The molecular mechanism of shade avoidance in crops--How data from Arabidopsis can help to identify targets for increasing yield and biomass production

In order to prevent or counteract shading,plants enact a complex set of growth and developmental adaptations when they sense a change in light quality caused by other plants in their vicinity.This shade avoidance response（SAR）typically includes increased stem elongation at the expense of plant fitness and yield,making it an undesirable trait in an agricultural context.Manipulating the molecular factors involved in SAR can potentially improve productivity by increasing tolerance to higher planting density.However,most of the investigations of the molecular mechanism of SAR have been carried out in Arabidopsis thaliana,and it is presently unclear in how far results of these investigations apply to crop plants.In this review,current data on SAR in crop plants,especially from members of the Solanaceae and Poaceae families,are integrated with data from Arabidopsis,in order to identify the most promising targets for biotechnological approaches.Phytochromes,which detect the change in light caused by neighboring plants,and early signaling components can be targeted to increase plant productivity.However,they control various photomorphogenic processes not necessarily related to shade avoidance.Transcription factors involved in SAR signaling could be better targets to specifically enhance or suppress SAR.Knowledge integration from Arabidopsis and crop plants also indicates factors that could facilitate the control of specific aspects of SAR.Candidates are provided for the regulation of plant architecture,flowering induction and carbohydrate allocation.Yet to-be-elucidated factors that control SAR-dependent changes in biotic resistance and cell wall composition are pointed out.This review also includes an analysis of publicly available gene expression data for maize to augment the sparse molecular data available for this important species.

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:ZmPHYB1^(Y98F)(mimicking Y104F of AtPHYB)and ZmPHYB1^(Y359F)(mimicking Y361F of AtPHYB).Ectopic expression of ZmPHYB1^(Y98F) and ZmPHYB1^(Y359F) 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 ZmPHYB1^(WT).Moreover,similar to the behavior of ZmPHYB1^(WT),ZmPHYB1Y98F and ZmPHYB1^(Y359F) proteins are localized to the nucleus after red light exposure,and could interact with PIF proteins of maize.In addition,expression of ZmPHYB1^(Y98F) and ZmPHYB1^(Y359F) 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 ZmPHYB1^(Y98F) and ZmPHYB1^(Y359F) for attenuating SAS and breeding high density-tolerant varieties of maize.

GmCRY1s modulate gibberellin metabolism to regulate soybean shade avoidance in response to reduced blue light

Soybean is an important legume crop that displays the classic shade avoidance syndrome(SAS),including exaggerated stem elongation,which leads to lodging and yield reduction under density farming conditions.Here,we compared the effects of two shade signals,low red light to far-red light ratio(R:FR)and low blue light(LBL),on soybean status and revealed that LBL predominantly induces excessive stem elongation.We used CRISPR-Cas9-engineered Gmcry mutants to investigate the functions of seven cryptochromes(GmCRYs)in soybean and found that the four GmCRY1s overlap in mediating LBL-induced SAS.Lightactivated GmCRY1s increase the abundance of the bZlP transcription factors STF1 and STF2,which directly upregulate the expression of genes encoding GA2 oxidases to deactivate GA1 and repress stem elongation.Notably,GmCRY1b overexpression lines displayed multiple agronomic advantages over the wild-type control under both dense planting and intercropping conditions.Our study demonstrates the integration of GmCRY1-mediated signals with the GA metabolic pathway in the regulation of LBL-induced SAS in soybean.It also provides a promising option for breeding lodging-resistant,high-yield soybean cultivars in the future.

Integration of light and hormone signaling pathways in the regulation of plant shade avoidance syndrome

As sessile organisms,plants are unable to move or escape from their neighboring competitors under high-density planting conditions.Instead,they have evolved the ability to sense changes in light quantity and quality(such as a reduction in photoactive radiation and drop in red/far-red light ratios)and evoke a suite of adaptative responses(such as stem elongation,reduced branching,hyponastic leaf orientation,early flowering and accelerated senescence)collectively termed shade avoidance syndrome(SAS).Over the past few decades,much progress has been made in identifying the various photoreceptor systems and light signaling components implicated in regulating SAS,and in elucidating the underlying molecular mechanisms,based on extensive molecular genetic studies with the model dicotyledonous plant Arabidopsis thaliana.Moreover,an emerging synthesis of the field is that light signaling integrates with the signaling pathways of various phytohormones to coordinately regulate different aspects of SAS.In this review,we present a brief summary of the various cross-talks between light and hormone signaling in regulating SAS.We also present a perspective of manipulating SAS to tailor crop architecture for breeding high-density tolerant crop cultivars.

ABNORMAL SHOOT 6 interacts with KATANIN 1 and SHADE AVOIDANCE 4 to promote cortical microtubule severing and ordering in Arabidopsis

Plant interphase cortical microtubules(cMTs)mediate anisotropic cell expansion in response to environmental and developmental cues.In Arabidopsis thaliana,KATANIN 1(KTN1),the p60 catalytic subunit of the conserved MT-severing enzyme katanin,is essential for cMT ordering and anisotropic cell expansion.However,the regulation of KTN1-mediated cMT severing and ordering remains unclear.In this work,we report that the Arabidopsis IQ67 DOMAIN(IQD)family gene ABNORMAL SHOOT 6(ABS6)encodes a MT-associated protein.Overexpression of ABS6 leads to elongated cotyledons,directional pavement cell expansion,and highly ordered transverse cMT arrays.Genetic suppressor analysis revealed that ABS6-mediated cMT ordering is dependent on KTN1 and SHADE AVOIDANCE 4(SAV4).Live imaging of cMT dynamics showed that both ABS6 and SAV4 function as positive regulators of cMT severing.Furthermore,ABS6 directly interacts with KTN1 and SAV4 and promotes their recruitment to the cMTs.Finally,analysis of loss-of-function mutant combinations showed that ABS6,SAV4,and KTN1 work together to ensure the robust ethylene response in the apical hook of dark-grown seedlings.Together,our findings establish ABS6 and SAV4 as positive regulators of cMT severing and ordering,and highlight the role of cMT dynamics in fine-tuning differential growth in plants.

Maize cryptochromes 1a1 and 1a2 promote seedling photomorphogenesis and shade resistance in Zea mays and Arabidopsis

Maize growth and development are regulated by light quality,intensity and photoperiod.Cryptochromes are blue/ultraviolet-A light receptors involved in stem elongation,shade avoidance,and photoperiodic flowering.To investigate the function of cryptochrome 1(CRY1) in maize,where it is encoded by Zm CRY1,we obtained two Zm CRY1a genes(Zm CRY1a1 and Zm CRY1a2),both of which share the highest similarity with other gramineous plants,in particular rice CRY1a by phylogenetic analysis.In Arabidopsis,overexpression of Zm CRY1a genes promoted seedling de-etiolation under blue and white light,resulting in dwarfing of mature plants.In seedlings of the maize inbred line Zong 31(Zm CRY1aOE),overexpression of Zm CRY1a genes caused a reduction in the mesocotyl and first leaf sheath lengths due to down-regulation of genes influencing cell elongation.In mature transgenic maize plants,plant height,ear height,and internode length decreased in response to overexpression of Zm CRY1a genes.Expression of Zm CRY1a were insensitive to low blue light(LBL)-induced shade avoidance syndrome(SAS) in Arabidopsis and maize.This prompted us to investigate the regulatory role of the gibberellin and auxin metabolic pathways in the response of Zm CRY1a genes to LBL treatment.We confirmed a link between Zm CRY1a expression and hormonal influence on the growth and development of maize under LBL-induced SAS.These results reveal that Zm CRY1a has a relatively conservative function in regulating maize photomorphogenesis and may guide new strategies for breeding high density-tolerant maize cultivars.

Shade adaptive response and yield analysis of different soybean genotypes in relay intercropping systems

Soybean is one of the major oil seed crops,which is usually intercropped with other crops to increase soybean production area and yield.However,soybean is highly sensitive to shading.It is unclear if soybean morphology responds to shading（i.e.,shade tolerance or avoidance）and which features may be suitable as screening materials in relay strip intercropping.Therefore,in this study,various agronomic characteristics of different soybean genotypes were analyzed under relay intercropping conditions.The soybean materials used in this study exhibited genetic diversity,and the coefficient of variations of the agronomic parameters ranged from 13.84 to 72.08%during the shade period and from 6.44 to 52.49%during the maturity period.The ratios of shading to full irradiance in stem mass fraction（SMF）were almost greater than 1,whereas opposite results were found in the leaves.Compared with full irradiance,the average stem length（SL）,leaf area ratio（LAR）and specific leaf area（SLA）for the two years（2013 and 2014）increased by 0.78,0.47 and 0.65 under shady conditions,respectively.However,the stem diameter（SD）,total biomass（TB）,leaf area（LA）,number of nodes（NN）on the main stem,and number of branches（BN）all decreased.During the shady period,the SL and SMF exhibited a significant negative correlation with yield,and the SD exhibited a significant positive correlation with yield.The correlation between the soybean yield and agronomic parameters during the mature period,except for SL,the first pod height（FPH）,100-seed weight（100-SW）,and reproductive growth period（RGP）,were significant（P〈0.01）,especially for seed weight per branch（SWB）,pods per plant（PP）,BN,and vegetative growth period（VGP）.These results provide an insight into screening the shade tolerance of soybean varieties and can be useful in targeted breeding programs of relay intercropped soybeans.

Shade-Inducible Gene Expression Change in Arabidopsis thaliana at Different Temperatures

We tested whether the plant response to an environmental factor could be affected by the context of another factor by using shade avoidance response at different temperatures. Depleting the red light (R;λmax = 660 nm) and/or enriching the far-red light (FR;λmax = 730 nm) results in a low R:FR ratio in the environment, which induces shade avoidance response such as elongation of petioles and reduction of plant pigments. On the other hand, warmer environmental temperature is known to mimic shade avoidance response under normal light condition, suggesting a potential crosstalk between the temperature and the light quality signals. Therefore, we investigated the patterns of gene expression responses to low R:FR ratio in different temperature contexts (22°C and 26°C) through microarray analyses. Similar, yet distinct patterns between the two responses were implicated by the levels of correlation in the commonly affected MapMan bins. However, the induction levels of typical shade genes such as ATHB2, IAA29, IAA19, HFR1, YUC8, and FT were very similar at both temperatures. Moreover, petiole length, chlorophylls, carotenoids, and anthocyanins contents did not support any statistically significant interaction between the light quality and the high temperature responses despite the obvious independent effect of each signal, which suggests cumulative effects of two independent responses. Nevertheless, other types of low R: FR-responsive genes with differential expression patterns at different temperatures were identified. They are overrepresented in secondary metabolism, lipid transport, oxidative stress, jasmonic acid, ethylene, light, pathogen defense responses, and extracellular region.

Height growth, diameter-height relationships and branching architecture of Pinus massoniana and Cunninghamia lanceolata in early regeneration stages in Anhui Province, eastern China: effects of light intensity and regeneration mode

To determine the growth strategies during early regeneration stages of two major coniferous species （Pinus massoniana and Cunninghamia lanceolata） in a secondary mixed coniferous forest in the Huangshan region of Anhui Province, eastern China, we examined height growth, diameter-height relationship and the relationship between main stem and lateral branch elongation in saplings, with a particular focus on the effects of light intensity and regeneration mode （seedlings versus sprouts）. When light intensity was sufficiently high, the extension growth of main stems was greater and more positively related to initial size for P. massoniana than for C. lanceolata. The slenderness of the stem form increased in the following order： C. lanceolata seedlings 〈 P. massoniana seedlings 〈 C. lanceolata sprouts. P. massoniana became less slender with increasing light intensity. P. massoniana had shorter branches than C. lanceolata given the same main stem elongation. Growth allocation depended more strongly on light intensity for P. massoniana than for C. lanceolata, with more growth allocated to the main stem under dark conditions. These results suggest that P. massoniana is a typical shade avoider; this species gives priority to extension growth of the main stem, especially when it is shaded. In contrast, C. lanceolata is a shade tolerator; this species allocates more biomass to radial growth of its main stems and to extension growth of branches. Based on these results, the ecological characteristics of P. massoniana and C. lanceolata and the roles of seedlings and sprouts are discussed in relation to stand dynamics of the mixed forests of P. massoniana and C. lanceolata in eastern China.

Carbon Nanoparticle Exerts Positive Growth Effects with Increase in Productivity by Down-Regulating Phytochrome B and Enhancing Internal Temperature in Rice

The effects of carbon nanoparticle(CNP)on rice variety Swarna(MTU7029)were investigated.CNP induced effects similar to shade avoidance response(SAR)of Arabidopsis,with increase in shoot length,root length,root number,cotyledon area,chlorophyll content and total sugar content in rice seedlings.In mature plants,CNP treatment resulted increase in plant height,number of productive tillers per plant,normalized difference vegetation index,quantum yield and root growth.A total of 320 mg of CNP per plant administered in four doses resulted in improved grain traits such as filled grain rate,100-grain weight,grain length/width ratio,hulling rate,milling rate and head rice recovery.Seeds from the CNP-treated plants showed increase in amylose,starch and soluble sugar contents compared to controls.Strikingly,CNP treatment showed an average of 17.5%increase in yield per plant.Upon investigation to the molecular mechanism behind CNP induction of SAR,a significant downregulation of phytochrome B transcript was found.Decrease in perception of red wavelengths led to responses similar to SAR.Increase in plant’s internal temperature by 0.5ºC±0.1ºC was recorded after CNP treatment.We suggest that the internalized CNP aggregates may serve to absorb extra photons thereby increasing the internal temperature of plants.Phytochrome B accounts the hike in internal temperature and initiates a feed-back reduction of its own transcription.We suggest that moderate SAR is beneficial for rice plants to improve agronomic traits and yield.It presents a potential non-transgenic method for improving rice yield by CNP treatment.

Shade-induced stem elongation in rice seedlings:Implication of tissue-specific phytohormone regulation

Summary A better understanding of shade avoidance syndrome （SAS） is an urgent need because of its effect on energy reallocation. Leverage-related mechanism in crops is of potential economic interest for agricultural applications. Here we report the SAS phenotype at tissue level rice seedlings. Tissue-specific RNA-sequencing indicates auxin plays different roles between coleoptile and the first leaf. Phenotypes of wild type treated by gibberellin and brassinosteroid biosynthesis inhibitors and of related mutants suggest these two hormones positively regulate SAS. Our work reveals the diversity of hormone responses in different organs and different species in shade conditions.

Diurnal Dependence of Growth Responses to Shade in Arabidopsis： Role of Hormone, Clock, and Light Signaling

We investigated the diurnal dependence of the hypocotyl-growth responses to shade under sunlight-night cycles in Arabidopsis thaliana. Afternoon shade events promoted hypocotyl growth, while morning shade was ineffective. The Ihy-D, elf3, lux, pif4 pifS, tocl, and quadruple della mutants retained the response to afternoon shade and the lack of response to morning shade while the Ihyccal mutant responded to both morning and afternoon shade. ThephyB mutant, plants overexpressing the multidrug resistance-like membrane protein ABCB19, and the iaa17/axr3 loss-of-function mutant failed to respond to shade. Transient exposure of sunlight-grown seedlings to synthetic auxin in the afternoon caused a stronger promotion of hypocotyl growth than morning treatments. The promotion of hypocotyl growth by afternoon shade or afternoon auxin required light perceived by phytochrome A or cryptochromes during the previous hours of the photoperiod. Although the ELF4-ELF3-LUX complex, PIF4, PIF5, and DELLA are key players in the generation of diurnal hypocotyl-growth patterns, they exert a minor role in the control of the diurnal pattern of growth responses to shade. We conclude that the strong diurnal dependency of hypocotyl-growth responses to shade relates to the balance between the antagonistic actions of LHY-CCA1 and a light-derived signal.

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

For shade-intolerant plants,a reduction in the red/far-red(R:FR)light ratio signals the close proximity of competitors and triggers shade-avoidance syndrome(SAS).Auxin,brassinosteroid,gibberellin and some transcriptional regulators have been reported to regulate shade-induced hypocotyl elongation.However,little is understood regarding the coordination of these multiple regulatory pathways.Here,combining time-lapse growth rates and transcriptomic data,we demonstrate that auxin and brassinosteroid affect two phases of shade-induced rapid growth,whereas gibberellin mainly contributes to the second rapid growth phase.PHYTOCHROME-INTERACTING FACTOR 7(PIF7)acts earlier than other PIFs.PIF4 and PIF5 modulate the second rapid growth phase.LONG HYPOCOTYL IN FAR-RED 1(HFR1)and PIF3-LIKE 1(PIL1)modulate two rapid growth phases.Our results reveal that hormonal and transcriptional regulatory programs act together to coordinate dynamic hypocotyl changes in an immediate response to a shade signal and provide a novel understanding of growth kinetics in a changing environment.

Light participates in the auxin-dependent regulation of plant growth

Light is the energy source for plant photosynthesis and influences plant growth and development.Through multiple photoreceptors, plant interprets light signals through various downstream phytohormones such as auxin. Recently, Chen et al.(2020) uncover a new layer of regulation in IPyA pathway of auxin biosynthesis by light. Here we highlight recent studies about how light controls plant growth through regulating auxin biosynthesis and signaling.

A Dual Mechanism Controls Nuclear Localization in the Atypical Basic-Helix-Loop-Helix Protein PAR1 of Arabidopsis thaliana

PAR1 is an atypical basic-helix-loop-helix （bHLH） protein that negatively regulates the shade avoidance syndrome in Arabidopsis thaliana acting as a transcriptional cofactor. Consistently with this function, PAR1 has to be in the nucleus to display biological activity. Previous structure-function analyses revealed that the N-terminal region of PAR1 drives the protein to the nucleus. However, truncated forms of PAR1 lacking this region still display biological activity, implying that PAR1 has additional mechanisms to localize into the nucleus. In this work, we compared the primary structure of PAR1 and various related and unrelated plant bHLH proteins, which led us to suggest that PAR1 contains a non-canonical nuclear localization signal （NLS） in the N-terminal region. By overexpressing truncated and mutated derivatives of PAR1, we have also investigated the importance of other regions of PAR1, such as the acidic and the extended HLH dimerization domains, for its nuclear localization. We found that, in the absence of the N-terminal region, a functional HLH domain is required for nuclear localization. Our results suggest the existence of a dual mechanism for PAR1 nuclear localization： （1） one mediated by the N-terminal non-consensus NLS and （2） a second one that involves interaction with other proteins via the dimerization domain,