Breeding upland rice for drought resistance

Journal of the Science of Food and Agriculture J Sci Food Agric 88:927–939 (2008)

ReviewBreeding upland rice for drought resistanceJerome Bernier,1,2∗ Gary N Atlin,1,† Rachid Serraj,1 Arvind Kumar1 and Dean Spaner2

1International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines2University of Alberta, Edmonton, Alberta, Canada T6G 2R3

Abstract: Upland rice, produced by smallholder farmers, is the lowest-yielding rice production system. Droughtstress is the most severe abiotic constraint in upland rice. Improving productivity of rice in the upland ecosystemis essential to meet rice food security needs of impoverished upland communities. Breeding drought-resistantupland rice is therefore an increasingly important goal. Numerous secondary characters have been suggested tohelp plant breeders in their selections. Most of these traits are not used in selection, as they are not practicalfor selection purposes, exhibit low heritability, or are not highly correlated with grain yield. The use of manageddrought stress, where drought stress can be imposed at specific periods, has been shown to increase the heritabilityof yield under stress to values similar to those obtained for yield in well-watered conditions. It has now beendemonstrated that drought-tolerant upland rice 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 efficientselection 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 nowbeen identified and may enable effective use of marker-assisted selection for drought resistance. 2008 Society of Chemical Industry

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

INTRODUCTIONA definition of drought generally accepted by plantbreeders is: ‘a shortfall of water availability sufficientto cause loss in yield’,1 or ‘a period of no rainfallor irrigation that affects crop growth’.2 Using asimilar definition, it has been estimated that 25%of the fields used for upland crop productionare prone to yield reduction as a consequence ofdrought.3 Drought may occur at any time duringthe growing season and may occur in most yearsin some areas. Plant breeding is only one tool foralleviating drought stress. However, drought-tolerantvarieties developed through plant breeding are moreaccessible to farmers than costly agronomic practicesor irrigation enhancements that may require largeinvestments.4

Rice – one of the most important crops in theworld – has the evolutionary particularity of beingsemi-aquatic. As a result, it has relatively few adap-tations to water-limited conditions and is extremelysensitive to drought stress.5 This paper attempts todefine the current status of breeding for droughtresistance, with a focus on upland rice. The globalimportance of rice, its different production systems,and the economic and social consequences of droughtstress on rice production are briefly reviewed. Themain physiological mechanisms contributing to yieldmaintenance during drought conditions are discussed,

and the breeding methodologies available to uplandrice breeders aiming to improve drought resistance arereviewed.

RICE: ORIGINS AND DOMESTICATIONRice (Oryza sativa L.) is a member of the Poaceaefamily, as are barley (Hordeum vulgare L.), wheat(Triticum aestivum L.), and corn (Zea mays L.). Thereare two species of cultivated rice. Oryza glaberrimaoriginates from West Africa and is presently onlygrown near its center of origin, while O. sativa,which is originally from Asia, is grown on allcontinents.6 In present-day Africa, O. glaberrima hasbeen almost completely replaced by O. sativa. Thisshift may be explained by the low yield potential anddifficulties associated with threshing and milling ofO. glaberrima.7 Some desirable characteristics of O.glaberrima (Steud.) have, however, been introgressedinto O. sativa genetic backgrounds; leading to thedevelopment of the increasingly popular ‘New ricefor Africa’ (NERICA) varieties.8 ‘Wild rice’ (Zizaniapalustris L.) of North America is not in the Oryzafamily, and is thus not a rice species.9 Henceforth,only O. sativa will be considered when referring torice.

There is evidence suggesting that rice was the firstcrop domesticated by humans, in the Yangtze river

∗ Correspondence to: Jerome Bernier, International Rice Research Institute, DAPO Box 7777, Metro Manila, PhilippinesE-mail: [email protected]†Present address : Centro Internacional de Mejoramiento de Maız y Trigo, Apdo. Postal 6-641 06600 Mexico, DF, Mexico(Received 23 March 2007; revised version received 4 October 2007; accepted 5 October 2007)Published online 2 January 2008; DOI: 10.1002/jsfa.3153

2008 Society of Chemical Industry. J Sci Food Agric 0022–5142/2008/$30.00

J Bernier et al.

basin as early as 13 000 years ago.10 The ancestor ofO. sativa is assumed to be Oryza rufipogon, whichis naturally distributed across Asia, from Pakistanto China.6 There are two main ecotypes withinnatural O. rufipogon populations: perennial and annualtypes. Cultivated rice originated from at least twoindependent domestication events, resulting in theindica and japonica ecotypes.11

RICE AND HUMAN NUTRITIONRice is the most important crop directly consumed byhumans. With around 600 Mt produced annually on149 Mha in 2003, rice accounts for 23% of the world’scaloric intake.12 In the same year, wheat was grownon a larger area, 207 Mha, but total production wasslightly lower.13

Most rice (90%) is grown in Asia, where it isestimated to supply 35–60% of the total caloricintake.6 Rice is especially important in the poorestAsian countries, such as Myanmar and Bangladesh,with annual per capita consumption in 2003 of 197and 160 kg, respectively. In the same year, the annualper capita consumption in the United Kingdom was5 kg, with a world average of 54 kg and an Asianaverage of 79 kg.13 Rice-based diets generally providelow iron, zinc and vitamin A intake; these nutrientdeficiencies are therefore common in regions relyingon rice for most of their caloric intake. Biofortificationprograms are underway to improve the nutritionalvalue of rice.12 Africa has roughly 3% of global rice-growing areas and produces a relatively small amountof rice. However, rice is gaining importance on thecontinent, with an increase in consumption of around6% annually.14 Rice production areas are consequentlyexpanding quickly to try to match the demand, butstill more than 40% of the rice consumed in Africa isimported.

Global rice production increased by 130% between1966 and 2000, while the population of low-incomecountries increased by an average of 90% over thesame period.15 The world population is predicted toreach approximately 8 billion by 2030,16 and there istherefore a need to further increase rice production by40% in the next 25 years.

RICE ECOSYSTEMS AND THEIRHYDROLOGICAL STATUSRice ecosystems are generally classified into four types:irrigated, rainfed lowland, deep-water and rainfedupland.9 Irrigated rice is the most common ecosystem,comprising 55% of the global production area. It isalso the most productive system and is responsiblefor 75% of global production. This can partly beexplained by the fact that irrigated rice productiongenerally takes place on well-drained, fertile soils thatare not subject to drought or flooding. More inputssuch as fertilizers are used in irrigated rice than in otherecosystems.6 This system has been the main focus of

the Green Revolution.17 High levels of investment infertilizers by farmers in irrigated systems are profitable,because the risk of crop loss due to drought or watersubmergence is low.

Deep-water rice is planted in areas that are naturallyflooded to depths greater than 50 cm for extendedperiods during the rainy season.9 In most deep-waterfields, seeds are broadcast a few weeks before thebeginning of the rainy (monsoon) season. The plantscan suffer from drought in the early stages of growth,but once the monsoon starts water levels rise andremain high until the end of the growing season. Stemselongate following the rise in water depth, sometimesup to 3 m. This rice ecosystem represents about 8% ofthe total rice cultivation area.6 The main productionareas are the deltas of the Ganges-Bramaputra River ofIndia and Bangladesh, the Mekong River of Vietnamand Cambodia, the Irrawaddy River in Myanmar andthe Chao Phraya River of Thailand.18

Rainfed lowland rice is the second most importantrice ecosystem, representing about 25% of total riceproduction area. Fields do not receive irrigation,relying entirely on rainfall or drainage from higherlands in a watershed. The defining feature of alowland field is the bund that surrounds it, permittingwater from rainfall or drainage from higher fields tobe impounded. Hydrological conditions in differentrainfed lowland fields vary substantially dependingon the position of the field in the toposequence, orsuccession of fields that drain into each other from thetop to the bottom of a rice-producing watershed. Inaddition to the use of bunds to impound water, wateris retained in many rainfed lowland fields throughtillage practices designed to reduce water losses viaseepage and percolation. Fields are often tilled whenwet (puddling), leading to the formation of a hard-panbelow the soil surface. This is desirable as it limitswater seepage, thereby facilitating ponding of water inthe field, but can also limit root growth and access towater stored in the lower regions of the soil profile.19

Finally, rainfed upland rice is grown in unbundedfields where good soil drainage and/or uneven landsurface renders the accumulation of water impossible.6

Upland rice is usually grown in systems wherelittle or no fertilizer is applied, and is direct-seeded into unpuddled, unsaturated soil.20 Mosttraditional upland rice varieties are low-yielding andprone to lodging, but are adapted to non-floodedsoils.21 Upland rice encompasses 12% of global riceproduction area and is generally the lowest-yieldingecosystem.6 Upland rice has a proportionately greaterimportance in Africa and Latin America, where itaccounts for around 40%22 and 45% of the rice-growing areas, respectively.23 In Asia and Africa,upland rice farmers are among the poorest in the worldand their holdings are often less than 0.5 ha in size.24

The situation is different in Latin America since muchof the upland rice production there is mechanized andfarms are larger.25

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Breeding upland rice for drought resistance

Recently, improved upland rice varieties withhigher harvest index, improved input responsivenessand higher yield potential have been developed atIRRI, in Brazil and in several Asian countries.Such ‘aerobic rice’ varieties combine the aerobicadaptations of traditional upland varieties with theinput responsiveness, lodging tolerance and yieldpotential of irrigated varieties.21 Aerobic rice mayreplace irrigated rice and rainfed lowland rice in someparts of the world facing decreasing water suppliesfor agriculture, as is already occurring in northeastChina.26

In the irrigated and deep-water rice ecosystems,water shortage does not normally occur, but in boththe rainfed upland and lowland cultivation systemsdrought stress is often the most important abiotic stressfactor limiting yields.27,28 Rainfed rice fields (bothupland and lowland) within a given watershed usuallydrain into one another from the highest to lowestelevation. The upper fields are the most drought-prone as they do not receive extra water from runoffor seepage from nearby fields.29,30 Upland rice isgenerally more prone to drought than lowland ricebecause water does not accumulate in the field, due tothe lack of a bund or hard-pan layer and, often, due toirregular, sloping topography.2,31,32

IMPACTS OF DROUGHT STRESS ON RICEPRODUCTIONEconomic impactsThe global reduction in rice production due todrought averages 18 Mt annually.17 This abiotic stressis therefore a major constraint to rice productionin water-limited environments. In Asia alone, it isestimated that a total of 23 Mha of rice fields(10 Mha in upland and 13 Mha in lowland) aredrought-prone.33 Drought is a particularly importantproduction constraint in eastern India, with more than10 Mha of drought-prone upland and lowland fields,where yield losses due to drought are reported tocost an average of US $250 million annually. Droughtaffects the poorest farmers disproportionately, causingthem to reduce their food consumption, withdraw theirchildren from school, migrate for employment or sellassets to meet immediate needs. Farmers growing ricein drought-prone environments are well aware of therisks involved and are consequently very reluctant touse expensive agricultural inputs such as fertilizers; thisfurther reduces yield potential in these regions.34 Withdiminishing water supplies for agriculture worldwide,the need to improve drought adaptation of rice isbecoming increasingly important.17

Types of droughtIt is not simply the lack of water that lowersyield potential, but also the timing and duration ofdrought stress related to phenological processes.35

There are three basic drought patterns affectingrice production: early (occurring during vegetative

growth, after establishment but before maximumtillering), intermittent, and late (occurring afterpanicle initiation) drought stresses.2 Early droughtsoften result in delayed sowing or transplanting.Yield reductions from early droughts are oftenminimal and result mainly from a reduction in tillernumbers.36,37 Intermittent or continuous droughts,occurring between the tillering and flowering stages,may greatly reduce yields despite no apparent droughtsymptoms (e.g., leaf rolling), mainly as a result ofreduced leaf expansion and photosynthesis.2 Whendrought occurs during later growing stages, especiallyduring flowering, reduced spikelet fertility is the mainfactor contributing to yield loss.38 Since the diversedrought patterns have different impacts on the crop, itis important to define which type of drought stress istargeted by a breeding program.2

MITIGATING THE IMPACT OF DROUGHT:POTENTIALLY USEFUL TRAITSRice is a notoriously drought-susceptible crop duein part to its shallow root system, and rapidstomatal closure and leaf senescence during mildwater stress.39 Rice, like other crops, can potentiallyresist drought stress using three different strategies:drought escape, drought avoidance, or droughttolerance. A proper timing of the life cycle, resultingin completion of the most sensitive developmentalstages while water is abundant, is considered tobe a drought escape strategy.40 Drought resistancemechanisms that are expressed even in the absenceof stress, such as deep rooting, are considereddrought avoidance mechanisms. Drought tolerancemechanisms are triggered by drought stress itself andare considered adaptative.41 Rice varieties possessingdrought avoidance and tolerance mechanisms arerequired in situations where the timing of droughtis mostly unpredictable.40 When stress is predictableand terminal, varieties that can escape drought bymaturing early may be the most appropriate choice forrice producers.

Drought escape through short duration varietiesIn drought-prone upland areas of eastern Indiaand Bangladesh, drought escape is an importantmechanism that allows rice to produce grain despitelimited water availability.6,41 In this region, the onsetof the rainy season is generally in June, and withdrawalcan occur as early as late September. Short-durationvarieties of the aus germplasm group are commonlyused in upland fields in this region,41 some ofwhich can reach maturity in as little as 80 days.6

Such varieties usually escape terminal drought, butthey are not necessarily drought-resistant. It shouldbe noted, however, that some aus varieties alsohave drought-resistant characteristics. The aus groupcomprises varieties adapted to the entire range of riceecosystems and may be used from irrigated to drought-prone upland fields.42 Short-duration varieties also

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occur within the tropical japonica germplasm group;these varieties are particularly important in rice-producing areas in West Africa and include drought-avoidant varieties such as WAB56-140, which wasused as a recurrent parent to produce some NERICAvarieties.43,44

Drought avoidance through deeper rootdistributionCompared with that of other cereal crops, it is clearthat the root system of rice is very poorly adaptedto water-limited conditions. Sorghum and rice canextract about the same amount of water from thetop 60 cm of soil. However, rice extracts little or nowater from below 60 cm, while sorghum maintainswater extraction potential at much greater depths.45 Adeeper root system has been shown to allow uplandrice to extract more water from the soil, resulting ina higher yield potential under drought46 and varietieswith a high deep-root weight to shoot weight ratioexhibit enhanced drought resistance in upland rice.2

The improvement of upland rice through a deeperroot system is thought by many to be a promisingway to increase water uptake, and ultimately grainyield, under drought stress conditions.2,46,47 Thecontribution of root depth to drought avoidancemay be site-specific, however, as the subsoil is ofteninhospitable to root growth due to unfavorable pHor nutrient deficiencies.48 Other root characteristics,such as increased xylem vessel size and root thickness,could also potentially improve water uptake.49,50

In addition to the drought avoidance benefits asso-ciated with the improved access to water associatedwith deeper roots, there is strong evidence from otherspecies that a reduction of root density in fast-dryingupper soil levels has resulted in reduced drought sen-sitivity. In maize, a 40% increase in yield under severestress resulting from eight cycles of recurrent selectionin a tropical population was associated with a 35%reduction in root mass within 0.5 m the soil surface.51

It is likely that a reduction in root biomass nearthe soil surface reduces root signals associated withintermittent soil drying, reducing premature stomatalclosure and reduced transpiration in response to mildstress.52

The ideal upland rice root system is thought to becomposed of deep roots with large xylem vessels, whichwould be capable of extracting water from the deepsoil layers.2,53 Irrigation in an upland rice screeningnursery can be managed so as to exert selectionpressure for root systems of this type. Infrequentirrigations that completely saturate the soil to a depthof 1 m or more, followed by extended periods of dryingthat result in low soil water potential in the upper 0.3 mbut conditions at or near field capacity in deeper layers,are preferable to frequent irrigations that only wet theupper soil layer.

Drought avoidance through stomatal controlOne basic mechanism for reducing the impact ofdrought is early stomatal closure at the beginning

of a period of water deficit. Stomatal closure reduceswater loss, but also reduces gas exchange betweenthe plant and the ambient air. The reduced CO2

intake then results in reduced photosynthesis.54,55 Thismechanism improves plant survival under droughtstress, but is also associated with yield reduction.1

Early stomatal closure may be desirable under somecircumstances, but not where droughts are short,frequent, and relatively mild. Regulation of stomatalconductance is very complex and poorly understood,but thought to be mainly a consequence of leaf cellresponse to water deficit, and, to a lesser extent, aconsequence of low root water status communicatedto the leaf via abscisic acid (ABA) signaling.56,57

Significant genetic variation for the sensitivity ofstomata to leaf water status has been reported inrice.58

In C3 species, carbon isotope discrimination(CID) is positively correlated with the ratio ofleaf internal CO2 leaf concentration to ambientair CO2 concentration,59 and this provides anintegrated measurement of transpiration efficiency.60

Higher CID generally indicates that stomata remainedopen for a greater proportion of the growingperiod.61,62 Plants with high CID tend to have higheryields in rainfed or irrigated environments becauseincreased transpiration enables increased biomassaccumultion.63 Under dryer conditions, ‘conservative’plants that grow more slowly and have a lower stomatalconductance (hence lower CID) may perform betteras they achieve a larger biomass accumulation pergram of water transpired.62,64 The ideal CID valuetherefore depends on the environment in which theplant is growing. In rice, because stomata tend to closeat relatively low levels of stress, enhancement of yieldin drought-prone environments seems more likely toresult from selection for high than for low CID. This isconsistent with unpublished data gathered up to nowat IRRI.

Drought tolerance traitsStability of flowering processesDrought stress at the beginning of the reproductivestage usually results in a delay in flowering in rice.65

This is mainly due to slowed elongation of the panicleand supporting tissues.5 This trait can be an effectivedrought avoidance mechanism if the period of waterdeficit is short, as panicle elongation resumes followinga brief period of stress. However, if flowering is delayedby more than a few days, severe yield losses usuallyoccur. It appears that rice has a predetermined amountof time when peduncle elongation can proceed andthat anthesis follows about a day thereafter. Slowpanicle elongation means that anthesis may occurwhile part of the panicle is still within the leafsheath.38 Unexerted spikelets are often sterile.66 It hasbeen reported that the greater the delay in flowering,the greater the yield and harvest index reductiondue to drought.40 Improving drought resistance maytherefore involve selection of plants exhibiting little



or no flowering delay due to drought.40,67 Thereis considerable genetic variation for flowering delayunder stress; some short-duration varieties actuallyexhibit accelerated flowering under drought stress.67,68

For production using water-saving irrigation methodsor for upper-toposequence rainfed fields that arefrequently dry, varieties that do not exhibit floweringdelay under non-saturated soil conditions could be animportant and achievable breeding objective.

Partitioning and stem reserve mobilizationAs photosynthesis becomes inhibited by drought, thegrain-filling process becomes increasingly reliant onstem reserve utilization.69 This drought tolerancemechanism is stimulated by a decrease in gibberellicacid concentration and an increase in abscisic acidconcentration in grains.70 Numerous studies havereported that stem reserve mobilization capacity isrelated to yield under water stress in wheat. In rice, afew studies also suggest that this mechanism maintainsgrain yield under water stress at the grain-fillingstage.70–72

BREEDING FOR DROUGHT RESISTANCE INUPLAND RICEProgress to date in breeding for droughtresistanceRice breeding programs focusing on drought resistancehave made little progress to date.2 This may beexplained by the fact that drought resistance is a traitcontrolled by many genes having different effects, andis affected by drought timing and severity. Another wayto explain the complexity of drought is that droughtresistance involves an interaction between the genesinvolved in yield potential per se (which are numerous)and the genes for drought resistance.1 However, muchof the reason for the lack of progress in rice canbe explained simply by the lack of investment thathas been made in screening for drought tolerancein variety development programs.17 Few programsexplicitly incorporate a drought tolerance screeningstep as part of their routine breeding activity, despitethe considerable effort that has been made on thegenetic and physiological analysis of traits thoughtto be related to genotypic differences in droughttolerance.

Modern plant breeding has been more successfulin favorable growing conditions than in unfavorableconditions.73,74 A study of 18 maize hybrids releasedby Pioneer Hi-Bred between 1953 and 2001 grownunder well-watered control conditions and fivedrought treatments confirmed this in maize. The rateof yield gain over 50 years of varietal developmentwas 189 kg ha−1 yr−1 under well-watered conditions.Under conditions of drought at flowering, yield gainswere also high (146 kg ha−1 yr−1). Conversely, yieldimprovements were no greater than 47 kg ha−1 yr−1

under four other simulated drought stress treatments(early-fill, mid-mill, late-fill, terminal drought).4

Similarly, improved rice varieties responsive to highlevels of inputs have been available to irrigated ricefarmers for a long time, but rainfed rice varieties havebeen little improved for drought tolerance and otherabiotic stresses. Many rainfed rice farmers still usetraditional low-yielding varieties.75,76

Selecting for drought-resistant upland riceIn most upland rice environments, droughts areunpredictable and do not occur every year. Farmersare not likely to be willing to sacrifice yield potentialfor greater yield in drought years. Plant breedersmust therefore select varieties capable of producingrelatively high yields in both favorable and unfavorableyears. Selection criteria needed to obtain high yieldsunder both stress and non-stress environments havebeen debated by breeders for decades.77 There arethree major breeding targets that may result inimproved grain yield under drought: increasing yieldpotential per se, timing flowering with periods whenwater is available, and improving drought resistance.78

Screening for increased yield potential is generallyperformed under ideal conditions. Such selectionenvironments will serve to improve yield underdrought if yield under drought and yield underwell-watered conditions are positively correlated.This is usually the case under mild and evensevere drought conditions in rice.67,79,80 Atlin et al.79

reported that even when the mean yield differencebetween stress and non-stress treatments is over50%, genotype means tend to be positively correlatedacross yield levels in populations of unselectedrecombinant inbred lines. This is because largedifferences among genotypes in height and harvestindex are often expressed in both stress and non-stress environments.79 Selection for yield potential istherefore an important element in developing varietiesthat produce acceptable yields under moderate levelsof stress.

Selecting genotypes that complete flowering beforethe onset of water stress is possible if the timingof drought is predictable and terminal. This is thecase for late-season stress in many areas where themonsoon 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 aroundflowering, occur unpredictably during the middle ofthe monsoon. Drought-resistant varieties are essentialin these areas.

Drought resistance is improved either if the crop isable to access more water or if it can use available watermore efficiently (higher transpiration efficiency).48

Selection for drought resistance can be performedby measuring yield under stress conditions and/ormeasuring a secondary character correlated with yieldunder stress conditions. A secondary trait is only usefulin breeding if it is inexpensive to measure, highlycorrelated to yield under drought and if it shows higherheritability than that of yield itself under stress.81


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Direct selection for yield under drought stressDirect selection for yield under favorable or water-limited conditions is the most commonly usedselection strategy used by cereal breeders to improveyield in water-limited environments.73,82 This methodhas not been widely used in rice until recently, butis now increasingly so, as drought resistance is beingrecognized as an important trait to improve in rice.2,17

Despite its increasing use, direct selection for yieldunder drought conditions poses problems; establishinguniform and repeatable drought stress in the field isdifficult and, at most screening sites, rainfall can alwaysoccur at undesirable moments, even during the dryseason.34 In upland rice, the application of manageddrought stress usually enables clear differentiationbetween resistant and susceptible lines on the basis ofyield only if yields are reduced by at least 70–80%relative to unstressed levels. At less severe stresslevels, yields may be more highly correlated withyield potential than with drought resistance.80 Recentstudies in upland rice conducted under artificiallyimposed stress in the dry season at IRRI demonstratethat yield under drought stress that is consistentlyand uniformly applied is usually as heritable as yieldestimated under non-stress conditions. When stressis very severe, H may even be higher under stress,with relatively little genotype × year interaction.67,79,80

Direct selection for yield under stress has been shownto result in significant gains in upland rice stresstolerance.80 Direct selection for yield under managedstress, when combined with concurrent selectionfor yield potential, is an effective and underutilizedapproach to developing stress-tolerant upland ricevarieties.

Secondary traits most commonly used by rice breedersCombining selection based on yield with secondarytraits into selection indices can improve selectiveresponse, if the physiological processes contribut-ing to grain yield in the target environment arewell understood and if the secondary traits canbe repeatably and inexpensively measured.73,83 Sec-ondary traits most commonly used by breeders aregenerally easily determined visually. The number ofdays to flower is normally measured under bothstress and non-stress conditions. Selection may beperformed for lines with ideal maturity dates inwell-watered conditions and no large flowering delayunder drought. Selection for lines that maintain ahigh spikelet fertility under drought stress and/or alow rate of leaf drying under drought stress is alsocommon.37,83 Flowering delay and spikelet fertilityhave both been reported to have moderate heritabili-ties and a high correlation with grain yield under stressat flowering.83

Other secondary traits that could be used in selectionSeveral authors have suggested that carbon isotopediscrimination (CID), an indirect but integrativemeasure of season-long stomatal conductance, could

be an effective selection criterion for grain yield underdrought.62,84–87 In wheat, grain yield was reportedto be positively correlated to stem CID in southernAustralia (r = 0.51–0.65)88 and to grain CID inSyria (r = 0.5),89 southern France (r = 0.44–0.70),86

and Spain (r = 0.5).90 Under the dry conditions ofnorthwest Mexico, high correlations were measuredbetween grain CID and yield in water treatmentssimulating post-anthesis water stress (r = 0.88 and0.89) and residual moisture conditions (r = 0.50and 0.66).62 At IRRI, positive or non-significantrelationships between grain CID and grain yield underdrought stress at flowering and grain-filling stages havealso been observed (unpublished).

Negative correlations between CID and grain yieldhave also been reported in some environments.62,91

Those are likely to occur in situations where cropsare grown on residual soil moisture.92 Under suchconditions, plants with a high CID may consumethe available soil water too quickly within theseason. Selection based on CID therefore requiresa solid understanding of the target environment.A backcross breeding program in Australia hasintroduced improved transpiration efficiency of thewheat variety Hartog by using Quarrion as a donor andselecting for lines with low CID (hence high water-use efficiency).93 Interestingly, CID measurementswere done using young plants growing under well-watered conditions and the desirable plants (thosewith low CID) were used for backcrossing. Thisresulted in the release of the drought-resistant wheatvariety ‘Drysdale’, which outperformed the local checkvariety by up to 40% under very dry conditions.93 Suchexamples have not occurred in rice to date.

Leaf or grain ash (mineral) content has beenproposed as an alternative selection criterion foryield under drought, thereby avoiding the high costof CID analysis.62,94 As most minerals are mainlytransported passively in the xylem and accumulatedin transpiring plant tissues, greater transpirationconsequently increases the amount of passivelytransported minerals into the leaves. Correlation wasfound between CID, leaf ash content, and grain yieldin different C3 species. In wheat, grain ash content waspositively correlated with grain yield under droughtstress, with correlation coefficients varying from 0.56to 0.9484,86 and with broad-sense heritabilities higherthan that of yield itself (H = 0.69 for grain ashcompared to H = 0.53 for yield).84 However, otherstudies failed to identify a significant associationbetween grain yield and grain ash content, but founda significant relationship with leaf ash content underflowering and grain-filling drought stress (r = 0.62 and0.68).62 No significant relationship between grain yieldand either leaf or grain ash content were identifiedunder pre-anthesis and residual moisture stresses.Despite encouraging results concerning the feasibilityof using ash content for selection, this trait has notbeen used to produce drought-resistant varieties in



any crop up to now, possibly due to the irregularity ofrelationships between grain yield and ash content.

Leaf water potential (LWP) under stress conditionsis a secondary trait presently employed by theThai rainfed lowland rice breeding program.37 Thismeasure is strongly correlated with spikelet sterilityunder drought stress and is less influenced bytiming of stress than spikelet sterility.35 Leaf waterpotential has been reported to have a relatively highcorrelation with grain yield (r = 0.69) when droughtstress was applied around flowering in an upland riceexperiment. Heritability values were not reported. Amajor limitation of LWP is that it is laborious tomeasure, with the result that only a small numberof lines can be tested at a time.35 The use ofLWP as a selection criterion in breeding programsis therefore limited to advanced generations, wheresmall population sizes, and consequently low possibleselection intensities, make it unlikely to achieve muchselection response.

Root characteristics are not widely used as secondaryselection traits by breeders because the root systemis difficult to study.95 Apart from contributingto drought avoidance, selecting for a better rootsystem could also improve weed competitivenessand nutrient absorption potential of upland rice.48,96

Most breeding programs are unable to select directlyfor root phenotypes, due to the high cost of suchscreening. However, as noted above, screening trialsand nurseries can be managed so as to exert selectionpressure for deep rooting by irrigating the soil profileto saturation at depth, then allowing stress to developover a long irrigation-free period wherein upper soillayers dry quickly, but lower layers retain plant-available water. Indirect selection for improved roottraits via marker-assisted selection (MAS) would alsobe feasible in theory, but success has so far been limited(see discussion on MAS below).97,98

When breeding for drought tolerance at the grain-filling stage, it has been suggested that breedersselect for plants with a high capacity to remobilizenon-structural carbohydrate stored in stems. This isroutinely done in some wheat breeding programs,78,99

but to our knowledge this selection criterion is notused by rice breeders. This may be due to the possiblenegative association between stem reserve storageand yield potential or lodging resistance, or to theimpossibility of combining this trait with resistance toleaf drying (stay-green).69

In farmers’ fields, the crop is not the only sourceof water loss. Evaporation of water from the surfaceof the soil, and water uptake by weeds, both serve tolimit the amount of water available for crop growth.48

Selecting for early leaf area production would increasecrop competitiveness against weeds and reduce soilevaporation, thereby indirectly contributing to droughtavoidance. This will be effective as long as it does notlead to excessive biomass production requiring morewater than is available at flowering.

Maximizing efficiency of drought resistancebreeding programsGiven the complexity of drought, there has beenmuch debate over the design of efficient droughtresistance rice breeding programs.77,82,100,101 Equa-tion (1) can be used to compare the efficacy of differ-ent breeding program designs and patterns of resourceallocation.100 Any breeding program can be consid-ered a form of indirect selection, wherein correlatedresponse in the target environment (CRT) results fromselection in some other environment (i.e., the nurs-eries and trials of the breeding program). Correlatedresponse depends on the selection intensity (i), thecorrelation between yields in the environment wherethe selection occurs and the target environment (rG)and the broad-sense heritability in the selection envi-ronment (Hs).

CRT ∝ i • rG • √Hs (1)

Careful management of yield trials so that theyreflect the conditions in which the farmers will begrowing the crop once a variety is released willmaximize rG. If a breeder wants to screen for resistanceto a stress that does not necessarily occur everyyear, the stress may have to be artificially imposedin the breeding environment. In the case of droughtresistance of upland rice, this can be achieved in somelocations by performing yield trials during the dryseason, with irrigation supplied to mimic droughtconditions. Dry season drought screening resultsmust be interpreted cautiously because off-seasonphotoperiod, solar radiation intensity, temperature,evaporative demand, and disease pressures oftendiffer from those characteristic of the wet season.However, there are locations (IRRI among them) inseveral South and Southeast Asian countries where dryseason conditions are suitable for drought screening.80

Rice breeding programs that have prioritized droughttolerance as an upland rice breeding objectiveshould develop an appropriate screening environment.An important element in developing a managed-stress screening system for drought tolerance isdemonstrating that the screen is predictive of resultsthat would be obtained in farmers’ fields undernaturally occurring stress in the wet season. At IRRI,recent selection studies under managed stress in thedry season exhibited heritability values averaging 0.39under drought stress, which is comparable to theaverage of 0.43 obtained under non-stress conditions(Table 1). Lines selected under managed droughtstress were shown to have a significantly higheryield under natural drought stress conditions thanunselected lines.80

Some plant breeders have suggested that breed-ing programs aiming to improve yields under sub-optimal environments (e.g., drought stress) couldconduct their screening only in high-yielding envi-ronments (e.g., well-watered fields). This wouldresult in a decrease in rG, but could increase


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Table 1. Comparison of heritability measured for grain yield under upland drought stress and non-stress conditions using different populations at

IRRI

PopulationRelative yield under

drought Stress H Non-stress H Source

Apo × IR64 0.17 0.23 0.46a Venuprasad et al.80

Apo × IR72 0.33 0.24 0.67a Venuprasad et al.80

Vandana × IR72 0.36 0.1 0.42a Venuprasad et al.80

IR64∗2/Azucena 0.16 0.43 0.33a Venuprasad et al.80

Vandana × Way Rarem 0.12 0.7 0.23 Bernier et al.67

IR55419-04 × Way Rarem 0.08 0.66 0.48 Kumar, unpublishedAverage 0.20 0.39 0.43

a Indicates that the non-stress trials were performed under transplanted lowland conditions.

Hs.79 Caution should be observed with this breed-ing method, as crossover interactions between thosetwo types of environments are commonly observedand progress in improving drought tolerance is usu-ally slower than using direct selection in unfavor-able environments.101–103 Recent studies suggest thatresponse to selection for yield in low-yielding envi-ronments is greater when selection is performed in alow-yielding environment than in a high-yielding envi-ronment in both rice80 and maize.82 If there is a highcorrelation between yields in stress and non-stressenvironments, breeding for improved yields underwater stress can also result in selection response underfavorable conditions.79 If a breeder wants to develop avariety that will yield well under both drought-stressedand non-stressed conditions, selection based on anindex of performance in both environments will be themost efficient selection criteria.77 It should be noted,however, that an unweighted average of mean yields instressed and non-stressed environments is not usuallythe most effective index, because lower means andgenetic variances in stress environments will result ina heavier weighting of means from non-stress environ-ments, even if H is the same in both screens. If equalweights are desired for stress and non-stress envi-ronments, selection should be based on standardizedmeans.

USE OF MOLECULAR MARKERS TO IMPROVEDROUGHT RESISTANCEA quantitative trait locus (QTL) is a chromosomalregion where one or more genes affect phenotypic val-ues of a quantitatively inherited trait such as grainyield or plant height.104 A QTL is detected bycorrelating phenotypic values of lines with differentmarker genotypes at a given chromosomal location(locus).105 There are three steps to QTL analysis:(1) phenotypic evaluation of a relatively large numberof plants from a population segregating for polymor-phic genetic markers; (2) genotyping part or all thepopulation; (3) statistical analyses to identify the locithat are affecting the trait(s) of interest.106 Such map-ping studies are performed to detect tight linkage of amolecular marker to a gene of interest. It then becomespossible to select for those desirable genes based on

marker genotype rather than field phenotype.35 Thistechnique, known as marker-assisted selection (MAS),is theoretically more reliable than selection based solelyon phenotype, as a marker tightly linked to the desir-able gene would represent selection with a heritabilityof near unity for that specific gene.107 Marker-assistedselection may be useful to improve traits that areeither controlled by a few genes or where phenotypicevaluation is difficult/costly to perform. The relativedifficulty associated with drought resistance phenotyp-ing suggests that there is scope for the use of MASin breeding for drought resistance.107 However, prob-lems such as the lack of identified QTL with largeeffects, as well as QTL × environment and QTL ×genetic background interactions, have thus far pre-vented widespread adoption of MAS by rice breedersinterested in drought resistance.

Identification of drought-related QTLDrought-related QTL have been mapped in a largenumber of crops including maize, barley, wheat,sorghum, cotton (Gossypium hirsutum L.) and Brassicaoleracea.108–113 In rice, QTL related to nearly allpreviously listed secondary drought resistance traitshave been identified.5 One study identified QTLfor leaf rolling and stomatal conductance.58 Anothergroup identified 28 QTL related to numerous roottraits.114 A third one compared the location of QTLlinked to root traits and OA. This experiment reported36 QTL related to root traits and five related toOA and concluded that these two drought resistancemechanisms are independent of each other.115 Someof the QTL identified corresponded to QTL previouslyidentified in other rice populations, and to QTLlocated in the corresponding syntenic regions in barleyand maize. However, co-location of QTL for root-related traits across populations or environments israre, due in part to generally large QTL × environmentinteraction affecting root traits. This constitutes asubstantial problem for using markers in selecting forimproved root phenotypes.116

Quantitative trait loci for yield and yield componentsunder different types of drought stress have alsobeen reported. The population CT9993/IR62266 wasused to perform QTL mapping for grain yield underdrought stress under upland conditions in southern



India31 and lowland conditions in eastern India117 andThailand.118 In southern India, five QTL related tograin yield were identified over two different trials. Onetrial consisted of a severe stress applied towards theend of the vegetative stage, while in the other stress wasmild, but applied at the flowering stage. The QTL withthe largest effects explained approximately 20% and28% of the genetic variation for yield in the vegetativeand reproductive-stage stress trials, respectively, butnone of the yield QTL observed were consistentacross trials.31 In eastern India, the same populationwas evaluated for 2 years under transplanted lowlandmanagement under severe stress. A single large-effectQTL affecting grain yield under stress conditions, butnot in the irrigated control, was detected at 206 cMon chromosome 1, between markers EM11 11 andRG109.117 This locus explained 32% of the geneticvariation for yield under stress over the 2 years,therefore explaining virtually all of the genetic variationfor yield under stress that was not associated with yieldpotential under non-stress conditions or phenology.The experiment performed in Thailand was doneusing five different water treatments in a transplantedtrial under line-source irrigation.118 Four QTL forgrain yield under water stress were reported, oneof which was consistent in three of the five watertreatments and one which was detected twice. Thelargest-effect QTL identified in this trial explainedabout 30% of the genetic variance for yield under verysevere stress. None of those QTL corresponded tothose previously identified in the same population byBabu et al.31 Overall, there was little correspondenceof QTL detected in the three experiments. This is aclear example of the problem QTL × environmentinteraction poses in understanding drought resistanceand breeding drought-tolerant rice cultivars; geneeffects are likely to be specific to particular hydrologicalenvironments and stress levels.

If MAS-based approaches to improvement of ricecultivars for drought tolerance are to be practical, itis likely that they will be based on the introgressionof alleles with large, additive effects on yield understress. Quantitative trait loci with these characteristicshave been recently reported by several groups. In apopulation of 180 recombinant inbred lines resultingfrom a cross between lowland variety Zhenshan 97and upland variety IRAT109, a QTL was detectedin two consecutive years affecting yield, biomass,and harvest index reduction under drought stressin rainout shelter conditions. The QTL identified inthis experiment (located on chromosome 9 betweenmarkers RM316 and RM219) was consistent andstress-specific, but of relatively small effect, explainingonly 14–25% of the total phenotypic variation.119

Another recent QTL mapping experiment identifieda yield-enhancing drought resistance QTL with thelargest effect to date in rice.67 This QTL (locatedon chromosome 12 between markers RM28048 andRM511) explained 51% of the genetic variance forgrain yield under drought stress in the field at the

flowering and grain-filling stages in a populationderived from a cross between the tolerant easternIndian variety Vandana and the susceptible Indonesianvariety Way Rarem at IRRI. This large-effect QTLwas consistently expressed at IRRI over two seasonsof reproductive-stage drought stress. A subsampleof the population was subsequently tested underupland drought stress in India and the QTL hada large and significant effect in two of the threelocations tested (unpublished). This demonstrates alow QTL × environment interaction under severeupland stress, indicating its potential usefulness forMAS. This QTL was also detected, although with amuch lesser effect, in another population (IR55419-04/Way Rarem) constituted from the donor parent,Way Rarem (unpublished data), raising hopes thatthis locus may contribute to drought resistance overa range of genetic backgrounds. It remains to be seenwhether introgressing the Way Rarem allele of thislocus into other genetic backgrounds will result inlarge and replicable increases in drought resistanceunder upland conditions. This hypothesis is currentlybeing tested at IRRI using a wide variety of cultivarsas recurrent parents. Fine-mapping is also under way,which will facilitate the introgression process.

In summary, many drought-related QTL have beenreported, but few are replicable over multiple environ-ments and/or populations. This lack of repeatability isa major impediment to the use of MAS to improvedrought resistance.5,68 Future research designed todetect QTL associated with rice drought toleranceshould focus on the detection and fine-mapping ofgenes with large effects. Such QTL have been reportedrecently and could lead to increased use of MAS bydrought resistance breeding programs.

Marker-assisted selection to improve droughtresistanceDespite great expectations, MAS has so far largelyfailed to deliver a useful way for plant breeders toimprove drought resistance. A notable exception canbe found in sorghum, where QTL related to the‘stay-green’ trait have received considerable attention.Stay-green is a trait similar to reduced leaf drying inrice. In sorghum, it has been demonstrated that linesmaintaining green leaves the longest under drought areable to accumulate more biomass and consequentlyproduce greater yields.120 Hybrids possessing the stay-green trait have yielded up to 50% more under post-flowering drought-stress compared to similar hybridsthat did not possess this trait.121 Numerous QTLhave been found to affect this trait, but four of them(explaining most of the genetic variation for the trait)seem to be relatively stable across both environmentsand genetic backgrounds.122 Stay-green QTL havebeen fine-mapped and are now used to improvedrought resistance of popular sorghum lines via MAS.

In rice, despite the small number of consistentQTL for use in MAS, a few attempts to introgressdrought resistance QTL into elite varieties have


J Bernier et al.

been made.1,114 There have been attempts to employmarkers linked to leaf water potential, spikelet sterilityand flowering delay for MAS.37 Most effort toimprove drought tolerance of rice through MAShas been devoted to the use of root-related QTL.Large chromosomal segments corresponding to QTLassociated with root length in a population derivedfrom a cross between the deep-rooted upland varietyAzucena and the shallow-rooted lowland varietyIR64 were introgressed into the IR64 background.Most of the lines carrying the desired introgressionsfailed to have deeper roots than IR64.97 The lackof effect of the QTL-containing segments on rootlength and yield may be because those QTL wereresponsible for a small proportion of the totalphenotypic variation (6–18%) and had not beenfine-mapped. Those QTL regions were very longand the desirable genes may have been lost due torecombination during backcrossing. Azucena root-related QTL have also been introduced into theindica variety Kalinga III, but only one of the fivetarget QTL had an effect on root length and nonehad a consistent effect on grain yield under water-limited conditions.98 These results indicate that onlyfine-mapped alleles with large confirmed effects onperformance under stress are appropriate targetsfor MAS.

Part of the reason for the limited success ofefforts to use molecular marker technology for ricedrought tolerance improvement is likely that sam-pling of the genetic variability within O. sativahas been inadequate. Only four mapping popula-tions (CO39/Moroberekan, CT9993/IR62266, Azu-cena/Bala and IR64/Azucena), all derived fromindica by japonica crosses, account for most of thedrought QTL experiments published to date. Inmost of those populations, the parents used werenot highly drought-tolerant. Thus, only a smallfraction of the available rice germplasm has beenassayed for alleles that might improve drought resis-tance. It is likely that many traditional varietiesfrom drought-prone areas have some resistance toreproductive-stage drought stress, but such varietieshave rarely been used as parents in QTL map-ping studies. The initial use of mapping populationsderived from indica by japonica crosses was neces-sary to provide adequate polymorphism for mappinganalyses.50 Presently, a large number of markersare available and more populations of more agro-nomically important varieties may be employed asparents.114 A more extensive survey of drought-resistant rice germplasm will hopefully lead to theidentification of lines carrying major genes confer-ring drought resistance. Such a survey is currentlybeing performed at IRRI and is yielding encouragingresults.67

CONCLUSIONThere is a need to develop upland rice varieties thatwill produce acceptable yields in both water-limitedand favorable environments. Many traits are knownto contribute to improving yield under drought, butthe anatomical, physiological, and molecular pathwayscontrolling them are not well understood. There isnow a concerted effort to understand the physiologicaland genetic basis of drought tolerance in rice. A betterunderstanding of the genetic basis of drought tolerancewill probably be achieved by using more diversemapping populations and by precisely identifying thegenes affecting variation in drought resistance throughfine-mapping, microarray analyses and proteomics.Mapping of QTL to identify chromosomal regionsimproving grain yield under water-limited conditionsis hampered by large genetic × environment effects,QTL × genetic background interactions, the largenumber of genes affecting yield, and the initial useof only a few populations derived from parents ofsimilar drought resistance, defined as yield under waterdeficit. As a result, individual locus with large effectson yield under stress have only recently been identified.Characterization of such genes at the physiological andmolecular level will be key factors in the applicationof molecular marker technology to the development ofmore drought-resistant upland rice varieties. This mayaid in increasing the food and income security of someof the poorest Asian and African smallholder farmers.

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Breeding upland rice for drought resistance