target environment.

  • Evaluate crop response to the major drought patterns (simulation modeling)

  • Match crop phenology (growth period, sowing, flowering, and seed filling) with most favorable period of soil moisture and climatic regimes

  • Develop a strategy for the optimal use of supplementary irrigation, when available

  • Increase available soil water to crop through agronomic management practices

  • Identify plant traits that would maximize (i) use of available soil moisture in transpiration (ii) production of biomass per unit water transpired, and (iii) partitioning into seed, thereby conferring enhanced crop water productivity.


Agronomic and genetic options that do not involve external input of irrigation can only partially alleviate drought effects, because yield is always lower than what can be achieved with irrigation.





Let's conclude




  • Good knowledge of the target environment is essential in drought breeding: what type of stress is more frequent?

  • Yield stability under drought scenarios and crop water productivity (ratio of yield achieved per water used) should be the target

  • Drought screening systems should be uniform, repeatable and differentiate genotypes

  • Field and irrigation management are critical for drought screening

  • Screening procedures are function of targets, needs and means. Each breeding program should adapt procedures to own environment and conditions.

  • Trait-based improvement needs careful choice and requires integration of breeding and other disciplines




Click here to see the references used in this lesson.







Next lesson


In the next lesson, we talk a bit more about drought. Lesson 4 describes the drought-prone environment.