Shade Avoidance Response Research Articles

Spatial Regulation of the Gene Expression Response to Shade in Arabidopsis Seedlings.

The shade avoidance response, which allows plants to escape from nearby competitors, is triggered by a reduction in the PFR form of phytochrome in response to shade. Classic physiological experiments have demonstrated that the shade signal perceived by the leaves is transmitted to the other parts of the plant. Recently, a simple method was developed to analyze the transcriptome in a single microgram tissue sample. In the present study, we adopted this method to conduct organ-specific transcriptomic analysis of the shade avoidance response in Arabidopsis seedlings. The shoot apical samples, which contained the meristem, basal parts of leaf primordia and short fragments of vasculature, were collected from the topmost part of the hypocotyl and subjected to RNA sequencing analysis. Unexpectedly, many more genes were up-regulated in the shoot apical region than in the cotyledons. Spotlight irradiation demonstrated that the apex-responsive genes were mainly controlled by phytochrome in the cotyledons. In accordance with the involvement of many auxin-responsive genes in this category, auxin biosynthesis was genetically shown to be essential for this response. In contrast, organ-autonomous regulation was more important for the genes that were up-regulated preferentially either in the cotyledons or in both the cotyledons and the apical region. Their responses to shade depended variously on auxin and PIFs (phytochrome-interacting factors), indicating the mechanistic diversity of the organ-autonomous response. Finally, we examined the expression of the auxin synthesis genes, the YUC genes, and found that three YUC genes, which were differently spatially regulated, co-ordinately elevated the auxin level within the shoot apical region.

Shade avoidance components and pathways in adult plants revealed by phenotypic profiling.

Shade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components.

Ectopic expression of a phytochrome B gene from Chinese cabbage (Brassica rapa L. ssp. pekinensis) in Arabidopsis thaliana promotes seedling de-etiolation, dwarfing in mature plants, and delayed flowering.

Phytochrome B (phyB) is an essential red light receptor that predominantly mediates seedling de-etiolation, shade-avoidance response, and flowering time. In this study, we isolate a full-length cDNA of PHYB, designated BrPHYB, from Chinese cabbage (Brassica rapa L. ssp. pekinensis), and we find that BrphyB protein has high amino acid sequence similarity and the closest evolutionary relationship to Arabidopsis thaliana phyB (i.e., AtphyB). Quantitative reverse transcription (RT)-PCR results indicate that the BrPHYB gene is ubiquitously expressed in different tissues under all light conditions. Constitutive expression of the BrPHYB gene in A. thaliana significantly enhances seedling de-etiolation under red- and white-light conditions, and causes dwarf stature in mature plants. Unexpectedly, overexpression of BrPHYB in transgenic A. thaliana resulted in reduced expression of gibberellins biosynthesis genes and delayed flowering under short-day conditions, whereas AtPHYB overexpression caused enhanced expression of FLOWERING LOCUS T and earlier flowering. Our results suggest that BrphyB might play an important role in regulating the development of Chinese cabbage. BrphyB and AtphyB have conserved functions during de-etiolation and vegetative plant growth and divergent functions in the regulation of flowering time.

RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean.

Weeds reduce yield in soybeans (Glycine max) through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate growing seasons. RNASeq data were collected from six biological samples of soybeans growing with or without weeds. Weed species and the methods to maintain weed-free controls varied between years to mitigate treatment effects, and to allow detection of general soybean weed responses. Soybean plants were not visibly nutrient- or water-stressed. We identified 55 consistently downregulated genes in weedy plots. Many of the downregulated genes were heat shock genes. Fourteen genes were consistently upregulated. Several transcription factors including a PHYTOCHROME INTERACTING FACTOR 3-like gene (PIF3) were included among the upregulated genes. Gene set enrichment analysis indicated roles for increased oxidative stress and jasmonic acid signaling responses during weed stress. The relationship of this weed-induced PIF3 gene to genes involved in shade avoidance responses in Arabidopsis provide evidence that this gene may be important in the response of soybean to weeds. These results suggest that the weed-induced PIF3 gene will be a target for manipulating weed tolerance in soybean.

Forced adaptation: plant proteins to fight climate change.

Increasing distress about climate change consequences is noticeable in daily press releases and science news articles. In the last 5 years more than 3 hundred thousand scientific articles included the terms “climate change,” “drought stress” and/or “climate adaptation” as a main topic. This build-up of energy devoted to understand climate change significance parallels the fact that any living organism must be able to cope with environmental changes to survive. Plant's sessile condition reinforces even more the need of an efficient adaptive response to counteract a suboptimal environment. Such adaptive strategies synchronize growth and development adjustments, as well as cellular and molecular activities, aimed at an efficient use of scarce resources, e.g., water. Plant hormones are often involved as systemic mediators of the perception and integration of environmental cues. For instance, abscisic acid (ABA) accumulation upon drought perception serves as an initial signal for long-term acclimation reactions, which eventually involve the differential expression of genes leading to changes in transcript and protein patterns (Valdes et al., 2013). Plant-specific homeodomain leucine-zipper (HD-Zip) class I genes have been for long time suggested as players in the signal transduction to adjust growth and development under stress circumstances (Soderman et al., 1996; Olsson et al., 2004), but it was not until recently that their specific regulatory mechanism within the drought-induced ABA signaling pathway was discovered (Valdes et al., 2012). The authors reported two Arabidopsis HD-Zip I transcription factors, named ATHB7 and ATHB12, down-regulating a number of genes encoding ABA-receptor proteins, in addition to up-regulating protein phosphatases type 2C. Both ABA receptors and protein phosphatases 2C are well established components of the ABA signaling pathway (Santiago et al., 2009). This fine modulation of the stress perception confers the plant with the capacity to adapt to exposure to constant levels of ABA, thus causing the ABA response to be transient in character and providing the plant with the possibility to turn on and off the adaptive response at will. Stress adaptation is essential to evolutionary fitness and, as such, it has been discovered that a similar biological function is retained by orthologous HD-Zip I proteins in many plant species (Song et al., 2012; Zhao et al., 2014). As previously mentioned, developmental changes and morphological alterations are part of the plant adaptation and, besides controlling stress responses, HD-Zip I genes have additional roles in controlling development (Ariel et al., 2010). An interesting point raised by Valdes et al. (2012) is that other HD-Zip genes sharing targets, but differing in expression patterns or dependence on specific external conditions may have similar functions in modulating the ABA signal perception. HD-Zip superfamily of transcription factors includes also class III, which are major polarity and patterning determinants (Prigge et al., 2005). A potential HD-Zip I/HD-Zip III antagonism in the control of ABA-receptor genes has been recently proposed (Brandt et al., 2014), manifesting that complex relationships between classes appear to lead the integration of environmental and developmental cues. Though class I and class III members do not seem to regulate the same ABA receptors (Liu et al., 2012; Valdes et al., 2012) it may be possible that both families oppositely regulate the expression of related genes in a cell-type specific manner (Brandt et al., 2014). Similar genetic interactions between proteins belonging to different class families have been described in the integration of shade escape control and leaf patterning (Brandt et al., 2012). Besides water availability, the plant environmental context is defined by additional, simultaneous external factors, e.g., light and temperature, and should these factors influence the transcript levels of HD-Zip proteins the dynamic behavior of the ABA-driven stress response becomes automatically dependent on such factors. This implies that cross-communication between different signaling systems should be mediated by the same HD-Zip proteins. In this sense, available genomic and proteomic data have predicted in silico interactions between genes early regulated in the shade-avoidance response and, ATHB7 and ATHB12 that highlight their potential participation also in light signaling pathways (Ciolfi et al., 2013). The intricate network established within this superfamily of transcription factors suggest that the plant-specific and evolutionary highly conserved HD-Zip proteins are crucial players modulating stress responses and may be linking patterning and adaptation by acting to adjust developmental programs to specific environmental situations.

Recipient of the 2014 molecular ecology prize: Johanna Schmitt.

Recipient of the 2014 molecular ecology prize: Johanna Schmitt.

How Potato Plants Take the Heat?

Potato is the third most important food crop in the world after rice and wheat. Because of its widely distributed cultivation and high yields, it is considered a critical species in terms of food security in face of a growing world population. However, potato is particularly vulnerable to high temperature during various stages of its life cycle. Elevated temperatures strongly suppress tuberization, negatively affect storage and shelf life of tubers and reduce fitness of seed potatoes. Breeding new heat-stress tolerant cultivars is therefore an urgent need for sustainable increases in potato production. To achieve this goal an integrated approach combining physiology, biochemistry and molecular genetics is followed to analyze the impact of elevated temperatures on source-sink relations of potato plants, potato tuber development, starch accumulation and tuber quality and tuber dormancy. First results indicate that heat effects source-sink relations by altered expression of the tuber inducing signal FT, by stimulating shade-avoidance responses of the shoot and by decreasing sink-strength of developing tubers. Sink strength of growing potato tubers is mainly regulated by the activity of sucrose synthase. Measuring sucrose synthase expression and activity of heat grown potato tubers revealed a significant down-regulation of the enzyme which is consistent with reduced tuber growth. Interestingly, genetic variation in the activity of sucrose synthase exists, potentially enabling selection of potato varieties with heat-tolerant sucrose synthase isoforms. Although FT seems to play a major role in regulating tuberization, sink-derived and additional source signals are likely to be involved in orchestrating the heat-induced shift in assimilate allocation. This assumption is based on experiments in which soil and air temperatures of pot grown potato plants were independently controlled in growth chambers and transcript as well as sugar and enzyme profiles were recorded. Results of this analysis and their implication to improve heat tolerance of potato plants will be discussed.

Shade Avoidance and the Regulation of Leaf Inclination in Rice

ABSTRACT: The shade avoidance syndrome is a morphologicaland physiological response when plants are exposed to shade. Recent work in Arabidopsis had begun to define the molecular components of the shade avoidance syndrome in dicotyledonous model plant. However, little is known about the shade avoidance response networks in agriculturally important monocotyledon crops such as rice. Here, we found that the degree of bending at the lamina joint is inversely proportional to the R:FR ratio. To elucidate which phytochrome is involved in this response, we did lamina joint inclination assay with the rice phytochrome-deficient mutants (osphyA, osphyB, and osphyC) and the wild type plants. Whereas the osphyA and osphyC knockout mutants bent at the lamina joint in the far-red rich condition as the wild type plants, the osphyB knockout mutants no longer bent at the lamina joint in the far-red rich condition. These results suggest that PHYB acts as a sole photoreceptor in the lamina joint inclination response in rice. Plant responses to shade (the reduced ratio of red light to far-red light) referred to as the shade avoidance syndrome (SAS). The phytochrome photoreceptors perceived R: FR ratio change, then control the adaptive responses such as stem elongation, leaf expansion, seed germination, leaf inclination, and flowering time

Different shades of JAZ during plant growth and defense.

Ever since their discovery as key regulators of the jasmonate (JA) signaling pathway, repressor proteins of the JASMONATE ZIM-domain (JAZ) family are rising stars in research on hormonal regulation of plant growth and defense. In plant cells, JAZ repressor proteins interact with an E3 ubiquitin ligase complex (SCFCOI1) that together functions as a JA receptor. In uninduced cells, JAZs block the activity of transcriptional regulators of JA responses by physically binding to them. Upon perception of bioactive JAs, JAZ proteins are rapidly degraded via the ubiquitin/26S proteasome-dependent proteolytic pathway. This releases the JAZ-bound transcription factors, resulting in the activation of downstream JA responses. JAs play a dominant role in regulating defense responses against herbivorous insects and necrotrophic pathogens, and in adaptive responses to beneficial soil-borne microbes. In addition, JAs have a signal function in a myriad of other processes, including abiotic stress reactions and plant growth responses to environmental cues. The JA pathway functions in the context of a complex network of hormone-regulated signaling pathways that, depending on the environmental or developmental condition, can act antagonistically or synergistically on each other to finely balance resource allocation between growth and defense and minimize fitness tradeoffs. In the process of balancing plant growth and defense, gibberellins (GAs) emerged as dominant antagonists of the JA signaling output. GAs regulate different aspects of plant growth via DELLA repressor proteins that block the activity of transcriptional regulators of GA responses by physically binding to them. Analogous to the role of JAZs in the JA pathway, DELLAs are degraded upon perception of GAs, resulting in the activation of downstream growth responses. Interestingly, DELLAs also interact with JAZs, thereby mutually limiting the cellular binding capacity to their cognate transcription factors. Consequently, GA-mediated degradation of DELLAs enhances the cellular binding capacity of JAZs to their cognate transcription factors, thus reducing the potential JA signaling output. This GA-mediated antagonistic effect on the JA pathway becomes apparent during the shade-avoidance response of plants that grow in dense vegetation stands. Shade-intolerant plant species respond to competition for light by increasing apical dominance and accelerating stem and petiole elongation. These growth and developmental responses occur in response to a drop in the red:far-red (R:FR) light ratio that is sensed by the phytochrome photoreceptors, predominantly phyB, and are GA-dependent through GA-mediated degradation of DELLA proteins. This allows them to outgrow neighboring plants, but at the cost of a reduced defensive capacity against necrotrophic pathogens and insect herbivores. In this issue of New Phytologist, Leone and co-workers zoomed in on the specific role of the Arabidopsis thaliana (Arabidopsis) JAZ10 protein in this process and shed light on the involvement of DELLAs in GA-JA crosstalk during the shade avoidance response. Besides growth-related hormones, also effector proteins of pathogens and plant growth-promoting mycorrhizal fungi have recently been shown to target JAZ repressor proteins, thereby changing the defense-related signaling circuitry for their own benefit. Hence, JAZ repressor proteins are emerging as central targets in the rewiring of the hormone-regulated signaling circuitry that regulates growth and defense.

CONSTANS-LIKE 7 (COL7) Is Involved in Phytochrome B (phyB)-Mediated Light-Quality Regulation of Auxin Homeostasis

Arabidopsis phytochrome B (phyB) is the major photoreceptor that senses the ratio of red to far-red light (R:FR) to regulate the shade-avoidance response (SAR). It has been hypothesized that altered homeostasis of phytohormones such as auxin and strigolactone is at least partially responsible for SAR, but the mechanism underlying phyB regulation of the hormonal change is not fully understood. Previously we reported that CONSTANS-LIKE 7 (COL7) enhances branching number under high R:FR but not under low R:FR, implying that COL7 may be involved in the phyB-mediated SAR. In this study, we provide evidence that COL7 reduces auxin levels in a high R:FR-dependent manner. We found that the phyB mutation suppresses the COL7-induced branching proliferation. Moreover, COL7 promotes mRNA expression of SUPERROOT 2 (SUR2), which encodes a suppressor of auxin biosynthesis, in high R:FR but not in low R:FR. Consistently with these results, deficiency of phyB suppresses the elevated transcription of SUR2 in COL7 overexpression plants grown in high R:FR. Taking these results together with data suggesting that photo-excited phyB is required for stabilization of the COL7 protein, we argue that COL7 is a critical factor linking light perception to changes in auxin level in Arabidopsis.

UV-B detected by the UVR8 photoreceptor antagonizes auxin signaling and plant shade avoidance.

Plants detect different facets of their radiation environment via specific photoreceptors to modulate growth and development. UV-B is perceived by the photoreceptor UV RESISTANCE LOCUS 8 (UVR8). The molecular mechanisms linking UVR8 activation to plant growth are not fully understood, however. When grown in close proximity to neighboring vegetation, shade-intolerant plants initiate dramatic stem elongation to overtop competitors. Here we show that UV-B, detected by UVR8, provides an unambiguous sunlight signal that inhibits shade avoidance responses in Arabidopsis thaliana by antagonizing the phytohormones auxin and gibberellin. UV-B triggers degradation of the transcription factors PHYTOCHROME INTERACTING FACTOR 4 and PHYTOCHROME INTERACTING FACTOR 5 and stabilizes growth-repressing DELLA proteins, inhibiting auxin biosynthesis via a dual mechanism. Our findings show that UVR8 signaling is closely integrated with other photoreceptor pathways to regulate auxin signaling and plant growth in sunlight.

Light intensity modulates the regulatory network of the shade avoidance response in Arabidopsis.

Plants such as Arabidopsis thaliana respond to foliar shade and neighbors who may become competitors for light resources by elongation growth to secure access to unfiltered sunlight. Challenges faced during this shade avoidance response (SAR) are different under a light-absorbing canopy and during neighbor detection where light remains abundant. In both situations, elongation growth depends on auxin and transcription factors of the phytochrome interacting factor (PIF) class. Using a computational modeling approach to study the SAR regulatory network, we identify and experimentally validate a previously unidentified role for long hypocotyl in far red 1, a negative regulator of the PIFs. Moreover, we find that during neighbor detection, growth is promoted primarily by the production of auxin. In contrast, in true shade, the system operates with less auxin but with an increased sensitivity to the hormonal signal. Our data suggest that this latter signal is less robust, which may reflect a cost-to-robustness tradeoff, a system trait long recognized by engineers and forming the basis of information theory.

Upland Cotton Gene GhFPF1 Confers Promotion of Flowering Time and Shade-Avoidance Responses in Arabidopsis thaliana

Extensive studies on floral transition in model species have revealed a network of regulatory interactions between proteins that transduce and integrate developmental and environmental signals to promote or inhibit the transition to flowering. Previous studies indicated FLOWERING PROMOTING FACTOR 1 (FPF1) gene was involved in the promotion of flowering, but the molecular mechanism was still unclear. Here, FPF1 homologous sequences were screened from diploid Gossypium raimondii L. (D-genome, n = 13) and Gossypium arboreum L. genome (A-genome, n = 13) databases. Orthologous genes from the two species were compared, suggesting that distinctions at nucleic acid and amino acid levels were not equivalent because of codon degeneracy. Six FPF1 homologous genes were identified from the cultivated allotetraploid Gossypium hirsutum L. (AD-genome, n = 26). Analysis of relative transcripts of the six genes in different tissues revealed that this gene family displayed strong tissue-specific expression. GhFPF1, encoding a 12.0-kDa protein (Accession No: KC832319) exerted more transcripts in floral apices of short-season cotton, hinting that it could be involved in floral regulation. Significantly activated APETALA 1 and suppressed FLOWERING LOCUS C expression were induced by over-expression of GhFPF1 in the Arabidopsis Columbia-0 ecotype. In addition, transgenic Arabidopsis displayed a constitutive shade-avoiding phenotype that is characterized by long hypocotyls and petioles, reduced chlorophyll content, and early flowering. We propose that GhFPF1 may be involved in flowering time control and shade-avoidance responses.

Interactions between Auxin, Microtubules and XTHs Mediate Green Shade- Induced Petiole Elongation in Arabidopsis

Plants are highly attuned to translating environmental changes to appropriate modifications in growth. Such phenotypic plasticity is observed in dense vegetations, where shading by neighboring plants, triggers rapid unidirectional shoot growth (shade avoidance), such as petiole elongation, which is partly under the control of auxin. This growth is fuelled by cellular expansion requiring cell-wall modification by proteins such as xyloglucan endotransglucosylase/hydrolases (XTHs). Cortical microtubules (cMTs) are highly dynamic cytoskeletal structures that are also implicated in growth regulation. The objective of this study was to investigate the tripartite interaction between auxin, cMTs and XTHs in shade avoidance. Our results indicate a role for cMTs to control rapid petiole elongation in Arabidopsis during shade avoidance. Genetic and pharmacological perturbation of cMTs obliterated shade-induced growth and led to a reduction in XTH activity as well. Furthermore, the cMT disruption repressed the shade-induced expression of a specific set of XTHs. These XTHs were also regulated by the hormone auxin, an important regulator of plant developmental plasticity and also of several shade avoidance responses. Accordingly, the effect of cMT disruption on the shade enhanced XTH expression could be rescued by auxin application. Based on the results we hypothesize that cMTs can mediate petiole elongation during shade avoidance by regulating the expression of cell wall modifying proteins via control of auxin distribution.

Light Regulation of Plant Defense

Precise allocation of limited resources between growth and defense is critical for plant survival. In shade-intolerant species, perception of competition signals by informational photoreceptors activates shade-avoidance responses and reduces the expression of defenses against pathogens and insects. The main mechanism underlying defense suppression is the simultaneous downregulation of jasmonate and salicylic acid signaling by low ratios of red:far-red radiation. Inactivation of phytochrome B by low red:far-red ratios appears to suppress jasmonate responses by altering the balance between DELLA and JASMONATE ZIM DOMAIN (JAZ) proteins in favor of the latter. Solar UVB radiation is a positive modulator of plant defense, signaling through jasmonate-dependent and jasmonate-independent pathways. Light, perceived by phytochrome B and presumably other photoreceptors, helps plants concentrate their defensive arsenals in photosynthetically valuable leaves. The discovery of connections between photoreceptors and defense signaling is revealing novel mechanisms that control key resource allocation decisions in plant canopies.

Photobiological Interactions of Blue Light and Photosynthetic Photon Flux: Effects of Monochromatic and Broad‐Spectrum Light Sources

Photosynthesis (Pn) and photomorphogenesis (Pm) are affected by light quality, light intensity and photoperiod. Although blue light (BL) is necessary for normal development, it is less efficient in driving Pn than other wavelengths of photosynthetically active radiation. The effects of BL on Pm are highly species dependent. Here we report the interacting effects of BL and photosynthetic photon flux (PPF) on growth and development of lettuce, radish and pepper. We used light-emitting diode (LED) arrays to provide BL fractions from 11% to 28% under broad-spectrum white LEDs, and from 0.3% to 92% under monochromatic LEDs. All treatments were replicated three times at each of two PPFs (200 and 500 μmol m(-2) s(-1)). Other than light quality, environmental conditions were uniformly maintained across chambers. Regardless of PPF, BL was necessary to prevent shade-avoidance responses in radish and lettuce. For lettuce and radish, increasing BL reduced stem length, and for both species, there were significant interactions of BL with PPF for leaf expansion. Increasing BL reduced petiole length in radish and flower number in pepper. BL minimally affected pepper growth and other developmental parameters. Pepper seedlings were more photobiologically sensitive than older plants. Surprisingly, there were few interactions between monochromatic and broad-spectrum light sources.

A reverse genetics approach identifies novel mutants in light responses and anthocyanin metabolism in petunia

Flower color and plant architecture are important commercially valuable features for ornamental petunias (Petunia x hybrida Vilm.). Photoperception and light signaling are the major environmental factors controlling anthocyanin and chlorophyll biosynthesis and shade-avoidance responses in higher plants. The genetic regulators of these processes were investigated in petunia by in silico analyses and the sequence information was used to devise a reverse genetics approach to probe mutant populations. Petunia orthologs of photoreceptor, light-signaling components and anthocyanin metabolism genes were identified and investigated for functional conservation by phylogenetic and protein motif analyses. The expression profiles of photoreceptor gene families and of transcription factors regulating anthocyanin biosynthesis were obtained by bioinformatic tools. Two mutant populations, generated by an alkalyting agent and by gamma irradiation, were screened using a phenotype-independent, sequence-based method by high-throughput PCR-based assay. The strategy allowed the identification of novel mutant alleles for anthocyanin biosynthesis (CHALCONE SYNTHASE) and regulation (PH4), and for light signaling (CONSTANS) genes.

Seedling development in buckwheat and the discovery of the photomorphogenic shade‐avoidance response

Numerous botanists of the early 19th century investigated the effect of sunlight on plant development, but no clear picture developed. One hundred and fifty years ago, Julius Sachs (1863) systematically analysed the light-plant relationships, using developing garden nasturtium (Tropaeolum majus) and seedlings of buckwheat (Fagopyron esculentum) as experimental material. From these studies, Sachs elucidated the phenomenon of photomorphogenesis (plant development under the influence of daylight) and the associated 'shade-avoidance response'. We have reproduced the classical buckwheat experiments of Sachs (1863) and document the original shade-avoidance syndrome with reference to hypocotyl elongation and cotyledon development in darkness (skotomorphogenesis), white light and shade induced by a canopy of green leaves. In subsequent publications, Sachs elaborated his concepts of 1863 and postulated the occurrence of 'flower-inducing substances'. In addition, he argued that the shade-avoidance response in cereals, such as wheat and maize, is responsible for lodging in crowded plant communities. We discuss these processes with respect to the red- to far-red light/phytochrome B relationships. Finally, we summarise the phytochrome B-phytohormone (auxin, brassinosteroids) connection within the cells of shaded Arabidopsis plants, and present a simple model to illustrate the shade-avoidance syndrome. In addition, we address the relationship between plant density and health of the corresponding population, a topic that was raised for the first time by Sachs (1863) in his seminal paper and elaborated in his textbooks.

Dynamics of the Shade-Avoidance Response in Arabidopsis

Shade-intolerant plants perceive the reduction in the ratio of red light (R) to far-red light (FR) as a warning of competition with neighboring vegetation and display a suite of developmental responses known as shade avoidance. In recent years, major progress has been made in understanding the molecular mechanisms underlying shade avoidance. Despite this, little is known about the dynamics of this response and the cascade of molecular events leading to plant adaptation to a low-R/FR environment. By combining genome-wide expression profiling and computational analyses, we show highly significant overlap between shade avoidance and deetiolation transcript profiles in Arabidopsis (Arabidopsis thaliana). The direction of the response was dissimilar at the early stages of shade avoidance and congruent at the late ones. This latter regulation requires LONG HYPOCOTYL IN FAR RED1/SLENDER IN CANOPY SHADE1 and phytochrome A, which function largely independently to negatively control shade avoidance. Gene network analysis highlights a subnetwork containing ELONGATED HYPOCOTYL5 (HY5), a master regulator of deetiolation, in the wild type and not in phytochrome A mutant upon prolonged low R/FR. Network analysis also highlights a direct connection between HY5 and HY5 HOMOLOG (HYH), a gene functionally implicated in the inhibition of hypocotyl elongation and known to be a direct target of the HY5 transcription factor. Kinetics analysis show that the HYH gene is indeed late induced by low R/FR and that its up-regulation depends on the action of HY5, since it does not occur in hy5 mutant. Therefore, we propose that one way plants adapt to a low-R/FR environment is by enhancing HY5 function.

Perception of low red:far‐red ratio compromises both salicylic acid‐ and jasmonic acid‐dependent pathogen defences in Arabidopsis

In dense stands of plants, such as agricultural monocultures, plants are exposed simultaneously to competition for light and other stresses such as pathogen infection. Here, we show that both salicylic acid (SA)-dependent and jasmonic acid (JA)-dependent disease resistance is inhibited by a simultaneously reduced red:far-red light ratio (R:FR), the early warning signal for plant competition. Conversely, SA- and JA-dependent induced defences did not affect shade-avoidance responses to low R:FR. Reduced pathogen resistance by low R:FR was accompanied by a strong reduction in the regulation of JA- and SA-responsive genes. The severe inhibition of SA-responsive transcription in low R:FR appeared to be brought about by the repression of SA-inducible kinases. Phosphorylation of the SA-responsive transcription co-activator NPR1, which is required for full induction of SA-responsive transcription, was indeed reduced and may thus play a role in the suppression of SA-mediated defences by low R:FR-mediated phytochrome inactivation. Our results indicate that foraging for light through the shade-avoidance response is prioritised over plant immune responses when plants are simultaneously challenged with competition and pathogen attack.