Quantitative Trait Loci and Crop Performance under Abiotic Stress: Where Do We Stand?: Table I.

The improvement of crop yield has been possible through the indirect manipulation of quantitative trait loci (QTLs) that control heritable variability of the traits and physiological mechanisms that determine biomass production and its partitioning. This article surveys how QTL-based approaches contribute to a better understanding of the genetic basis of crop performance under environmentally constrained conditions and critically analyzes how this knowledge can assist breeders accelerate the release of cultivars better able to cope with abiotic constraints. Crop performance is the end result of the action of thousands of genes and their interactions with environmental conditions and cultural practices. During the past century, conventional breeding has been very successful in constantly raising the yield potential of crops (Campos et al., 2004; Borlaug and Dowswell, 2005; Duvick, 2005). This was mainly achieved with little or no knowledge of the factors governing the genetic variability exploited by breeders for crop improvement (Blum, 1988; Borlaug, 2007). However, this approach may now be insufficient, because the pressure to provide improvements at a rapid pace will mount if global climate change increases the frequency and severity of abiotic constraints. Heat stress, drought, water-logging, and salinity will probably become more prevalent in certain areas, while there will be an increased demand for agricultural products and reduced availability of agricultural land and natural resources such as water and fertilizers. Consequently, the genetic dissection of the quantitative traits controlling the adaptive response of crops to abiotic stress is a prerequisite to allow cost-effective applications of genomics-based approaches to breeding programs aimed at improving the sustainability and stability of yield under adverse conditions. Robertson (1985) postulated that qualitative mutant alleles and QTL alleles represent the extremes of a possible range of effects, with QTLs resulting from the segregation of natural alleles with smaller effects. The cloning of a number of plant QTLs has confirmed Robertson’s hypothesis, in as much as the types of mutations, genes, and metabolic pathways determining quantitative traits are not distinct from those underlying Mendelian traits and in some cases involve the same loci for which a strong mutation was already known (Salvi and Tuberosa, 2005; Bortiri et al., 2006). Examples of the latter are provided by studies of Arabidopsis (Arabidopsis thaliana) tolerance to water deficit (Masle et al., 2005), salinity (Rus et al., 2006), and aluminum (Al) toxicity (Hoekenga et al., 2006). QTLs can be categorized according to the stability of their effects across environmental conditions. A “constitutive” QTL is consistently detected across most environments, while an “adaptive” QTL is detected only in specific environmental conditions or increases in expression with the level of an environmental factor (e.g. a QTL that is expressed more strongly with increasing temperature; Vargas et al., 2006). The presence and magnitude of these adaptive QTLs, therefore, vary greatly between experiments, while the sensitivity of the same trait to environmental conditions can be underscored by stable QTLs across a range of environments (see below on modeling). The sensitivity to environmental conditions may be due to the responsiveness of regulation (e.g. transcription) of the QTL gene to an environmental cue. Alternatively, differences in response may have an indirect cause (e.g. genotypes with larger root systems will be less affected by water shortage or nutrient deficit, so genes controlling root development may underpin QTLs defined by abscisic acid [ABA] content, stomatal conductance, or biomass accumulation). Additionally, QTLs that alter flowering time often influence yield under water or nutrient deficit because the duration of the crop life cycle affects the timing and intensity of the stress experienced by the plants (Reynolds and Tuberosa, Consequently, the basis for the differences between adaptive and QTLs is less is often and the of the effects by most QTLs on yield in environmental conditions not be to and the of a is of the to the of QTL This is for stress tolerance which are by the intensity of the in the and in the control stomatal and therefore, the of and plant et al., factors that influence plant and the of genotypes to be by plants to and defined of demand and water potential that can provide these conditions et al., et al., 2007). to factors are to the of QTLs for genetic A QTL in genetic may not because the may already be in Additionally, the effects of the may not be to due to interactions et al., only a (e.g. a tolerance QTL in et al., a tolerance QTL in et al., and a flowering time QTL in et al., et al., et al., QTLs from a genetic smaller effects or in under conditions. Consequently, the knowledge from QTL and studies a for the is by of the most by the and to be a approach with the et al., 2005; et al., and not for this of the traits that determine crop yield under the conditions of the of of QTLs that these and of to the QTL A number of have the most to be in QTL approaches for crop improvement and et al., and et al., 2004; et al., and et al., and and The QTL studies for of these and provide a of how and with can with the During their life crops are to abiotic that The in of the has dissection of the physiological and traits underlying stress tolerance mechanisms to an level et al., and et al., and 2007). of studies and have QTLs that may a in the effects of abiotic However, has very little to the release of cultivars with tolerance to abiotic and this is with only a et al., et al., et al., et al., interactions between are to performance under conditions involve of genes and QTLs for tolerance to abiotic and factors that root and such as in et al., and 2005; et al., 2006), in and 2005; et al., et al., and toxicity in et al., and et al., 2007). A of to drought, and flowering and of is a of This of has been to a range of metabolic (e.g. of of in the cycle the of et al., and and et al., 2007). 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The gene approach to be most successful a specific underlying the tolerance trait is known (e.g. of an or as in the is to be of in the cloning of QTLs for yield under and physiological because the underlying of these traits is are some loci that a gene the availability of of have been in with the that and tolerance and such by a gene approach may a gene the and plant genes to abiotic stress tolerance and a in the level of differences in and to be the most basis for the between differences in expression are to a very from or crop can be to et al., et al., et al., 2007). However, the of this in QTL cloning is by the number of genes that expression differences to stress or of such has to the of a stress tolerance QTL is provided by the in genes from that are by stress, genes, and tolerance in plants and while more genetic for a of these genes to tolerance in plants was only by QTL and mutant et al., 2005; et al., et al., et al., 2007). of from studies and and will allow better understanding of in plants et al., and better of genes to be in determining The of can be by knowledge of the genes in a QTL defined by can be known from most of the gene of an can be by the in gene and that between crops and (e.g. between and the Arabidopsis and between the and and the of and the the in the is by of genes, the genes the can be for as as for to the the gene and and genes with and genes, and genes of these loci et al., et al., et al., et al., et al., et al., et al., cases will to be to or not abiotic stress tolerance genes more often types of The the of adaptive traits may vary with environmental conditions a time of some (e.g. stomatal or water to (e.g. of The genetic of such traits a to cope with the variability of of a that QTL interactions et al., 2006). A of to its with environmental conditions. This the development of able to these and to the of genotypes in a range of environmental conditions. quantitative traits (e.g. of or biomass from environmental such as and water is that the of gene regulation is in such a that a plant in a to a environmental to a at the plant level an approach has been for the and genetic of the sensitivity of to environmental conditions et al., et al., et al., response of to and water which stable of the genotypes in conditions. The of these for of and et al., et al., 2007). This the of in as defined by their QTL alleles et al., et al., 2007). This therefore, the of QTLs of plant in not a to the performance of with a of alleles in This is a is at to very traits and genetic crop development as a of environmental conditions. Consequently, allow for the of the effects of traits on the of crop water and et al., et al., However, their so the effects of genes or QTLs be at the crop level for traits (e.g. et al., et al., 2005), for traits to environmental (e.g. flowering response to et al., or QTL at the level can be with crop et al., now has been to a trait will have a a of et the of a trait to across this trait a under or stress a under The of this approach is to the potential of a trait in a by and Additionally, the same approach to the of a QTL a QTL to and that be in the improvement of abiotic stress tolerance of crops will on the QTL The dissection of QTLs governing the for crop yield and its sustainability will a more and of cultivars with an performance under abiotic et al., et al., and is to to QTL-based will breeding aimed at improving tolerance to abiotic The of such effects have been The and cloning of QTLs may be in the by a number of the improvement of (e.g. or and Tuberosa, and approaches (e.g. et al., types of genetic (e.g. et al., and et al., in (e.g. et al., 2004; et al., and and et al., et al., with that the of in environments et al., et al., and increasing availability of (e.g. of and et al., et al., and for genes (e.g. et al., and and et al., a to cloning QTLs in that are in or a in QTL and cloning has been possible through the of the et al., QTL on with a with on a of and et al., the most QTL dissection for The this have the of this the only factor the of to of the in the by on the the the of these and the rapid a is for the the improvement in due to the rapid of is exploited while its (e.g. the for strong genes or a of by the from the to the et al., However, if the effects of the QTLs are by to a improvement may be and the potential to yield at such a may be to for the or yield to to the trait by at loci et al., 2006). Arabidopsis and plants (e.g. will to the genetic and basis of to abiotic stress et al., and will provide to the of of Arabidopsis as a are the availability of a a of genetic and a very life and the to at a of the for is the in Arabidopsis of QTLs controlling the of root et al., 2005; et al., et al., 2006), a factor for crop performance under a number of abiotic et al., 2007). of will be the of QTLs in response to environmental and and the in gene expression et al., 2007). this knowledge will the release of better crops will on to the at the loci and to their effects in crops under conditions et al., 2007). a in of crops and in an to alleles those that the and have and et al., et al., et al., QTL and will be in alleles not the this on as provide a of et al., A QTL approach on will gene and will on the mechanisms that allow plants to to a approach a of the at the physiological and the of the most et al., et al., that the to are provided by gene interactions at the and metabolic and their to environmental an of et al., et al., and et al., et al., in the regulation of gene expression under stress conditions. approaches to on the of and how these may influence variability et al., approaches are to become as more become a understanding of natural will only by differences between natural in et al., et al., 2007). while the gene approach be the such as cloning of natural QTLs, will to a in in understanding of the control of stress of QTL a breeding aimed at improving tolerance to abiotic will be achieved a able to provide the to the mechanisms of crops with the of the at the and was by the the the and the of This from a of to was by the and the