Accepted Manuscript Title: To grow or not to grow: A stressful decision for plants Author: Rudy Dolferus PII: DOI: Reference:
S0168-9452(14)00243-X http://dx.doi.org/doi:10.1016/j.plantsci.2014.10.002 PSL 9061
To appear in:
Received date: Revised date: Accepted date:
4-9-2014 6-10-2014 9-10-2014
Please cite this article as: R. Dolferus, To grow or not to grow: a stressful decision for plants, Plant Science (2014), http://dx.doi.org/10.1016/j.plantsci.2014.10.002 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
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To grow or not to grow: a stressful decision for plants
11 Rudy Dolferus
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GPO Box 1600
Canberra ACT 2601 Australia
E-mail: [email protected]
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Abstract ..................................................................................................3 1. Introduction .......................................................................................4
1.2. Plant growth and the environment ......................................................................5
1.3. Can we exploit plant adaptive capacity?.............................................................6
1.4. The virtue of model plants ..................................................................................7
1.5. Are domesticated plants different? .....................................................................8
2. Genetic approaches for improving abiotic stress tolerance.............9
2.2. Avoidance and escape reactions .......................................................................10
2.3. Constitutive vs. inducible stress tolerance ........................................................11
2.4. QTL analysis in the genomics era.....................................................................15
2.5. Next generation phenotyping methods .............................................................16
3. Components of abiotic stress responses ..........................................17
3.2. First things first: establishment of cellular protection ......................................19
3.3. Taking care of metabolic adjustment................................................................20
3.4. Do abiotic stress response pathways overlap? ..................................................22
3.5. Selection for tolerance to multiple abiotic stresses...........................................23
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1.1. Abiotic stresses: definition and impact on agriculture........................................4
2.1. Field or controlled environment phenotyping?...................................................9
3.1. The power of transcriptomics ...........................................................................17
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3.6. Transgenic approaches for abiotic stress tolerance...........................................25
4. Coordination of growth responses to abiotic stress........................27 4.1. Do plants have brains? ......................................................................................27 4.2. Growth inhibition responses .............................................................................28 4.3. Growth stimulation responses...........................................................................30 4.4. An old legend born again: auxins .....................................................................32 4.5. Coordination of environmental responses ........................................................33
5. Conclusions.......................................................................................35 Acknowledgements ..............................................................................37 References ............................................................................................38 Figure Legends.....................................................................................59
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Progress in improving abiotic stress tolerance of crop plants using classic breeding
and selection approaches has been slow. This has generally been blamed on the lack
of reliable traits and phenotyping methods for stress tolerance. In crops, abiotic stress
tolerance is most often measured in terms of yield-capacity under adverse weather
conditions. “Yield” is a complex trait and is determined by growth and developmental
processes which are controlled by environmental signals throughout the light cycle of
the plant. The use of model systems has allowed us to gradually unravel how plants
grow and develop, but our understanding of the flexibility and opportunistic nature of
plant development and its capacity to adapt growth to environmental cues is still
evolving. There is genetic variability for the capacity to maintain yield and
productivity under abiotic stress conditions in crop plants such as cereals.
Technological progress in various domains has made it increasingly possible to mine
that genetic variability and develop a better understanding about the basic mechanism
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human nutrition, the cereals.
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of plant growth and abiotic stress tolerance. The aim of this paper is not to give a detailed account of all current research progress, but instead to highlight some of the current research trends that may ultimately lead to strategies for stress-proofing crop species. The focus will be on abiotic stresses that are most often associated with climate change (drought, heat and cold) and those crops that are most important for
Abiotic stress/plant development/senescence/hormone regulation/cereals/crop yield
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1.1. Abiotic stresses: definition and impact on agriculture
Plants are immobile and depend on their environment for growth and development.
This environment is variable and challenges plants with abiotic stress situations
throughout their life cycle: light (quality and quantity), mineral nutrition (depletion
and toxicity, salinity), temperature (heat, cold) and water availability (drought,
flooding). Plant development is therefore flexible and adjustable to the environment.
During evolution, wild plant species have learned to adapt to their natural
environment and this has determined their geographical distribution. In agricultural
environments, crop productivity is usually well controlled by agronomical practices,
but crop losses due to extreme and unexpected weather events are unavoidable. The
prospect of having to meet food demands for a 34% increase of the global population
by 2050 is imminent . Crop yields will need boosting, but the higher frequency and
intensity of drought, heat and cold spells will also require crops that are better able to
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therefore be based on a thorough understanding of the complexity of plant growth and
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maintain productivity under sub-optimal conditions. The concept of “tolerance” and “sensitivity” of plants to abiotic stress situations can be difficult to measure. In model plants like Arabidopsis, tolerance is often measured as “survival”. In crop species like cereals maintenance of “yield” and “productivity” is for economical reasons more important than “survival”. The criteria to evaluate stress tolerance in crop plants must
developmental processes that ultimately correlate with maintenance of productivity.
Unfortunately, this knowledge is still evolving.
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5 Progress in cereal yield improvements has generally been slow and is starting to reach
a plateau, falling short of the annual yield increases required to meet 2050 food
demands . In rice and wheat it is estimated that annual rate of yield increase has so
far been primarily achieved through improved managing practices (mechanisation)
rather than through breeding and genetic gain [3, 4]. During the last decade significant
progress has been made in improving our understanding about plant physiology and
molecular biology and new technologies have placed us now in a better position to
improve the efficiency of crop breeding. Improved knowledge and advanced new
technologies may now provide us with an opportunity to improve the speed and
efficiency of breeding to boost crop yield and abiotic stress tolerance.
1.2. Plant growth and the environment
Plants continuously adjust growth and development, growing prolifically when
conditions are optimal and slowing down, arresting and even reversing growth (e.g.
abscission, senescence and cell death responses) under sub-optimal conditions - even
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is therefore not surprising that crop productivity attributes (yield, quality) are strongly
influenced by environmental variability (gene-environment interactions, GxE).
Consequently, the responsiveness of crop plants to abiotic stresses is equally variable
and is controlled by complex gene networks with epistatic interactions . In the
field, crop plants are continuously challenged by a combination of stresses which are
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when conditions are not life-threatening. This bidirectional growth adjustment mechanism is quite remarkable and poorly understood, but it may hold the key for improving abiotic stress tolerance. Plant growth is a measure of environmental input and adaptive capacity to a particular environment; some conditions can be controlled by humans (irrigation, fertilization etc.), but others are at the mercy of the weather. It
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6 often typical for that environment. Breeding activities are usually focused on specific
target environments, but this approach tends to improve adaptive traits that are
constitutively present and are relevant for that environment only. This approach may
have resulted in the loss of genetic variation from current breeding stock that would
allow the plant to maintain productivity under unexpected and/or more extreme stress
conditions. To identify germplasm that is better able to maintain productivity under
more challenging abiotic stress conditions, it will be necessary to increase the
selection standards and identify germplasm that is able to perform well under stress
1.3. Can we exploit plant adaptive capacity?
Plants in general (higher and lower plants) have a staggering capacity to adapt to
extreme environments and they can be found in most ecosystems of the globe. Some
grasses and flowering plants can be found on the Antarctic Peninsula , resurrection
plants are adapted to extremely hot and dry conditions [7, 8], while seagrasses are
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stress signalling and metabolic and developmental adaption mechanisms [8, 10].
Proof-of-concept transgenic approaches can be used to evaluate some of these
adaptation mechanisms (e.g., cryo- and osmo-protectants) in crop species such as
cereals. However, this may be difficult to achieve if genes of an entire metabolic
pathway need to be transferred and it may also compromise important yield and
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land plants that have re-adapted to life in a marine environment, surviving conditions of low light, high salt and anoxia in the sediment . Adaptation of plants to extreme environments requires complex morphological, developmental and metabolic adaptations. Exploring the molecular mechanisms of drought tolerance in resurrection plants and salt tolerance of halophytes has benefited our understanding about abiotic
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7 quality traits. Important morphological and developmental components that contribute
to abiotic stress tolerance simply cannot be transferred to cereals. Sourcing abiotic
stress tolerance traits from the available genetic variability in crop species, landraces
and progenitor species may be a more desirable approach.
1.4. The virtue of model plants
A small genome size has been an important criterion for the selection of model plants.
The simple dicot Arabidopsis has been a workhorse for advancing our understanding
of various plant biological processes, including plant development and response to
various abiotic stresses. Comparative genomics is starting to reveal important
differences between different model systems, suggesting that care is needed when
extrapolating information from model systems to other plants. For example, some
genes are missing in Arabidopsis that are present in other plants , while other
genes have diverged and evolved different functions in other plants. The control of
flowering and flower development differs considerably between eudicots
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has become faster and cheaper, which has made it possible to sequence larger plant
genomes. In addition to the rice genome, the genome sequences of four other
cultivated grasses (maize, sorghum, barley and wheat; www.gramene.org) and one
wild grass (Brachypodium; www.brachypodium.org) are now available, providing a
wealth of information for comparative genomics studies into the evolution of these
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(Arabidopsis) and monocots (rice, Brachypodium), even though the regulatory genes (e.g. MADS-box genes) identified in Arabidopsis are also present in monocots . In addition, it has been shown plants that many of the proteins with completely unknown function (POFs; proteins with obscure features) are species-specific and have no homologues in other species [15, 16]. In recent times, sequencing technology
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genomes (synteny, gene loss/conservation, gene divergence). This unstoppable
progress in sequencing technologies and genomics will ultimately reduce the reliance
on model systems.
1.5. Are domesticated plants different?
Domestication has turned wild ancestor varieties into cultivated crops that have a
different architecture and look vastly different from their progenitor species (e.g., rice:
Fig. 1). Selection for desirable traits has affected many plant developmental
processes, including yield-related traits (seed size and number), seed shattering, seed
dormancy, photoperiod and flowering time, palatability and overall shape and body
architecture [17, 18]. Comparative genomics is slowly revealing the effect of
domestication at the DNA level . Comparison of the wild rice (Oryza rufipogon)
and cultivated rice (O. sativa japonica) genome sequences reveals significant gene
loss in the cultivated species . A comparison between domesticated and wild
tomato revealed genes that underwent positive selection and many genes that showed
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ancestor plants and landraces are often more tolerant to abiotic stresses and this
genetic variability could be re-introduced in domesticated crops. This process has
started for cereals such as rice  and maize  using wide crosses between
progenitors and interbreeding relatives. In bread wheat, the reconstruction of synthetic
hexaploids from the respective wild ancestors aims to achieve a similar goal .
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shifts in gene expression levels . Some gene deletions, mutations and variation in gene expression may have directly or indirectly affected abiotic stress tolerance. In beans, two DREB2 loci (dehydration-responsive element binding transcription factor) shared high levels of sequence diversity in one bean locus but no variation in the other, suggesting that domestication may have affected one of these genes . Wild
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9 This process can be complicated by the lack of molecular markers for precision
breeding and the possible introduction of undesirable traits. These problems will be
discussed in more detail in the following chapter. Comparative genomics could also
be used to compare adaptation of crop species to abiotic stresses in different
environments and to compare genetic variability in stress tolerance . The
difference in growth responses to environmental conditions can also reside in more
subtle changes in gene functions (e.g., base pair substitutions). Identifying those
differences will take additional effort.
2. Genetic approaches for improving abiotic stress tolerance
2.1. Field or controlled environment phenotyping?
Controlled environments allow control over occurrence and timing of a stress during
plant development, as well as its duration and severity. It is also possible to
investigate the effect of a single abiotic stress at a time. This is a significant advantage
over field studies, where environmental conditions are typically variable and
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unpredictable. However, field environments remain difficult to simulate in growth chambers, even though technology is improving . Air humidity, variation of light quantity and quality throughout the day (blue and red light enrichments at sunrise and sunset, respectively) control important plant physiological processes, yet are often
ignored in controlled environments. Additionally, heat load caused by light bulbs can
sometimes cause heat stress problems [28, 29] and soil drought and frost events are
extremely hard to simulate in controlled environments. In the field, environmental
changes that cause stress in plants most often occur over several hours (in the case of
heat during the day or frosts overnight) or even over several days (in the case of
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10 drought). These gradual changes are difficult to replicate in controlled environments
and stresses are often imposed abruptly, causing a shock situation by not allowing the
plant to gradually adapt to the stress. Additionally, growing plants in pots that are too
small affects root development, which in the case of drought stress affects the severity
and the speed with which the stress is imposed [30, 31]. Despite these issues,
controlled environments are the only tool that allows the comparison between
different stress responses independently and when used with due care and reasonable
attention, they can help to analyse stress responses in terms of sensitivity of different
plant developmental stages and effect of treatment duration and severity. This is very
important for designing phenotyping methods and to make sure that lines with
different flowering times are stressed at the same developmental stage when
comparing different lines. Communication with breeders and farmers can identify
germplasm that performs better/worse in field stress conditions and this material can
then provide an excellent benchmark to establish “realistic” stress treatment
conditions that give identical rankings in growth chambers. It is equally important to
replicate controlled environment results under field conditions.
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flowering time [32, 33]. This is particularly troublesome when screening large
populations that segregate for flowering time genes. Flowering time is important for
optimizing grain yield in wheat, as flowering too early can result in cold and frost
damage and late flowering can result in poor yields due to drought and heat stress [34,
35]. Manipulating flowering time can also have adverse effects on yield; early-
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2.2. Avoidance and escape reactions Selecting germplasm that is tolerant to abiotic stress under field conditions is compromised by escape or avoidance responses. In wheat, the damage caused by terminal drought can be alleviated by escaping drought through alteration of
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11 maturing varieties have less chance to accumulate biomass compared to late maturing
varieties, which indirectly affects grain yield in wheat . Plants can also avoid
stress damage by adapting metabolic activity and growth rate. Accelerated growth
requires faster metabolism and mobilization of resources, while slowing down
metabolism and growth saves vital resources for passive survival of abiotic stress
conditions. Plants can use any of these tactics for survival in a particular environment.
In rice, ethylene response transcription factors (ERF) play an important role in
flooding tolerance [37, 38]. The ERF genes SNORKEL1 and 2 are important in deep-
water rice varieties, where elongation growth and outgrowing rising water levels
(escape response) is important for longer-term survival and grain production. In
contrast, another ERF-family member, SUBMERGENCE-1A (SUB1A), is important
in rice varieties that have to survive occasional short-term submergence and flooding
by transiently keeping growth and metabolic activity quiescent. Analysis of the
molecular basis indicates that the plant hormone ethylene plays an important role in
regulating elongation growth under stress conditions. The example of flooding
tolerance in rice illustrates the importance of regulating plant growth rate and
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2.3. Constitutive vs. inducible stress tolerance
Selection for yield-related traits in field environments has dominated crop breeding.
Traits such as growth vigour, biomass accumulation, harvest index (reproductive
biomass), stem carbohydrate levels, tiller number, plant height, water use and
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metabolic activity under stress conditions. Avoidance and escape reactions generally provide protection against abiotic stress through adjustment of growth rate and developmental processes. Understanding the molecular basis of these processes is important for understanding abiotic stress tolerance.
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12 transpiration efficiency, carbon isotope discrimination and root depth are important in
cereal breeding. These traits, together with improved management practises, have
improved vegetative growth of cereal crops, resulting in higher yield and productivity
[32, 33, 39-41]. Interestingly, for Australian wheat the yield gain was found to be
proportionally higher in the driest years compared to the better years even though
those traits were not specifically targeting drought conditions . This illustrates that
yield-based traits that boost vegetative growth, biomass accumulation and water use
efficiency generally benefit plant growth and resilience and contribute to higher yields
under abiotic stress conditions [3-5, 41, 42]. However, unexpected and more extreme
abiotic stress conditions still result in massive yield penalties, indicating that growth
vigour and biomass accumulation does not necessarily result in a better capacity to
maintain that yield potential when growth conditions during reproductive
development are not favourable . It is clear that an additional tolerance mechanism
is needed to convert or maintain the yield potential generated during the vegetative
stage to successful reproductive development and grain productivity. Sensitivity of
crops to various abiotic stresses are usually associated with phenotypes that are
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compromised as growth repression saves resources for later growth when conditions
have returned to normal . Even when this occurs, yield can never be recovered
because it is too late in the growing season and previously established biomass and
productivity has been lost. In many crops, growth repression can be an exaggeration
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indicative of growth arrest, generally including leaf senescence or cell death, severe tissue necrosis (e.g., frosts and salinity), stomatal closure and arrest of photosynthesis . At the reproductive stage, pollen sterility and abortion of grain development are similar growth repression phenotypes that cause major yield losses in cereals. Under shorter-duration or unexpected stress periods, survival of the plant is often not
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13 or an overly sensitive response to stress conditions. There may therefore be an
opportunity for increasing the threshold level at which growth repression takes place
in response to stresses, in order to maintain growth and productivity for as long as
possible. Interestingly, the two flooding tolerance mechanisms described earlier for
rice (section 2.2: growth acceleration versus metabolic quiescence) may be more
widely applicable for other abiotic stresses and the molecular understanding of
flooding tolerance may stimulate research on other abiotic stresses. An intriguing
question is whether avoidance and escape strategies should also be seen as part of the
plants overall strategy to tolerate abiotic stresses.
To identify crops that maintain growth and yield potential under adverse growth
conditions it is necessary to complement constitutively expressed yield traits with
traits that are induced and specifically expressed under stress conditions. Identifying
more stress-induced traits will have a positive effect for breeding stress-tolerant crops,
but also for improving our understanding of the underlying physiological and
molecular mechanism. Under stress conditions, plants require mechanisms to protect
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(irrigated, rain-fed, rainout shelter plots to compare water stress conditions) .
However, controlled environments offer significant advantages if precision-
phenotyping is required (see section 2.1). Leaf senescence is a stress-induced
phenotype and has received a lot of attention as a stress-induced trait. Selecting for
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their cellular machinery, metabolic adaptations and their capacity to sustain growth and development (see section 3). Selection for stress-inducible traits is more difficult to achieve, considering the unpredictability of field conditions and interference of avoidance and escape reactions. Field plots can be selected to target certain abiotic stresses (drought, heat, frost) or can be artificially modified to create stress conditions
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14 delayed foliar senescence (stay-green) and maintenance of stomatal conductance,
transpiration and photosynthesis during stress conditions are relatively easy
phenotypes to score . Significant improvements in drought tolerance have resulted
from proof-of-concept transgenic approaches manipulating cytokinin levels,
confirming that this trait contributes to stress tolerance . Leaf rolling is another
distinctive and easy to score heat and drought-induced phenotype. Reduction in leaf
area prevents transpiration and water loss and genetic variation for leaf rolling is
available in wheat and rice. However, leaf rolling does not always correlate with
drought tolerance, suggesting that it could be an escape rather than tolerance
mechanism [47, 48]. Osmotic adjustment is an inducible drought adaptation
mechanism that maintains leaf water potential through the synthesis of osmotically
active substances [44, 50]. Osmotic adjustment delays leaf senescence and leaf
rolling, maintains stomatal conductance and turgor pressure, thereby sustaining
growth under drought conditions . Despite its importance, osmotic adjustment has
so far remained a difficult trait to phenotype . Many abiotic stresses cause pollen
sterility and loss of fertility and grain yield in cereals [53, 54]. A phenotyping method
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building up a higher yield potential, stress-inducible traits are essential to sustain that
higher yield potential under adverse environmental conditions to maintain growth and
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for cold and drought-induced pollen sterility was established using controlled environments [55, 56] and the plant hormone abscisic acid (ABA) was shown to play a role in stress-induced pollen abortion [53, 57, 58]. Stress-inducible traits are less likely to have negative effects on productivity of crops under non-stress conditions. While yield traits that improve vegetative plant growth and development contribute to
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2.4. QTL analysis in the genomics era
Identifying genetic variation for abiotic stress tolerance in crops requires the tedious
and laborious process of establishing linkage maps using DNA-based molecular
markers: restriction fragment length polymorphism (RFLP), amplified fragment
length polymorphism (AFLP), random amplification of polymorphic DNA (RAPD),
cleaved amplified polymorphic sequences (CAPS) and simple sequence repeat (SSR,
microsatellite) markers. In the last decade, the shift to high-throughput technologies
such as Diversity Arrays (DArT; ) and Single Nucleotide Polymorphism markers
(SNP; ) has made the construction of high density genomic maps easier. The
identification of SNP markers was boosted by the availability of the genome sequence
for many crop species. 160,000 SNPs were identified in the non-repetitive genome
fraction of 20 different rice varieties . The availability of annotated genome
sequences and accurate high density SNP maps makes it easier to identify candidate
genes within QTL (Quantitative Trait Loci) regions [61, 62] and the lowering in
sequencing costs has made it possible to carry out genotyping by sequencing (GBS),
which further facilitates fine-mapping QTL . Genome-wide association studies
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(GWAS, ) also benefit from high density SNP maps and can be used for mapping abiotic stress tolerance loci. In wheat, the development of multi-parent advanced inter-cross populations (MAGIC) provides a powerful tool for mapping QTL .
Abiotic stress tolerance is typically controlled by a large number of QTL with
epistatic interactions and low phenotypic contribution and heritability. A
comprehensive overview of QTL for various abiotic stress-related traits can be
accessed at the Gramene and Plant Stress websites (archive.gramene.org/qtl/;
www.plantstress.com/files/qtls_for_ resistance.htm). Abiotic stress QTL mapping and
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16 genomic selection (GS) has so far not led to markers for routine use in marker-
assisted selection (MAS) for abiotic stress tolerance [41, 66, 67]. With the bottleneck
of genotyping removed, mapping of abiotic stress tolerance loci will depend on the
availability of reliable traits for phenotyping. The case of salinity tolerance in rice is a
good example that QTL analysis can lead to identification of candidate genes
provided that reliable phenotyping methods are available .
2.5. Next generation phenotyping methods
Considering the difficulties involved in direct selection for abiotic stress tolerance in
field or controlled environments, shifting from “observable” to molecular or
secondary traits that are highly correlated with abiotic stress tolerance, may improve
reliability of phenotyping procedures . Our understanding about the physiological
and molecular basis of stress responses has improved and technological progress in
the last decade has provided opportunities for high-throughput phenotyping.
Metabolomics is a promising technology that can now be used at a scale that is
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used to quantitatively and qualitatively evaluate components of cellular protection.
Hormone measurements can be used as indicators of developmental responses in
sensitive and tolerant germplasm (senescence or growth). Proteomics can also be used
for phenotyping abiotic stress responses, but protein expression profiling can be
technically more challenging (e.g., resolution limits of two-dimensional
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compatible with population screening and mQTL mapping. This technology was used to identify genes controlling several metabolites and quality-related traits [70-72], but can also be used to map mQTL for metabolite changes associated with abiotic stresses [73, 74]. Measuring diagnostic metabolites can be informative about the physiological state of plant tissues in response to drought, heat and cold and metabolomics can be
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17 electrophoresis and detection limits of mass spectrometry) and is harder to adapt for
high throughput screening . The development in recent years of various digital
imaging technologies has added even more opportunities for phenotyping [67, 76].
Non-destructive imaging can measure canopy properties that contribute to biomass
accumulation, as well as stress-related traits (photosynthesis, transpiration and leaf
senescence). This technology can be applied for high-throughput screening under
field or controlled environments [77-79]. New generation phenotyping technologies
are powerful but require some knowledge about the molecular and physiological basis
of abiotic stress phenotypes and the questions to be addressed.
3. Components of abiotic stress responses
3.1. The power of transcriptomics
While GxE interactions are considered problematic and something to avoid in plant
breeding, molecular biologists have used differential gene expression of stress-treated
versus unstressed plant material as a standard method to study abiotic stress
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responses. In the recent decade, large-scale transcriptome analyses using microarrays and more recently new generation sequencing technologies (RNA-seq) have proven to be a powerful tool for identifying genes and cellular processes that are affected by abiotic stresses . A massive amount of transcriptome information for different stresses and plant species is currently available in public databases.
Transcriptome information is starting to reveal how plants respond to various abiotic
stresses, but the full potential is still unexplored . Currently, about 40% of the
proteins encoded by a eukaryotic genome have an unknown function . It is
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18 estimated that between 18 and 38% of the eukaryotic proteome consists of proteins
without any defined domain or motif . Interestingly, when comparing the
Arabidopsis and rice proteins with totally unknown features (POFs) nearly half were
found to be species-specific and had no homolog in the other genome .
Obviously, identifying the function of these proteins will require species-specific
studies and this will be a major challenge. Finding the exact physiological function for
members of large gene families (e.g., transcription factors) can also be a complicated
and time-consuming process. In model plants such as Arabidopsis and rice, insertion
mutagenesis using T-DNA and transposons can be used to identify gene functions and
support the gene annotation process. In rice, about 60.49% of the nuclear genes have
been tagged with T-DNA or Tos17 transposon insertions , but the functional
characterization of these insertion mutants remains a major effort. In addition, the
function of some genes for which the insertion mutant phenotype is lethal cannot be
investigated. Another limitation is gene redundancy and lack of a clear phenotype for
some mutations. Over-expression and RNAi technology can also be used to reveal the
function of candidate genes in plants that can be transformed. Transcriptome analysis
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triggering early developmental responses, are likely to be present all the time and
simply require activation by upstream signals (e.g., phosphorylation). Identifying
those genes will require more fundamental approaches, ideally using model systems
in the first place (e.g., using mutagenesis approaches).
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needs support from other technologies to speed up the identification of unknown gene functions. A systems biology approach combining transcriptomics with proteomics and metabolomics can help this process [84, 85]. It is also important to realize that transcriptomics focuses on differentially expressed genes, while some genes that play an important role in the early stress signal perception and transduction events, or those
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3.2. First things first: establishment of cellular protection
Bacteria, yeast and animals have a general cellular stress response mechanism that
protects essential macromolecules (DNA, proteins and lipids) against oxidative stress
and removes damaged cells using a cell death response. The conservation of this
response in different life forms suggests that it is an ancient protection mechanism
against general stress situations. The minimal cellular stress response proteome
consists of 44 proteins with known function, including molecular chaperones (e.g.
heat shock proteins), various enzymes that repair DNA damage and various proteins
that protect against oxidative stress and reactive oxygen species (ROS), such as
superoxide dismutase and glutathione antioxidant defence pathway proteins .
Plants also activate a cellular protection mechanism in response to various stresses.
Little is known about macromolecule protection in plants, but chaperone proteins (e.g.
heat shock proteins) are induced by all abiotic stresses and their importance is
illustrated by the fact that an Escherichia coli gene encoding a cold shock protein that
functions as RNA chaperone can significantly improve tolerance to multiple stresses
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(cold, drought, heat) in transgenic rice and maize . The transformation of light into chemical energy during photosynthesis and the mitochondrial electron transport chain produce damaging free radicals . Regulation of intracellular redox homeostasis has been shown to control important metabolic pathways such as photosynthesis [89, 90] and is also important for regulating root and leaf
developmental processes [91, 92]. Superoxide, hydrogen peroxide and hydroxyl
radical production is induced in response to abiotic and biotic stresses and results in
activation of genes encoding ROS-detoxifying enzymes [93, 94]. Active oxygen
species such as hydrogen peroxide are generally considered as local and systemic
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20 signals in response to various stress situations [95, 96]. This indicates that plants may
have turned this early stress defence mechanism into a systemic warning signal to
protect different plant parts. Some oxidative stress-related genes are expressed in cells
associated with the vascular bundles , which is compatible with a systemic
signalling function of ROS [98-100]. Resistance to the ROS-generating herbicide
paraquat in Conyza bonariensis is correlated with a highly expressed constitutive
ROS detoxification system and cross-tolerance to environmental oxidants [101, 102].
Paraquat resistance in wheat and barley has been correlated with tolerance to water
stress and paraquat treatment has been evaluated as a screening system for abiotic
stress tolerance [103, 104]. Overexpression of peroxidase, catalase, superoxide
reductase and superoxide dismutase in transgenic plants has resulted in improved
tolerance to cold, drought, salinity and heat stress [105-108], while an ascorbate
deficient mutant in Arabidopsis caused a stress-sensitive phenotype . Cellular
protection in plants may also function as an intracellular and systemic signal to
regulate developmental processes. As a stress defence mechanism it may be essential
for all other aspects of the stress response to function and it could therefore act as an
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“enabling” mechanism that needs to be activated before other aspects of stress responses (biotic and abiotic) can be established (Fig. 2).
3.3. Taking care of metabolic adjustment
Changes in plant growth and development under abiotic stress conditions must be
associated with metabolic activity to provide the energy required to establish the
response. Firstly, the altered cellular environment requires changes in the cellular
machinery to be put in place; adaptations of translation initiation and protein folding
are commonly observed in stress-induced transcriptomes [110, 111]. Then, specially
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21 adapted metabolic proteins are induced early in the stress response (Fig. 2). Many
abiotic stresses shut down photosynthesis, while photosynthates are a crucial source
of energy. Sugars are transported from source to sink tissues via the phloem and are
important signals for growth and development, as well as response to various abiotic
stresses. Sugar signalling and metabolism are therefore tightly linked to growth
responses . ABA regulates stomatal conductance and photosynthetic activity,
causing vegetative growth retardation. This has been shown to contribute to
vegetative stage abiotic stress tolerance, but this growth repression also has a negative
effect on reproductive processes . Abiotic stresses repress the sucrose cleaving
enzyme cell wall invertase in anthers, preventing hexose supply for pollen
development and causing pollen sterility. ABA accumulation was shown to directly or
indirectly repress cell wall invertase expression. Tolerant wheat and rice germplasm
displayed different anther ABA homeostasis, maintaining lower ABA levels than
sensitive lines in response to cold and drought stress [55-57, 113]. Sugars and ABA
are known to regulate ethylene and senescence responses . Sugars are an
important growth signal in plants and are therefore tightly connected with the decision
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osmotic stresses such as drought, cold and salt stress and are tightly integrated with
signalling pathways for sugars, essential nutrients (nitrogen) and various hormones
[118-120]. The yeast SnRK (Sucrose non-fermenting related kinase) related protein
kinases KIN10 and KIN11 play a central role in coordinating sugar, stress and
517 518 519 520
to grow or repress growth and respond to abiotic stress (Fig. 2). The glycolytic enzyme hexokinase (HXK) is a cellular sugar sensor that cross-talks to several phytohormones . Other cellular components involved in regulation of metabolism in plants show some similarity to yeast. The Mitogen-Activated Protein Kinase (MAPK) [116, 117] and the Salt Overly Sensitive (SOS) pathways respond to
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22 developmental signals with metabolic pathways, activating gene expression via bZIP
transcription factors [121, 122]. The General Control Non-repressible related protein
kinase (GCN-2) phosphorylates translation initiation factor 2 (eIF2α) and is able to
sense free amino acid levels, respond to osmotic stresses and control protein synthesis
[123, 124]. Both SnRK1 and GCN-2 regulate nitrate reductase and nitrogen
metabolism [120, 121]. Further research is required to establish how this complex
metabolic regulation mechanism is controlled by environmental stimuli. The
conservation of the kinases that regulate fundamental metabolic pathways between
plants, yeast and animals illustrates their evolutionary importance.
3.4. Do abiotic stress response pathways overlap?
It has been demonstrated that treatment with one abiotic stress can provide “cross-
tolerance” or “hardening” to other stresses, including biotic stresses [125, 126]. Pre-
treatment of plants with the stress hormone ABA has a similar effect [127-129]. This
already suggests that there must be some functional overlap in the signalling and
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pollen fertility, induction of osmo-protectants by drought, cold and salinity) are also
shared by different stresses. Communication between sink and source tissues is
especially important under abiotic stress conditions when growth can be limited by
available resources. To fully understand the impact of abiotic stresses on plant growth
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response pathways of abiotic stresses. Osmotic stresses (drought, cold, salinity, heat) involve ABA and are therefore expected to share common components. Furthermore, transcriptome analyses have confirmed that early macromolecule and oxidative stress protection is recruited by most stresses and is a general stress response (Fig. 2). Some developmental and metabolic responses (e.g., growth adaptation, leaf senescence,
Page 22 of 65
it is essential to further unravel the relationships between metabolism and
552 Due to gene redundancy, different gene copies encoding proteins with the same
function can be activated under different stresses, suggesting that overlap between
different stresses could be larger at the protein level than at the transcript level. In
economical terms, it seems logical that plants will share the response to the initial
threat and mount stress-specific responses once the general response has created the
environment to make this possible (Fig. 2). A shared initial stress response may not
require many genes and some may have so far remained undetected in differential
gene expression studies. Regulation at the protein level, such as targeted protein
degradation using the ubiquitin proteasome, is commonly used by plant hormones to
regulate downstream developmental signalling . It is therefore possible that a
rather small - but critically important - part of the overlap between different abiotic
stress responses has so far escaped detection.
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arrest is taken in this early response mechanism and it is an important factor for
determining productivity and abiotic stress tolerance in crops. Selection for adaptation
to specific environments and productivity traits has affected many developmental
properties and may also have modified the early response mechanism to stress (Fig.
2). Selection against seed dormancy may have affected homeostasis of hormones that
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3.5. Selection for tolerance to multiple abiotic stresses Genetic diversity for abiotic stress tolerance is more likely to occur in the early response mechanism than in the stress-specific responses that depend on the initial response (Fig. 2). The decision to continue growth or induce senescence and growth
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24 play a role in stress tolerance (ABA, GA). Adaptation to seasonal conditions and
different environments in cereals has modified important growth processes such as
duration of photosynthesis, adaptation to day-length and altered rate of leaf
senescence, which may also have changed the interaction between plant hormones
(ethylene, cytokinins). The stay-green trait has therefore been thought of as a potential
domestication trait [45, 131]. Analysis of stay-green QTL (e.g., sorghum) could lead
to positional cloning and identification of new genes involved in this process [45,
In nature, frequent exposure to a combination of stresses may have selected a shared
genetic adaptation mechanism to those stresses. This may be the case for heat and
drought stress which often occur at the same time in field conditions [126, 133]. It
therefore makes sense to select germplasm that is tolerant to more than one abiotic
stress , especially since different abiotic stress responses may already share a
common initial response mechanism (Fig. 2). Germplasm that establishes the initial
response successfully may also be better able to establish a stress-specific response
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wheat lines that are tolerant to multiple abiotic stresses individually (drought, heat,
shading and cold). QTL mapping using this tolerant germplasm can also be used to
identify overlapping general stress-response QTL, as well as QTL that are specific for
different stresses. Obtaining high levels of abiotic stress tolerance may ultimately
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(Fig. 2). However, selecting germplasm that is tolerant to more than one stress using the combination of those stresses may be difficult to achieve because of quantitative and qualitative differences in tolerance to the combination of stresses and the difficulty to choose physiologically relevant selection conditions for the combination of stresses. We are currently using a step-wise selection procedure to first identify
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25 require combining both general stress response and stress-specific QTL. However, for
some traits it may be difficult to obtain tolerance to a combination of stresses; some
traits for drought (stomata closed to prevent water loss) and heat stress (open stomata
to reduce leaf temperature) are mutually exclusive .
3.6. Transgenic approaches for abiotic stress tolerance
It is common practice in molecular biology to use proof-of-concept transgenic
approaches (over-expression, RNAi) to evaluate candidate genes for their effect on
abiotic stress tolerance. Many genes have indeed been shown to improve abiotic stress
tolerance (; see Plant Stress website for a comprehensive listing:
www.plantstress.com/ files/abiotic-stress_gene.htm). These include transcription and
regulatory factors, osmo-protectants, hormone and oxidative stress-related genes,
molecular chaperones, transporters and various metabolic genes. Abiotic stress
tolerance for most of these genes was evaluated under controlled environment or
glasshouse conditions, using model systems such as Arabidopsis or tobacco and some
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tolerance may also be a contributing factor; in model plants tolerance is usually
measured as survival under vegetative stage stresses, while in crops maintenance of
productivity during reproductive stage stresses is important [136, 137]. The choice of
promoter to drive transgene expression is also important. Strong constitutive
promoters lead to ectopic expression of a transgene, potentially causing adverse
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were also evaluated in cereals (rice, wheat, barley, maize). Relatively few transgenic lines have so far made any impact for improving field abiotic stress tolerance . Potential explanations are that the field environment is much harsher, transgenes only partially improve the abiotic stress response or they improve response to one stress and not a combination of stresses. Differences in evaluation criteria for abiotic stress
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26 secondary effects on crop productivity. CBF/DREB transcription factors can improve
osmotic stress tolerance but result in stunted growth when using constitutive
promoters ; plants look normal when a strong drought-inducible promoter is
used that expresses the transgene only when required . The quantitative and
qualitative properties of the promoter driving a transgene may be particularly critical
in the case of transcription factors, hormone metabolic and signal transduction genes.
Using Arabidopsis as a model system it may be extremely difficult or impossible to
fully evaluate and predict potential adverse effects in crop species . In the case
of multigene families it is often difficult to find out which gene to use for
transformation. For instance, only a few aquaporin gene family members are affected
by stress and lead to improvement of drought tolerance in transgenic plants . For
large transcription factor families, trial and error approaches can identify which gene
has a positive effect on stress tolerance . Some transgenic approaches may result
in morphologically different plants where stress phenotypes are simply delayed (e.g.,
smaller leaf area reduce transpiration under drought), giving transgenics an unfair
advantage . Manipulation of cytokinin levels using a stress-induced promoter led
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multiple stresses (cold, drought and heat) in field experiments , suggesting that
focusing on the manipulation of the top of the stress signalling cascade using general
stress responsive genes may yield positive results.
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to delayed senescence and improved drought tolerance in rice under glasshouse conditions . It is possible that these transgenic lines may also perform well under field drought conditions, considering the field experience with stay-green plants. Interestingly, transgenic rice and maize plants expressing an E. coli cold shock protein
that acts as RNA chaperone in cellular protection resulted in improved tolerance to
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4. Coordination of growth responses to abiotic stress
4.1. Do plants have brains?
How are the early responses to abiotic stresses orchestrated by signals from the
environment? Higher animals are mobile and react to stress by escaping
environmental challenges. The brain processes environmental signals via the central
nervous system and regulates this mobility and escape reaction. The flexibility of
plant development in response to environmental change indicates that they have an
efficient systemic signalling mechanism that coordinates and orchestrates the
response to adverse environmental conditions. The plant vascular system bears some
resemblance to an animal central nervous system, sparking some speculation that
plants have a cellular communication mechanism similar to animals . Specific
proteins known to play a role as neurotransmitters in animals (e.g., glutamate
receptors, 14-3-3 proteins) are also encoded in plant genomes but they acquired
different functions when plants evolved into multicellular organisms. The vascular
system plays an important role in coordinating growth and development between the
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different plant parts , but the signalling mechanism is vastly different to that of animals. Plants have evolved their own systemic signals to drive growth and development (Fig. 2). Being photosynthetic organisms, they use photosynthates and the capacity to produce sugars as a resource signal for growth. They also adapted reactive oxygen species as a signal for abiotic stress. Plants have evolved their own
hormone signals, which are totally unlike animal hormones, to signal developmental
and growth responses. An emerging theme in plant biology is the observation that
many genes involved in hormone synthesis and signalling, e.g. those involved in ABA
synthesis and signalling [146, 58], are expressed in vascular parenchyma cells. This
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28 allows rapid signal perception and distribution via the vascular system, similar to a
nervous system but at a slower pace. Environmental signals can therefore be sensed in
any plant part and quickly spread throughout the plant, suggesting that plants have
essentially obviated the need for a central nervous system. Despite its importance, the
signal transmitting function of the vascular system still needs to be unravelled .
Understanding of how the signals (hormones, ROS, metabolites) themselves work is
gradually emerging. Auxins can be transported all over the plant using directional
efflux carriers and long-distance transporters and tissue-specific response mechanisms
make it possible to mount different auxin responses in different plant parts .
These different plant parts are pre-programmed to react differently to plant hormone
signals, explaining how environmental signals can have different but coordinated
responses. Hormonal signals therefore form an important link between the
environment and developmental processes. Plant evolution and global diversity is
testimony that plants have evolved efficient systems to manage and adapt to
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development and have been implicated in abiotic stress responses. A lot of progress
has been made in recent years in understanding their function. Plant hormones can be
growth-retarding (ABA, ethylene, jasmonic acid) or growth-promoting (auxin,
gibberellic acid, cytokinin). Two recently discovered plant hormones, brassinosteroids
 and strigolactones  act in conjunction with auxins and can be classified as
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4.2. Growth inhibition responses The key to understanding abiotic stress tolerance resides in understanding the plant’s capacity to accelerate/maintain or repress growth. Interaction between plant hormones must play an important role in this phenomenon. Most plant hormones play a role in
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29 growth promoting hormones, while salicylic acid functions in plant defence responses
to pathogens . The stress hormone ABA is implicated in stomatal closure and
regulation of plant water balance, which impairs photosynthesis and restricts growth
. ABA levels are up-regulated in response to osmotic stresses (drought, cold,
salinity) and heat stress. Higher ABA levels improve stress tolerance at the vegetative
level, but there is a compromise at the reproductive level. QTL analysis in maize
indicated that lines with higher root ABA levels had lower grain yield  and our
own work demonstrated that lower ABA levels in stressed anthers was correlated with
better cold and drought tolerance, as well as maintenance of anther sink strength in
rice . The ABA signalling pathway interacts with other hormones and sugar
signalling via the SnRK network [98, 123]. ABA’s restriction of photosynthesis and
photosynthate allocation to sink tissues may help in shorter periods of abiotic stress,
but is destructive under longer term stress conditions such as terminal drought. The
opposing effect of ABA on vegetative and reproductive structures indicates that it is
important to understand the effect of abiotic stress during plant development. The
success of transgenic approaches for manipulation of abiotic stress tolerance will
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tapetum [153, 154]. External application and stress-induced accumulation of ABA
results in senescence, but the role of ABA in this process is still unclear. ABA may
interact with the oxidative stress response that protects against senescence , but
may also cause senescence via interaction with ethylene. The role of ethylene in
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depend on carefully targeting the control of ABA homeostasis to particular tissues and growth stages.
Growth repression under abiotic stress conditions is associated with induction of leaf senescence (Fig. 3) or programmed cell death responses in tissues such as the anther
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30 inducing leaf senescence and inhibition of root elongation has been well investigated.
Antisense repression of ethylene biosynthesis inhibits senescence, and the limitation
of ethylene production has in many cases resulted in improved abiotic stress tolerance
. Ethylene can induce the biosynthesis of the growth-promoting hormone auxin
in a tissue-specific manner . The role of ethylene can therefore also be growth-
promoting; low light (etiolation) and shading conditions cause elongation growth in
shading-sensitive plants . Ethylene is therefore in a unique position to control
plant developmental processes: it can act as an inhibitor of growth, but also as a
growth promoter (Fig. 4).
Jasmonic acid can also induce senescence. In Arabidopsis, jasmonate-induced
senescence involves induction of the transcription factor WRKY57, which is
repressed by the growth hormone auxin . In addition, jasmonate induces
expression of ICE (Inducer of CBF Expression), thereby promoting freezing tolerance
in Arabidopsis . Ethylene and jasmonate can regulate each other’s homeostasis
via feedback regulation, producing a fine balance between growth repression
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Cytokinins counteract the effect of ethylene, preventing senescence and stimulating
sugar metabolism and sink strength. Over-expression of the cytokinin biosynthetic
gene isopentenyl transferase has been used to produce plants that show delayed
senescence (stay-green trait), increased biomass production and improved stress
tolerance [45, 131]. However, the stay-green trait is not always associated with
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(jasmonic acid) and growth stimulation (ethylene).
4.3. Growth stimulation responses The growth hormone group of cytokinins plays a role in controlling cell division.
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increased yield and productivity , suggesting that increased cytokinin levels
benefit vegetative growth but not reproductive development.
751 Gibberellins (GA) play a crucial role in the promotion of plant elongation growth. In
the absence of GA, elongation growth is restrained by DELLA nuclear proteins. In the
presence of GA, DELLA proteins bind to the GA-GID1 receptor complex, targeting it
for degradation by the ubiquitin-26S proteasome and thereby activating GA signalling
and elongation growth . Some DELLA mutants are unable to bind the GA-GID1
complex, causing it to escape proteasome degradation. This suppresses elongation
growth, causing a semi-dwarf phenotype. Other DELLA mutants abolish its
repression activity, resulting in a tall stature (slender); these mutants are also male
sterile, suggesting that DELLA proteins play a role in pollen development .
Mutations in GA biosynthesis genes and DELLA proteins with a semi-dwarf
phenotype increase yield in cereals and have formed the basis of the Green
Revolution . However, some GA-insensitive dwarf mutants in wheat (reduced
height; Rht) also have reduced pollen viability, which has been associated with
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CBF1 was shown to induce DELLA gene expression and activate GA catabolic genes,
causing growth repression [168, 169]. Stress-induced accumulation of ABA
antagonizes GA action by controlling DELLA activity . In addition, DELLA
proteins play a role in mounting a protective response to oxidative stress [169, 171].
765 766 767 768
reduced tolerance to abiotic stresses such as heat and drought [162, 164]. Interestingly, the growth-stimulation of GA can be counteracted by environmental stresses and hormones such as ethylene and auxins, which affect the growth restraining activity of DELLA proteins [165-167]. In Arabidopsis, the CBF/DREB cold-inducible transcription factors activate cold acclimation and freezing tolerance.
Page 31 of 65
The DELLA proteins obviously form a hub of hormonal and environmental
interactions that determine continuation or repression of growth in function of
environmental cues .
4.4. An old legend born again: auxins
Auxins were the first plant hormone to be discovered. The growth-promoting
properties of auxins have gained increasing prominence in recent years because of
their role in regulating development and response to abiotic stress. Auxins are
synthesized in the shoot apical meristem and are transported to neighbouring tissues
and over longer distances using efflux carriers and polar transporters respectively.
Auxins stimulate root growth and other tissue-specific responses throughout the plant
such as leaf and fruit senescence . In Arabidopsis this requires cross-talk with
jasmonic acid signalling and the transcription factor WRKY57 [161, 173, 174].
One of the oldest known effects of auxins is the control of apical dominance and
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have a role in stamen development and are actively synthesized in the anther,
controlling pollen development and anther dehiscence . Apical dominance may
play an important role in promoting reproductive development and grain yield in
cereals. Auxins are synthesized in the anthers towards maturity where they play a role
in anther senescence [178, 179]. At the start of reproductive development in cereals
789 790 791 792
shoot branching (tillering in cereals). Cutting the main stem of a plant removes the apical meristem where auxins are made, resulting in increased branching. The branching response involves interaction with strigolactone and requires adequate sugar supply to support axillary bud outgrowth [175, 176]. It has been demonstrated that auxin treatment improves fertility in heat-stressed barley plants . Auxins
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33 the shoot apex where auxins are synthesized changes into a flowering meristem. It
then develops into a spike containing the reproductive organs. The presence of auxin
biosynthesis in the floral organs at this stage might signify that apical dominance is
controlled by the reproductive structures. This function may be essential to direct
resources to the reproductive structures for seed production rather than investing them
in further vegetative growth. Abiotic stresses in cereals cause pollen sterility in
sensitive lines, resulting in increased tillering after the stress period (Fig. 3). This may
reflect the loss in apical dominance as a result of pollen sterility. An intriguing aspect
of auxins is that they regulate some aspects of plant development such as lateral root
development synergistically with ethylene and other hormones, while for some
aspects both hormones act antagonistically . Recent progress in understanding
plant hormone action is illustrating the complexity of cross-talk between different
plant hormones and the importance of controlling hormone homeostasis.
Understanding the intricacies of these interactions is important to unravel how genetic
variability in the network can affect how plants adapt to environmental change.
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in photomorphogenesis. Phytochromes respond to darkness (etiolation) and changes
in the red to far-red light ratio, which warns the plant about competing vegetation
(shade avoidance) . Phytochromes control many growth processes from seed
germination to reproductive development and they are well known to modulate biotic
and abiotic stress responses .The activated form of phytochrome moves to the
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4.5. Coordination of environmental responses Progress made in unravelling how plants react to low light conditions provided a clue as to how environmental signals regulate plant growth. Phytochrome photoreceptors react to changes in the ratio between red and far-red light and play an important role
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34 nucleus and forms a complex with members of the basic helix-loop-helix (bHLH)
transcription factors, the Phytochrome Interacting Factors (PIF). PIFs interact with
DELLA proteins; in the absence of GA, DELLA proteins bind to PIFs, preventing
them from regulating their target genes. In the presence of GA, DELLA proteins are
degraded, PIFs become functional and elongation growth is activated [161, 182, 183]
(Fig. 4). PIF transcription factors also activate auxin biosynthesis and their own
expression is controlled by the circadian clock; the Arabidopsis bZIP transcription
factor Hy5 (Elongated Hypocotyl) promotes photomorphogenesis by antagonizing PIF
action and the RING-motif E3 ligase COP1 (Constitutive Morphogenic) inhibits Hy5.
This pathway also influences CBF function and freezing tolerance . PIFs form in
combination with DELLA proteins a hub for the integration of signals from various
hormones [183, 185-187], day-length [184, 188], light quality [158, 184], as well as
sugars  (Fig. 4). Light quality is also important for the induction of CBF
transcription factors and activation of cold and frost tolerance [190, 191] and PIFs
play a role in regulating expression of DREB transcription factors that are required for
drought responses . Low red to far-red ratios lead to increased levels of ethylene
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converge into a single, complicated signalling hub that orchestrates plant growth
responses. This environmental response hub may explain why one abiotic stress can
improve the response to other stresses (section 3.4).
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, which affects the stability of the DELLA proteins  (Fig. 4). Induction of the ERF transcription factor SUB1A under flooding conditions prevents elongation growth by increasing DELLA levels, thereby inhibiting GA-mediated elongation growth [37, 38]. The PIF transcription factors also mediate cross-talk with ROS signalling . These findings demonstrate how different environmental stimuli
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In the last decade important progress has been made using model plants in
understanding how plants grow and develop and how they respond to changes in the
environment. This know-how is still fragmentary and needs to be extended to crop
plants. In important crop species such as cereals, it is important to maintain
productivity under abiotic stress conditions during the reproductive stage. Some crop
plants appear to overreact and switch to growth arrest too quickly, even when survival
is not immediately under threat. One way of improving stress tolerance and grain
productivity in cereals would be to increase the threshold level at which plants switch
from promotion to arrest of growth. At the vegetative stage, the stay-green trait has
achieved this by selecting for delayed senescence. Maybe an equivalent of the stay-
green trait is required to protect the reproductive stage and grain formation in cereals.
Seed production itself is a stress survival mechanism; seed can survive prolonged
stress conditions in dehydrated state and this guarantees the plant’s next generation.
This potential may have been lost from crop plants, but genetic diversity to
reintroduce this trait may still be available in breeding lines, landraces or wild
866 867 868 869
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progenitor species. This material can also be used to further improve our understanding of the hormonal interactions that control growth.
A lesson could be learned from flooding tolerance research, which showed that both growth arrest and acceleration can be beneficial – depending on the circumstances.
This response requires ethylene and ERF transcription factors. The molecular basis of
how flooding tolerance interacts with the environmental response hub can serve as a
guideline for other abiotic stresses. Response to shading also shares some of the hub
components used by flooding stress. Importantly, the example of flooding stress
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36 indicates that avoidance and/or escape reactions should not necessarily be treated as
different or independent from true tolerance responses. The common denominator is
“growth regulation”. It is crucial that we learn to understand how plants regulate
growth in function of environmental restraints; this may lead to strategies to
manipulate the threshold levels to switch from growth arrest to maintenance of
growth. Crop plants such as cereals, combined with current technologies, can help us
to reach that level of understanding.
Having a single regulatory hub to integrate all environmental responses and regulate
plant growth and development makes a lot of sense, but a lot of questions still need to
be answered. We need to get a better understanding about systemic signalling and the
relationship between vegetative and reproductive growth. During the stage of
flowering and seed production, a plant behaves quite differently from a plant during
vegetative growth. Even though there is a shared response system to the environment,
growth signals still need to be relayed to different plant parts and the effect in
different plant parts can be interpreted very differently. For instance, nitrogen
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environment. The use of Green Revolution genes in cereals has shown that reducing
stem elongation growth using semi-dwarf genes benefits grain yield, but there is a
trade-off in terms of abiotic stress tolerance and pollen fertility. Some semi-dwarf
mutations affect the function of DELLA proteins in the central hub controlling growth
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application can stimulate vegetative growth and repress reproductive development. In cereals, grain yield depends on successful interaction between both vegetative and reproductive growth. While management, agronomy and breeding practices have focused a lot on the vegetative establishment phase of cereals, relatively little is known about the control of reproductive development and its interaction with the
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37 and abiotic stress responses (Fig. 4). This raises the question whether high yield and
high abiotic stress tolerance are compatible – or not. There is a strong need to fully
understand the function of the central environmental response hub (e.g., role of PIF
family members, identification of still unknown components), but the use of model
systems only may not allow us to achieve this and genetic variation in crop species
should be included in these studies. Analysing this genetic variation using new
generation genotyping and phenotyping technologies has vastly improved and
identification of candidate stress tolerance genes is made easier using genomics.
Proof-of-function transgenic approaches may also lead to identification of genes that
can be used for stress-proofing cereals.
The technological revolution of the last decade has provided renewed hope for
improving abiotic stress tolerance in crops such as cereals, but it is clear that this
effort will increasingly require close interaction between plant scientists of different
disciplines, including bioinformaticians and engineers.
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of cited references in this review paper has been limited by journal policy. The author
apologises to those authors whose publications were not cited in this paper.
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R.D. is supported by grants from the Grains Research and Development corporation (GRDC, grants CSP00130, CSP00143 and CSP00175). The author thanks Jane Edlington and Holly Staniford for their help in preparing the manuscript. The number
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1. FAO, How to feed the world in 2050, http://www.fao.org, 2009.
2. G. Edmeades, T. Fischer, D. Byerlee, Can we feed the world in 2050? In: ‘Food security from sustainable agriculture, Proceedings of the 15th Agronomy
Conference 2010, 2010, Lincoln, New Zealand, pp. 15-19.
3. A.J. Hall, R.A. Richards, Prognosis for genetic improvement of yield potential
and water-limited yield of major grain crops, Field Crops Res. 143 (2013) 18-33.
4. R.A. Richards, J.R. Hunt, J.A. Kirkegaard, J.B. Passioura, Yield improvement and
adaptation of wheat to water-limited environments in Australia - a case study,
Crop Past. Sci. 65 (2014) 676-689.
935 936 937 938 939 940 941 942 943
6. L.A. Bravo, M. Griffith, Characterization of antifreeze activity in Antarctic plants,
adaptation in cereals, Crit. Rev. Plant Sci. 27 (2008) 377-412.
J. Exp. Bot. 56 (2005) 1189-1196.
5. J.L. Araus, G.A. Slafer, C. Royo, D. Serret, Breeding for yield potential and stress
7. D. Bartels, F. Salamini, Desiccation tolerance in the resurrection plant Craterostigma plantagineum. A contribution to the study of drought tolerance at
Ac ce p
the molecular level, Plant Physiol. 127 (2001) 1346-1353.
8. T.S. Gechev, C. Dinakar, M. Benina, V. Toneva, D. Bartels, Molecular mechanisms of desiccation tolerance in resurrection plants, Cell. Mol. Life Sci. 69 (2012) 3175-3186.
9. L. Wissler et al., Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life, BMC Evol. Biol. 11 (2011) 8.
10. S. Shabala, Learning from halophytes: physiological basis and strategies to
improve abiotic stress tolerance in crops, Ann. Bot. 112 (2013) 1209-1221
Page 38 of 65
948 949 950 951 952
effector, Plant J. 76 (2013) 800-810. 12. H. Yoshida, Y. Nagato, Flower development in rice, J. Exp. Bot. 62 (2011) 47194730.
11. J.P.B. Lloyd, B. Davies, SMG1 is an ancient nonsense-mediated mRNA decay
13. M. Ciaffi, A.R. Paolacci, O.A. Tanzarella, E. Porceddu, Molecular aspects of flower development in grasses, Sex. Plant Reprod. 24 (2011) 247-282.
14. K. Matsubara, K. Hori, E. Ogiso-Tanaka, M. Yano, Cloning of quantitative trait genes from rice reveals conservation and divergence of photoperiod flowering
pathways in Arabidopsis and rice, Front. Plant Sci. 5 (2014) 1-7.
958 959 960
16. M. Gollery, J. Harper, J. Cushman, T. Mittler, R. Mittler, POFs: what we don't know can hurt us, Trends Plant Sci. 12 (2007) 492-496. 17. B.L Gross, K.M. Olsen, Genetic perspectives on crop domestication, Trends Plant Sci. 15 (2010) 529-537.
18. R.S. Meyer, M.D. Purugganan, Evolution of crop species: genetics of
Ac ce p
obscure features. Genome Biol. 7 (2006) R57.
15. M. Gollery et al., What makes species unique? The contribution of proteins with
21. D. Koenig et al., Comparative transcriptomics reveals patterns of selection in
domesticated and wild tomato, Proc. Natl Acad. Sci. USA 110 (2013) E2655-
962 963 964 965
domestication and diversification. Nat. Rev. Genet. 14 (2013) 840-852.
19. K.M. Olsen, J.F. Wendel, A bountiful harvest: genomic insights into crop domestication phenotypes, Annu. Rev. Plant Biol. 64 (2013) 47-70.
20. H. Sakai, T. Itoh, Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis, BMC Genom. 11 (2010) 121-134.
Page 39 of 65
40 22. A.J. Cortés, D. This, C. Chavarro, S. Madriñán, M.W. Blair, Nucleotide diversity
patterns at the drought-related DREB2 encoding genes in wild and cultivated
common bean (Phaseolus vulgaris L.), Theor. Appl. Genet. 125 (2012) 1069-
23. B.J. Atwell, H. Wang, A.P. Scafaro, Could abiotic stress tolerance in wild
relatives of rice be used to improve Oryza sativa? Plant Sci. 215-216 (2014) 48-
981 982 983 984
wheat wild relatives and landraces, J. Exp. Bot. 58 (2007) 177-186. 26. .K. Mochida, K. Shinozaki K., Unlocking Triticeae genomics to sustainably feed the future, Plant Cell Physiol. 54 (2013) 1931-1950. 27. H. Poorter et al., The art of growing plants for experimental purposes: a practical guide for the plant biologist, Func. Plant Biol. 39 (2012) 821-838. 28. R.J. Downs, H. Hellmers, Environment and the experimental control of plant
Ac ce p
25. M. Reynolds, F. Dreccer, R. Trethowan, Drought-adaptive traits derived from
utilization, J. Biosci. 37 (2012) 843-855.
24. B.M. Prasanna, Diversity in global maize germplasm: characterization and
30. J.B. Passioura, the perils of pot experiments, Func. Plant Biol. 33 (2006) 1075-
986 987 988 989
growth, in: J.F. Sutcliffe, P. Mahlburg, Experimental Botany Vol. 6, 1975, Academic Press, London-New York-San Francisco, pp. 125-140.
29. I.G. Cummings, J.B. Reid, A. Koutoulis, Red to far-red ratio correction in plant growth chambers - growth responses and influence of thermal load on garden pea, Physiol. Plant. 131 (2007) 171-179.
Page 40 of 65
31. H. Poorter, J. Climent, D. Van Dusschoten, J. Bühler, J. Postma, Pot size matters:
a meta-analysis on the effect of rooting volume on plant growth, Func. Plant Biol.
39 (2012) 839-850. 32. D. Fleury, S. Jefferies, H. Kuchel, P. Langridge, Genetic and genomic tools to
improve drought tolerance in wheat, J. Exp. Bot. 61 (2010) 3211-3222.
33. R.A. Richards et al., Breeding for improved water productivity in temperate
cereals: phenotyping, quantitative trait loci, markers and the selection environment, Func. Plant Biol. 37 (2010) 85-97.
34. A. Greenup, W.J. Peacock, E.S. Dennis, B. Trevaskis, The molecular biology of
seasonal flowering-responses in Arabidopsis and the cereals, Ann. Bot. 103
35. B. Zheng, B. Biddulph, D. Li, H. Kuchel, S. Chapman, Quantification of the effects of VRN1 and Ppd-D1 to predict spring wheat (Triticum aestivum) heading
time across diverse environments, J. Exp. Bot. 64 (2013) 3747-3761. 36. P.A. Riffkin, P.M. Evans, J.F. Chin, G.A. Kearney, Early-maturing spring wheat outperforms late-maturing winter wheat in the high rainfall environment of south-
Ac ce p
39. R.A. Fischer, Understanding the physiological basis of yield potential in wheat, J.
1009 1010 1011 1012
1015 1016 1017
western Victoria. Austral. J. Agric. Res. 54 (2003) 193-202.
37. J. Bailey-Serres, L.A. Voesenek, Life in the balance: a signaling network controlling survival of flooding, Curr. Opin. Plant Biol. 13 (2010) 489-494.
38. J. Bailey-Serres et al., Making sense of low oxygen sensing, Trends Plant Sci. 17 (2012) 129-138.
Agric. Sci. 145 (2007) 99-113. 40. R.A. Fischer, Wheat physiology: a review of recent developments, Crop Pasture Sci. 62 (2011) 95-114.
Page 41 of 65
41. N.C. Collins, F. Tardieu, R. Tuberosa, Quantitative trait loci and crop
performance under abiotic stress: where do we stand? Plant Physiol. 147 (2008)
42. M.M. Chaves, J.P. Maroco, J.S. Pereira, Understanding plant responses to drought - from genes to the whole plant, Func. Plant Biol. 30 (2003) 239-264.
43. A. Guiboileau, R. Sormani, C. Meyer, C. Masclaux-Daubresse, Senescence and
death of plant organs: Nutrient recycling and developmental regulation, Comptes
Rendus Biologies 333 (2010) 382-391.
44. H. Sprigg, R. Belford, S. Milroy, S.J. Bennett, D. Bowran, Adaptations for
growing wheat in the drying climate of Western Australia, Crop Past. Sci. 65
45. H. Thomas, H. Ougham, The stay-green trait, J. Exp. Bot. 65 (2014) 3889-3900.
46. R.M. Rivero et al., Delayed leaf senescence induces extreme drought tolerance in
47. X.R.R. Sirault, A.G. Condon, G.J. Rebetzke, G.D. Farquhar, Genetic analysis of leaf rolling in wheat, in: R. Appels, R. Eastwood, E. Lagudah, P. Langridge, M.M.
Ac ce p
a flowering plant, Proc. Natl Acad. Sci. USA 104 (2007) 19631-19636.
49. J.M. Morgan, Osmoregulation and water stress in higher plants, Annu. Rev. Plant
1034 1035 1036 1037
Lynne (Eds.), Proceedings of the 11th International Wheat Genetic Symposium, Brisbane, Australia.
48. S. Bunnag, P. Pongthai, Selection of rice (Oryza sativa L.) cultivars tolerant to drought stress at the vegetative stage under field conditions, Am. J. Plant Sci. 4 (2013) 1701-1708.
Physiol. 35 (1984) 299-319.
Page 42 of 65
50. J.M. Morgan, Growth and yield of wheat lines with differing osmoregulative
capacity at high soil water deficit in seasons of varying evaporative demand, Field
Crops Res. 40 (1995) 143-152. 51. T.C. Hsiao, J.C. O'Toole, E.B. Yambao, N.C. Turner, Influence of osmotic
adjustment on leaf rolling and tissue death in rice (Oryza sativa L.), Plant Physiol.
75 (1984) 338-341.
52. R.C. Babu, M.S. Pathan, A. Blum, H.T. Nguyen, Comparison of measurement
methods of osmotic adjustment in rice cultivars, Crop Sci. 39 (1999) 150-158.
53. H.S. Saini, D. Aspinall, Sterility in wheat (Triticum aestivum L.) induced by water
deficit or high temperature: possible mediation by abscisic acid. Austral. J. Plant
Physiol. 9 (1982) 529-537.
54. N. Powell, X. Ji, R. Ravash, J. Edlington, R. Dolferus, Yield stability for cereals in a changing climate, Func. Plant Biol. 39 (2012) 539-552.
55. S.N. Oliver et al., Cold-induced repression of the rice anther-specific cell wall
invertase gene OSINV4 is correlated with sucrose accumulation and pollen
sterility, Plant Cell Envir. 28, (2005) 1534-1551.
1058 1059 1060 1061 1062 1063 1064
Ac ce p
56. X. Ji et al., Importance of pre-anthesis anther sink strength for maintenance of grain number during reproductive stage water stress in wheat, Plant Cell Envir. 33 (2010) 926-942.
57. S.N. Oliver, E.S. Dennis, R. Dolferus, ABA regulates apoplastic sugar transport and is a potential signal for cold-induced pollen sterility in rice, Plant Cell Physiol. 48 (2007) 1319-1330. 58. X. Ji et al., Control of ABA catabolism and ABA homeostasis is important for reproductive stage stress tolerance in cereals, Plant Physiol. 156 (2011) 647-662.
Page 43 of 65
59. D. Jaccoud, K. Peng, D. Feinstein, A. Kilian, Diversity arrays: a solid state
technology for sequence information independent genotyping, Nucl. Ac. Res. 29
60. J. Mammadov, R. Aggarwal, R. Buyyarapu, S. Kumpatla, SNP markers and their impact on plant breeding, Int. J. Plant Genom. 2012 (2012) 728398.
61. K.L. McNally et al., Genomewide SNP variation reveals relationships among
landraces and modern varieties of rice, Proc. Natl Acad. Sci. U.S.A 106 (2009)
62. M.W. Ganal et al., Large SNP arrays for genotyping in crop plants, J. Biosci. 37 (2012) 821-828.
63. J. Spindel et al, Bridging the genotyping gap: using genotyping by sequencing
(GBS) to add high-density SNP markers and new value to traditional bi-parental
mapping and breeding populations, Theor. Appl. Genet. 126 (2013) 2699-2716.
1080 1081 1082 1083 1084 1085
64. P.K. Gupta, P.L. Kulwal, V. Jaiswal, Association mapping in crop plants: opportunities and challenges, Adv. Genet. 85 (2014) 109-147. 65. B.E. Huang et al., A multiparent advanced generation inter-cross population for
Ac ce p
genetic analysis in wheat, Plant Biotechnol. J. 10 (2012) 826-839.
66. A. Nakaya, S.N. Isobe, Will genomic selection be a practical method for plant breeding? Ann. Bot. 110 (2012) 1303-1316.
67. J.N. Cobb, G. De Clerck, A. Greenberg, R. Clark, S. McCouch, Next-generation phenotyping: requirements and strategies for enhancing our understanding of
genotype-phenotype relationships and its relevance to crop improvement, Theor.
Appl. Genet. 126 (2013) 867-887.
Page 44 of 65
68. S. Negrão, B. Courtois, N. Ahmadi, I. Abreu, N. Saibo, M. Oliveira, Recent
updates on salinity stress in rice: from physiological to molecular responses, Crit.
Rev. Plant Sci. 30 (2011) 329-377. 69. J. Feng et al., Characterization of metabolite quantitative trait loci and metabolic
networks that control glucosinolate concentration in the seeds and leaves of
Brassica napus, New Phytol. 193 (2012) 96-108.
70. N. Carreno-Quitero et al., Untargeted metabolic quantitative trait loci analyses reveal a relationship between primary metabolism and potato tuber quality, Plant
Physiol. 158 (2012) 1306-1318.
71. Y. Wahyuni et al., Genetic mapping of semi-polar metabolites in pepper fruits
(Capsicum sp.): towards unraveling the molecular regulation of flavonoid
quantitative trait loci, Mol. Breeding 33 (2014) 503-518. 72. U. Roessner et al., Metabolic profiling allows comprehensive phenotyping of
genetically or environmentally modified plant systems, Plant Cell 13 (2001) 11-
73. C. Caldana et al., High density kinetic analysis of the metabolomics and
Ac ce p
75. I.A. Abreu et al., Coping with abiotic stress: Proteome changes for crop
1104 1105 1106 1107
1110 1111 1112
transcriptomic response of Arabidopsis to eight environmental conditions, Plant J. 67 (2011) 869-884.
74. C.B. Hill et al., Whole-genome mapping of agronomic and metabolomics trait to identify novel quantitative trait loci in bread wheat grown in a water-limited environment, Plant Physiol. 162 (2013) 1266-1281.
improvement, J. Prot. 93 (2013) 145-168. 76. F. Fiorani, U. Schurr, Future scenarios for plant phenotyping, Annu. Rev. Plant Biol. 64 (2013) 267-291.
Page 45 of 65
77. N. Honsdorf, T.J. March, B. Berger, M. Tester, K. Pillen, High-throughput
phenotyping to detect drought tolerance QTL in wild barley introgression lines,
Plos One 9 (2014) e97047.
78. B. Masuka, J.L. Araus, B. Das, K. Sonder, J.E. Cairns, Phenotyping for abiotic stress tolerance in maize, J. Integr. Plant Biol. 54 (2012) 238-249.
79. A. Ballvora et al., “Deep phenotyping” of early plant response to abiotic stress
using non-invasive approaches in barley, in: G. Zhang et al. (Eds.), Advance in
barley sciences: proceeding of 11th International Barley Genetics Symposium,
Chapter 26, Zhejiang University and Springer Science, Dordrecht, pp. 317-326.
80. O. Morozova, M.A. Marra, Applications of next-generation sequencing
technologies in functional genomics, Genomics 92 (2008) 255-264.
81. J. Kilian, F. Peschke, K.W. Berendzen, K. Harter, D. Wanke, Prerequisites, performance and profits of transcriptional profiling the abiotic stress response,
Biochim. Biophys. Acta 1819 (2012) 166-175. 82. K. Horan et al., Annotating genes of known and unknown function by large-scale coexpression analysis, Plant Physiol. 147 (2008) 41-57.
Ac ce p
Genet. 7 (2011) e1002020.
1129 1130 1131 1132
83. N. Wang, T. Long, W. Yao, L. Xiong, Q. Zhang, C. Wu, Mutant resources for the functional analysis of the rice genome, Mol. Plant 6 (2013) 596-604.
84. G.R. Cramer, K. Urano, S. Delrot, M. Pezzotti, K. Shinozaki, Effects of abiotic stress on plants: a systems biology perspective, BMC Plant Biol. 11 (2011) 163.
85. Y-S. Seo et al., Towards establishment of a rice stress response interactome, PLoS
86. D. Kültz, Molecular and evolutionary basis of the cellular stress response, Ann. Rev. Physiol. 67 (2005) 225-257.
Page 46 of 65
87. P. Castiglioni et al., Bacterial RNA chaperones confer abiotic stress tolerance in
plants and improved grain yield in maize under water-limited conditions. Plant
Physiol. 147 (2008) 446-455. 88. F.J. Schmitt et al., Reactive oxygen species: re-evaluation of generation,
monitoring and role in stress-signaling in phototrophic organisms, Biochim.
Biophys. Acta. 1837 (2014) 835-848.
Ann. Bot. 99 (2007) 3-8.
89. S. Debolt, V. Melino, C.M. Ford, Ascorbate as a biosynthetic precursor in plants,
90. A. Nunes-Nesi, R. Sulpice, Y. Gibon, A.R. Fernie, The enigmatic contribution of
mitochondrial function in photosynthesis, J. Exp. Bot. 59, 1675-1684.
91. Z. Chen, D.R. Gallie, Dehydroascorbate reductase affects leaf growth,
development and function, Plant Physiol. 142 (2006) 775-787. 92. E. Olmos, G. Kiddle, T.K. Pellny, S. Kumar, C.H. Foyer, Modulation of plant
morphology, root architecture, and cell structure by low vitamin C in Arabidopsis
thaliana, J. Exp. Bot. 57 (2006) 1645-1655.
1153 1154 1155 1156 1157
93. G. Noctor, A. Mhamdi, C.H. Foyer, The roles of reactive oxygen metabolism in
Ac ce p
drought: not so cut and dried, Plant Physiol. 164 (2014) 1636-1648.
94. M. Fujita et al., Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks, Curr. Opin. Plant Biol. 9 (2006) 436-442.
95. G.M. Pastori, C.H. Foyer, Common components, networks, and pathways of
cross-tolerance to stress. The central role of “redox” and abscisic acid-mediated
controls, Plant Physiol. 129 (2002) 460-468.
96. G. Kocsy et al., Redox control of plant growth and development, Plant Sci. 211 (2013) 77-91.
Page 47 of 65
97. D. Hérouart, M. Van Montagu, D. Inzé, Developmental and environmental
regulation of the Nicotiana plumbaginifolia cytosolic Cu/Zn-superoxide dismutase
promoter in transgenic tobacco, Plant Physiol. 104 (1994) 873-880.
and auxin perspective, Plant Cell Environ. 35 (2012) 321-333.
99. A. Baxter, R. Mittler, N. Suzuki, ROS as key players in plant stress signaling, J.
98. V.B. Tognetti, P. Mühlenbock, F. Van Breusegem, Stress homeostasis - the redox
Exp. Bot. 65 (2014) 1229-1240. 100.
A. Krishnamurthy, B. Rathinasabapathi, Oxidative stress tolerance in plants -
novel interplay between auxin and reactive oxygen species signaling, Plant Signal.
Behav. 8 (2013) e25761-1 - e25761-5. 101.
B. Ye, J. Gressel, Transient, oxidant-induced antioxidant transcript and
enzyme levels correlate with greater oxidant-resistance in paraquat-resistant
Conyza bonariensis, Planta 211 (2000) 50-61. 102.
Y. Shaaltiel, A. Glazer, P.F. Bocion, J. Gressel, Cross tolerance to herbicidal
and environmental oxidants of plant biotypes tolerant to paraquat, sulfur dioxide
and ozone, Pest. Biochem. Physiol. 31 (1988) 13-23.
1178 1179 1180 1181 1182 1183 1184
Ac ce p
A. Altinkut, K. Kazan, Z. Ipekci, N. Gozukirmizi, Tolerance to paraquat is
correlated with the traits associated with water stress tolerance in segregating F2 populations of barley and wheat, Euphytica 121 (2001) 81-86.
H.R. Lascano, M.N. Melchiorre, C.M. Luna, V.S. Trippi, Effect of photo-
oxidative stress induced by paraquat in two wheat cultivars with differential tolerance to water stress, Plant Sci. 164 (2003) 841-848.
Y.H. Kim et al., Overexpression of sweet potato swpa4 peroxidase results in
increased hydrogen peroxide production and enhances stress tolerance in tobacco,
Planta 227 (2008) 867-881.
Page 48 of 65
T. Matsumura, N. Tabayashi, Y. Kamagata, C. Souma, H. Saruyama, Wheat
catalase expressed in transgenic rice can improve tolerance against low
temperature stress, Physiol. Plant. 1167 (2002) 317-327. 107.
Y.J. Im, M. Ji, A. Lee, R. Killens, A.M. Grunden, W.F. Boss, Expression of
Pyrococcus furiosus superoxide reductase in Arabidopsis Enhances heat tolerance,
Plant Physiol. 151 (2009) 893-904.
S.R. Prashanth, V. Sadhasivam, A. Parida, Over expression of cytosolic
copper/zinc superoxide dismutase from a mangrove plant Avicennia marina in
indica Rice var Pusa Basmati-1 confers abiotic stress tolerance, Transgenic Res.
17 (2008) 281-291.
C. Huang, W. He, J. Guo, X. Chang, P. Su, L. Zhang, Increased sensitivity to
salt stress in an ascorbate-deficient Arabidopsis mutant, J. Exp. Bot. 56 (2005)
1202 1203 1204 1205 1206 1207
S. Echevarría-Zomeño et al., Regulation of translation initiation under biotic
and abiotic stresses, Int. J. Mol. Sci. 14 (2013) 4670-4683. 111.
J.X. Liu, S.H. Howell, Endoplasmic reticulum protein quality control and its
Ac ce p
relationship to environmental stress responses in plants, Plant Cell 22 (2010) 2930-2942.
Y.L. Ruan, Sucrose metabolism: gateway to diverse carbon use and sugar
signaling, Annu. Rev. Plant Biol. 65 (2014) 33-67.
N. Sreenivasulu, V.T. Harshavardhan, G. Govind, C. Seiler, A. Kohli,
Contrapuntal role of ABA: does it mediate stress tolerance or plant growth
retardation under long-term drought stress? Gene 506 (2012) 265-273.
Page 49 of 65
A. Wingler, T. Roitsch, Metabolic regulation of leaf senescence: interactions
of sugar signalling with biotic and abiotic stress responses, Plant Biol. 10 Suppl 1
1216 1217 1218 1219
networks controllng plant growth, Curr. Opin. Plant Biol. 13 (2010) 273-278. 116.
C. Jonak, L. Okrész , L. Bögre, H. Hirt, Complexity, cross talk and integration
S. Smeekens, J. Ma, J. Hanson, F. Rolland, Sugar signals and molecular
of plant MAP kinase signaling, Curr. Opin. Plant Biol. 5 (2002) 415-424. 117.
B. Wurzinger, A. Mair, B. Pfister, M. Teige, Cross-talk of calcium-dependent
protein kinase and MAP kinase signaling, Plant Signal. Behav. 6 (2011) 8-12. 118.
V. Chinnusamy, K. Schumaker, J.K. Zhu, Molecular genetic perspectives on
cross-talk and specificity in abiotic stress signalling in plants, J. Exp. Bot. 55
(2004) 225-236. 119.
H. Ji, J.M. Pardo, G. Batelli, M.J. Van Oosten, R.A. Bressan, X. Li, The Salt
Overly Sensitive (SOS) pathway: established and emerging roles, Mol. Plant 6
1226 1227 1228 1229 1230 1231 1232 1233
J. Martínez-Atienza et al., Conservation of the salt overly sensitive pathway in
Ac ce p
rice, Plant Physiol. 143 (2007) 1001-1012.
E. Baena-Gonsalez, F. Rolland, J.M. Thevelein, J. Sheen, A central integrator
of transcription networks in plant stress and energy signaling, Nature 448 (2007) 938-943.
J. Hanson, J. Smeekens, Sugar perception and signaling - an update, Curr.
Opin. Plant Biol. 12 (2009) 562-567. 123.
S.J. Hey, E. Byrne, N.G. Halford, The interface between metabolic and stress
signaling, Ann. Bot. 105 (2010) 197-203.
Page 50 of 65
E.H. Byrne et al., Overexpression of GCN2-type protein kinase in wheat has
profound effects on free amino acid concentration and gene expression, Plant
Biotech. J. 10 (2012) 328-340.
controlling cross-tolerance, Trends Plant Sci. 5 (2000) 241-246. 126.
R. Mittler, Abiotic stress, the field environment and stress combination,
Trends Plant Sci. 11 (2006) 15-19. 127.
C. Bowler, R. Fluhr, The role of calcium and activated oxygens as signals for
P.C. Larosa, A.K. Handa, P.M. Hasegawa, R.A. Bressan, Abscisic acid
accelerates adaptation of cultured tobacco cells to salt, Plant Physiol. 79 (1985)
A.J. Robertson, M. Ishikawa, L.V. Gusta, S.L. MacKenzie, Abscisic acid-
induced heat tolerance in Bromus inermis Leyss cell-suspension cultures. Heat-
stable, abscisic acid-responsive polypeptides in combination with sucrose confer
enhanced thermostability, Plant Physiol. 105 (1994) 181-190. S. Lu, W. Su, H. Li, Z. Guo, Abscisic acid improves drought tolerance of
triploid Bermuda grass and involves H2O2- and NO-induced antioxidant enzyme
Ac ce p
1250 1251 1252 1253
activities, Plant Physiol. Biochem. 47 (2009) 132-138.
D.R. Kelley, M. Estelle, Ubiquitin-mediated control of plant hormone
signaling, Plant Physiol. 160 (2012) 47-55.
P.L. Gregersen, A. Culetic, L. Boschian, K. Krupinska, Plant senescence and
crop productivity, Plant Mol. Biol. 82 (2013) 603-622. K. Harris et al., Sorghum stay-green QTL individually reduce post-flowering
drought-induced leaf senescence, J. Exp. Bot. 58 (2007) 327-338.
Page 51 of 65
K.S.V. Jagadish, J.E. Cairns, A. Kumar, I.M. Somayanda, P.Q. Craufurd,
Does susceptibility to heat stress confound screening for drought tolerance in rice?
Func. Plant Biol. 38 (2011) 261-269.
P. Ahmad et al., Role of transgenic plants in agriculture and biopharming,
Biotechnol. Adv. 30 (2012) 524-530. 135.
J. Deikman, M. Petracek, J.E. Heard, Drought tolerance through
biotechnology: improving translation from the laboratory to farmers' fields, Curr.
Opin. Biotechnol. 23 (2012) 243-250. 136.
Z. Peleg, M.P. Apse, E. Blumwald, Engineering salinity and water-stress
tolerance in crop plants: getting closer to the field, Adv. Bot. Res. 57 (2011) 405-
M. Reguera, Z. Peleg, E. Blumwald, targeting metabolic pathways for genetic
engineering abiotic stress-tolerance in crops, Biochim. Biophys. Acta 1819 (2012)
S.J. Oh, C.W. Kwon, D.W. Choi, S.I. Song, J.K. Kim, Expression of barley
HvCBF4 enhances tolerance to abiotic stress in transgenic rice. Plant Biotech. J. 5
Ac ce p
1273 1274 1275 1276
M. Kasuga, S. Miura, K. Shinozaki, K. Yamaguchi-Shinozaki, A combination
of the Arabidopsis DREB1A gene and stress-inducible rd29A promoter improved drought- and low-temperature stress tolerance in tobacco by gene transfer. Plant Cell Physiol. 45 (2004) 346-350. M. Ayada et al., Functional analysis of the durum wheat gene TdPIP2;1 and its
promoter region in response to abiotic stress in rice, Plant Physiol. Biochem. 79
Page 52 of 65
53 1281 1282 1283
S.J. Oh et al., Overexpression of the transcription factor AP37 in rice improves
grain yield under drought conditions. Plant Physiol. 150 (2009) 1368-1379. 142.
D.L. Lawlor, Genetic engineering to improve plant performance under
drought: physiological evaluation of achievements, limitations, and possibilities, J.
Exp. Bot. 64 (2013) 83-108. 143.
Z. Peleg, M. Reguera, E. Tumimbang, H. Walia, E. Blumwald, Cytokinin-
mediated source/sink modifications improve drought tolerance and increase grain
yield in rice under water-stress, Plant Biotechnol J. 9 (2011) 747-758.
A. Alpi et al., Plant neurobiology: no brain, no gain? Trends Plant Sci. 12
(2007) 135-136. 145.
K. Brackmann, T. Greb, Long- and short-distance signaling in the regulation
of lateral plant growth, Physiol. Plant. 151 (2013) 134-141. 146.
A. Endo et al., Drought induction of Arabidopsis 9-cis-epoxycarotenoid
dioxygenase occurs in vascular parenchyma cells, Plant Physiol. 147 (2008) 1984-
1297 1298 1299 1300 1301 1302 1303 1304
R. Spicer, Symplasmic networks in secondary vascular tissues: parenchyma
Ac ce p
distribution and activity supporting long-distance transport, J. Exp. Bot. 65 (2014) 1829-1848.
S. Vanneste, J. Friml, Auxin: a trigger for change in plant development, Cell
136 (2009) 1005-1016.
Y. Fridman, S. Savaldi-Goldstein, Brassinosteroids in growth control: how,
when and where, Plant Sci. 209 (2013) 24-31. 150.
P.B. Brewer, H. Koltai, C.A. Beveridge, Diverse roles of strigolactones in
plant development, Mol. Plant. 6 (2013) 18-28.
Page 53 of 65
54 1305 1306 1307
Z.Q. Fu, X. Dong, Systemic acquired resistance: turning local infection into
global defense, Annu. Rev. Plant Biol. 64 (2013) 839-863. 152.
P. Landi et al., Root-ABA1 QTL effects root lodging, grain yield, and other
agronomic traits in maize grown under well-watered and water-stressed
conditions, J. Exp. Bot. 58 (2006) 319-326.
1314 1315 1316 1317 1318
R.W. Parish, H.S. Phan, S. Iacunone, S.F. Li, Tapetal development and abiotic
stress: a centre of vulnerability, Func. Plant Biol. 39 (2012) 553-559. 155.
S. Gepstein, B.R. Glick, Strategies to ameliorate abiotic stress-induced plant
senescence, Plant Mol. Biol. 82 (2013) 623-633. 156.
P.O. Lim, H.J. Kim, H.G. Nam, Leaf senescence, Ann. Rev. Plant Biol. 58
A.N. Stepanova, J.M. Alonso, Ethylene signaling and response: where
different regulatory modules meet, Curr. Opin. Plant Biol. 12 (2009) 548-555. 157.
R. Pierik, D. Tholen, H. Poorter, E.J.W. Visser, L.A.C.J. Voesenek, The Janus
face of ethylene: growth inhibition and stimulation, Trends Plant Sci. 11 (2006)
1321 1322 1323 1324 1325
Ac ce p
K.A. Franklin, Shade avoidance, New Phytol. 179 (2008) 930-944.
Y. Jiang, G. Liang, S. Yang, D. Yu, Arabidopsis WRKY57 functions as a node
of convergence for jasmonic acid- and auxin-mediated signaling in jasmonic acidinduced leaf senescence, Plant Cell 26 (2014) 230-245.
Y. Hu, L. Jiang, F. Wang, D. Yua, Jasmonate regulates the INDUCER OF
FACTOR1 cascade and freezing tolerance in Arabidopsis, Plant Cell 25 (2013)
Page 54 of 65
55 1329 1330 1331
H. Claeys, S. De Bodt, D. Inzé, Gibberellins and DELLAs: central nodes in
growth regulatory networks, Trends Plant Sci. 19 (2014) 231-239. 162.
A.R.G. Plackett et al., DELLA activity is required for successful pollen
development in the Columbia ecotype of Arabidopsis, New Phytol. 210 (2014)
P. Hedden, The genes of the Green Revolution, Trends Genet. 19 (2003) 5-9.
F. Alghabari, M. Lukac, H.E. Jones, M.J. Gooding, Effect of Rht alleles on the
tolerance of wheat grain set to high temperature and drought stress during booting
and anthesis, J. Agron. Crop Sci. 200 (2014) 36-45.
P. Achard et al., Integration of plant responses to environmentally activated
phytohormonal signals, Science 311 (2006) 91-94. 166.
E.H. Colebrook, S.G. Thomas, A.L. Phillips, P. Hedden, The role of
gibberellin signalling in plant responses to abiotic stress, J. Exp. Biol. 217 (2014)
1345 1346 1347 1348 1349 1350 1351
X. Fu, N.P. Harberd, Auxin promotes Arabidopsis root growth by modulating
gibberellin response, Nature 421 (2003) 740-743.
Ac ce p
P. Achard et al., The cold-inducible CBF1 factor-dependent signalling
pathway modulates the accumulation of the growth-repressing DELLA proteins via its effect on gibberellin metabolism, Plant Cell 20 (2008) 2117-2129.
L.V. Kurepin et al., Role of CBFs as integrators of chloroplast Redox,
phytochrome and plant hormone signalling during cold acclimation, Int. J. Mol. Sci. 14 (2013) 12729-12763.
D. Golldack, C. Li, H. Mohan, N. Probst, Gibberellins and abscisic acid signal
crosstalk: living and developing under unfavorable conditions, Plant Cell Rep. 32
Page 55 of 65
P. Achard, J.P. Renou, R. Berthome, N.P. Harberd, P. Genschik, Plant
DELLAs retrain growth and promote survival of adversity by reducing the levels
of reactive oxygen species, Cur. Biol. 18, 656-660. 172.
Y. Jiang, G, Liang, S. Yang, D. Yu, Arabidopsis WRKY57 functions as a node
of convergence for jasmonic acid- and auxin-mediated signaling in jasmonic acid-
induced leaf senescence, Plant Cell 26 (2014) 230-245.
Q. Ma et al., Comprehensive insights on how 2,4-dichlorophenoxyacetic acid
retards senescence in post-harvest citrus fruits using transcriptomic and proteomic
approaches, J. Exp. Bot. 65 (2014) 61-74. 174.
C. Böttcher, C.A. Burbidge, P.K. Boss, C. Davies, Interactions between
ethylene and auxin are crucial to the control of grape (Vitis vinifera L.) berry
ripening, BMC Plant Biol. 13 (2013) 222.
1368 1369 1370 1371 1372 1373 1374 1375 1376
E.A. Dun, P.B. Brewer, C.A. Beveridge, Strigolactones: discovery of the
elusive shoot branching hormone, Trends Plant Sci. 14 (2009) 364-372. 176.
M.G. Mason, J.J. Ross, B.A. Babst, B.N. Wienclaw, C.A.Beveridge, Sugar
demand, not auxin, is the initial regulator of apical dominance, Proc. Natl Acad.
Ac ce p
Sci. USA. 111 (2014) 6092-6097.
T. Sakata et al., Auxins reverse plant male sterility caused by high
temperatures, Proc. Natl Acad. Sci. USA 107 (2010) 8569-8574.
V. Cecchetti, M.M. Altamura, G. Falasca, P. Costantino, M. Cardarelli, Auxin
regulates Arabidopsis anther dehiscence, pollen maturation, and filament elongation, Plant Cell 20 (2008) 1760-1774.
K. Hirano et al., Comprehensive transcriptome analysis of phytohormone
biosynthesis and signaling genes in microspore/pollen and tapetum of rice, Plant
Cell Physiol. 49 (2008) 1429-1450.
Page 56 of 65
1380 1381 1382 1383
F. Wang, X. Cui, Y. Sun, C.H. Dong, Ethylene signaling and regulation in
plant growth and stress responses, Plant Cell Rep. 32 (2013) 1099-1109. 181.
R.F. Carvalho, M.L. Campos, R.A. Azevedo, The role of phytochrome in
stress tolerance, J. Integr. Plant Biol. 53 (2011) 920-929. 182.
A. Castillon, H. Shen, E. Huq, Phytochrome Interacting Factors: central
players in phytochrome-mediated light signaling networks, Trends Plant Sci. 12,
P. Hornitschek et al., Phytochrome interacting factors 4 and 5 control seedling
growth in changing light conditions by directly controlling auxin signaling, Plant
J. 71 (2012) 699-711. 184.
P. Maibam et al., the influence of light quality, circadian rhythm, and
photoperiod on the CBF-mediated freezing tolerance, Int. J. Mol. Sci. 14 (2013)
K.A. Franklin et al., Phytochrome-interacting factor 4 (PIF4) regulates auxin
biosynthesis at high temperature, Proc. Natl Acad. Sci. USA 108 (2011) 20231-
1395 1396 1397 1398 1399 1400 1401 1402
Ac ce p
P. Leivar, P.H. Quail, PIFs: pivotal components in a cellular signaling hub,
Trends Plant Sci. 16 (2011) 19-28.
S.L. Lau, X.W. Deng, Plant hormone signaling lights up: integrators of light
and hormones, Curr. Opin. Plant Biol. 13 (2010) 571-577.
A. Sanchez, J. Shin, S.J. Davis, Abiotic stress and the circadian clock, Plant
Sign. Behav. 6 (2011) 223-231. 189.
I. Sairanen et al., Soluble carbohydrates regulate auxin biosynthesis via PIF
proteins in Arabidopsis, Plant Cell 24 (2012) 4907-4916.
Page 57 of 65
58 1403 1404 1405
K.A. Franklin, G.C. Whitelam, Light-quality regulation of freezing tolerance
in Arabidopsis thaliana, Nat. Genet. 39 (2007) 1410-1413. 191.
Z. Bieniawska et al., Disruption of the Arabidopsis circadian clock is
responsible for extensive variation in the cold-responsive transcriptome, Plant
Physiol. 147 (2008) 263-279. 192.
S. Kidokoro et al., The phytochrome-interacting factor PIF7 negatively
regulates DREB1 expression under circadian control in Arabidopsis, Plant
Physiol. 151 (2009) 2046-2057. 193.
D. Chen et al., Antagonistic basic helix-loop-helix/bZIP transcription factors
form transcriptional modules that integrate light and reactive oxygen species
signaling in Arabidopsis, Plant Cell 25 (2013) 1657-1673.
Ac ce p
Page 58 of 65
59 1414 1415
Figure Legends Figure 1: Effect of domestication in rice. Oryza rufipogon (top panel) is
considered to be the ancestor of cultivated rice (Oryza sativa; bottom panel). The
changes in development and overall appearance between the two lines are very
Figure 2: Proposed components of abiotic stress responses in plants.
Early responses to abiotic stress are likely to be general stress responses: cellular
protection of macromolecules and oxidative stress, metabolic adjustments and
hormonal changes that lead to developmental responses. Genetic variation in crop
species can lead to different responses in reaction to certain threshold levels of
abiotic stresses. Some germplasm will initiate a senescence response and stop
growth, with negative yield consequences. Other germplasm is more resilient and
1429 1430 1431 1432
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will maintain growth and productivity as much as possible. The latter phenotype will require successful interaction between the different early responses to establish stress-specific responses. Genetic variation can occur at different levels of the response pathway. QTL (stars with letter “Q”) in different parts of the general stress response will affect response to different abiotic stresses. QTL in
the stress-specific responses are predicted to only affect response to a particular
stress. Targeting the genetic variation in the general stress response could be more
successful, but may require additional QTL in the stress-specific responses. QTL
for stress-specific responses may have negative effects for other stresses.
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60 1437 Figure 3: Effect of drought stress at the reproductive stage in wheat. Drought
stress leads to extensive leaf senescence in wheat (top left). Re-watering results in
the development of new freshly green tillers that will flower and produce grains,
while grain development in the older stressed tillers is either aborted or leads to
spikes without grain (top right). The close-up pictures at the bottom show prolific
initiation of new tillers in response to re-watering after drought treatment.
Figure 4: Simplified schematic representation of the components involved in the
environmental response module that controls plant growth, based on the shade
avoidance response pathway in Arabidopsis. The PIF and DELLA proteins are
central regulators of growth and environmental responses in plants.
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61 Abiotic stresses affect yield and productivity of crop plants. Stress tolerance in crops correlates with maintenance of growth and productivity. Early stress-responsive genes control growth responses Selection strategies should use stress-induced traits and focus on early general stress response. Plant hormone interactions control development and abiotic stress tolerance.
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Oxidative Stress Q
Temperature Q Stress
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Stress Specific Responses
General Stress Response
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