The tomato Blind gene encodes a MYB transcription factor that controls the formation of lateral meristems

Transcriptome analysis reveals the key network of axillary bud outgrowth modulated by topping in citrus

Topping, an important tree shaping and pruning technique, can promote the outgrowth of citrus axillary buds. However, the underlying molecular mechanism is still unclear. In this study, spring shoots of Citrus reticulata 'Huagan No.2' were topped and transcriptome was compared between axillary buds of topped and untopped shoots at 6 and 11 days after topping (DAT). 1944 and 2394 differentially expressed genes (DEGs) were found at 6 and 11 DAT, respectively. KEGG analysis revealed that many DEGs were related to starch and sucrose metabolism, signal transduction of auxin, cytokinin and abscisic acid. Specially, transcript levels of auxin synthesis, transport, and signaling-related genes (SAURs and ARF5), cytokinin signal transduction related genes (CRE1, AHP and Type-A ARRs), ABA signal responsive genes (PYL and ABF) were up-regulated by topping; while transcript levels of auxin receptor TIR1, auxin responsive genes AUX/IAAs, ABA signal transduction related gene PP2Cs and synthesis related genes NCED3 were down-regulated. On the other hand, the contents of sucrose and fructose in axillary buds of topped shoots were significantly higher than those in untopped shoots; transcript levels of 16 genes related to sucrose synthase, hexokinase, sucrose phosphate synthase, endoglucanase and glucosidase, were up-regulated in axillary buds after topping. In addition, transcript levels of genes related to trehalose 6-phosphate metabolism and glycolysis/tricarboxylic acid (TCA) cycle, as well to some transcription factors including Pkinase, Pkinase_Tyr, Kinesin, AP2/ERF, P450, MYB, NAC and Cyclin_c, significantly responded to topping. Taken together, the present results suggested that topping promoted citrus axillary bud outgrowth through comprehensively regulating plant hormone and carbohydrate metabolism, as well as signal transduction. These results deepened our understanding of citrus axillary bud outgrowth by topping and laid a foundation for further research on the molecular mechanisms of citrus axillary bud outgrowth.

A systematic regulatory network related to bulbil formation in Lilium lancifolium based on metabolome and transcriptome analyses

BACKGROUND

Lilium lancifolium is a special wild triploid species native to China and can produce abundant bulbils on its stem under natural conditions, which is very valuable to study bulbil organogenesis in plants. Although similar to the lateral and tillering principles, the molecular mechanism underlying bulbil formation has remained incompletely understood.

RESULTS

The metabolome and transcriptome of L. lancifolium bulbils across four development stages were analyzed. The pairwise comparison of metabolomes across the four stages identified 17 differential hormones, predominantly auxin (IAA), cytokinin (CK), and jasmonic acid (JA). Short Time-series Expression Miner (STEM) trend analysis of differential genes revealed four significant trends across these stages. The KEGG enrichment analysis of the four clusters highlighted pathways, such as plant hormone signal transduction, which were speculated to play a crucial role in development stages. these pathways were speculated to play a crucial role in development stages. To explore the key differential expressed genes and transcription factors associated with bulbil occurrence, two periods were focused on: Ll_UN and Ll_DN, which represented the stages with and without bulbils, respectively. Through correlation analysis and qRT-PCR analysis, 11 candidate differentially expressed genes and 27 candidate transcription factors were selected. By spraying exogenous hormones to validate these candidates, LlbHLH128, LlTIFY10A, LlbHLH93, and LlMYB108, were identified as the key genes for L. lancifolium bulbils.

CONCLUSION

A regulatory network of L. lancifolium bulbil development was predicted. LlTIFY10A and LlbHLH93 might be involved in the JA and auxin signal transduction pathways, which jointly formed a regulatory network to affect the occurrence of L. lancifolium bulbil. This study not only provided more information about the differentially expressed genes and metabolites through transcriptome and metabolomics analyses, but also provided a clearer understanding of the effect of hormones on bulbil formation in lily.

The diversification of the shoot branching system: A quantitative and comparative perspective in meristem determinacy

Reiterative shoot branching largely defines important yield components of crops and is essentially controlled by programs that direct the initiation, dormancy release, and differentiation of meristems in the axils of leaves. Here, we focus on meristem determinacy, defining the number of reiterations that shape the shoot architectures and exhibit enormous diversity in a wide range of species. The meristem determinacy per se is hierarchically complex and context-dependent for the successively emerged meristems, representing a crucial mechanism in shaping the complexity of the shoot branching. In addition, we have highlighted that two key components of axillary meristem developmental programs may have been co-opted in controlling flower/ear number of an axillary inflorescence in legumes/maize, hinting at the diversification of axillary-meristem-patterning programs in different lineages. This begs the question how axillary meristem patterning programs may have diversified during plant evolution and hence helped shape the rich variation in shoot branching systems.

The tomato WRKY-B transcription factor modulates lateral branching by targeting BLIND, PIN4, and IAA15

Lateral branching is a crucial agronomic trait that impacts crop yield. In tomato ( Solanum lycopersicum ), excessive lateral branching is unfavorable and results in substantial labor and management costs. Therefore, optimizing lateral branching is a primary objective in tomato breeding. Although many genes related to lateral branching have been reported in tomato, the molecular mechanism underlying their network remains elusive. In this study, we found that the expression profile of a WRKY gene, WRKY-B (for WRKY-BRANCING), was associated with the auxin-dependent axillary bud development process. Wrky-b mutants generated by the CRISPR/Cas9 editing system presented fewer lateral branches, while WRKY-B overexpression lines presented more lateral branches than did wild-type plants. Furthermore, WRKY-B can directly target the well-known branching gene BLIND (BL) and the auxin efflux carrier gene PIN4 to activate their expression. Both the bl and pin4 mutants exhibited reduced lateral branching, similar to the wrky-b mutant. The IAA contents in the axillary buds of the wrky-b, bl, and pin4 mutant plants were significantly higher than those in the wild-type plants. In addition, WRKY-B can also directly target the AUX/IAA gene IAA15 and repress its expression. In summary, WRKY-B works upstream of BL, PIN4, and IAA15 to regulate the development of lateral branches in tomato.

Transcription factor FveMYB117a inhibits axillary bud outgrowth by regulating cytokinin homeostasis in woodland strawberry

Shoot branching affects plant architecture. In strawberry (Fragaria L.), short branches (crowns) develop from dormant axillary buds to form inflorescences and flowers. While this developmental transition contributes greatly to perenniality and yield in strawberry, its regulatory mechanism remains unclear and understudied. In the woodland strawberry (Fragaria vesca), we identified and characterized 2 independent mutants showing more crowns. Both mutant alleles reside in FveMYB117a, a R2R3-MYB transcription factor gene highly expressed in shoot apical meristems, axillary buds, and young leaves. Transcriptome analysis revealed that the expression of several cytokinin pathway genes was altered in the fvemyb117a mutant. Consistently, active cytokinins were significantly increased in the axillary buds of the fvemyb117a mutant. Exogenous application of cytokinin enhanced crown outgrowth in the wild type, whereas the cytokinin inhibitors suppressed crown outgrowth in the fvemyb117a mutant. FveMYB117a binds directly to the promoters of the cytokinin homeostasis genes FveIPT2 encoding an isopentenyltransferase and FveCKX1 encoding a cytokinin oxidase to regulate their expression. Conversely, the type-B Arabidopsis response regulators FveARR1 and FveARR2b can directly inhibit the expression of FveMYB117a, indicative of a negative feedback regulation. In conclusion, we identified FveMYB117a as a key repressor of crown outgrowth by inhibiting cytokinin accumulation and provide a mechanistic basis for bud fate transition in an herbaceous perennial plant.

Genomic analysis of a spontaneous unifoliate mutant reveals gene candidates associated with compound leaf development in Vigna unguiculata [L] Walp

Molecular mechanisms which underpin compound leaf development in some legumes have been reported, but there is no previous study on the molecular genetic control of compound leaf formation in Vigna unguiculata (cowpea), an important dryland legume of African origin. In most studied species with compound leaves, class 1 KNOTTED-LIKE HOMEOBOX genes expressed in developing leaf primordia sustain morphogenetic activity, allowing leaf dissection and the development of leaflets. Other genes, such as, SINGLE LEAFLET1 in Medicago truncatula and Trifoliate in Solanum lycopersicum, are also implicated in regulating compound leaf patterning. To set the pace for an in-depth understanding of the genetics of compound leaf development in cowpea, we applied RNA-seq and whole genome shotgun sequence datasets of a spontaneous cowpea unifoliate mutant and its trifoliate wild-type cultivar to conduct comparative reference-based gene expression, de novo genome-wide isoform switch, and genome variant analyses between the two genotypes. Our results suggest that genomic variants upstream of LATE ELONGATED HYPOCOTYL and down-stream of REVEILLE4, BRASSINOSTERIOD INSENSITIVE1 and LATERAL ORGAN BOUNDARIES result in down-regulation of key components of cowpea circadian rhythm central oscillator and brassinosteroid signaling, resulting in unifoliate leaves and brassinosteroid-deficient-like phenotypes. We have stated hypotheses that will guide follow-up studies expected to provide more insights.

CsRAXs negatively regulate leaf size and fruiting ability through auxin glycosylation in cucumber

Leaves are the main photosynthesis organ that directly determines crop yield and biomass. Dissecting the regulatory mechanism of leaf development is crucial for food security and ecosystem turn-over. Here, we identified the novel function of R2R3-MYB transcription factors CsRAXs in regulating cucumber leaf size and fruiting ability. Csrax5 single mutant exhibited enlarged leaf size and stem diameter, and Csrax1/2/5 triple mutant displayed further enlargement phenotype. Overexpression of CsRAX1 or CsRAX5 gave rise to smaller leaf and thinner stem. The fruiting ability of Csrax1/2/5 plants was significantly enhanced, while that of CsRAX5 overexpression lines was greatly weakened. Similarly, cell number and free auxin level were elevated in mutant plants while decreased in overexpression lines. Biochemical data indicated that CsRAX1/5 directly promoted the expression of auxin glucosyltransferase gene CsUGT74E2. Therefore, our data suggested that CsRAXs function as repressors for leaf size development by promoting auxin glycosylation to decrease free auxin level and cell division in cucumber. Our findings provide new gene targets for cucumber breeding with increased leaf size and crop yield.

Far-red light inhibits lateral bud growth mainly through enhancing apical dominance independently of strigolactone synthesis in tomato

The ratio of red light to far-red light (R:FR) is perceived by light receptors and consequently regulates plant architecture. Regulation of shoot branching by R:FR ratio involves plant hormones. However, the roles of strigolactone (SL), the key shoot branching hormone and the interplay of different hormones in the light regulation of shoot branching in tomato (Solanum lycopersicum) are elusive. Here, we found that defects in SL synthesis genes CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7) and CCD8 in tomato resulted in more lateral bud growth but failed to reverse the FR inhibition of lateral bud growth, which was associated with increased auxin synthesis and decreased synthesis of cytokinin (CK) and brassinosteroid (BR). Treatment of auxin also inhibited shoot branching in ccd mutants. However, CK released the FR inhibition of lateral bud growth in ccd mutants, concomitant with the upregulation of BR synthesis genes. Furthermore, plants that overexpressed BR synthesis gene showed more lateral bud growth and the shoot branching was less sensitive to the low R:FR ratio. The results indicate that SL synthesis is dispensable for light regulation of shoot branching in tomato. Auxin mediates the response to R:FR ratio to regulate shoot branching by suppressing CK and BR synthesis.

The transcription factor SPL13 mediates strigolactone suppression of shoot branching by inhibiting cytokinin synthesis in Solanum lycopersicum

Plant architecture imposes a large impact on crop yield. IDEAL PLANT ARCHITECTURE 1 (IPA1), which encodes a SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor, is a target of molecular design for improving grain yield. However, the roles of SPL transcription factors in regulating tomato (Solanum lycopersicum) plant architecture are unclear. Here, we show that the expression of SPL13 is down-regulated in the lateral buds of strigolactone (SL)-deficient ccd mutants and is induced by GR24 (a synthetic analog of SL). Knockout of SPL13 by CRISPR/Cas9 resulted in higher levels of cytokinins (CKs) and transcripts of the CK synthesis gene ISOPENTENYL TRANSFERASES 1 (IPT1) in the stem nodes, and more growth of lateral buds. GR24 suppresses CK synthesis and lateral bud growth in ccd mutants, but is not effective in spl13 mutants. On the other hand, silencing of the IPT1 gene inhibited bud growth of spl13 mutants. Interestingly, SL levels in root extracts and exudates are significantly increased in spl13 mutants. Molecular studies indicated that SPL13 directly represses the transcription of IPT1 and the SL synthesis genes CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7) and MORE AXILLARY GROWTH 1 (MAX1). The results demonstrate that SPL13 acts downstream of SL to suppress lateral bud growth by inhibiting CK synthesis in tomato. Tuning the expression of SPL13 is a potential approach for decreasing the number of lateral shoots in tomato.

Bridging pathways: SBP15 regulates GOBLET in modulating tomato axillary bud outgrowth

This article comments on:

Barrera-Rojas CH, Vicente MH, Brito DAP, Silva EM,Muñoz Lopez A, Ferigolo LF, Carmo RM, Silva CMS, Silva GFF, Correa JPO, Notini MM, Freschi L, Cubas P, Nogueira FTS. 2023. Tomato miR156-targeted SlSBP15 represses shoot branching by modulating hormone dynamics and interacting with GOBLET and BRANCHED1b. Journal of Experimental Botany 74, 5124–5139.

Characterization of the Molecular Events Underlying the Establishment of Axillary Meristem Region in Pepper

Plant architecture is a major motif of plant diversity, and shoot branching patterns primarily determine the aerial architecture of plants. In this study, we identified an inbred pepper line with fewer lateral branches, 20C1734, which was free of lateral branches at the middle and upper nodes of the main stem with smooth and flat leaf axils. Successive leaf axil sections confirmed that in normal pepper plants, for either node n, Pn (Primordium n) < 1 cm and Pn+1 < 1 cm were the critical periods between the identification of axillary meristems and the establishment of the region, whereas Pn+3 < 1 cm was fully developed and formed a completely new organ. In 20C1734, the normal axillary meristematic tissue region establishment and meristematic cell identity confirmation could not be performed on the axils without axillary buds. Comparative transcriptome analysis revealed that "auxin-activated signaling pathway", "response to auxin", "response to abscisic acid", "auxin biosynthetic process", and the biosynthesis of the terms/pathways, such as "secondary metabolites", were differentially enriched in different types of leaf axils at critical periods of axillary meristem development. The accuracy of RNA-seq was verified using RT-PCR for some genes in the pathway. Several differentially expressed genes (DEGs) related to endogenous phytohormones were targeted, including several genes of the PINs family. The endogenous hormone assay showed extremely high levels of IAA and ABA in leaf axils without axillary buds. ABA content in particular was unusually high. At the same time, there is no regular change in IAA level in this type of leaf axils (normal leaf axils will be accompanied by AM formation and IAA content will be low). Based on this, we speculated that the contents of endogenous hormones IAA and ABA in 20C1734 plant increased sharply, which led to the abnormal expression of genes in related pathways, which affected the formation of Ams in leaf axils in the middle and late vegetative growth period, and finally, nodes without axillary buds and side branches appeared.

Genome-wide analysis of MdPLATZ genes and their expression during axillary bud outgrowth in apple (Malus domestica Borkh.)

BACKGROUND

Branching is a plastic character that affects plant architecture and spatial structure. The trait is controlled by a variety of plant hormones through coordination with environmental signals. Plant AT-rich sequence and zinc-binding protein (PLATZ) is a transcription factor that plays an important role in plant growth and development. However, systematic research on the role of the PLATZ family in apple branching has not been conducted previously.

RESULTS

In this study, a total of 17 PLATZ genes were identified and characterized from the apple genome. The 83 PLATZ proteins from apple, tomato, Arabidopsis, rice, and maize were classified into three groups based on the topological structure of the phylogenetic tree. The phylogenetic relationships, conserved motifs, gene structure, regulatory cis-acting elements, and microRNAs of the MdPLATZ family members were predicted. Expression analysis revealed that MdPLATZ genes exhibited distinct expression patterns in different tissues. The expression patterns of the MdPLATZ genes were systematically investigated in response to treatments that impact apple branching [thidazuron (TDZ) and decapitation]. The expression of MdPLATZ1, 6, 7, 8, 9, 15, and 16 was regulated during axillary bud outgrowth based on RNA-sequencing data obtained from apple axillary buds treated by decapitation or exogenous TDZ application. Quantitative real-time PCR analysis showed that MdPLATZ6 was strongly downregulated in response to the TDZ and decapitation treatments, however, MdPLATZ15 was significantly upregulated in response to TDZ, but exhibited little response to decapitation. Furthermore, the co-expression network showed that PLATZ might be involved in shoot branching by regulating branching-related genes or mediating cytokinin or auxin pathway.

CONCLUSION

The results provide valuable information for further functional investigation of MdPLATZ genes in the control of axillary bud outgrowth in apple.

Regulation of capsule spine formation in castor

Castor (Ricinus communis L.) is a dicotyledonous oilseed crop that can have either spineless or spiny capsules. Spines are protuberant structures that differ from thorns or prickles. The developmental regulatory mechanisms governing spine formation in castor or other plants have remained largely unknown. Herein, using map-based cloning in 2 independent F2 populations, F2-LYY5/DL01 and F2-LYY9/DL01, we identified the RcMYB106 (myb domain protein 106) transcription factor as a key regulator of capsule spine development in castor. Haplotype analyses demonstrated that either a 4,353-bp deletion in the promoter or a single nucleotide polymorphism leading to a premature stop codon in the RcMYB106 gene could cause the spineless capsule phenotype in castor. Results of our experiments indicated that RcMYB106 might target the downstream gene RcWIN1 (WAX INDUCER1), which encodes an ethylene response factor known to be involved in trichome formation in Arabidopsis (Arabidopsis thaliana) to control capsule spine development in castor. This hypothesis, however, remains to be further tested. Nevertheless, our study reveals a potential molecular regulatory mechanism underlying the spine capsule trait in a nonmodel plant species.

The Secrets of Meristems Initiation: Axillary Meristem Initiation and Floral Meristem Initiation

The branching phenotype is an extremely important agronomic trait of plants, especially for horticultural crops. It is not only an important yield character of fruit trees, but also an exquisite ornamental trait of landscape trees and flowers. The branching characteristics of plants are determined by the periodic initiation and later development of meristems, especially the axillary meristem (AM) in the vegetative stage and the floral meristem (FM) in the reproductive stage, which jointly determine the above-ground plant architecture. The regulation of meristem initiation has made great progress in model plants in recent years. Meristem initiation is comprehensively regulated by a complex regulatory network composed of plant hormones and transcription factors. However, as it is an important trait, studies on meristem initiation in horticultural plants are very limited, and the mechanism of meristem initiation regulation in horticultural plants is largely unknown. This review summarizes recent research advances in axillary meristem regulation and mainly reviews the regulatory networks and mechanisms of AM and FM initiation regulated by transcription factors and hormones. Finally, considering the existing problems in meristem initiation studies and the need for branching trait improvement in horticulture plants, we prospect future studies to accelerate the genetic improvement of the branching trait in horticulture plants.

Epistatic interaction between CsCEN and CsSHBY in regulating indeterminate/determinate growth of lateral branch in cucumber

KEY MESSAGE

Two genetic loci, det-ma (CsCEN) and det-lb, showed epistatic interaction on indeterminate/determinate growth of LB in cucumber. CsSHBY was identified as the candidate gene for det-lb locus. Plant architecture depends on the spatial regulation of meristems from both main axis (MA) and lateral branches (LBs). Fate (indeterminate or determinate) of these meristems is a crucial source of architectural diversity determining crop productivity and management. CENTRORADIALIS/TERMINAL FLOWER 1/SELF-PRUNING (CETS) gene family have been well known as pivotal regulators for indeterminate/determinate growth of MA. Nevertheless, genes that regulate LB indeterminacy/determinacy remained unclear. Cucumber (Cucumis sativus L.) has typical monopodial growth and multiple lateral branches. Both MA and LBs had indeterminate or determinate growth, and indeterminate/determinate growth of LB was controlled by two distinct loci, det-ma (CsCEN) and det-lb. In our study, based on bulked segregant analysis (BSA) method, the det-lb locus was mapped on a 60.6 kb region on chromosome 1 harboring only one gene CsaV3_1G044330, which encoded a putative vacuolar-sorting protein (designated as CsSHBY). Multipoint mutations in CsSHBY were identified in D082 and D226, compared with CCMC, including nonsynonymous SNP mutations and a 6-bp deletion in exons. Further, qPCR showed that CsSHBY was highly expressed in lateral bud of CCMC, suggesting that CsSHBY might play an active role in regulating indeterminate/determinate growth of LB. Genetic analyses showed that det-ma (CsCEN) had an epistatic effect on det-lb (CsSHBY), and CsCEN could activate CsSHBY promoter by Dual luciferase and GUS activity assays. Meanwhile, Cscen or Csshby was found to influence auxin contents and CsYUCs and CsPINs expression levels. These findings provided new insights into precisely optimizing plant architecture for yield improvements.

Spectral light quality regulates the morphogenesis, architecture, and flowering in pepper (Capsicum annuum L.)

Transparent plastic films with poor light transmittance seriously affect the mass composition of visible light in many greenhouses, which leads to the reduction of photosynthesis in vegetable crops. Understanding the regulatory mechanisms of monochromatic light in the vegetative and reproductive growth of vegetable crops is of great importance for the application of light-emitting diodes (LEDs) in the greenhouse. In this study, three monochromatic light treatments (red-, green- and blue-light) were simulated by using LEDs to explore light quality-dependent regulation from the stage of seedling to flowering in pepper (Capsicum annuum L.). The results showed that light quality-dependent regulation guides the growth and morphogenesis in pepper plants. Red- and blue-light played opposite roles in determining the plant height, stomatal density, axillary bud growth, photosynthetic characteristics, flowering time and hormone metabolism, while green light treatment resulted in taller plants and fewer branches, which was similar to the red-light treatment. The weighted correlation network analysis (WGCNA) based on mRNA-seq results revealed that the two modules named "MEred" and "MEmidnightblue" were positively correlated with red- and blue-light treatment, respectively, exhibiting high correlations with the traits such as plant hormone content, branching and flowering. Moreover, our results suggest that the light response factor ELONGATED HYPOCOTYL 5 (HY5) is essential for blue light-induced plant growth and development by regulating photosynthesis in pepper plants. Hence, this study uncovers crucial molecular mechanisms of how light quality determines the morphogenesis, architecture, and flowering in pepper plants, thus providing a basic concept of manipulating light quality to regulate pepper plant growth and flowering under greenhouse conditions.

Transcriptional regulatory network of high-value active ingredients in medicinal plants

High-value active ingredients in medicinal plants have attracted research attention because of their benefits for human health, such as the antimalarial artemisinin, anticardiovascular disease tanshinones, and anticancer Taxol and vinblastine. Here, we review how hormones and environmental factors promote the accumulation of active ingredients, thereby providing a strategy to produce high-value drugs at a low cost. Focusing on major hormone signaling events and environmental factors, we review the transcriptional regulatory network mediating biosynthesis of representative active ingredients. In this network, many transcription factors (TFs) simultaneously control multiple synthase genes; thus, understanding the molecular mechanisms affecting transcriptional regulation of active ingredients will be crucial to developing new breeding possibilities.

Stem Cell Basis of Shoot Branching

During their postembryonic development, plants continuously form branches to conquer more space and adapt to changing environments. In seed plants, this is achieved by lateral branching, in which axillary meristems (AMs) initiate at the leaf axils to form axillary buds. The developmental potential of AMs to form shoot branches is the same as that of embryonic shoot apical meristems (SAMs). Recent studies in Arabidopsis thaliana have revealed the cellular origin of AMs and have identified transcription factors and phytohormones that regulate sequential steps leading to AM initiation. In particular, a group of meristematic cells detached from the SAM are key to AM initiation, which constitutes an excellent system for understanding stem cell fate and de novo meristem formation.

Control of vegetative reproduction in Marchantiapolymorpha by the KAI2-ligand signaling pathway

In vegetative reproduction of Marchantia polymorpha (M. polymorpha), propagules, called gemmae, are formed in gemma cups. Despite its significance for survival, control of gemma and gemma cup formation by environmental cues is not well understood. We show here that the number of gemmae formed in a gemma cup is a genetic trait. Gemma formation starts from the central region of the floor of the gemma cup, proceeds to the periphery, and terminates when the appropriate number of gemmae is initiated. The MpKARRIKIN INSENSITIVE2 (MpKAI2)-dependent signaling pathway promotes gemma cup formation and gemma initiation. The number of gemmae in a cup is controlled by modulating the ON/OFF switch of the KAI2-dependent signaling. Termination of the signaling results in the accumulation of MpSMXL, a suppressor protein. In the Mpsmxl mutants, gemma initiation continues, leading to the formation of a highly increased number of gemmae in a cup. Consistent with its function, the MpKAI2-dependent signaling pathway is active in gemma cups where gemmae initiate, as well as in the notch region of the mature gemma and midrib of the ventral side of the thallus. In this work, we also show that GEMMA CUP-ASSOCIATED MYB1 works downstream of this signaling pathway to promote gemma cup formation and gemma initiation. We also found that the availability of potassium affects gemma cup formation independently from the KAI2-dependent signaling pathway in M. polymorpha. We propose that the KAI2-dependent signaling pathway functions to optimize vegetative reproduction by adapting to the environment in M. polymorpha.

R2R3-MYB transcription factor GEMMA CUP-ASSOCIATED MYB1 mediates the cytokinin signal to achieve proper organ development in Marchantia polymorpha

Cytokinin, a plant hormone, plays essential roles in organ growth and development. The type-B response regulator-mediated cytokinin signaling is repressed by type-A response regulators and is conserved in the liverwort Marchantia polymorpha. Its signal coordinates the development of diverse organs on the thallus body, such as the gemma cup, rhizoid, and air pores. Here we report that the type-B response regulator MpRRB upregulates the expression of the R2R3-MYB transcription factor GEMMA CUP-ASSOCIATED MYB1 (MpGCAM1) in M. polymorpha. Whereas both Mpgcam1 and Mprrb knockout mutants exhibited defects in gemma cup formation, the Mpgcam1 Mprra double mutant, in which cytokinin signaling is activated due to the lack of type-A response regulator, also formed no gemma cups. This suggests that MpGCAM1 functions downstream of cytokinin signaling. Inducible overexpression of MpGCAM1 produced undifferentiated cell clumps on the thalli of both wild-type and Mprrb. However, smaller thalli were formed in Mprrb compared to the wild-type after the cessation of overexpression. These results suggest that cytokinin signaling promotes gemma cup formation and cellular reprogramming through MpGCAM1, while cytokinin signals also participate in activating cell division during thallus development.

Emerging roles of the ubiquitin-proteasome pathway in enhancing crop yield by optimizing seed agronomic traits

Ubiquitin-proteasome pathway has the potential to modulate crop productivity by influencing agronomic traits. Being sessile, the plant often uses the ubiquitin-proteasome pathway to maintain the stability of different regulatory proteins to survive in an ever-changing environment. The ubiquitin system influences plant reproduction, growth, development, responses to the environment, and processes that control critical agronomic traits. E3 ligases are the major players in this pathway, and they are responsible for recognizing and tagging the targets/substrates. Plants have a variety of E3 ubiquitin ligases, whose functions have been studied extensively, ranging from plant growth to defense strategies. Here we summarize three agronomic traits influenced by ubiquitination: seed size and weight, seed germination, and accessory plant agronomic traits particularly panicle architecture, tillering in rice, and tassels branch number in maize. This review article highlights some recent progress on how the ubiquitin system influences the stability/modification of proteins that determine seed agronomic properties like size, weight, germination and filling, and ultimately agricultural productivity and quality. Further research into the molecular basis of the aforementioned processes might lead to the identification of genes that could be modified or selected for crop development. Likewise, we also propose advances and future perspectives in this regard.

The Role of Transcription Factors in the Regulation of Plant Shoot Branching

Transcription factors, also known as trans-acting factors, balance development and stress responses in plants. Branching plays an important role in plant morphogenesis and is closely related to plant biomass and crop yield. The apical meristem produced during plant embryonic development repeatedly produces the body of the plant, and the final aerial structure is regulated by the branching mode generated by axillary meristem (AM) activities. These branching patterns are regulated by two processes: AM formation and axillary bud growth. In recent years, transcription factors involved in regulating these processes have been identified. In addition, these transcription factors play an important role in various plant hormone pathways and photoresponses regulating plant branching. In this review, we start from the formation and growth of axillary meristems, including the regulation of hormones, light and other internal and external factors, and focus on the transcription factors involved in regulating plant branching and development to provide candidate genes for improving crop architecture through gene editing or directed breeding.

Transcriptome Analysis to Explore the Cause of the Formation of Different Inflorescences in Tomato

The number of inflorescence branches is an important agronomic character of tomato. The meristem differentiation and development pattern of tomato inflorescence is complex and its regulation mechanism is very different from those of other model plants. Therefore, in order to explore the cause of tomato inflorescence branching, transcriptome analysis was conducted on two kinds of tomato inflorescences (single racemes and compound inflorescences). According to the transcriptome data analysis, there were many DEGs of tomato inflorescences at early, middle, and late stages. Then, GO and KEGG enrichments of DEGs were performed. DEGs are mainly enriched in metabolic pathways, biohormone signaling, and cell cycle pathways. According to previous studies, DEGs were mainly enriched in metabolic pathways, and FALSIFLORA (FA) and ANANTHA (AN) genes were the most notable of 41 DEGs related to inflorescence branching. This study not only provides a theoretical basis for understanding inflorescence branching, but also provides a new idea for the follow-up study of inflorescence.

Newly Discovered Alleles of the Tomato Antiflorigen Gene SELF PRUNING Provide a Range of Plant Compactness and Yield

In tomato cultivation, a rare natural mutation in the flowering repressor antiflorigen gene SELF-PRUNING (sp-classic) induces precocious shoot termination and is the foundation in determinate tomato breeding for open field production. Heterozygous single flower truss (sft) mutants in the florigen SFT gene in the background of sp-classic provide a heterosis-like effect by delaying shoot termination, suggesting the subtle suppression of determinacy by genetic modification of the florigen–antiflorigen balance could improve yield. Here, we isolated three new sp alleles from the tomato germplasm that show modified determinate growth compared to sp-classic, including one allele that mimics the effect of sft heterozygosity. Two deletion alleles eliminated functional transcripts and showed similar shoot termination, determinate growth, and yields as sp-classic. In contrast, amino acid substitution allele sp-5732 showed semi-determinate growth with more leaves and sympodial shoots on all shoots. This translated to greater yield compared to the other stronger alleles by up to 42%. Transcriptome profiling of axillary (sympodial) shoot meristems (SYM) from sp-classic and wild type plants revealed six mis-regulated genes related to the floral transition, which were used as biomarkers to show that the maturation of SYMs in the weaker sp-5732 genotype is delayed compared to sp-classic, consistent with delayed shoot termination and semi-determinate growth. Assessing sp allele frequencies from over 500 accessions indicated that one of the strong sp alleles (sp-2798) arose in early breeding cultivars but was not selected. The newly discovered sp alleles are potentially valuable resources to quantitatively manipulate shoot growth and yield in determinate breeding programs, with sp-5732 providing an opportunity to develop semi-determinate field varieties with higher yields.

Atlas of phenotypic, genotypic and geographical diversity present in the European traditional tomato

The Mediterranean basin countries are considered secondary centres of tomato diversification. However, information on phenotypic and allelic variation of local tomato materials is still limited. Here we report on the evaluation of the largest traditional tomato collection, which includes 1499 accessions from Southern Europe. Analyses of 70 traits revealed a broad range of phenotypic variability with different distributions among countries, with the culinary end use within each country being the main driver of tomato diversification. Furthermore, eight main tomato types (phenoclusters) were defined by integrating phenotypic data, country of origin, and end use. Genome-wide association study (GWAS) meta-analyses identified associations in 211 loci, 159 of which were novel. The multidimensional integration of phenoclusters and the GWAS meta-analysis identified the molecular signatures for each traditional tomato type and indicated that signatures originated from differential combinations of loci, which in some cases converged in the same tomato phenotype. Our results provide a roadmap for studying and exploiting this untapped tomato diversity.

Increased branching independent of strigolactone in cytokinin oxidase 2-overexpressing tomato is mediated by reduced auxin transport

Tomato production is influenced by shoot branching, which is controlled by different hormones. Here we produced tomato plants overexpressing the cytokinin-deactivating gene CYTOKININ OXYDASE 2 (CKX2). CKX2-overexpressing (CKX2-OE) plants showed an excessive growth of axillary shoots, the opposite phenotype expected for plants with reduced cytokinin content, as evidenced by LC-MS analysis and ARR5-GUS staining. The TCP transcription factor SlBRC1b was downregulated in the axillary buds of CKX2-OE and its excessive branching was dependent on a functional version of the GRAS-family gene LATERAL SUPPRESSOR (LS). Grafting experiments indicated that increased branching in CKX2-OE plants is unlikely to be mediated by root-derived signals. Crossing CKX2-OE plants with transgenic antisense plants for the strigolactone biosynthesis gene CAROTENOID CLEAVAGE DIOXYGENASE (CCD7-AS) produced an additive phenotype, indicating independent effects of cytokinin and strigolactones on increased branching. On the other hand, CKX2-OE plants showed reduced polar auxin transport and their bud outgrowth was reduced when combined with auxin mutants. Accordingly, CKX2-OE basal buds did not respond to auxin applied in the decapitated apex. Our results suggest that tomato shoot branching depends on a fine-tuning of different hormonal balances and that perturbations in the auxin status could compensate for the reduced cytokinin levels in CKX2-OE plants.

The SINGLE FLOWER (SFL) gene encodes a MYB transcription factor that regulates the number of flowers produced by the inflorescence of chickpea

Legumes usually have compound inflorescences, where flowers/pods develop from secondary inflorescences (I2), formed laterally at the primary inflorescence (I1). Number of flowers per I2, characteristic of each legume species, has important ecological and evolutionary relevance as it determines diversity in inflorescence architecture; moreover, it is also agronomically important for its potential impact on yield. Nevertheless, the genetic network controlling the number of flowers per I2 is virtually unknown. Chickpea (Cicer arietinum) typically produces one flower per I2 but single flower (sfl) mutants produce two (double-pod phenotype). We isolated the SFL gene by mapping the sfl-d mutation and identifying and characterising a second mutant allele. We analysed the effect of sfl on chickpea inflorescence ontogeny with scanning electron microscopy and studied the expression of SFL and meristem identity genes by RNA in situ hybridisation. We show that SFL corresponds to CaRAX1/2a, which codes a MYB transcription factor specifically expressed in the I2 meristem. Our findings reveal SFL as a central factor controlling chickpea inflorescence architecture, acting in the I2 meristem to regulate the length of the period for which it remains active, and therefore determining the number of floral meristems that it can produce.

D-type cyclin OsCYCD3;1 is involved in the maintenance of meristem activity to regulate branch formation in rice

D-type cyclins (CYCDs) are involved in a wide range of biological processes, as one of the major regulators of cell cycle activity. In Arabidopsis (Arabidopsis thaliana), three members of CYCD3 subgroup genes play important roles in plant development such as leaf development and branch formation. In rice (Oryza sativa), there is only one gene (OsCYCD3;1) belonging to the CYCD3 subgroup; its function is unknown. In this study, in order to elucidate the function of OsCYCD3;1, we generated knockout mutants of the gene and conducted developmental analysis. The knockout mutants showed a significantly reduced number of branches compared with a wild type, suggesting that OsCYCD3;1 promotes branch formation. Histological analysis showed that the activities of the axillary meristem and the shoot apical meristem (SAM) were compromised in these mutant plants. Our results suggest that OsCYCD3;1 promotes branch formation, probably by regulating cell division to maintain the activities of the axillary meristem and the SAM.

Reflections on the Triptych of Meristems That Build Flowering Branches in Tomato

Branching is an important component determining crop yield. In tomato, the sympodial pattern of shoot and inflorescence branching is initiated at floral transition and involves the precise regulation of three very close meristems: (i) the shoot apical meristem (SAM) that undergoes the first transition to flower meristem (FM) fate, (ii) the inflorescence sympodial meristem (SIM) that emerges on its flank and remains transiently indeterminate to continue flower initiation, and (iii) the shoot sympodial meristem (SYM), which is initiated at the axil of the youngest leaf primordium and takes over shoot growth before forming itself the next inflorescence. The proper fate of each type of meristems involves the spatiotemporal regulation of FM genes, since they all eventually terminate in a flower, but also the transient repression of other fates since conversions are observed in different mutants. In this paper, we summarize the current knowledge about the genetic determinants of meristem fate in tomato and share the reflections that led us to identify sepal and flower abscission zone initiation as a critical stage of FM development that affects the branching of the inflorescence.

The branchless gene Clbl in watermelon encoding a TERMINAL FLOWER 1 protein regulates the number of lateral branches

A SNP mutation in Clbl gene encoding TERMINAL FLOWER 1 protein is responsible for watermelon branchless. Lateral branching is one of the most important traits, which directly determines plant architecture and crop productivity. Commercial watermelon has the characteristics of multiple lateral branches, and it is time-consuming and labor-costing to manually remove the lateral branches in traditional watermelon cultivation. In our present study, a lateral branchless trait was identified in watermelon material WCZ, and genetic analysis revealed that it was controlled by a single recessive gene, which named as Clbl (Citrullus lanatus branchless). A bulked segregant sequencing (BSA-seq) and linkage analysis was conducted to primarily map Clbl on watermelon chromosome 4. Next-generation sequencing-aided marker discovery and a large mapping population consisting of 1406 F₂ plants were used to further map Clbl locus into a 9011-bp candidate region, which harbored only one candidate gene Cla018392 encoding a TERMINAL FLOWER 1 protein. Sequence comparison of Cla018392 between two parental lines revealed that there was a SNP detected from C to A in the coding region in the branchless inbred line WCZ, which resulted in a mutation from alanine (GCA) to glutamate (GAA) at the fourth exon. A dCAPS marker was developed from the SNP locus, which was co-segregated with the branchless phenotype in both BC₁ and F₂ population, and it was further validated in 152 natural watermelon accessions. qRT-PCR and in situ hybridization showed that the expression level of Cla018392 was significantly reduced in the axillary bud and apical bud in branchless line WCZ. Ectopic expression of ClTFL1 in Arabidopsis showed an increased number of lateral branches. The results of this study will be helpful for better understanding the molecular mechanism of lateral branch development in watermelon and for the development of marker-assisted selection (MAS) for new branchless watermelon cultivars.

RGN1 controls grain number and shapes panicle architecture in rice

Yield in rice is determined mainly by panicle architecture. Using map-based cloning, we identified an R2R3 MYB transcription factor REGULATOR OF GRAIN NUMBER1 (RGN1) affecting grain number and panicle architecture. Mutation of RGN1 caused an absence of lateral grains on secondary branches. We demonstrated that RGN1 controls lateral grain formation by regulation of LONELY GUY (LOG) expression, thus controlling grain number and shaping panicle architecture. A novel favourable allele, RGN1^C , derived from the Or-I group in wild rice affected panicle architecture by means longer panicles. Identification of RGN1 provides a theoretical basis for understanding the molecular mechanism of lateral grain formation in rice; RGN1 will be an important gene resource for molecular breeding for higher yield.

The molecular and genetic regulation of shoot branching

The architecture of flowering plants exhibits both phenotypic diversity and plasticity, determined, in part, by the number and activity of axillary meristems and, in part, by the growth characteristics of the branches that develop from the axillary buds. The plasticity of shoot branching results from a combination of various intrinsic and genetic elements, such as number and position of nodes and type of growth phase, as well as environmental signals such as nutrient availability, light characteristics, and temperature (Napoli et al., 1998; Bennett and Leyser, 2006; Janssen et al., 2014; Teichmann and Muhr, 2015; Ueda and Yanagisawa, 2019). Axillary meristem initiation and axillary bud outgrowth are controlled by a complex and interconnected regulatory network. Although many of the genes and hormones that modulate branching patterns have been discovered and characterized through genetic and biochemical studies, there are still many gaps in our understanding of the control mechanisms at play. In this review, we will summarize our current knowledge of the control of axillary meristem initiation and outgrowth into a branch.

CRISPR/Cas9-Mediated SlMYBS2 Mutagenesis Reduces Tomato Resistance to Phytophthora infestans

Phytophthora infestans (P. infestans) recently caused epidemics of tomato late blight. Our study aimed to identify the function of the SlMYBS2 gene in response to tomato late blight. To further investigate the function of SlMYBS2 in tomato resistance to P. infestans, we studied the effects of SlMYBS2 gene knock out. The SlMYBS2 gene was knocked out by CRISPR-Cas9, and the resulting plants (SlMYBS2 gene knockout, slmybs2-c) showed reduced resistance to P. infestans, accompanied by increases in the number of necrotic cells, lesion sizes, and disease index. Furthermore, after P. infestans infection, the expression levels of pathogenesis-related (PR) genes in slmybs2-c plants were significantly lower than those in wild-type (AC) plants, while the number of necrotic cells and the accumulation of reactive oxygen species (ROS) were higher than those in wild-type plants. Taken together, these results indicate that SlMYBS2 acts as a positive regulator of tomato resistance to P. infestans infection by regulating the ROS level and the expression level of PR genes.

The miR164-GhCUC2-GhBRC1 module regulates plant architecture through abscisic acid in cotton

Branching determines cotton architecture and production, but the underlying regulatory mechanisms remain unclear. Here, we report that the miR164-GhCUC2 (CUP-SHAPED COTYLEDON2) module regulates lateral shoot development in cotton and Arabidopsis. We generated OE-GhCUC2m (overexpression GhCUC2m) and STTM164 (short tandem target mimic RNA of miR164) lines in cotton and heterologous expression lines for gh-miR164, GhCUC2 and GhCUC2m in Arabidopsis to study the mechanisms controlling lateral branching. GhCUC2m overexpression resulted in a short-branch phenotype similar to STTM164. In addition, heterologous expression of GhCUC2m led to decreased number and length of branches compared with wild type, opposite to the effects of the OE-gh-pre164 line in Arabidopsis. GhCUC2 interacted with GhBRC1 and exhibited similar negative regulation of branching. Overexpression of GhBRC1 in the brc1-2 mutant partially rescued the mutant phenotype and decreased branch number. GhBRC1 directly bound to the NCED1 promoter and activated its transcription, leading to local abscisic acid (ABA) accumulation and response. Mutation of the NCED1 promoter disrupted activation by GhBRC1. This finding demonstrates a direct relationship between BRC1 and ABA signalling and places ABA downstream of BRC1 in the control of branching development. The miR164-GhCUC2-GhBRC1-GhNCED1 module provides a clear regulatory axis for ABA signalling to control plant architecture.

Super determinant1A, a RAWULdomain-containing protein, modulates axillary meristem formation and compound leaf development in tomato

Shoot branching and complex leaf development relies on the establishment of boundaries that precedes the formation of axillary meristems (AMs) and leaflets. The tomato (Solanum lycopersicum) super determinant mutant is compromised in both processes, due to a mutation in Sde1A. Sde1A encodes a protein with a RAWUL domain, which is also present in Polycomb Group Repressive Complex 1 (PRC1) RING finger proteins and WD Repeat Domain 48 proteins. Genetic analysis revealed that Sde1A and Bmi1A cooperate, whereas Bmi1C antagonizes both activities, indicating the existence of functionally opposing PRC1 complexes that interact with Sde1A. Sde1A is expressed at early stages of boundary development in a small group of cells in the center of the leaf-axil boundary, but its activity is required for meristem formation at later stages. This suggests that Sde1A and Bmi1A promote AM formation and complex leaf development by safeguarding a pool of cells in the developing boundary zones. Genetic and protein interaction analyses showed that Sde1A and Lateral suppressor (Ls) are components of the same genetic pathway. In contrast to ls, sde1a mutants are not compromised in inflorescence branching, suggesting that Sde1A is a potential target for breeding tomato cultivars with reduced side-shoot formation during vegetative development.

VvMYB114 mediated by miR828 negatively regulates trichome development of Arabidopsis

Trichome is a specialized structure differentiated during the morphogenesis of plant leaf epidermal cells. In recent years, with the continuous researches on trichome development of Arabidopsis and other plants, more and more genes related to trichome morphogenesis have been discovered, including R2R3-type MYB genes. In this study, we cloned a R2R3-type MYB family gene from grape, VvMYB114, a target gene of vvi-miR828. qRT-PCR showed that VvMYB114 mRNA accumulated during grape fruit ripening, and VvMYB114 protein had transcriptional activation activity. Heterologous overexpression of VvMYB114 in Arabidopsis reduced the number of trichome on leaves and stems. Mutating the miR828-binding site in VvMYB114 without altering amino-acid sequence had no effect on trichome development in Arabidopsis. The results showed a different role of the regulation of miR828 to VvMYB114 in Arabidopsis from in grape, which indicated the functional divergence of miRNA targeting homoeologous genes in different species played an important roles in evolution and useful trait selection.

Molecular mechanism of MdWUS2-MdTCP12 interaction in mediating cytokinin signaling to control axillary bud outgrowth

Shoot branching is an important factor that influences the architecture of apple trees and cytokinin is known to promote axillary bud outgrowth. The cultivar 'Fuji', which is grown on ~75% of the apple-producing area in China, exhibits poor natural branching. The TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) family genes BRANCHED1/2 (BRC1/2) are involved in integrating diverse factors that function locally to inhibit shoot branching; however, the molecular mechanism underlying the cytokinin-mediated promotion of branching that involves the repression of BRC1/2 remains unclear. In this study, we found that apple WUSCHEL2 (MdWUS2), which interacts with the co-repressor TOPLESS-RELATED9 (MdTPR9), is activated by cytokinin and regulates branching by inhibiting the activity of MdTCP12 (a BRC2 homolog). Overexpressing MdWUS2 in Arabidopsis or Nicotiana benthamiana resulted in enhanced branching. Overexpression of MdTCP12 inhibited axillary bud outgrowth in Arabidopsis, indicating that it contributes to the regulation of branching. In addition, we found that MdWUS2 interacted with MdTCP12 in vivo and in vitro and suppressed the ability of MdTCP12 to activate the transcription of its target gene, HOMEOBOX PROTEIN 53b (MdHB53b). Our results therefore suggest that MdWUS2 is involved in the cytokinin-mediated inhibition of MdTCP12 that controls bud outgrowth, and hence provide new insights into the regulation of shoot branching by cytokinin.

Plant design gets its details: Modulating plant architecture by phase transitions

Plants evolved different strategies to better adapt to the environmental conditions in which they live: the control of their body architecture and the timing of phase change are two important processes that can improve their fitness. As they age, plants undergo two major phase changes (juvenile to adult and adult to reproductive) that are a response to environmental and endogenous signals. These phase transitions are accompanied by alterations in plant morphology and also by changes in physiology and the behavior of gene regulatory networks. Six main pathways involving environmental and endogenous cues that crosstalk with each other have been described as responsible for the control of plant phase transitions: the photoperiod pathway, the autonomous pathway, the vernalization pathway, the temperature pathway, the GA pathway, and the age pathway. However, studies have revealed that sugar is also involved in phase change and the control of branching behavior. In this review, we discuss recent advances in plant biology concerning the genetic and molecular mechanisms that allow plants to regulate phase transitions in response to the environment. We also propose connections between phase transition and plant architecture control.

Inhibition of lateral shoot formation by RNA interference and chemically induced mutations to genes expressed in the axillary meristem of Nicotiana tabacum L

BACKGROUND

Lateral branches vigorously proliferate in tobacco after the topping of the inflorescence portions of stems for the maturation of the leaves to be harvested. Therefore, tobacco varieties with inhibited lateral shoot formation are highly desired by tobacco farmers.

RESULTS

Genetic inhibition of lateral shoot formation was attempted in tobacco. Two groups of genes were examined by RNA interference. The first group comprised homologs of the genes mediating lateral shoot formation in other plants, whereas the second group included genes highly expressed in axillary bud primordial stages. Although "primary" lateral shoots that grew after the plants were topped off when flower buds emerged were unaffected, the growth of "secondary" lateral shoots, which were detected on the abaxial side of the primary lateral shoot base, was significantly suppressed in the knock-down lines of NtLs, NtBl1, NtREV, VE7, and VE12. Chemically induced mutations to NtLs, NtBl1, and NtREV similarly inhibited the development of secondary and "tertiary" lateral shoots, but not primary lateral shoots. The mutations to NtLs and NtBl1 were incorporated into an elite variety by backcrossing. The agronomic characteristics of the backcross lines were examined in field trials conducted in commercial tobacco production regions. The lines were generally suitable for tobacco leaf production and may be useful as new tobacco varieties.

CONCLUSION

The suppressed expression of NtLs, NtBl1, NtREV, VE7, or VE12 inhibited the development of only the secondary and tertiary lateral shoots in tobacco. The mutant lines may benefit tobacco farmers by minimizing the work required to remove secondary and tertiary lateral shoots that emerge when farmers are harvesting leaves, which is a labor-intensive process.

Overexpression of GmMYB14 improves high-density yield and drought tolerance of soybean through regulating plant architecture mediated by the brassinosteroid pathway

MYB transcription factors (TFs) have been reported to regulate the biosynthesis of secondary metabolites, as well as to mediate plant adaption to abiotic stresses, including drought. However, the roles of MYB TFs in regulating plant architecture and yield potential remain poorly understood. Here, we studied the roles of the dehydration-inducible GmMYB14 gene in regulating plant architecture, high-density yield and drought tolerance through the brassinosteroid (BR) pathway in soybean. GmMYB14 was shown to localize to nucleus and has a transactivation activity. Stable GmMYB14-overexpressing (GmMYB14-OX) transgenic soybean plants displayed a semi-dwarfism and compact plant architecture associated with decreased cell size, resulting in a decrease in plant height, internode length, leaf area, leaf petiole length and leaf petiole angle, and improved yield in high density under field conditions. Results of the transcriptome sequencing suggested the involvement of BRs in regulating GmMYB14-OX plant architecture. Indeed, GmMYB14-OX plants showed reduced endogenous BR contents, while exogenous application of brassinolide could partly rescue the phenotype of GmMYB14-OX plants. Furthermore, GmMYB14 was shown to directly bind to the promoter of GmBEN1 and up-regulate its expression, leading to reduced BR content in GmMYB14-OX plants. GmMYB14-OX plants also displayed improved drought tolerance under field conditions. GmBEN1 expression was also up-regulated in the leaves of GmMYB14-OX plants under polyethylene glycol treatment, indicating that the GmBEN1-mediated reduction in BR level under stress also contributed to drought/osmotic stress tolerance of the transgenic plants. Our findings provided a strategy for stably increasing high-density yield and drought tolerance in soybean using a single TF-encoding gene.

Overexpression of MusaSNAC1 improves shoot proliferation in transgenic banana lines

Augmenting shoot multiplication through genetic engineering is an emerging biotechnological application desirable in optimizing regeneration of genetically modified plants on selection medium and rapid clonal propagation of elite cultivars. Here, we report the improved shoot multiplication in transgenic banana lines with overexpression of MusaSNAC1, a drought-associated NAC transcription factor in banana. Overexpression of MusaSNAC1 induces hypersensitivity of transgenic banana lines toward 6-benzylaminopurine ensuing higher shoot number on different concentrations of 6-benzylaminopurine. Altered transcript levels of multiple genes involved in auxin signaling (Aux/IAA and ARFs) and cytokinin signaling pathways (ARRs) in banana plants overexpressing MusaSNAC1 corroborate the hypersensitivity of transgenic banana plants toward 6-benzylaminopurine. Modulation in expression of ARRs reported to be involved in ABA-hypersensitivity and closure of stomatal aperture correlates with the function of MusaSNAC1 as a drought-responsive NAC transcription factor. Present study suggests a prospective cross talk between shoot multiplication and drought responses coordinated by MusaSNAC1 in banana plants.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02744-5.

Tomato SlBL4 plays an important role in fruit pedicel organogenesis and abscission

Abscission, a cell separation process, is an important trait that influences grain and fruit yield. We previously reported that BEL1-LIKE HOMEODOMAIN 4 (SlBL4) is involved in chloroplast development and cell wall metabolism in tomato fruit. In the present study, we showed that silencing SlBL4 resulted in the enlargement and pre-abscission of the tomato (Solanum lycopersicum cv. Micro-TOM) fruit pedicel. The anatomic analysis showed the presence of more epidermal cell layers and no obvious abscission zone (AZ) in the SlBL4 RNAi lines compared with the wild-type plants. RNA-seq analysis indicated that the regulation of abscission by SlBL4 was associated with the altered abundance of genes related to key meristems, auxin transporters, signaling components, and cell wall metabolism. Furthermore, SlBL4 positively affected the auxin concentration in the abscission zone. A dual-luciferase reporter assay revealed that SlBL4 activated the transcription of the JOINTLESS, OVATE, PIN1, and LAX3 genes. We reported a novel function of SlBL4, which plays key roles in fruit pedicel organogenesis and abscission in tomatoes.

The AtMYB2 inhibits the formation of axillary meristem in Arabidopsis by repressing RAX1 gene under environmental stresses

AtMYB2 protein represses the formation of axillary meristems in response to environmental stresses so that plants can undergo a shorter vegetative development stage under environmental stresses. Shoot branching is an important event determined by endogenous factors during the development of plants. The formation of axillary meristem is also significantly repressed by environmental stresses and the underlying mechanism is largely unknown. The REGULATOR OF AXILLARY MERISTEMS (RAX) genes encode the R2R3 MYB transcription factors that have been shown to regulate the formation of axillary meristems in Arabidopsis. The AtMYB2 is also a member of R2R3 MYB gene family whose expression is usually induced by the environmental stresses. In this study, our results showed that AtMYB2 protein plays a pivotal negative regulatory role in the formation of axillary meristem. AtMYB2 is mainly expressed in the leaf axils as that of RAX1. The environmental stresses can increase the expression of AtMYB2 protein which further inhibits the expression of RAX1 gene by binding to its promoter. Therefore, AtMYB2 protein represses the formation of axillary meristems in response to environmental stresses so that plants can undergo a shorter vegetative development stage under environmental stresses.

Activation tagging identifies Arabidopsis transcription factor AtMYB68 for heat and drought tolerance at yield determining reproductive stages

Heat stress occurring at reproductive stages can result in significant and permanent damage to crop yields. However, previous genetic studies in understanding heat stress response and signaling were performed mostly on seedling and plants at early vegetative stages. Here we identify, using a developmentally defined, gain-of-function genetic screen with approximately 18 000 Arabidopsis thaliana activation-tagged lines, a mutant that maintained productive seed set post-severe heat stress during flowering. Genome walking indicated this phenotype was caused by the insertion of 35S enhancers adjacent to a nuclear localized transcription factor AtMYB68. Subsequent overexpression analysis confirmed that AtMYB68 was responsible for the reproductive heat tolerance of the mutant. Furthermore, these transgenic Arabidopsis plants exhibited enhanced abscisic acid sensitivity at and post-germination, reduced transpirational water loss during a drought treatment, and enhanced seed yield under combined heat and drought stress during flowering. Ectopic expression of AtMYB68 in Brassica napus driven either by 35S or by heat-inducible promoter recapitulated the enhanced reproductive heat stress and drought tolerance phenotypes observed in the transgenic Arabidopsis. The improvement to heat stress is likely due to enhanced pollen viability observed in the transgenic plants. More importantly, the transgenic canola showed significant yield advantages over the non-transgenic controls in multiple locations, multiple season field trials under various drought and heat stress conditions. Together these results suggest that AtMYB68 regulate plant stress tolerance at the most important yield determining stage of plant development, and is an effective target for crop yield protection under current global climate volatility.

Gemma cup and gemma development in Marchantia polymorpha

The basal land plant Marchantia polymorpha efficiently propagates in favourable environments through clonal progeny called gemmae. Gemmae develop in cup-shaped receptacles known as gemma cups, which are formed on the gametophyte body. Anatomical studies have described the developmental processes involved over a century ago; however, little is known about the underlying molecular mechanisms. Recent studies have started to unravel the mechanism underlying genetic and hormonal regulation of gemma cup and gemma development, showing that it shares some regulatory mechanisms with several sporophytic organs in angiosperms. Further study of these specialized organs will contribute to our understanding of the core regulatory modules underlying organ development in land plants and how these became so diversified morphologically over the course of evolution.

Control of cell fate during axillary meristem initiation

Axillary meristems (AMs) are located in the leaf axil and can establish new growth axes. Whereas their neighboring cells are differentiated, the undifferentiated cells in the AM endow the AM with the same developmental potential as the shoot apical meristem. The AM is, therefore, an excellent system to study stem cell fate maintenance in plants. In this review, we summarize the current knowledge of AM initiation. Recent findings have shown that AMs derive from a stem cell lineage that is maintained in the leaf axil. This review covers AM progenitor cell fate maintenance, reactivation, and meristem establishment. We also highlight recent work that links transcription factors, phytohormones, and epigenetic regulation to AM initiation.

Insights into the Diversification and Evolution of R2R3-MYB Transcription Factors in Plants

As one of the largest families of transcription factors (TFs) in plants, R2R3-MYB proteins play crucial roles in regulating a series of plant-specific biological processes. Although the diversity of plant R2R3-MYB TFs has been studied previously, the processes and mechanisms underlying the expansion of these proteins remain unclear. Here, we performed evolutionary analyses of plant R2R3-MYB TFs with dense coverage of streptophyte algae and embryophytes. Our analyses revealed that ancestral land plants exhibited 10 subfamilies of R2R3-MYB proteins, among which orthologs of seven subfamilies were present in chlorophytes and charophycean algae. We found that asymmetric gene duplication events in different subfamilies account for the expansion of R2R3-MYB proteins in embryophytes. We further discovered that the largest subfamily of R2R3-MYBs in land plants, subfamily VIII, emerged in the common ancestor of Zygnematophyceae and embryophytes. During plant terrestrialization, six duplication events gave rise to seven clades of subfamily VIII. Subsequently, this TF subfamily showed a tendency for expansion in bryophytes, lycophytes, and ferns and extensively diversified in ancestral gymnosperms and angiosperms in clades VIII-A-1, VIII-D, and VIII-E. In contrast to subfamily VIII, other subfamilies of R2R3-MYB TFs have remained less expanded across embryophytes. The findings regarding phylogenetic analyses, auxiliary motifs, and DNA-binding specificities provide insight into the evolutionary history of plant R2R3-MYB TFs and shed light on the mechanisms underlying the extensive expansion and subsequent sub- and neofunctionalization of these proteins.

Control of Plant Branching by the CUC2/CUC3-DA1-UBP15 Regulatory Module

Lateral branches are important for plant architecture and production, but how plants determine their lateral branches remains to be further understood. Here, we report that the CUP-SHAPED COTYLEDON2 (CUC2)/CUC3-DA1-UBIQUITIN-SPECIFIC PROTEASE15 (UBP15) regulatory module controls the initiation of axillary meristems, thereby determining the number of lateral branches in Arabidopsis (Arabidopsis thaliana). Mutation in the ubiquitin-dependent peptidase DA1 causes fewer lateral branches due to defects in the initiation of axillary meristems. The transcription factors CUC2 and CUC3, which regulate the axillary meristem initiation, directly bind to the DA1 promoter and activate its expression. Further results show that UBP15, which is a direct substrate of DA1 peptidase, represses the initiation of axillary meristems. Genetic analyses support that CUC2/CUC3, DA1, and UBP15 function, at least in part, in a common pathway to regulate the initiation of axillary meristems. Therefore, our findings establish a genetic and molecular framework by which the CUC2/CUC3-DA1-UBP15 regulatory module controls the initiation of axillary meristems, thereby determining plant architecture.

Plant Inflorescence Architecture: The Formation, Activity, and Fate of Axillary Meristems

The above-ground plant body in different plant species can have very distinct forms or architectures that arise by recurrent redeployment of a finite set of building blocks-leaves with axillary meristems, stems or branches, and flowers. The unique architectures of plant inflorescences in different plant families and species, on which this review focuses, determine the reproductive success and yield of wild and cultivated plants. Major contributors to the inflorescence architecture are the activity and developmental trajectories adopted by axillary meristems, which determine the degree of branching and the number of flowers formed. Recent advances in genetic and molecular analyses in diverse flowering plants have uncovered both common regulatory principles and unique players and/or regulatory interactions that underlie inflorescence architecture. Modulating activity of these regulators has already led to yield increases in the field. Additional insight into the underlying regulatory interactions and principles will not only uncover how their rewiring resulted in altered plant form, but will also enhance efforts at optimizing plant architecture in desirable ways in crop species.

Downregulation of SlGRAS15 manipulates plant architecture in tomato (Solanum lycopersicum)

GRAS family transcription factors (TF) are involved in multiple biological processes in plants. In recent years among the 54 identified GRAS proteins, only few have been studied functionally in tomato (Solanum lycopersicum). In the present study, a novel and previously uncharacterized member of tomato GRAS transcription factors family SlGRAS15 was isolated and functionally characterized. It was observed that SlGRAS15 preferably expressed in roots, followed by young leaves, stem, and comparatively low transcripts levels were noticed in all other tissues. To explore the SlGRAS15 function in detail, an RNA interference (RNAi) vector targeting SlGRAS15 was constructed and transformed into tomato plants. The transgenic plants carrying SlGRAS15-RNAi displayed pleiotropic phenotypes associated with multiple agronomical traits including reduced plant height and small leaf size with pointed margins, increased node number, lateral shoots, and petiolules length. In addition, transcriptional analysis revealed that silencing SlGRAS15 altered vegetative growth by downregulating gibberellin (GA) biosynthesis genes and stimulating the GA deactivating genes, thus lowering the endogenous GA content in tomato transgenic lines. Moreover, the GA signaling downstream gene (SlGAST1) was downregulated but the negative regulator of GA signaling (SlDELLA) was upregulated by SlGRAS15 silencing. The root and hypocotyl length in SlGRAS15-RNAi lines showed reduced growth under normal conditions (Mock) as compared with the wild type (WT) control plants. Taken together, these findings enhanced our understanding that suppression of SlGRAS15 lead to a series of developmental processes by modulating gibberellin signaling and demonstrate an association between the SlGRAS15 and GA signaling pathway during vegetative growth in tomato.