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Chapter 7

Genetics Options for Improving theProductivity of Wheat in Water-Limited andTemperature-Stressed EnvironmentsR.M. Trethowan and T. Mahmood

Introduction

Predicted climate change will reduce the capac-ity of agricultural systems to maintain and in-crease food production. However, there will beboth limitations and opportunities for agricul-ture in this changing scenario. While crop pro-duction in some environments will decrease dueto increased temperature, water shortages, andgreater climate variability, other regions, par-ticularly those at higher latitudes, will benefitfrom the shift in temperature and increased lev-els of CO2. However, when combined with waterstress, it is more difficult to predict plant responseas elevated CO2 both increases water use by in-creasing leaf area and reduces water use by re-ducing stomatal conductance (Cure and Acock1986). Nevertheless, the productivity of food-producing regions closer to the equator, wherethe bulk of the world’s poorer population live,will need to be maintained or stabilized in achanging climate to avoid significant unrest anduncontrolled migration to less affected areas.

Wheat and rice are the primary foodstuffs ofthe world, providing the major share of calories

to vast numbers of poor people (Roberts andSchlenker 2009). Improving the stress toleranceof these vital crop species, in conjunction withimproved agronomic practices and enabling gov-ernment policies, will reduce the impact of cli-mate change. This chapter will focus on wheat,a crop grown on more than 200 m ha world-wide, producing in excess of 600 m tones annu-ally (USDA 2010), and a staple food for 35%of the world’s population (Shao et al. 2006).Wheat is particularly important in a changingclimate because it already has a broad adap-tive range and can be found from the equatorto 60◦N and from sea level to more than 3000 min altitude (Slafer and Satorre 1999). The geneticdiversity available in farmers’ fields, in centersof origin and diversity, in plant breeding pro-grams, and in gene banks is examined in thischapter with particular reference to wheat. Theextent of our knowledge of the genetic controlof moisture and temperature stress tolerance andstrategies to increase rates of genetic gain foryield in a more hostile cropping environment arediscussed.

Crop Adaptation to Climate Change, First Edition. Edited by Shyam S. Yadav, Robert J. Redden, Jerry L. Hatfield,Hermann Lotze-Campen and Anthony E. Hall.c© 2011 John Wiley & Sons, Ltd. Published 2011 by John Wiley & Sons, Ltd.

218



GENETICS OPTIONS FOR IMPROVING THE PRODUCTIVITY OF WHEAT 219

Traits that influence plantresponse to drought and hightemperature

Crop establishment and early growth

Vigorous early crop growth tends to reduceevaporative loss of water from the soil surfaceand suppresses weeds, thus reducing compe-tition for water. Plants that rapidly cover theground tend to have thinner, wider leaves withlower specific leaf weight and a more prostrategrowth habit (Richards 1996; Richards et al.2001, 2002). Richards and Lukacs (2002) alsosuggested that larger seed and embryos con-tribute to improved early vigor. Vigor is likelyto be useful in environments subject to terminalstress as early biomass coverage reduces waterloss and promotes biomass production (Reynoldset al. 2007a). However, in environments wherecrops are grown on stored soil moisture, earlybiomass development could be a disadvantage.In these environments, longer coleoptiles willtend to offer an advantage as seeds could besown deeper, thus taking advantage of moisturedeeper in the soil profile (Trethowan et al. 2005).When grown under combined drought and hightemperature stress, plant growth and leaf areaof wheat is reduced, thus reducing transpira-tion and soil water loss (Machado and Paulsen2001). Clearly, increasing the temperature toler-ance of wheat would also improve its water-useefficiency.

Root growth and water uptake

Plant breeders have made significant progressin improving above ground traits in most crops,with largely indirect progress on below groundtraits. Nevertheless, a more water-efficient rootsystem will improve grain yield and productivityof crop species such as wheat, although a moreefficient root system is not necessarily larger ormore extensive. Reynolds et al. (2007b) foundthat the yield advantage of synthetic-derivedwheat over their adapted parents was due to

greater investment in root biomass at depth, notin overall increase in total root biomass. Rootsare difficult to measure, and indirect assessmentsare necessary if genetic progress in root archi-tecture and physiology are to be realized. Traitslinked to water status or temperature tolerancecan be useful indicators of root characteristics,and these include measures of relative leaf watercontent, stomatal conductance, and canopy tem-perature (CT) (Reynolds et al. 2005; Reynoldset al. 2007b). Of these traits, CT is the most eas-ily measured and displays an association withroot length density and grain yield under stress(Reynolds and Trethowan 2007). Carbon isotopediscrimination (CID) of plant tissue can also beused to estimate plant response to stress, andthose with better access to water will show higherCID (Sayre et al. 1995; Monneveux et al. 2005).CID was used to indirectly estimate the yieldof wheat in Australia, culminating in the releaseof two wheat cultivars with improved water-useefficiency (Rebetzke et al. 2002).

Osmotic adjustment under drought stress mayalso improve plant response to stress, althoughthis tends to promote survival rather than pro-ductivity (Serraj and Sinclair 2002). There is ge-netic variation for osmotic adjustment in wheat,and characters such as continued leaf elongationunder stress (Turner 1986), delayed leaf senes-cence (Hsiao 1973), maintenance of root devel-opment, stabilization of soil moisture extraction,and adjustments to stomatal and photosyntheticprocesses are linked to improved osmotic adjust-ment (Reynolds et al. 2007a). Evidence suggeststhat osmotic adjustment is controlled by a singlegene in wheat (Morgan 1991, 2000; Morgan andTan 1996), and the character can be measuredunder controlled conditions in the greenhouseand used to select for improved grain yield un-der drought stress in the field (Moinuddin et al.2005).

Roots tend to be more sensitive to higher tem-perature than above ground biomass (Porter andGawith 1999), and this increased sensitivity islinked to fluctuations in diurnal temperature (Petr1991). Temperature in excess of 35◦C will reduce



220 CROP ADAPTATION TO CLIMATE CHANGE

terminal root growth, thus increasing senescence(Wardlaw and Moncur 1995).

Phenology

One of the primary causes of poor water-use ef-ficiency is inappropriate crop phenology. Yieldand adaptation will improve if phenological de-velopment matches the most probable avail-able moisture distribution in the crop season. Inthe simplest sense, early flowering will avoiddrought and temperature stress in environmentswhere terminal stress is likely to occur. Thegenes controlling photoperiod and vernaliza-tion response in wheat are well understood, andmolecular markers are available for most genesof major effect (Yan 2009). These genes canbe manipulated to better target crop genotypesto farming systems and regions, thus improv-ing water-use efficiency and regional yield andproductivity.

Partitioning of photosyntheticassimilates

High preanthesis biomass may be a disadvan-tage under severe stress if water becomes lim-iting during the grain-filling period. However,fructans stored in stems prior to heading cancontribute to grain filling and yield and canbe particularly useful when photosynthetic ca-pacity is reduced by postanthesis stress (Blumet al. 1983; Blum 1998). In a study of solidand nonsolid stem wheat lines derived from thesame cross, Saint Pierre et al. (2010a) found thatmaterials with solid stem had higher levels ofwater-soluble stem carbohydrates and that thesematerials were higher yielding under droughtstress. Other traits that may contribute to in-creased fructan storage include long and thickstem internodes (Reynolds et al. 2007b). The in-heritance of water-soluble stem carbohydrates iscomplex and many minor quantitative trait loci(QTL) contribute to the expression of the trait,nevertheless heritability is high, particularly un-der terminal drought stress, indicating that phe-

notypic selection should be effective (Rebetzkeet al. 2007b).

Spike photosynthesis can also be an impor-tant contributor to grain fill, particularly underdrought stress, as spikes (including awns) havea higher water-use efficiency than leaves as theycan refix respiratory carbon (Bort et al. 1994;Bort et al. 1996). While gas-exchange is difficultto measure on spikes, chlorophyll fluorescencecould be used as a more rapid measure to aidselection in plant breeding programs (Reynoldset al. 2007b).

Plant height, harvest index, and othermorphological traits

Many consider taller plants to be more toler-ant to severe drought stress than shorter plants.This likely arises from the comparison of talllandrace cultivars, still grown in more marginalenvironments, with modern semidwarf cultivarstested in the same regions. Nevertheless, bet-ter relative partitioning of assimilates to spikeand grain growth could be expected to re-sult in higher harvest index, thus improvingyield under drought as water is saved by notgenerating the additional biomass (Reynoldsand Trethowan 2007). Mathews et al. (2007)tested a range of isogenic pairs of wheat cul-tivars across a range of water-limited environ-ments globally and concluded that in almostall instances, the shorter lines out performedtheir taller counterparts. Under high temperaturestress, we would expect to see a reduction in har-vest index among less-tolerant materials as spikeinitiation and development is retarded (Ballaand Veisz 2008).

There is evidence that a range of differentleaf morphologies can influence plant responseto drought and high temperature. Leaf glau-cousness (Richards et al. 1986), rolling (Ayenehet al. 2002), pubescence, and erect habit (Innesand Blackwell 1983) can reduce radiation loadon the leaf surface, thus reducing transpiration.These traits show a largely facultative responseto drought and therefore would not be associated




with reduced radiation-use efficiency under fa-vorable conditions (Reynolds et al. 2007b).

Antioxidants and ABA

It is likely that there is a link between plantadaptation to high temperature and drought as adegree of thermal and radiation tolerance wouldbe an advantage in high-radiation environments,typical of many dry areas (Reynolds et al.2007b). Reduced stomatal conductance is likelyto increase leaf radiation load beyond thatrequired to fix carbon, thereby increasing theaccumulation of active oxygen species. Thexanthophylls cycle, for example, can dissipateup to 75% of absorbed light energy (Niyogi1999). Barley landraces can adapt to stressby rapid xanthophyll cycling and reducedleaf chlorophyll, mechanisms that increasephoto-protection (Tardy et al. 1998; Havaux andTardy 1999). However, adaptive chlorophyllloss is likely to be a yield disadvantage undermore productive conditions.

Abscisic acid (ABA) is a growth regulatorsynthesized in response to stress. Increased ABAtends to reduce seed-set (Morgan 1980; Westgateet al. 1996), leaf transpiration rate, cell expan-sion, and cell division, and increases partition-ing of assimilates to root growth (Turner 1986).These responses are highly conservative andlikely to be a disadvantage under more produc-tive conditions. Selection for high ABA has notresulted in improved productivity under stress(Loss and Siddique 1994).

Sources of genetic variation fordrought and heat tolerance

The yield of wheat has increased globally bysome 1% per annum over the past 50 years(Trethowan et al. 2001). Nevertheless, rates ofgenetic gain in recent years have reached aplateau (Lobell et al. 2005; Chatrath et al. 2007),indicating a possible exhaustion of genetic diver-sity for yield. To improve yield potential further,it will be necessary to radically alter crop archi-tecture and/or physiology. However, increasing

yield potential under highly productive condi-tions is unlikely to increase regional and globalfood production. Grain crops such as wheat arerarely grown under optimal conditions. Improv-ing the stress tolerance of crops will likely in-crease total production, particularly as climatechange or increased climate variability is likelyto increase the intensity and occurrence of stress.Identification of sources of genetic diversity forstress tolerance is critical if better adapted wheatcultivars are to be developed.

Diversity for plant response to droughtand high temperature in the primarywheat gene pool

Plant breeders have steadily exploited genetic di-versity for stress tolerance over the past 50 yearsand considerable progress in yield and adaptationhas been made (Trethowan et al. 2007). Never-theless, rates of progress are significantly lowerthan that of other more simply inherited traits. Asignificant component of improved yield poten-tial is maintenance of disease resistance (Sayreet al. 1998). Disease resistance is simply inher-ited and easily assessed both in the field andunder controlled conditions. This ease of assess-ment and relative simplicity of inheritance hasdriven the development of molecular markers fordisease resistance in wheat. Molecular markershave allowed the plant breeder to pyramid dis-ease genes both in the presence and absence ofthe disease (William et al. 2007). In contrast, thecomplexity of inheritance and response to envi-ronment has hampered attempts at establishingaccurate phenotypes for the abiotic stresses.

Variability in the environment can be con-trolled using growth chambers; however, theseresponses are rarely transferable to the field. Ifplant breeders are to increase rates of geneticprogress for yield under stress, it will be impor-tant to base screening in the field. Field-basedmanaged stress environments have been used atthe International Maize and Wheat ImprovementCentre (CIMMYT) to improve the stress toler-ance of wheat (Trethowan et al. 2001; Trethowan




et al. 2005). Trials are sown in an arid, irri-gated environment in northwestern Mexico nearCiudad Obregon (latitude 27◦N, 60 m abovesea level) and limited irrigation used to gen-erate repeatable drought stress regimes. Thesestress regimes represent the dominant stress pat-terns found in the environments targeted by theCIMMYT wheat-breeding program. Delayedplanting dates are used to generate terminal heatstress, and combinations of delayed sowing andrestricted irrigation simulate both stresses. Acombination of gravity, drip, and overhead irriga-tion is used by CIMMYT wheat breeders to cre-ate the targeted stress patterns. Materials selectedin this way are distributed to many environmentsaround the world in the Semi-Arid Wheat YieldTrial (SAWYT) and the data generated collatedand analyzed by CIMMYT. Historically, the ma-terials were tested using one dominant postan-thesis stress regime; however, the lines selectedin this way tended to be well adapted in a subsetof global environments only (Trethowan et al.2001). Nevertheless, rates of genetic gain over a19-year period were found to be 4% per annum inlow-yielding environments and less than 1% un-der more productive conditions (Trethowan et al.2002). The results indicated that global rates ofgenetic gain could be increased by increasing therelevance of materials in regions where CIM-MYT germplasm performed poorly. Similarly,an analysis of CIMMYT’s High TemperatureWheat Yield Trial showed that screening materi-als under terminal heat stress at Ciudad Obregonin northwestern Mexico, did identify materialsrelevant to a wide range of environments glob-ally (Lillemo et al. 2005).

Several families of germplasm with superiorperformance under drought and heat stress wereidentified. These include lines derived from theparent “Baviacora” for drought response and“Kauz” for performance under high terminaltemperatures. Wherever possible, breeders haveattempted to use adapted materials in crossesas reduced linkage drag is expected. However,landrace or traditional cultivars have also beenused to extend the genetic diversity for stress

response. Recent work at CIMMYT identifiedMexican landraces with superior water extrac-tion from depth and high levels of stem solu-ble stem carbohydrates, particularly at or beforeflowering (Reynolds et al. 2007b). These materi-als were crossed to adapted materials, and lineswith superior stress response in good agronomicbackgrounds have been derived (Reynolds, per-sonal communication).

Clearly, there is significant variation fordrought and heat response in the primary wheatgene pool, and there is scope to improve plantresponse further. Progress is to some extent lim-ited by phenotyping and breeding strategy. Nev-ertheless, the additive nature of drought and heatstress tolerance will require new sources of alle-les if rates of genetic gain are to be lifted beyondthe current rate of 1% per annum.

Diversity for plant response to droughtand high temperature in the secondarywheat gene pool

Synthetic hexaploid wheat, produced by cross-ing tetraploid wheat, both modern and ances-tral, with Aegilops tauschii, the donor of theD-genome of hexaploid wheat, offers excitingnew variation for stress tolerance. Primary syn-thetic wheat was first reported by McFadden andSears in 1946. Over the past 20-years, many newprimary synthetics have been made at CIMMYTand other organizations (van Ginkel and Ogbon-naya 2007). These primaries have largely beenbased on modern cultivated durum wheat al-though tetraploid emmer wheat has also beenused to expand the genetic base of the A and Bgenomes (Lage et al. 2004). The primary synthet-ics, particularly those based on emmer wheat,have poor agronomic type and are difficult tothresh, which complicates their evaluation forstress tolerance. Morphological, phenological,and disease data are more easily assessed andmake up most of the available phenotypic infor-mation. Nevertheless, some evidence suggeststhat the primary synthetics do express a degree ofdrought and heat tolerance under field conditions




(Villareal et al. 1998; Villareal and Mujeeb-Kazi1999).

The primary synthetics are a potential sourceof new, largely additive, genetic variation for re-sponse to limited moisture. In crosses betweenprimary synthetics and adapted wheat cultivars,plant breeders at CIMMYT observed an im-proved response to drought among the derivedprogeny (Trethowan et al. 2000, 2003, 2007).These responses were initially observed in north-western Mexico in the Sonoran desert under lim-ited irrigation and then internationally once theselected progeny were distributed in CIMMYT’sSAWYT (Lage and Trethowan 2008). The syn-thetic derivatives developed in Mexico were alsoevaluated in Australia and many of the mate-rials identified as superior under limited mois-ture in Mexico also performed well compared totheir recurrent parents and locally developed cul-tivars under Australian conditions (Ogbonnayaet al. 2007; Dreccer et al. 2007). In a differ-ent comparison, Gororo et al. (2002) tested syn-thetic hexaploid derivatives developed from pri-mary synthetics produced in Australia in bothAustralia and Mexico and found that the de-rived lines exceeded the check for yield in 38of 42 multienvironment comparisons across bothcountries.

The physiological basis of improved adapta-tion to limited moisture of synthetic-derived ma-terial is unclear although preliminary evidenceindicates that greater investment in root biomassdeeper in the soil profile by synthetic-derivedmaterials is an advantage in Mexico (Reynoldset al. 2007b). In this study, the greater investmentin deeper roots led to a lower root : shoot ratio un-der drought stress. Synthetic derivatives are alsoable to maintain seed weight under drought andhigh-temperature stress (Trethowan et al. 2005).

While the primary synthetics carry usefulvariation for stress adaptation, there is also con-siderable linkage drag associated with poor agro-nomic type and quality. Empirical selection foryield under stress has captured only a smallproportion of the primary synthetic genomein the agronomically superior, drought-adapted

progeny, as evidenced by microsatellite analysis(Zhang et al. 2005) and coefficients of parentageof more recently derived materials (Lage andTrethowan 2008).

Significant variation for response to high-temperature stress has been observed among theancestral species of wheat, including A. tauschi(Zaharieva et al. 2001). This tolerance is oftenexpressed in the primary synthetics, althoughexpression can be linked to poor yield underoptimal growing conditions. Yang et al. (2002)found that yield in primary synthetics was supe-rior to adapted cultivars in the temperature range25◦C/30◦C but inferior at optimal temperature.This lack of response at lower temperature mostlikely reflects linkage drag associated with theprimary background; when the stress is removed,the “yield engine” is exposed. Nevertheless, ev-idence suggests that stress tolerance and highyield potential are not intrinsically negativelylinked. Breeding can remove this yield crossovereffect under more productive conditions. Lageand Trethowan (2008) demonstrated this with thesynthetic derivative “Vorobey” (Fig. 7.1). Thiswas compared to the best locally adapted culti-vars in environments where yield ranged from 1to 8 tons. In almost all instances, Vorobey yieldedmore than the locally adapted materials.

Reynolds et al. (1994) found that stay-greenor green leaf duration was linked to high tem-perature tolerance. In a later study, Reynoldset al. (2007) reported that the yield of synthetic-derived materials in late sown, irrigated yieldtrials in the Sonoran desert was 30% higher thanthe adapted check cultivars at temperatures inexcess of 35◦C during anthesis and grain filling.

While the synthetic wheats do provide use-ful variation for cold tolerance in the vegetativephase (Limin and Fowler 1982, 1993), the evi-dence of frost tolerance during reproductive de-velopment is inconclusive. Maes et al. (2001)found that floret death was delayed in some pri-mary synthetics under freezing temperatures byup to 4 minutes. While statistically significant,the value of this trait under frost in the field isunclear.




R2 = 0.96R2 = 0.93R2 = 0.82

R2 = 0.84

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1086420

Average yield of SAWYT at site (t/ha)

Yie

ld o

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Top yielder

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Bottom yielder

Fig. 7.1. The yield of the synthetic derivative “Vorobey” compared to the highestyielding line, highest yielding local check cultivar, and lowest yielding line in theSemiArid Wheat Yield Trial (SAWYT) at 45 locations. (Reproduced from Lage andTrethowan 2007.)

Diversity for plant response to droughtand high temperature in the tertiarywheat gene pool

The tertiary gene pool is a last resort for plantbreeders searching for genetic variation for traitsof economic importance, as this diversity is dif-ficult to introgress into adapted materials. Whilesynthetic wheat combines materials representingone or more of the hexaploid wheat genome, ter-tiary genomes are nonhomologous with wheat,complicating gene transfer. Nevertheless, cy-togeneticists have made considerable progressin transferring alien segments, generally target-ing disease resistance, particularly rust genes inwheat (Tomar and Menon 2001; Zhang and Ren2001; Aghaee-Sarbarzeh et al. 2002; Mago et al.2005). The identification of the ph mutants inwheat (Sears 1976) promoted homologous pair-ing and made the development of addition andsubstitution lines possible, which in turn revo-lutionized the transfer of chromosome segmentsfrom alien species.

The 1BL.1RS translocation in wheat is oneof the better known alien translocations to im-pact wheat breeding for both biotic and abioticstresses. The translocation was found in the win-ter wheat cultivar Kavkaz and later transferred tospring wheat by CIMMYT breeders, eventuallygiving rise to the Veery wheats (Rajaram et al.

1990). Apart from carrying genes for disease re-sistance, the segment was also linked with highyield in many environments, even in the absenceof disease (Trethowan et al. 2007). This superior-ity is likely linked to a more vigorous root growthconferred by the translocated segment (Ehdaieet al. 2003; Waines and Ehdaie 2007). Unfortu-nately, lines carrying the 1BL.1RS translocationexpress inferior industrial quality in some back-grounds, which has limited the deployment ofthese materials in some environments (Amiouret al. 2002). Other rye translocations such as1AL.1RS, 2BS.2RL, and 6BS.6RL have been re-ported and are linked in some cases to improve-ments in disease resistance (Rabinovich 1998).However, none of these have expressed agro-nomic performance equivalent to 1BL.1RS.

Alien species found in harsh environmentscan also provide useful sources of stress tol-erance. Aegilops geniculata has been shown toexpress relatively low CID, a trait indicative ofhigh transpiration efficiency and therefore toler-ance to drought (Zaharieva et al. 2001), whichcould be a source of useful variation if trans-ferred to adapted wheat. A translocated seg-ment of Agropyron elongatum carrying the leafrust resistance gene Lr-19 has been observedto increase yield potential in some environ-ments and in some backgrounds by improving




radiation-use efficiency and grain number(Reynolds et al. 2001), although the evidenceunder stress is less conclusive (Monneveux et al.2003).

Unfortunately, there are relatively few exam-ples of successful alien gene transfer into adaptedwheat that improve adaptation to abiotic stresses.The complex inheritance of abiotic stress toler-ance, meiotic instability, and linked deleteriouseffects limit the widespread application of thetertiary gene pool in applied wheat breeding.

Diversity for plant response to droughtand high temperature throughtransgenesis

The transfer of genes beyond the tertiary genepool through genetic engineering is another toolavailable to the plant breeder to increase geneticdiversity for stress tolerance. However, the ex-pression of drought tolerance in transgenic wheatproduced at CIMMYT based on the Dreb1Atranscription factor from Arabidopsis thalianawas not transferable from the greenhouse to thefield (Pellegrineschi et al. 2004; Saint Pierreet al. 2010b). Nevertheless, improved response todrought has been noted in other transgenic cropssuch as soybean. Ronde et al. (2004) comparedtransgenics based on the pyrroline-5-carboxylatereductase gene (P5CR) with their controls andfound that transformed plants had higher freeproline and higher relative water content un-der drought. Proline has been linked with plantresponse to drought and can be accumulatedin various plant structures, including leaf tis-sue, meristems, and root apical regions (Rhodeset al. 1999). Proline may contribute to osmoticadjustment by protecting proteins and cellularmembranes in plants under stress. Wang et al.(2006) also reported a twofold increase in pro-line of transgenic wheat plants transformed us-ing the Dreb transcriptional factor; however, thedrought response was not confirmed under fieldconditions.

Perhaps, the most promising recent story isdrought-tolerant transgenic maize. Monstanto

and BASF have discovered a gene from the bac-teria Bacillus subtilise that improves drought tol-erance in maize (BASF 2009). Moves are under-way to test and ultimately release this cultivar insub-Saharan Africa. While little published evi-dence is available on the performance of trans-genic crops under drought, these new improvedmaterials are potentially an exciting new sourceof variation for plant breeders, particularly asperfect molecular markers exist for the trans-genes making their introgression into wider ge-netic backgrounds possible through conventionalmarker-assisted selection.

Combining genetic variation fordrought and heat tolerance inapplied wheat breeding

The plant breeding process can be divided into aseries of steps, spanning the identification of par-ents through to the release of improved cultivarsto farmers. Breeding strategies for transferringgenetic diversity for stress tolerance into wheatare outlined.

Crossing strategies

The importance of choosing parents for crossingthat maximize the probability of achieving thedesired phenotype can never be under underes-timated. If this is not done efficiently, all subse-quent investment in the resulting populations islargely wasted. Selection for drought or heat tol-erance is normally conducted within the framework, a breeding program that targets a rangeof other economically important traits such asdisease resistance and end-use market quality.Given the vagaries of environment and the influ-ence of environment on the expression of stresstolerance, it is important that prospective parentsare tested widely for stress response in the targetenvironment.

The cost and accuracy of genotyping technol-ogy has improved significantly in recent years.In addition to background genotype, the number




of simply inherited traits with linked orperfect markers has increased and the breederwill have layers of information available onparental materials. Advances in genotyping hasalso provided a platform for association geneticsstudies within whole breeding programs; mostmature programs will have access to historicalperformance data and residue seed, at least, ofthe parents and selected progeny.

One such example comes from the CIM-MYT wheat breeding program (Crossa et al.2007). Lines entering CIMMYT’s internationaltrial network were maintained in a gene bank andwere therefore available for genotyping. Breed-ers were able to associate genotype with yieldperformance across a 25-year period. The analy-sis identified genomic regions associated withsuperior yield in many environments globally(Table 7.1). The chromosome regions in high-light in Table 7.1 indicate significant DArT mark-ers that are not linked to genes of major effectsuch as vernalization, photoperiod response, ormajor disease-resistance genes. These regionsand their associated markers can be combinedin crossing to improve yield response.

It is also wise to determine the physiolog-ical response of parents to drought and heat.These data complement the molecular charac-terization of materials and allow the breederto combine complementary physiological char-acters in crosses. This was the approach usedby Reynolds and Trethowan (2007) to improvedrought stress tolerance. The yield performanceof the derived lines exceeded that of conventionalcrosses made among the best drought-tolerant orwater-use-efficient genotypes based on yield un-der stress alone (Manes Y, personal communi-cation). However, while the grain yield of thesematerials has improved, it is yet to be confirmedthat different physiological traits have been pyra-mided and are responsible for the enhanced re-sponse. Within the primary gene pool, simple bi-parental crosses are often sufficient to combineuseful variation. However, a degree of backcross-ing is essential when combining variability fromthe secondary and tertiary pools.

Selection strategies

The probability of obtaining the desired stresstolerance phenotype from crosses combining tar-get traits is dependent upon the chosen selectionstrategy. Practicality will limit population sizein the early generations; however, the breedershould strive to maximize the number of plantsscreened in each cross. For example, materialshave historically been selected for water-use ef-ficiency at CIMMYT using two alternating stresspatterns during the segregating phase, contin-uous drought stress, and no stress. The F2 isscreened under well-watered conditions as effec-tive screening for simply inherited but vital char-acters such as disease resistance, plant height,and flowering time is best conducted withoutdrought stress. Materials are screened for thefirst time under drought stress at the F3. Typ-ically up to 3000 plants are grown at F2, ofwhich 200–300 may be selected and bulked onthe basis of disease resistance and other sim-ply inherited characters. Around 1500 plants arethen sown in F3 under stress and around 10% ofthese materials selected on the basis of spike size,seed size, and tiller number. Terminal heat stressis generated by late planting. The nurseries arewell-watered to avoid the confounding effects ofdrought stress and large F3 populations are sownand stem rust susceptible plants removed, as thisdisease is prevalent in the Yaqui Valley at hightemperature. The remaining plants are bulk har-vested and the seed separated for seed size anddensity on a gravity table. The selected portionof seed is then resown under heat stress in thefield for further selection.

If molecular markers for known genes areavailable, they should be used to increase thefrequency of desired alleles in the segregatingphase. Allele enrichment in the earliest seg-regating generations using markers for knowngenes will greatly increase the frequency oftarget genes in the population (Bonnett et al.2005). However, QTL of significant effect withassociated flanking markers tend to be rare inwheat. Most QTL for stress tolerance have been



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6706

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6,39

83,5

672,

4125

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7P

pd2

3132

,935

0,73

50,9

336,

2135

,33

78,7

360,

0049

Eps

QT

L00

94,0

950,

4210

QT

L

2D41

44P

pd1R

ht8

QT

L44

13E

ps—

QT

L

3A93

69,1

681

QT

L77

56,2

698,

7992

,293

8,47

25,

9268

,440

7,16

88—

—E

ps

3B03

65,0

995,

5716

,701

5,83

52,8

983,

7142

,931

0,42

09,9

510,

5390

,917

0,60

47,5

105,

6802

,888

6,02

80,0

384,

8238

,809

6,44

12,8

845

——

QT

L93

68,2

757

Vrn

QT

L

(Con

tinu

ed)

227



Tab

le7.

1.(C

onti

nued

)

Shor

tar

m(S

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arm

(L)

Unk

now

nar

m

DA

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Gen

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65,9

401

——

QT

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Ppd

QT

L

4A27

88Q

TL

7280

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4,37

95,7

807,

8271

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20,2

533

QT

L46

60,7

924

Eps

4B39

08,6

149

Rht

-1,Q

TL

1505

,829

2Q

TL

3608

,526

5E

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TL

4D—

Rht

-2—

QT

L—

Eps

5A11

65,0

605

—52

31V

rn-A

1QT

L42

49Q

TL

5B61

36,1

420,

9666

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5—

9467

,010

3,49

96,7

101,

5896

,30

30,9

598

Vrn

-A2

QT

L44

18,4

703,

4936

QT

L

5D14

00—

—V

rn-A

3V

rn-4

—Q

TL

6A74

75,0

864,

8006

,793

8,90

75—

9690

,257

3,09

59,7

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—Q

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6B95

32,1

922,

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——

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QT

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L33

93,6

495

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66,4

553,

4748

QT

L

7B—

—62

73,9

925,

7887

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3,89

21,

5547

,528

0,01

94,6

156,

4300

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08,6

320,

0504

QT

L15

33,9

746

Vrn

B4,

Vrn

5Eps

,Q

TL

228




identified in biparental populations and tend tobe background specific or environment specificin their effect. These QTL generally representonly a small portion of the total expression ofthe trait.

An alternative is to identify QTL within eachpopulation specific to that population. These canthen be combined in a marker-assisted recur-rent selection scheme (MARS) (Bernardo andCharcosset 2006). MARS schemes have gener-ally been used in open-pollinated crops such asmaize (Eathington et al. 2007), but there is noreason, apart from limitations with crossing, thatthis will not be equally effective in wheat. Fig-ure 7.2 outlines a possible MARS scheme forwheat. In a MARS scheme, the parents and in-termediate generations are genotyped (generallyF3 or F4). It is also important to select adaptedparents that do not differ greatly in floweringdate and plant height, as phenotypic assessmentof stress tolerance is a key component of thescheme, and differences in phenology will con-found determination of the stress response. InFig. 7.2, 300 F2-derived F3 progeny are geno-typed and the F4 tested in multiple environ-ments for response to stress. The significance ofeach marker-allele is then calculated, thus pro-viding an estimated breeding value. The selectedprogeny, based on phenotypic response, are re-combined in crosses on the basis of the signifi-cance of each marker-allele. In this way, the sig-nificant markers for stress response are combinedwithin each population. Another variant on thisstrategy is genome-wide selection. In this case,all breeding values, not just the significant geneeffects, are used to drive crossing and recombi-nation (Bernardo and Yu 2007). Nevertheless, aswith all selection schemes, the determination ofthe stress phenotype is the rate-limiting step. Ef-fective selection for stress tolerance (and hencethe accuracy of each gene effect estimation) de-pends on the prevailing conditions in the yearof selection. The heritability of selection is oftenlow in most stressed environments as year effectsare large (Ribaut et al. 1996; Ahmed and Bajelan2008).

It is often better to select materials usingmanaged stress conditions that most closelymimic the most probably environment type forthe target region. This has been the philoso-phy at CIMMYT, and wheat materials are se-lected using limited irrigation and delayed plant-ing dates to generate dominant drought and heatstress patterns, respectively, that are typical ofthe wider target environments (Trethowan et al.2005).

While it is generally time consuming to mea-sure physiological traits, the application of phys-iological tools are not necessarily limited toscreening small numbers of parents. Some traits,such as canopy temperature depression (CTD),are easy to measure using an infrared thermome-ter and are highly correlated with stress response(Reynolds et al. 2007). CTD has been success-fully used in the F4 generation to favorably skewgene frequency, resulting in a higher propor-tion of drought-adapted materials with coolercanopies (Trethowan and Turner 2009). How-ever, Saint Pierre et al. (2010b) studied gene ac-tion for CTD across diverse environments andconcluded that selection should be delayed un-til higher levels of homozygosity are reachedbecause of significant dominance and epistaticeffects. These authors also confirmed the signif-icant relationship between yield under droughtand heat stress and CTD.

Although the inheritance of osmotic adjust-ment is simple (Morgan and Tan 1996; Morgan2000) and the relationship between greenhouseand field response relatively robust (Moinuddinet al. 2005), it is difficult to use this charac-ter for selection of large numbers of lines be-cause of the difficulty and time required to as-sess the character. However, selection would befacilitated by the identification of robust molec-ular markers linked to the trait. Similarly, water-soluble stem carbohydrate is an excellent candi-date for marker-assisted selection and is linkedto improved performance under stress in someenvironments. However, phenotypic screeningshould be conducted on early sown materialsgrown without drought stress as these conditions




Parent 1 X Parent 2

Pop

ulat

ion

deve

lopm

ent

F1

F2

F3

F3:4

F3:5 (if needed)

Single seed descent

300 F3 progenies

300 progenies

Multilocation phenotyping

1st Recombination cycle A B C D E F G H

F1 F1 F1 F1

F1 F1

F1

F2

F3

2nd Recombination cycle

3rd Recombination cycle

Multilocation phenotyping

F3:4

Rec

ombi

natio

n P

op

ulat

ion

deve

lop

men

t

10 plants/family (A-H), 6 sets of 8 families/cross

Bi-parental population

QTL detection

Genotyping

Genotyping

Genotyping

Genotyping

Genotyping

Fig. 7.2. An example of a marker-assisted recurrent selection scheme to improve the stress adaptation of wheat. (Courtesyof Xavier Delannay.)

have the highest heritability of expression of thetrait (Dreccer et al. 2009).

Double haploids produced using the maize-wheat system or microspore culture provides auseful additional tool for the rapid production ofhomozygous lines (Kisana et al. 2006). Doublehaploids are often used to develop random pop-

ulations from F1 progeny for genetic mappingstudies. However, if applied on F2 or BC1F1progeny following screening for highly herita-ble traits, using either traditional techniques ormolecular markers, they can speed up the breed-ing process considerably. Nevertheless, the ap-plication of double haploids is limited by their




expense and the genetic complexity of stress tol-erance, which requires large numbers of progenyto be screened.

Confirmation of stress response infixed line progeny

The expression of stress response in fixed lineprogeny from any selection scheme must be con-firmed as the stress phenotype up until this pointhas been determined in relatively few environ-ments on small seed quantities of large numbersof individual lines. In some programs such asthe wheat breeding program at CIMMYT, newfixed line progenies are tested under managedstress conditions in the field (Trethowan et al.2005). Over the past decade, four basic stresspatterns were generated in the field using lim-ited irrigation at an arid location in northwesternMexico; these patterns were continuous droughtstress, preanthesis stress, postanthesis stress, andno drought stress. Irrigation was controlled usinga combination of drip and gravity-fed irrigation.In the Sonoran desert, most of the annual precipi-tation falls during the summer, and in most years,there is on average 100 mm of available water inthe soil profile at planting. The continuous stressregime was generated by planting into dry soilfollowed by the application of up to 60 mm ofwater in three separate irrigations. These irriga-tions were generally applied at planting, jointing,and mid-boot stage but were varied dependingon unseasonal rainfall. The aim was to producea constant but not lethal stress throughout thegrowth phase; an average yield of 1–1.5 t/hawas targeted. The preanthesis stress regimewas identical to the continuous stress pat-tern until flowering after which the stresswas relieved by two additional irrigations of40 mm each; one applied at flowering, the othermid-grainfill. The targeted average yield was 2t/ha. The postanthesis stress was generated byapplying 90 mm of water during the preanthe-sis phase in three separate irrigations: one aftersowing, one at jointing, and the final irrigation inmid-boot. No irrigation was applied after mid-

boot and 2 t/ha average yield was targeted. Theoptimal treatment was managed by applying upto 6 irrigations of 40 mm each throughout thegrowth cycle to avoid drought stress. Yield of6 t/ha or greater was targeted. However, not allmaterials are tested under all regimes. Optimaland continuous stress patterns have been used toscreen preliminary materials and the full range ofstress patterns applied to only the most advancedmaterials. The intensity of selection is relativelyhigh under drought stress with 10–20% of mate-rials selected from preliminary yield testing.

Following evaluation under managed stressesin northwestern Mexico over a 3-year period,with the range of stresses increasing as the num-ber of selected lines decreases, the materials aresent globally in coordinated yield trials for exten-sive testing in the target environments. Materialsdeveloped and deployed in this way have adaptedwell to a wide range of growing conditions inthe wheat-growing areas of the developing world(Trethowan et al. 2001, 2003).

Screening for high-temperature stress toler-ance at CIMMYT is managed by late planting.Wheat is normally sown in November in theYaqui Valley and flowers during February whiletemperatures are still cool. Average maximumand minimum temperatures for the critical Jan-uary to April growth period (representing spikeinitiation to physiological maturity) are 26.5◦Cand 12.5◦C, respectively. However, when plant-ing is delayed until January, spike initiation takesplace in late February/early March and physio-logical maturity in May. The respective averagemaximum and minimum temperatures for thesame growth period become 29.0◦C and 15◦C.

In other wheat breeding programs, such asthose in Australia, fixed lines are tested widelyin multienvironment trials across the target en-vironment over a number of years to reduce theimpact of large genotype × location × year in-teractions (Chapman et al. 2000). Genotypes areselected for release on the basis of their highand stable yield performance over time. In manydeveloping countries, lines are generally testedin multienvironment yield trials on a network




of government research stations for economicand logistical reasons, which do not necessar-ily represent on-farm conditions (Ceccarelli andGrando 2007). For this reason, some have advo-cated farmer participatory varietal selection asone avenue to ensure the relevance of releasedcultivars to farmers (Witcombe et al. 1996). Inthis instance, fixed lines with disease resistanceand market quality and tested in a series of on-farm demonstrations and farmer feedback usedto identify lines for release.

Managing plant breedinginformation to make betterdecisions: The importanceof informatics

In recent years, the volume of information avail-able to the wheat breeder has increased exponen-tially with advances in genotyping technology.Many plant breeders use dedicated software, of-ten developed in house, to manage the day-to-dayoperations of their breeding programs. These op-erations include updating pedigrees, producingfield books, and storing linked phenotypic andmolecular data. However, few plant breeders inthe public sector make efficient use of the fourtiers of available data representing pedigree, phe-notype, background genotype, and foregroundgenotype. In addition, increasing operating costs,more challenging research objectives, and con-cerns over intellectual property and the properdocumentation of germplasm flow have madedata management an imperative. The Interna-tional Crop Information System (ICIS) is a pub-licly available integrated database that housesthe four tiers of plant breeding data (DeLacyet al. 2009). However, ICIS is an evolving sys-tem and many of the tools required to interrogatethe warehoused data are still in development. In-creasing rates of genetic gain under stress is morethan ever dependent upon the efficient access anduse of available information.

Commercial companies have invested signif-icant sums in informatics to support their cropbreeding effort. One of the best examples is

maize breeding at Monstanto. Monsanto madea decision to centralize its database system usingpurpose built software (Eathington et al. 2007).This system required uniform nomenclature, traitdefinitions, and rating scales to be adopted acrosstheir global maize breeding effort. All pedigree,phenotypic, and genotypic data are now managedin this way. Monstanto breeders have access topredictive tools base on gene effects estimatedacross the database to improve their rates of ge-netic advance. Plant breeder access to equivalentinformatics support for wheat and rice; key cropsfor global food security and largely bred in thepublic sector, is essential if rates of genetic gainare to keep pace with those in commercial sectormaize.

Integrating genetic improvementand conservation agriculture toincrease productivity under stress

While genetic improvement of stress toleranceis an important avenue to improve yield andproductivity in an increasingly hostile produc-tion environment, the new materials must be de-veloped within the framework of a water andresource conserving agricultural system. Ensur-ing that newly developed lines are well adaptedto conservation agricultural practices is a plantbreeding objective. Already there is evidence thatgenotype × farming system interactions exist forwheat for yield and product quality (Gutierrez2006); these interactions can be exploited to de-velop more relevant crop cultivars. However, theevidence of genotype × tillage interactions hashistorically been inconclusive, largely becausesmall numbers of genotypes have been testedand most of the materials evaluated were devel-oped under conventional tillage (Trethowan et al.2010).

To effectively breed for adaptation to conser-vation agriculture, the plant breeder must firstevaluate potential parents under both tilled anduntilled regimes to classify genotype responses.Segregating populations should also be selectedunder locally adopted conservation agricultural




techniques. Trethowan et al. (2010) reported thatselection of segregating materials from the samecross under zero-tillage produced lines that per-formed well under both zero-tillage and conven-tionally tilled systems.

However, if the response can be brokendown into discrete traits with higher heritabil-ity, then genetic progress can be significantlyadvanced. Earlier work has identified coleop-tile length (Rebetzke et al. 2007a; Trethowanet al. 2001), coleoptile thickness (Rebetzke et al.2004), emergence from depth (Trethowan et al.2005), seedling vigor (Liang and Richards 1999),rate of stubble decomposition (Joshi et al. 2007),root depth (Reynolds and Trethowan 2007), al-lelopathy (Bertholdsson 2005), N-use efficiency(van Ginkel et al. 2001), disease resistance(Trethowan et al. 2005), and seedling temper-ature tolerance (Boubaker and Yamada 1991) ashaving some influence on plant response to un-tilled soil. Genetic variation for all these charac-ters can be found in both the primary and sec-ondary wheat gene pools, hence progress in im-proving should not be onerous.

Conclusion

There is sufficient variation in the primary, sec-ondary, and tertiary wheat gene pools to sig-nificantly improve the response of wheat toan increasingly variable climate, including ex-tended periods of in-season drought and increas-ing temperature. The complexity of inheritanceof stress tolerance, difficulty in determining ac-curate stress phenotypes, and the limitations oftraditional wheat breeding strategies are majorimpediments to progress. In the short term, therate of genetic gain for yield is likely to remainflat, as evidence by a recent lack of progressglobally in wheat (Lobell et al. 2005; Chatrathet al. 2007). To some extent, we have exhaustedgenetic variation for yield potential within theprimary wheat gene pool and must look to thesecondary and tertiary gene pools for new ge-netic diversity. In the short to medium term, aconcerted effort to improve the stress tolerance

of wheat will likely pay greater dividends region-ally, thus improving food security globally. Evi-dence from the secondary wheat gene pool, par-ticularly synthetic wheat and other amphiploids,offers real potential to increase overall stress tol-erance and hence productivity and yield stabilityin highly variable environments. Managing theexponential increase of molecular informationand marrying phenotype and genotype in effi-cient cross-predictive software will also be animportant contributor to improvement of overallrates of genetic gain.

In the longer term, the prognosis for increas-ing yield under stress is good. New transgenesthat improve plant response to drought and heatare likely to extend the genetic variation availableto plant breeders. Nevertheless, wheat is a com-plex hexaploid and genes tend to be located ingene-rich regions along the chromosome, inter-spersed with gene-poor regions. Rates of recom-bination also tend to be higher at distal ends of thechromosome and lower closer to the centromere.Clearly, increased recombination in wheat wouldpotentially unlock considerable genetic diversityresiding in the primary gene pool (Akhunov et al.2003).

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