Review Breeding Upland Rice for Drought Resistance

8/6/2019 Review Breeding Upland Rice for Drought Resistance

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Title:

Review: Breeding upland rice for drought resistance

By: Jrme Bernier,1,3* Gary N. Atlin1,2, Rachid Serraj1, Arvind

Kumar1 and Dean Spaner3

1- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

2- Present adress : Centro Internacional de Mejoramiento de Maz y Trigo, Apdo. Postal

6-641 06600 Mexico, D.F., Mexico

3- University of Alberta, Edmonton, Alberta, Canada, T6G 2R3

*Corresponding author:

ABSTRACT

Upland rice, produced by smallholder farmers, is the lowest-yielding rice production system. Drought

stress is the most severe abiotic constraint in upland rice. Improving productivity of rice in the upland

ecosystem is essential to meet rice food security needs of impoverished upland communities. In this

context, breeding drought-resistant rice is an increasingly important goal. Numerous secondary

characters have been suggested to help plant breeders in their selections, but most of these traits are

not used in selection, as they are not practical for selection purposes, exhibit low heritability, or are not

highly correlated with grain yield. Standardization of drought screening has been shown to increase

the heritability of yield under stress to values similar to those obtained for yield in well-watered

conditions. It has now been demonstrated that drought tolerant upland s can be bred by directly

selecting for yield in stress environments. The use of molecular markers to perform selection may

eventually provide plant breeders with more efficient selection methods. To date, many quantitative

trait loci (QTL) for drought resistance have been identified in rice, but few are suitable for use in

marker-assisted selection. However, large-effect drought resistance QTL have now been identified and

may enable effective use of marker-assisted selection for drought resistance.


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Keywords: upland rice, drought, selection method, marker-assisted

selection

INTRODUCTION

A definition of drought generally accepted by plant breeders is: a shortfall of water availability

sufficient to cause loss in yield,1 or a period of no rainfall or irrigation that affects crop growth.2

Using a similar definition, it has been estimated that 25% of the fields used for upland crop production

are prone to yield reductions as a consequence of drought.3 Drought therefore has a major impact on

world agriculture. Drought may happen at anytime during the growing season and may occur every

year in some areas. Plant breeding is only one tool for alleviating drought stress. However, drought

tolerant varieties developed through plant breeding are more accessible to farmers than costlyagronomic practices or irrigation enhancements that might require large investments by farmers.4

Rice, one of the most important crops of the world, has the evolutionary particularity of being semi-

aquatic. As a result, rice has relatively few adaptations to water-limited conditions and is extremely

sensitive to drought stress.5 This paper attempts to define the current status of breeding for drought

resistance with a focus on upland rice. The global importance of rice, its different production systems,

and the economic and social consequences of drought stress on rice production are briefly reviewed.

The physiological mechanisms contributing to maintain grain yield under drought conditions arediscussed, and the breeding methodologies available to upland rice breeders aiming to improve

drought resistance are reviewed.

RICE: ORIGINS AND DOMESTICATION

Rice (Oryza sativa L.) is a member of the Poaceae family, as are barley (Hordeum vulgare L.), wheat

(Triticum aestivum L.) and corn (Zea mays L.). There are two species of cultivated rice. Oryza

glaberrima originates from West Africa and is presently only grown near its center of origin, while O.

sativa, which is originally from Asia, is grown on all continents.6 In present day Africa, O. glaberrima

has been almost completely replaced by O. sativa. This shift may be explained by the low yield

potential and difficulties associated with threshing and milling ofO. glaberrima.7 Some desirable

characteristics ofO. glaberrima have, however, been introgressed into O. sativa genetic backgrounds;

leading to the development of the increasingly popular New rice for Africa (NERICA) varieties.8


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Wild rice (Zizania palustris L.) of North America is not in the Oryza family, and is thus not a rice

species.9 Henceforth, only O. sativa will be considered when referring to rice.

There is evidence suggesting that rice was the first crop domesticated by humans in the Yangtze riverbasin as early as 13000 years ago.10 The ancestor ofO. sativa is assumed to be Oryza rufipogon, which

is naturally distributed across Asia, from Pakistan to China.6 There are two main ecotypes within

natural O. rufipogon populations; perennial and annual types. Cultivated rice originated from at least

two independent domestication events, resulting in the indica andjaponica ecotypes.11

RICE AND HUMAN NUTRITION

Rice is the most important crop directly consumed by humans. With around 600 M t produced

annually on 149 M ha in 2003, rice accounts for 23% of the worlds caloric intake.12 In the same year,

wheat was grown on a larger area, 207 M ha, but total production was slightly lower.13

Most rice (90%) is grown in Asia, where it is estimated to supply 35 to 60% of the total caloric

intake.6 Rice is especially important in the poorest Asian countries, such as Myanmar and Bangladesh,

with annual per capita consumption in 2003 of 197 and 160 kg, respectively. In the same year, the

annual per capita consumption in the United Kingdom was 5 kg, with a world average of 54 kg and an

Asian average of 79 kg.13 Rice-based diets generally provide low iron, zinc and vitamin A intake;

these nutrient deficiencies are therefore common in regions relying on rice for most of their caloric

intake. Biofortification programs are underway to improve the nutritional value of rice.12

Rice production increased by 130% between 1966 and 2000, while the population of low income

countries increased by an average of 90% over the same period.14 The world population is predicted to

reach approximately 8 billion by 2030,15 and there is therefore a need to further increase rice

production by 40% in the next 25 years.14

RICE ECOSYSTEMS AND THEIR HYDROLOGICAL STATUSRice ecosystems are generally classified into 4 types: irrigated, rainfed lowland, deep-water and

rainfed upland.9 Irrigated rice is the most common ecosystem, comprising 55% of the global

production area. It is also the most productive system and is responsible for 75% of global production.

This can partly be explained by the fact that irrigated rice production generally takes place on well-

drained, fertile soils that are not subject to drought or flooding. More inputs such as fertilizers are used


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in irrigated rice than in other ecosystems.6 This system has been the main focus of the Green

Revolution.16 High levels of investment in fertilizers by farmers in irrigated systems are profitable,

because the risk of crop loss due to drought or flooding is low.

Deep-water rice is planted in areas that are naturally flooded to depths greater than 50 cm for extended

periods during the rainy season.9 In most deep-water fields, seeds are broadcast a few weeks before the

beginning of the rainy (monsoon) season. The plants can suffer from drought in the early stages of

growth, but once the monsoon starts, water levels rise and remain high until the end of the growing

season. Stems elongate following the rise in water depth, sometimes up to 3 m. This rice ecosystem

represents about 8% of the total rice cultivation area.6 The main production areas are the deltas of the

Ganges-Bramaputra river of India and Bangladesh, the Mekong river of Vietnam and Cambodia, the

Irrawady river in Myanmar and the Chao Phraya river of Thailand.

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Rainfed lowland rice is the second most important rice ecosystem, representing about 25% of total rice

production area. Fields do not receive irrigation, relying entirely on rainfall or drainage from higher

lands in a watershed. The defining feature of a lowland field is the bund that surrounds it, permitting

water from rainfall or drainage from higher fields to be impounded. Hydrological conditions in

different rainfed lowland fields vary substantially depending on the position of the field in the

toposequence, or succession of fields that drain into each other from the top to the bottom of a rice-

producing watershed. In addition to the use of bunds to impound water, water is retained in manyrainfed lowland fields through tillage practices designed to reduce water losses via seepage and

percolation. Fields are often tilled when wet (puddling), leading to the formation of a hard-pan below

the soil surface. This is desirable as it limits water seepage, thereby preventing or retarding the onset

of drought-stress, but can also limit root growth and access to water stored in the lower parts of the

soil profile.18

Finally, rainfed upland rice is grown in unbunded fields where good soil drainage and/or uneven land

surface renders the accumulation of water impossible.6 Upland rice is usually grown in systems where

little or no fertilizer is applied, and is direct-seeded into unpuddled, unsaturated soil.19 Most traditional

upland rice varieties are low-yielding and prone to lodging, but are adapted to non-flooded soils.20

Upland rice encompasses 12% of global rice production area and is generally the lowest yielding

ecosystem.6 Upland rice farmers are among the poorest in the world and their holding are often less

than 0.5 ha in size.21


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Types of drought

It is not simply the lack of water that lowers yield potential, but also the timing and duration of

drought stress related to phenological processes.31 There are three basic drought patterns affecting rice

production: early, intermittent and late drought stresses.2

Early droughts often result in delayed sowing

or transplanting. Yield reductions from early droughts (occurring during vegetative growth, after

establishment but before maximum tillering) are often minimal, and result from a reduction in tiller

numbers.32, 33 Intermittent or continuous droughts (occurring between the tillering and flowering

stages), may greatly reduce yields despite no apparent drought symptoms (eg: leaf rolling), mainly as a

result of reduced leaf expansion and photosynthesis.2 When drought occurs during later growing

stages ( following panicle initiation and especially during flowering), spikelet fertility is reduced and

this becomes the main factor contributing to yield loss.34 Since the diverse drought patterns have

different impacts on the crop, it is important to define which type of drought stress is targeted by abreeding program.2

MITIGATING THE IMPACT OF DROUGHT

Rice is a notoriously drought-susceptible crop due in part to its small root system, and rapid stomatal

closure and leaf senescence during mild water stress.35 Rice, like other crops, can potentially resist

drought stress using three different strategies: drought escape, drought avoidance, or drought

tolerance. A proper timing of lifecycle, resulting in the completion of the most sensitive

developmental stages while water is abundant, is considered to be a drought escape strategy.36

Avoiding water-deficit stress with a root system capable of extracting water from deep soil layers, or

by reducing evapotranspiration without affecting yields, is considered as drought avoidance.36

Mechanisms such as osmotic adjustment (OA) whereby a plant maintains cell turgor pressure under

reduced soil water potential are categorized as drought tolerance mechanisms.36 Drought avoidance

mechanisms can be expressed even in the absence of stress and are then considered constitutive.

Drought tolerance mechanisms are the result of a response triggered by drought stress itself and are

therefore considered adaptative.37 When the stress is terminal and predictable, drought escape through

the use of shorter duration varieties is often the preferable method of improving yield potential.

Drought avoidance and tolerance mechanisms are required in situations where the timing of drought is

mostly unpredictable.38

Drought escape through short duration varieties


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regulated by aquaporins, which are small transmembrane proteins that act as water channels.49 The

apoplastic pathway contributes a great deal more to plant water uptake than water uptake via

aquaporins.47

Roots taper down as they grow, which increases their axial resistance, eventually rendering upward

water flow impossible.2 An increased xylem vessel size has been hypothesized to be a useful trait to

improve water extraction from deeper soil layers.50 Basal root thickness has been reported to be

correlated with yield in upland rice (rG=0.33).51

Rice roots have also been reported to be highly susceptible to cavitation (the collapse of a continuous

water column in the xylem due to air bubble formation).52 Cavitation occurs when axial water flow in

the xylem vessels cannot keep up with the transpiration rate.

53

Root pressure, the mechanism by whichrice is thought to overcome cavitation at night, has been reported to be a potentially important

component of drought resistance.52

The ideal upland rice root system is thought to be composed of only a few thick and long roots with

large xylem vessels capable of extracting water in the deep soil layers.2, 54 This type of root system is

usually associated with plants having a moderate tillering capacity. A high tillering capacity is linked

to extensive production of adventitious roots, which in turn reduces the amount of assimilates

available for existing roots to grow deeper.

54

Stomatal control and transpiration efficiency

One basic mechanism for reducing the impact of drought is early stomatal closure at the beginning of

a period of water deficit. Stomatal closure reduces water loss, but also reduces the gas exchange

between the plant and the ambient air. The reduced CO2 intake then results in reduced

photosynthesis.55, 56 This mechanism is therefore useful to improve plant survival under drought stress,

but is also associated with yield reduction.1 Early stomatal closure may be desirable under some

circumstances, but not where droughts are short, frequent, and relatively mild.

1

Regulation of stomatalconductance is very complex and poorly understood, but thought to be mainly a consequence of leaf

cell response to water deficit, and, to a lesser extent, a consequence of low root water status

communicated to the leaf via abscisic acid (ABA) signaling.57, 58 Significant genetic variation for the

sensitivity of stomata to leaf water status has been reported in rice.59


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In C3 species, carbon isotope discrimination (CID) is positively correlated to the ratio of internal CO2

leaf concentration to ambient air CO2 concentration,60 and this provides an integrated measurement of

transpiration efficiency61. Higher CID generally indicates that stomata were kept open for a greater

proportion of the growing period.62, 63

Plants with high CID tend to have higher yields in rainfed orirrigated environments because increased transpiration enables an increased biomass accumultion.64

Under dryer conditions, conservative plants that grow more slowly, and have a lower stomatal

conductance (hence lower CID), may perform better as they achieve a larger biomass accumulation

per gram of water transpired.63, 65

Drought tolerance traits

Osmotic adjustment

As a plant detects a water-deficit stress, it may accumulate a variety of osmotically active compounds

such as amino acids, sugars and ions inside its cells, resulting in a lowering of the cell osmotic

potential.66 Water present in inter-cellular spaces then flows towards the inside of those cells.2, 54 This

process, called osmotic adjustment (OA), was proposed as a potential factor that could enable plants

to maintain turgor and survive better at low water status. It has, however, been argued that osmotic

adjustment probably does not allow the plant to draw much extra water from the soil and that this

could come at a cost in yield potential.67 In rice, despite much previous research focus and

investments, the usefulness of OA in improving grain yield under drought stress has not beendocumented,31, 68 The failure to demonstrate any tangible benefit of OA on yield is probably related to

the fact that the hypothetical benefits are expressed only when crop survival is threatened. Osmotic

adjustment could contribute to drought resistance via osmolyte accumulation in roots that would

maintain or increase root development into deeper soil layers, thereby increasing available water for

crop use.69, 70

Cell membrane stability

The ability to survive dehydration is influenced by a cells ability to survive at reduced water content.This can be considered complementary to OA because both traits will help maintain leaf growth (or

prevent leaf death) during drought.1 Rice varieties differ in dehydration tolerance and an important

factor for such differences is the capacity of the cell membrane to prevent electrolyte leakage at

decreasing water content, or cell membrane stability (CMS).71 The maintenance of membrane

function is assumed to mean that cell activity is also maintained. Measurements of CMS have been


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used in other crops and are known to be correlated with yields under high temperature and possibly

under drought stress.71

Epicuticular waxIn sorghum (Sorghum bicolorL. Moench), drought resistance is a trait that is highly correlated with

the thickness of the epicuticular wax layer. It has been estimated that the thickness of the epicuticular

wax in rice is about 20% that of sorghum.54 The resistance of the rice cuticule to water loss is therefore

low and rice loses water even if its stomata are closed.2, 39 Experiments have demonstrated that rice

varieties with a thick cuticle layer retain their leaf turgor for longer periods of time after the onset of a

water-stress, however, the effects on yield have not been thoroughly investigated.54 A thick wax layer

may also reflect more sunlight away from the leaf, thereby preventing leaf heating without requiring

transpiration.

72

Partitioning and stem reserve mobilization

As photosynthesis becomes inhibited by drought, the grain filling process becomes increasingly reliant

on stem reserve utilization.72 Numerous studies have reported that stem reserve mobilization capacity

is related to yield under water-stress in wheat.72 In rice, a few studies also indicated that this

mechanism maintains grain yield under water stress at the grain filling stage.73-75 This drought

tolerance mechanism is stimulated by a decrease in gibberellic acid concentration and an increase in

abscisic acid concentration.

75

Stability of flowering processes

Drought stress applied at the beginning of the reproductive stage usually results in a delay in

flowering.76 This is mainly due to slowed elongation of the panicle and supporting tissues.5 This trait

can be an effective drought avoidance mechanism if the period of water deficit is short, as panicle

elongation resumes after relief from a brief period of stress. However, if flowering is delayed by more

than a few days, severe yield losses usually occur. It appears that rice has a pre-determined amount of

time when peduncle elongation can proceed and that anthesis follows about a day thereafter. Slow

panicle elongation means that anthesis may occur while part of the panicle is still within the leaf

sheath.34 Unexerted spikelets will be sterile.77 It has been reported that the greater the delay in

flowering, the greater the yield and harvest index reduction due to drought. 38 Improving drought

resistance may therefore involve selection for plants exhibiting little or no flowering delay due to

drought.38, 78 Nevertheless, the highly drought-resistant variety Moroberekan exhibited greater


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effect.93, 94 A large number of genes are activated by one hormone and repressed by the other. It is

likely that a large part of the differential response of different rice varieties to drought is related to

their responses to the ABA/GA antagonistic effects.75, 90, 91 Salicylic acid, cytokinins and ethylene can

also be involved in drought response.76, 95

RNA-based microarray technology is now being used to analyze drought resistance pathways in rice

by comparing levels of gene expression between resistant and susceptible genotypes. This is a very

powerful tool because the expression of thousands of genes can be assayed at once.96 Over the last five

years, many genomic studies on the model plantArabidopsis thaliana have given important

indications of the physiological mechanisms that allow plants to survive drought. There are at least

four different biochemical pathways that are activated whenArabidopsis is exposed to an abiotic stress

such as drought, salt or cold. Two of those mechanisms are ABA-dependant and two are ABA-independent.97 Those four response pathways are not totally independent, as can be seen from the fact

that many genes that are induced by both drought and cold stress have an ABRE (ABA responsive

element) and a DRE (dehydration responsive element) motif in their promoter region.97 The ABRE

motif responds to the presence of ABA while the DRE region induces transcription in the presence of

a protein from the DREB1 protein family (a response to cold-stress) or DREB2 family (a response to

salt or drought).98

Drought and salinity stress both result in reduced soil water potential that renders water absorptionmore difficult and requires similar osmotic and growth regulation response components.85, 99 In the

case of drought, the perception of water stress occurs by sensing of membrane tension, while saline

stresses are sensed by osmosensors. Both sensing mechanisms result in ABA production that then

activates a common response mechanism.89 Resistance pathways to salt, cold and drought stress have

many shared components. Microarray technology has enabled scientists to identify 351 genes of

Arabidopsis that are induced by either drought, cold or high salinity stress.81 Of all those genes, 128

were specifically responsive to drought; 21 to cold; 51 to high salt; 8 were induced by either drought

or cold; 2 by either cold or salinity; and 119 by either drought or salinity. A further group of 22 genes

was found to be up-regulated by all three environmental stresses.81 Such results demonstrate the

complexity of the mechanisms involved in stress response and suggest the existence of large

interactions between drought and salt-stress response. Identification of genes involved in resistance to

multiple stresses would facilitate the development of crop varieties with multiple stress resistance.100


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However, the experimental protocols used in many studies lead to rapid stresses development in

conditions that are not representative of agricultural situations and therefore might be misleading.101

In rice, the knowledge of the biochemistry involved in stress resistance is more limited than inArabidopsis. An experiment using two-dimensional polyacrylamide gel electrophoresis identified 42

proteins that were present in a significantly higher or lower concentration during drought stress.102

Among the proteins that had an increased concentration under drought were enzymes of carbon

metabolism, actin depolymerizing factor (involved in cell shape regulation), RUBISCO activase and

various other proteins.102 Evidence of shared responses between cold, drought and salinity stress are

also available at the proteomic level, as the protein superoxide dismutase is known to be accumulated

as a result of any such stress.103

BREEDING FOR DROUGHT RESISTANCE IN UPLAND RICE

Progress to date in breeding for drought resistance

Rice breeding programs focussing on drought resistance have made little progress to date.2 This may

be explained by the fact that drought resistance is a trait controlled by many genes having different

effects, and is dependent on drought timing and severity. Another way to explain the complexity of

drought is that drought resistance involves an interaction between the genes involved in yield potential

per se (which are numerous) and the genes for drought resistance.1 However, much of the reason for

the lack of progress in rice can be explained simply by the lack of investment that has been made in

screening for drought tolerance in variety development programs.16 Few programs explicitly

incorporate a drought tolerance screening step as part of their routine breeding activity, despite the

considerable effort that has been made on the genetic and physiological analysis of traits thought to be

related to genotypic differences in drought tolerance.

Modern plant breeding has been more succesful in favorable growing conditions than in unfavorable

conditions.104, 105 A study of 18 maize hybrids released by Pionner Hi-Bred between 1953 and 2001

grown under well-watered control conditions and five drought treatments confirmed this in maize. The

rate of yield gain over 50 years of varietal development was 189 kg ha-1 year-1 under well-watered

conditions. Under conditions of drought at flowering, yield gains were also high (146 kg ha-1 year-1),

but was no more than 47 kg ha-1 year-1 under 4 other simulated drought stress treatments (early-fill,

mid-mill, late-fill, terminal drought).4 Similarly, in rice, improved varieties responsive to high levels


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of inputs have been available to irrigated rice farmers for a long time, but rainfed rice varieties have

been little improved. Many rainfed rice farmers still use traditional low yielding varieties.106, 107

Selecting for drought-resistant upland riceIn most upland rice environments, droughts are unpredictable and will not occur every year. Farmers

are not likely to be willing to sacrifice yield potential for greater yield in drought years. Plant breeders

must therefore select varieties capable of producing well in both favorable and unfavorable years.

Selection criteria to be used in order to obtain high yields under both stress and non-stress

environments have been debated by breeders for decades.108 There are 3 major breeding targets that

may result in improved grain yield under drought: increasing yield potentialper se, timing flowering

with periods when water is available, and improving drought resistance.109

Screening for increased yield potential is generally performed under ideal conditions. Such selection

environments will serve to improve yield under drought if yield under drought and yield under well-

watered conditions are positively correlated. This is usually the case under mild and even severe

drought conditions in rice.78, 110, 111 Atlin et al. (2004) demonstrated that, even when the mean yield

difference between stress and non-stress treatments is over 50%, genotype means tend to be positively

correlated across yield levels in populations of unselected recombinant inbred lines. This is explained

because large differences among genotypes in height and harvest index are often expressed in both

stress and non-stress environments.110

Selection for yield potential is therefore an important element indeveloping varieties that produce acceptable yields under moderate levels of stress.

Selecting genotypes that complete their flowering before the onset of water stress is possible if the

timing of drought is predictable and terminal. This is the case for late-season stress in many areas

where the monsoon tends to withdraw predictably and sharply, as in much of eastern India, Thailand,

and Laos. However, in many areas where upland rice is grown, brief periods of drought stress,

particularly around flowering, occur unpredictably during the middle of the monsoon. Drought

resistant varieties are essential in these areas.

Drought resistance is improved either if the crop is able to access more water or if it can use available

water more efficiently (higher transpiration efficiency).45 Selection for drought resistance can be

performed by measuring yield under stress conditions and/or measuring a secondary character

correlated with yield under stress conditions. A secondary trait is only useful in breeding if it is


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stress at flowering stage.113 Selection for a low rate of leaf drying is similar to selection for stay-

green in sorghum. In sorghum, it has been demonstrated that lines maintaining green leaves the

longest under drought are able to accumulate more biomass and consequently produce greater

yields.114

Other secondary traits that could be used in selection

Several authors have suggested that carbon isotope discrimination (CID), an indirect measure of

stomatal conductance, could be an effective selection criterion for grain yield under drought.63, 115-118 In

wheat, grain yield was found to be positively correlated to stem CID under the conditions of South

Australia (r=0.51 to 0.65)119 and to grain CID in the conditions of Syria (r=0.5),120 south of France

(r=0.44 to 0.70)117 and Spain (r=0.5).121 Significant correlation was found, under the dry conditions of

north-west Mexico, between grain CID and yield, in water treatments simulating post-anthesis waterstress (r=0.88 and 0.89) and residual moisture conditions (r=0.50 and 0.66).63 The correlation was

significant in only one of two trials for pre-anthesis water stress (r=0.58).63 At IRRI, positive or non-

significant relationships between grain CID and grain yield under drought stress at flowering and grain

filling stages have also been observed (unpublished).

There are few circumstances where negative correlations between grain yield and CID have been

observed, despite that fact that it is generally assumed that lower CID indicates higher transpiration

efficiency. This may be due to the fact that lower CID leads to slower crop growth under the absenceof water deficit and that a higher transpiration rate does not necessarily imply faster rate of soil water

depletion.116 A negative CID has however been demonstrated to be advantageous in Australia. A

backcross breeding program has introduced improved transpiration efficiency of the wheat variety

Hartog by using Quarrion as a donor and selecting for lines with a low CID (hence high water-use

efficiency).122 Interestingly, CID measurements were done using young plants growing under well-

watered conditions and the desirable plants (those with low CID) were used for backcrossing. This

resulted in the release of the drought-resistant wheat variety Drysdale, which outperformed the local

check variety by up to 40% under very dry conditions.122 Such examples have not occurred in rice so

far.

Leaf or grain ash (mineral) content was proposed as an alternative selection criterion for yield under

drought, thereby avoiding the high cost of CID analysis.63, 123 As most minerals are mainly transported

passively in the xylem and accumulated in transpiring plant tissues, greater transpiration consequently


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compared the location of QTL linked to root traits and OA. This experiment reported 36 QTL related

to root traits and 5 related to OA and concluded that these two drought resistance mechanisms are

independent of each other.144 Some of the QTL identified in this study corresponded to QTL

previously identified in other rice populations, as well as in the corresponding syntenic regions inbarley and maize.144 However, co-location of QTL for root related traits across populations or

environments is rare, due in part to generally large QTL x environment interaction affecting root traits.

This constitutes a substantial problem for using markers in selecting for improved root phenotypes.145

Quantitative trait loci for yield and yield components under different types of drought stress have also

been reported. The population CT9993 x IR62266 was used to perform QTL mapping for grain yield

under drought stress under upland conditions in southern India27 and lowland conditions in Thailand.

146 In southern India, five QTL related to grain yield were identified over two different trials. One trial

consisted of a severe stress applied towards the end of the vegetative stage while in the other, stress

was mild, but applied at the flowering stage. The QTL with the largest effects explained

approximately 20% and 28% of the genetic variation for yield in the vegetative and reproductive-stage

stress trials, respectively, but none of the yield QTL observed were consistent across trials.27 The

experiment performed in Thailand was done using 5 different water treatments in a transplanted trial

under line-source irrigation.146 Four QTL for grain yield under water stress were reported, one of

which was consistent in 3 of the 5 water treatments and one which was detected twice. The largest-

effect QTL identified in this trial explained about 30% of the genetic variance for yield under very

severe stress.146 None of those QTL corresponded to those previously identified in the same population

by Babu et al. (2003). This is a clear example of the problem of QTL x environment interaction poses

in understanding drought resistance.

In a population of 180 recombinant inbred lines resulting from a cross between lowland variety

Zhenshan 97 and upland variety IRAT109, a QTL has been detected in two consecutive years

affecting yield, biomass and harvest index reduction under drought stress in rainout shelter conditions.

The QTL identified in this experiment (located on Chromosome 9 between markers RM316 and

RM219) was consistent and stress-specific, but of relatively small effect, explaining only 14-25% of

the total phenotypic variation.147 A recent QTL mapping experiment identified a QTL explaining 51%

of the genetic variance for grain yield under drought stress in the field at the flowering and grain

filling stages in a Vandana x Way Rarem population at IRRI. This large-effect QTL was consistently


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expressed over two seasons of reproductive-stage drought tolerance and is now being fine-mapped.78

This QTL, which exhibited a low level of QTL x environment interaction, seems to have potential use

in MAS. This is reinforced by the fact that this QTL was also detected, although with a lesser effect, in

another population (IR55419-04 x Way Rarem) constituted from the donor parent, Way Rarem(unpublished data). Trials are currently under way to evaluate the effect of this QTL at multiple

locations in India.

In summary, many drought-related QTL have been reported, but few are replicable over multiple

environments and/or populations. These are major impediments to the implementation of MAS to

improve drought resistance.5, 80 Future research designed to detect QTLs associated with rice drought

tolerance should focus on the detection and fine-mapping of genes with large effects. Such QTL have

been reported recently and could lead to increased use of MAS by drought resistance breeding

programs.

Marker-assisted selection to improve drought resistance in rice

Despite the small number of consistent QTL for use in MAS, a few attempts to introgress drought

resistance QTL into elite varieties have been made.1, 143 Large chromosomal segments corresponding

to QTL associated with root length in a population derived from a cross between the deep-rooted

upland variety Azucena and shallow-rooted lowland variety IR64 were introgressed into the IR64

background. Most of the lines carrying the desired introgressions failed to have deeper roots than

IR64.126 The lack of effect of the QTL-containing segments on root length and yield may be because

those QTL were responsible for a small proportion of the total phenotypic variation (6 to 18%) and

had not been fine-mapped. Those QTL regions were very long and the desirable genes may have been

lost due to recombination during backcrossing. Azucena root-related QTL have also been introduced

into the indica variety Kalinga III, but only one of the five target QTL had an effect on root length and

none had a consistent effect on grain yield under water-limited conditions.127 These results indicate

that only fine-mapped alleles with large confirmed effects on performance under stress are appropriate

targets for MAS.

Molecular marker technology has so far failed to be extensively used as a breeding tool by drought

breeders in any crop, because of the fact that no QTL responsible for a large enough effect on grain


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yield has been discovered and fine-mapped.5 In rice, there are now attempts to employ markers linked

to leaf water potential, spikelet sterility and flowering delay.33 Only five mapping populations account

for most of the drought QTL experiments published to date, most of which were derived from parents

that do not differ widely in their drought resistance characteristics.36

Thus, only a very small fractionof the available rice germplasm has been assayed for alleles that might improve drought resistance. It

is likely that many traditional varieties from drought-prone areas have some resistance to reproductive-

stage drought stress, but such varieties have rarely been used as parents in QTL mapping studies. To

date, the lines used as parents in most QTL mapping studies were derived from indica xjaponica

crosses.51 This was done initially because such diverse crosses were needed to provide adequate

polymorphism for mapping analyses. Presently, a large number of markers are available and more

populations of more agronomically important varieties may be employed as parents.143 A more

extensive survey of drought-resistant rice germplasm will hopefully lead to the identification of linescarrying major genes conferring drought resistance. Such a survey is currently being performed at

IRRI and is yielding encouraging results.78

CONCLUSION

There is a need to develop upland rice varieties that will produce acceptable yields under both water-

limited and favourable environments. Many traits are known to contribute to improving yield under

drought, but the anatomical, physiological, and molecular pathways controlling them are not well

understood. There is now a concerted effort to understand the physiological and genetic basis of

drought tolerance in rice. A better understanding of the genetic basis of drought tolerance will

probably be achieved by using more diverse mapping populations and by precisely identifying the

genes affecting variation in drought resistance through fine-mapping, microarray analyses and

proteomics. Mapping of QTL to identify chromosomal regions improving grain yield under water

limited conditions is hampered by large genetic x environment effects, QTL x genetic background

interactions, the large number of genes affecting yield, and a mistaken initial use of populations

derived from parents that did not differ greatly in drought tolerance. As a result, individual loci withlarge effects on yield under stress have only recently been identified. Characterization of such genes

and their anatomical, physiological, and molecular genetic effects, will be key factors in the

application of molecular marker technology to the development of more drought-resistant upland rice

varieties. This may aid in increasing the food and income security of some of the poorest Asian and

African smallholders.


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Review Breeding Upland Rice for Drought Resistance