Shade Avoidance Syndrome Research Articles

Functional analysis of PHYB polymorphisms in Arabidopsis thaliana collected in Patagonia.

Arabidopsis thaliana shows a wide range of natural genetic variation in light responses. Shade avoidance syndrome is a strategy of major adaptive significance that includes seed germination, elongation of vegetative structures, leaf hyponasty, and acceleration of flowering. Previously, we found that the southernmost Arabidopsis accession, collected in the south of Patagonia (Pat), is hyposensitive to light and displays a reduced response to shade light. This work aimed to explore the genetic basis of the shade avoidance response (SAR) for hypocotyl growth by QTL mapping in a recently developed 162 RIL population between Col-0 and Pat. We mapped four QTL for seedling hypocotyl growth: WL1 and WL2 QTL in white light, SHADE1 QTL in shade light, and SAR1 QTL for the SAR. PHYB is the strongest candidate gene for SAR1 QTL. Here we studied the function of two polymorphic indels in the promoter region, a GGGR deletion, and three non-synonymous polymorphisms on the PHYB coding region compared with the Col-0 reference genome. To decipher the contribution and relevance of each PHYB-Pat polymorphism, we constructed transgenic lines with single or double polymorphisms by using Col-0 as a reference genome. We found that single polymorphisms in the coding region of PHYB have discrete functions in seed germination, seedling development, and shade avoidance response. These results suggest distinct functions for each PHYB polymorphism to the adjustment of plant development to variable light conditions.

Genetic and transcriptome analyses reveal the candidate genes and pathways involved in the inactive shade-avoidance response enabling high-density planting of soybean.

High-density planting is a major way to improve crop yields. However, shade-avoidance syndrome (SAS) is a major factor limiting increased planting density. First Green Revolution addressed grass lodging problem by using dwarf/semi-dwarf genes. However, it is not suitable for soybean, which bear seeds on stalk and whose seed yield depends on plant height. Hence, mining shade-tolerant germplasms and elucidating the underlying mechanism could provide meaningful resources and information for high-yield breeding. Here, we report a high-plant density-tolerant soybean cultivar, JiDou 17, which exhibited an inactive SAS (iSAS) phenotype under high-plant density or low-light conditions at the seedling stage. A quantitative trait locus (QTL) mapping analysis using a recombinant inbred line (RIL) population showed that this iSAS phenotype is related to a major QTL, named shade-avoidance response 1 (qSAR1), which was detected. The mapping region was narrowed by a haplotype analysis into a 554 kb interval harboring 44 genes, including 4 known to be key regulators of the SAS network and 4 with a variance response to low-light conditions between near isogenic line (NIL) stems. Via RNA-seq, we identified iSAS-specific genes based on one pair of near isogenic lines (NILs) and their parents. The iSAS-specific genes expressed in the stems were significantly enriched in the “proteasomal protein catabolic” process and the proteasome pathway, which were recently suggested to promote the shade-avoidance response by enhancing PIF7 stability. Most iSAS-specific proteasome-related genes were downregulated under low-light conditions. The expression of genes related to ABA, CK, and GA significantly varied between the low- and normal-light conditions. This finding is meaningful for the cloning of genes that harbor beneficial variation(s) conferring the iSAS phenotype fixed in domestication and breeding practice.

ParentalDNAmethylation influences plasticity of early offspring traits, but offspringDNAmethylation influences trait plasticity throughout life

AbstractPlants alter their phenotypes in response to both their own environment and that of their parents. Parental environments are hypothesized to more strongly regulate early life stages of offspring, while offspring environments regulate later life stages, since offspring perception becomes more accurate throughout development. DNA methylation in plants is known to respond to environmental conditions and can be transmitted across generations, so DNA methylation of both parents and offspring may be involved in regulating responses to environments within and across generations. However, the relative contribution of each generation's epigenetic regulation is not known. We quantified phenotypic responses to parent and offspring canopy environment and tested whether parental or offspring DNA methylation mediated those responses. To quantify the response to parental versus offspring canopy, we used green filter during the growth of either parents or offspring. To test the contribution of parental versus offspring DNA methylation to regulate offspring phenotypic responses to canopy shade at seed, seedling, and adult life stages, we manipulated parental or offspring DNA methylation using 5‐azacytidine. Both parent and offspring shade affected offspring traits. Parental DNA demethylation affected trait responses to both parental and offspring canopy, but it did so only at early life stages, while offspring DNA demethylation influenced responses throughout life. Trait correlations were significantly altered by chemical demethylation of parents and offspring, indicating that DNA methylation in both generations influences integrated phenotypic responses to canopy. These results demonstrate that the influence of parental methylation on offspring phenotypes measured in this study were manifest only early in the life of offspring, while offspring phenotypes were more strongly influenced by their own epigenetic regulation at mature stages. DNA methylation of both parents and offspring appears to coordinate multitrait responses like the “shade avoidance syndrome.”

Comparative proteomics analysis of Arabidopsis thaliana response to light-emitting diode of narrow wavelength 450 nm, 595 nm, and 650 nm

Incident light is a central modulator of plant growth and development. However, there are still open questions surrounding wavelength-specific plant proteomic responses. Here we applied tandem mass tag based quantitative proteomics technology to acquire an in-depth view of proteome changes in Arabidopsis thaliana response to narrow wavelength blue (B; 450 nm), amber (A; 595 nm), and red (R; 650 nm) light treatments. A total of 16,707 proteins were identified with 9120 proteins quantified across all three light treatments in three biological replicates. This enabled examination of changes in the abundance for proteins with low abundance and important regulatory roles including transcription factors and hormone signaling. Importantly, 18% (1631 proteins) of the A. thaliana proteome is differentially abundant in response to narrow wavelength lights, and changes in proteome correlate well with different morphologies exhibited by plants. To showcase the usefulness of this resource, data were placed in the context of more than thirty published datasets, providing orthogonal validation and further insights into light-specific biological pathways, including Systemic Acquired Resistance and Shade Avoidance Syndrome. This high-resolution resource for A. thaliana provides baseline data and a tool for defining molecular mechanisms that control fundamental aspects of plant response to changing light conditions, with implications in plant development and adaptation. SignificanceUnderstanding of molecular mechanisms involved in wavelength-specific response of plant is question of widespread interest both to basic researchers and to those interested in applying such knowledge to the engineering of novel proteins, as well as targeted lighting systems. Here we sought to generate a high-resolution proteomic profile of plant leaves, based on exposure to specific narrow-wavelength lights. Although changes in plant physiology in response to light spectral composition is well documented, there is limited knowledge on the roles of specific light wavelengths and their impact. Most previous studies have utilized relatively broad wavebands in their experiments. Such multi-wavelengths lights trigger diverse and complex signaling networks that pose major challenges in inference of wavelength-specific molecular processes that underly the plant response. Moreover, most studies have compared the effect of blue and red wavelengths comparing with FL, as control. As FL light consists the mixed spectra composition of both red and blue as well as numerous other wavelengths, comparing undeniably results in inconsistent and overlapping responses that will hamper effects to elucidate the plant response to specific wavelengths [1, 2]. Monitoring plant proteome response to specific wavelengths and further contrasting the changes with one another, rather than comparing plants proteome to FL, is thus necessary to gain detailed insights on underlying biological pathways and their consequences in plant physiology. Here, we employed narrow wavelength LED lights in our design to eliminate a potential overlap in molecular responses by ensuring non-overlapping wavelengths in the light treatments. We further applied TMT-labeling technology to gain a high-resolution view on the proteome changes. Our proteomics data provides an in-depth coverage suitable for system-wide analyses, providing deep insights on plant molecular response particularly because of the tremendous increase in the coverage of identified proteins which outreach the other biological data.

Creation of two hyperactive variants of phytochrome B1 for attenuating shade avoidance syndrome in maize

Increasing the planting density of maize is an effective measure to improve its yield. However, plants under high planting density tend to trigger shade avoidance syndrome (SAS), reducing lodging resistance and ultimately yield drop. Phytochrome B (phyB) plays a dominant role in mediating shade avoidance response. This study constructed two hyperactive mutated alleles of maize PHYB1: ZmPHYB1Y98F (mimicking Y104F of AtPHYB) and ZmPHYB1Y359F (mimicking Y361F of AtPHYB). Ectopic expression of ZmPHYB1Y98F and ZmPHYB1Y359F under the control of the ZmPHYB1 promoter in the Arabidopsis phyB-9 background rendered enhanced activity on complementing the phyB-9 related phenotypes compared with ZmPHYB1WT. Moreover, similar to the behavior of ZmPHYB1WT, ZmPHYB1Y98F and ZmPHYB1Y359F proteins are localized to the nucleus after red light exposure, and could interact with PIF proteins of maize. In addition, expression of ZmPHYB1Y98F and ZmPHYB1Y359F variants under the control of the native ZmPHYB1 promoter attenuated SAS of maize seedlings subjected to simulated shade treatment. It effectively reduced mature maize's plant height and ear height in field conditions. The results combined demonstrate the utility of ZmPHYB1Y98F and ZmPHYB1Y359F for attenuating SAS and breeding high density-tolerant varieties of maize.

Effects of Light Quality on Colonization of Tomato Roots by AMF and Implications for Growth and Defense.

Beneficial soil microbes can enhance plant growth and defense, but the extent to which this occurs depends on the availability of resources, such as water and nutrients. However, relatively little is known about the role of light quality, which is altered during shading, resulting a low red: far-red ratio (R:FR) of light. We examined how low R:FR light influences arbuscular mycorrhizal fungus (AMF)-mediated changes in plant growth and defense using Solanum lycopersicum (tomato) and the insect herbivore Chrysodeixis chalcites. We also examined effects on third trophic level interactions with the parasitoid Cotesia marginiventris. Under low R:FR light, non-mycorrhizal plants activated the shade avoidance syndrome (SAS), resulting in enhanced biomass production. However, mycorrhizal inoculation decreased stem elongation in shaded plants, thus counteracting the plant’s SAS response to shading. Unexpectedly, activation of SAS under low R:FR light did not increase plant susceptibility to the herbivore in either non-mycorrhizal or mycorrhizal plants. AMF did not significantly affect survival or growth of caterpillars and parasitoids but suppressed herbivore-induced expression of jasmonic acid-signaled defenses genes under low R:FR light. These results highlight the context-dependency of AMF effects on plant growth and defense and the potentially adverse effects of AMF under shading.

Development and carotenoid synthesis in dark-grown carrot taproots require PHYTOCHROME RAPIDLY REGULATED1.

Light stimulates carotenoid synthesis in plants during photomorphogenesis through the expression of PHYTOENE SYNTHASE (PSY), a key gene in carotenoid biosynthesis. The orange carrot (Daucus carota) synthesizes and accumulates high amounts of carotenoids in the taproot that grows underground. Contrary to other organs, light impairs carrot taproot development and represses the expression of carotenogenic genes, such as DcPSY1 and DcPSY2, reducing carotenoid accumulation. By means of RNA sequencing, in a previous analysis, we observed that carrot PHYTOCHROME RAPIDLY REGULATED1 (DcPAR1) is more highly expressed in the underground grown taproot compared with those grown in light. PAR1 is a transcriptional cofactor with a negative role in shade avoidance syndrome regulation in Arabidopsis (Arabidopsis thaliana) through the dimerization with PHYTOCHROME-INTERACTING FACTORs (PIFs), allowing a moderate synthesis of carotenoids. Here, we show that overexpressing AtPAR1 in carrot increases carotenoid production in taproots grown underground as well as DcPSY1 expression. The high expression of AtPAR1 and DcPAR1 led us to hypothesize a functional role of DcPAR1 that was verified through in vivo binding to AtPIF7 and overexpression in Arabidopsis, where AtPSY expression and carotenoid accumulation increased together with a photomorphogenic phenotype. Finally, DcPAR1 antisense carrot lines presented a dramatic decrease in carotenoid levels and in relative expression of key carotenogenic genes as well as impaired taproot development. These results suggest that DcPAR1 is a key factor for secondary root development and carotenoid synthesis in carrot taproot grown underground.

A genome-wide analysis suggests pleiotropic effects of Green Revolution genes on shade avoidance in wheat.

A classic example of phenotypic plasticity in plants is the suit of phenotypic responses induced by a change in the ratio of red to far-red light (R∶FR) as a result of shading, also known as the shade avoidance syndrome (SAS). While the adaptive consequences of this syndrome have been extensively discussed in natural ecosystems, how SAS varies within crop populations and how SAS evolved during crop domestication and breeding remain poorly known. In this study, we grew a panel of 180 durum wheat (Triticum turgidum ssp. durum) genotypes spanning diversity from wild, early domesticated, and elite genetic compartments under two light treatments: low R:FR light (shaded treatment) and high R:FR light (unshaded treatment). We first quantified the genetic variability of SAS, here measured as a change in plant height at the seedling stage. We then dissected the genetic basis of this variation through genome-wide association mapping. Genotypes grown in shaded conditions were taller than those grown under unshaded conditions. Interaction between light quality and genotype did not affect plant height. We found six QTLs affecting plant height. Three significantly interacted with light quality among which the well-known Rht1gene introgressed in elite germplasm during the Green Revolution. Interestingly at three loci, short genotypes systematically expressed reduced SAS, suggesting a positive genetic correlation between plant height and plant height plasticity. Overall, our study sheds light on the evolutionary history of crops and illustrates the relevance of genetic approaches to tackle agricultural challenges.

Unraveling the Dynamic Integration of Auxin, Brassinosteroid and Gibberellin in Early Shade-Induced Hypocotyl Elongation.

The online version contains supplementary material available at 10.1007/s43657-022-00044-3.

GmBICs Modulate Low Blue Light-Induced Stem Elongation in Soybean.

Blue-light inhibitors of cryptochromes (BICs) promote hypocotyl elongation by suppressing the activity of cryptochromes in Arabidopsis. Nevertheless, the roles of BICs in other plant species are still unclear. Here we investigate their functions by genetic overexpression and CRISPR/Cas9 engineered mutations targeting the six GmBIC genes in soybean. We showed that the GmBICs overexpression (GmBICs-OX) lines strongly promoted stem elongation, while the single, double, and quadruple mutations in the GmBIC genes resulted in incremental dwarfing phenotypes. Furthermore, overexpression of GmBIC2a abolished the low blue light (LBL)-induced stem elongation, demonstrating the involvement of GmBICs in regulating cryptochrome-mediated LBL-induced shade avoidance syndrome (SAS). The Gmbic1a1b2a2b quadruple mutant displayed reduced stem elongation under LBL conditions, which was reminiscent of the GmCRY1b-OX lines. Taken together, this study provided essential genetic resources for elucidating GmBICs functional mechanisms and breeding of shade-tolerant soybean cultivars in future.

PIF7 controls leaf cell proliferation through an AN3 substitution repression mechanism

Plants are agile, plastic organisms able to adapt to everchanging circumstances. Responding to far-red (FR) wavelengths from nearby vegetation, shade-intolerant species elicit the adaptive shade-avoidance syndrome (SAS), characterized by elongated petioles, leaf hyponasty, and smaller leaves. We utilized end-of-day FR (EODFR) treatments to interrogate molecular processes that underlie the SAS leaf response. Genetic analysis established that PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) is required for EODFR-mediated constraint of leaf blade cell division, while EODFR messenger RNA sequencing data identified ANGUSTIFOLIA3 (AN3) as a potential PIF7 target. We show that PIF7 can suppress AN3 transcription by directly interacting with and sequestering AN3. We also establish that PIF7 and AN3 impose antagonistic control of gene expression via common cis-acting promoter motifs in several cell-cycle regulator genes. EODFR triggers the molecular substitution of AN3 to PIF7 at G-box/PBE-box promoter regions and a switch from promotion to repression of gene expression.

Effects of Green Light on Elongation Do Not Interact with Far-Red, Unless the Phytochrome Photostationary State (PSS) Changes in Tomato.

Simple SummaryThis paper focuses on the role of phytochromes (phys) in the interaction between green light and far-red light effects on “shade avoidance syndrome”. We grew wild type and phy mutants of tomato under a set of light conditions with different combinations of green, blue, red, and far-red light. Partial (20%) replacement of red/blue by green light in the absence of far-red light hardly affected the tomato plant morphology. However, when the spectrum contained far-red light, partially replacing red/blue by green light resulted in more elongation, which was associated with a lower phytochrome photostationary state (PSS) value. There was no effect of partial substitution of red/blue with green light when the PSS was kept constant. Thus, this study has revealed an interaction between green and far-red light effects on elongation unless PSS was kept constant. Green light was often a bit neglected in photobiology, but now an increasing number of researchers are realizing that green light deserves more attention. This study advances the understanding of light quality and plant growth and finding the optimal spectrum when growing plants under LED lighting in controlled environment agriculture.Green light (G) could trigger a “shade avoidance syndrome” (SAS) similarly to far-red light. We aimed to test the hypothesis that G interacts with far-red light to induce SAS, with this interaction mediated by phytochromes (phys). The tomato (Solanum lycopersicum cv. Moneymaker) wild-type (WT) and phyA, phyB1B2, and phyAB1B2 mutants were grown in a climate room with or without 30 µmol m−2 s−1 G on red/blue and red/blue/far-red backgrounds, maintaining the same photosynthetically active radiation (400–700 nm) of 150 µmol m−2 s−1 and red/blue ratio of 3. G hardly affected the dry mass accumulation or leaf area of WT, phyA, and phyB1B2 with or without far-red light. A lower phytochrome photostationary state (PSS) by adding far-red light significantly increased the total dry mass by enhancing the leaf area in WT plants but not in phy mutants. When the background light did not contain far-red light, partially replacing red/blue with G did not significantly affect stem elongation. However, when the background light contained far-red light, partially replacing red/blue with G enhanced elongation only when associated with a decrease in PSS, indicating that G interacts with far-red light on elongation only when the PSS changes.

Parental UV-B radiation regulates the habitat selection of clonal Duchesnea indica in heterogeneous light environments.

Habitat selection behaviour is an effective strategy adopted by clonal plants in heterogeneous understorey light environments, and it is likely regulated by the parental environment's ultraviolet-B radiation levels (UV-B) due to the photomorphogenesis of UV-B and maternal effects. Here, parental ramets of Duchesnea indica were treated with two UV-B radiation levels [high (UV5 group) and low (UV10 group)], newborn offspring were grown under a heterogeneous light environment (ambient light vs shade habitat), and the growth and DNA methylation variations of parents and offspring were analysed. The results showed that parental UV-B affected not only the growth of the parent but also the offspring. The offspring of different UV-B-radiated parents showed different performances. Although these offspring all displayed a tendency to escape from light environments, such as entering shade habitats earlier, and allocating more biomass under shade (33.06% of control, 42.28% of UV5 and 72.73% of UV10), these were particularly obvious in offspring of the high UV-B parent. Improvements in epigenetic diversity (4.77 of control vs 4.83 of UV10) and total DNA methylation levels (25.94% of control vs 27.15% of UV10) and the inhibition of shade avoidance syndrome (denser growth with shorter stolons and internodes) were only observed in offspring of high UV-B parents. This difference was related to the eustress and stress effects of low and high UV-B, respectively. Overall, the behaviour of D. indica under heterogeneous light conditions was regulated by the parental UV-B exposure. Moreover, certain performance improvements helped offspring pre-regulate growth to cope with future environments and were probably associated with the effects of maternal DNA methylation variations in UV-B-radiated parents.

Comparative phenotypic and transcriptomic analyses unravel conserved and distinct mechanisms underlying shade avoidance syndrome in Brassicaceae vegetables

BackgroundPlants grown under shade are exposed to low red/far-red ratio, thereby triggering an array of altered phenotypes called shade avoidance syndrome (SAS). Shade negatively influences plant growth, leading to a reduction in agricultural productivity. Understanding of SAS is crucial for sustainable agricultural practices, especially for high-density indoor farming. Brassicaceae vegetables are widely consumed around the world and are commonly cultivated in indoor farms. However, our understanding of SAS in Brassicaceae vegetables and their genome-wide transcriptional regulatory networks are still largely unexplored.ResultsShade induced common signs of SAS, including hypocotyl elongation and reduced carotenoids/anthocyanins biosynthesis, in two different Brassicaceae species: Brassica rapa (Choy Sum and Pak Choy) and Brassica oleracea (Kai Lan). Phenotype-assisted transcriptome analysis identified a set of genes induced by shade in these species, many of which were related to auxin biosynthesis and signaling [e.g. YUCCA8 (YUC8), YUC9, and INDOLE-3-ACETIC ACID INDUCIBLE (IAAs)] and other phytohormones signaling pathways including brassinosteroids and ethylene. The genes functioning in plant defense (e.g. MYB29 and JASMONATE-ZIM-DOMAIN PROTEIN 9) as well as in biosynthesis of anthocyanins and glucosinolates were repressed upon shade. Besides, each species also exhibited distinct SAS phenotypes. Shade strongly reduced primary roots and elongated petioles of B. oleracea, Kai Lan. However, these SAS phenotypes were not clearly recognized in B. rapa, Choy Sum and Pak Choy. Some auxin signaling genes (e.g. AUXIN RESPONSE FACTOR 19, IAA10, and IAA20) were specifically induced in B. oleracea, while homologs in B. rapa were not up-regulated under shade. Contrastingly, shade-exposed B. rapa vegetables triggered the ethylene signaling pathway earlier than B. oleracea, Kai Lan. Interestingly, shade induced the transcript levels of LONG HYPOCOTYL IN FAR-RED 1 (HFR1) homolog in only Pak Choy as B. rapa. As HFR1 is a key negative regulator of SAS in Arabidopsis, our finding suggests that Pak Choy HFR1 homolog may also function in conferring higher shade tolerance in this variety.ConclusionsOur study shows that two Brassicaceae species not only share a conserved SAS mechanism but also exhibit distinct responses to shade, which will provide comprehensive information to develop new shade-tolerant cultivars that are suitable for high-density indoor farms.

Domestication reduces phenotypic plasticity in chaya (<em>Cnidoscolus aconitifolius</em> (Mill.) I.M. Johnst)

Background: Natural selection optimizes phenotypic plasticity in plants found in environmentally variable habitats. However, it is unclear how artificial selection has affected the phenotypic plasticity of crops. Reduced plasticity in crop yield is often considered a desirable feature in cultivated plants; however, limited phenotypic plasticity in this and other traits may also affect the ability of crops to cope with environmental variation. Study species: Wild and domesticated chaya (Cnidoscolus aconitifolius (Mill.) I.M. Johnst). Question: How domestication has affected the phenotypic plasticity of vegetative traits in response to the light environment? Methods: Leaf area, leaf perimeter, leaf specific area, leaf production, trichome density, stem elongation, growth in stem diameter and slenderness were measured in clones of wild and domesticated plants. These clones were allocated to two contrasting light treatments: fully exposed to sun vs. placement beneath a shade cloth. The phenotypic traits and reaction norms were compared between the genotypes of wild and domesticated plants. Results: Lower plasticity in leaf production and slenderness was observed in the domesticated compared to the wild plants. Leaf production and slenderness are associated with the shade avoidance syndrome, which was evident in wild plants but not manifested in domesticated plants. Reduced plasticity in leaf production also suggests yield stability. Conclusion: Artificial selection reduces phenotypic plasticity in the yield of chaya and in its response to variation in light availability.

Effects of partial replacement of red by green light in the growth spectrum on photomorphogenesis and photosynthesis in tomato plants

The artificial light used in growth chambers is usually devoid of green (G) light, which is considered to be less photosynthetically efficient than blue (B) or red (R) light. To verify the role of G light supplementation in the spectrum, we modified the RB spectrum by progressively replacing R light with an equal amount of G light. The tomato plants were cultivated under 100 µmol m–2 s–1 of five different combinations of R (35–75%) and G light (0–40%) in the presence of a fixed proportion of B light (25%) provided by light-emitting diodes (LEDs). Substituting G light for R altered the plant’s morphology and partitioning of biomass. We observed a decrease in the dry biomass of leaves, which was associated with increased biomass accumulation and the length of the roots. Moreover, plants previously grown under the RGB spectrum more efficiently utilized the B light that was applied to assess the effective quantum yield of photosystem II, as well as the G light when estimated with CO2 fixation using RB + G light-response curves. At the same time, the inclusion of G light in the growth spectrum reduced stomatal conductance (gs), transpiration (E) and altered stomatal traits, thus improving water-use efficiency. Besides this, the increasing contribution of G light in place of R light in the growth spectrum resulted in the progressive accumulation of phytochrome interacting factor 5, along with a lowered level of chalcone synthase and anthocyanins. However, the plants grown at 40% G light exhibited a decreased net photosynthetic rate (Pn), and consequently, a reduced dry biomass accumulation, accompanied by morphological and molecular traits related to shade-avoidance syndrome.

Explaining variation in productivity requires intraspecific variability in plant height among communities

AbstractWhile recent studies have shown the importance of intraspecific trait variation in the processes of community assembly, we still know little about the contributions of intraspecific trait variability to ecosystem functions. Here, we conducted a functional group removal experiment in an alpine meadow in Qinghai-Tibetan Plateau over 4 years to investigate the relative importance of inter- and intraspecific variability in plant height for productivity. We split total variability in plant height within each of 75 manipulated communities into interspecific variability (TVinter) and intraspecific variability within a community (ITVwithin). Community-weighted mean height among communities was decomposed into fixed community-weighted mean (CWMfixed) and intraspecific variability among communities (ITVamong). We constructed a series of generalized additive mixed models and piecewise structural equation modeling to determine how trait variability (i.e. TVinter, ITVwithin, CWMfixed and ITVamong) indirectly mediated the changes in productivity in response to functional group removal. Community productivity was not only affected directly by treatment manipulations, but also increased with both inter- and intraspecific variability (i.e. CWMfixed and ITVamong) in plant height indirectly. This suggests that both the ‘selection effect’ and a ‘shade-avoidance syndrome’ can incur higher CWMfixed and ITVamong, and may simultaneously operate to regulate productivity. Our findings provide new evidence that, besides interspecific variability, intraspecific trait variability in plant height also plays a role in maintaining net primary productivity.

Shade avoidance syndrome in 4D: illuminating a role for transcriptional repression of protein biogenesis genes.

Shade avoidance syndrome in 4D: illuminating a role for transcriptional repression of protein biogenesis genes.

Development of micropropagation system of Zingiber officinale var. rubrum Theilade using different spectrum light-emitting diode (LED) irradiation

Halia Bara, a popular variety of Zingiber officinale Theilade in Malaysia valued for medicinal values was successfully micropropagated using light-emitting diodes (LEDs) to produce disease-free planting materials. This study aimed to establish LED-induced organogenesis of Halia Bara and to evaluate their biochemical profile. Basal part explants were irradiated with white (400−700 nm), far-red (720 nm), blue (460 nm), green (530 nm), red (660 nm), and purple (400–660 nm) LEDs to study the impact of light quality on vegetative growth of 12-week-old Halia Bara plantlets and their biochemical profile such as superoxide dismutase antioxidant enzyme, pigmentation in addition to total carbohydrate content and accumulation of proline amino acid. Generally, shade avoidance syndrome driven growth by red (660 nm) LED significantly promoted shoot length to 12.07 cm producing taller plants with long and thin leaves. The number of shoots (5.57) and leaves (20) were significantly higher on plants irradiated with dichromatic purple (400–660 nm) LED. Root formation of Halia Bara was also significantly promoted by monochromatic red (13.29). However, microshoot formation was fairly enhanced by white, far-red (720 nm), and blue (460 nm) LEDs in the range of 5–5.9 while exhibiting the insignificant difference in green, red, and purple irradiance. First-line defense by superoxide dismutase (SOD) enzyme was significantly upregulated on Halia Bara plantlets irradiated by blue (460 nm) (0.186 ± 0.001 SOD U/mg) and green (530 nm) (0.183 ± 0.001 SOD U/mg). In general, pigmentation such as total chlorophyll (0.516 to 0.541 μg/mL) and carotenoid (1917–2109 μg/g) were notably higher in Halia Bara plants irradiated by white, blue, green, and purple LEDs than the red and far-red irradiation meanwhile porphyrin (14.143 ± 1.930 μg/g) was highly produced following green LED irradiation. Light-regulated accumulation of total carbohydrate and proline were the highest in far-red (109.098 ± 3.223 mg/g) and control white (0.101 ± 0.008 mmol/mg) LED irradiated Halia Bara plants, respectively. In short, vegetative traits and biochemical profile of in vitro Halia Bara is differentially influenced by the quality of light. Based on the photomorphogenetic and physiological traits, the present study emphasizes the suitability of adoption of the LED irradiance for the sustainable production of micropropagated Halia Bara plants to be supplied to small-scale farmers.

Low light intensity delays vegetative phase change.

Plants that develop under low light (LL) intensity often display a phenotype known as the “shade tolerance syndrome (STS)”. This syndrome is similar to the phenotype of plants in the juvenile phase of shoot development, but the basis for this similarity is unknown. We tested the hypothesis that the STS is regulated by the same mechanism that regulates the juvenile vegetative phase by examining the effect of LL on rosette development in Arabidopsis (Arabidopsis thaliana). We found that LL prolonged the juvenile vegetative phase and that this was associated with an increase in the expression of the master regulators of vegetative phase change, miR156 and miR157, and a decrease in the expression of their SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) targets. Exogenous sucrose partially corrected the effect of LL on seedling development and miR156 expression. Our results suggest that the response of Arabidopsis to LL is mediated by an increase in miR156/miR157 expression and by factors that repress SPL gene expression independently of miR156/miR157, and is caused in part by a decrease in carbohydrate production. The effect of LL on vegetative phase change does not require the photoreceptors and transcription factors responsible for the shade avoidance syndrome, implying that light intensity and light quality regulate rosette development through different pathways.