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Abstract Background The shoot apical meristem (SAM), from which all above-ground tissues of plants are derived, is critical to plant morphology and development. In maize (Zea mays), loss-of-function mutant studies have identified several SAM-related genes, most encoding homeobox transcription factors (TFs), located upstream of hierarchical networks of hundreds of genes. Results Here, we collect 46 transcriptome and 16 translatome datasets across 62 different tissues or stages from the maize inbred line B73. We construct a dynamic regulome for 27 members of three SAM-related homeobox subfamilies (KNOX, WOX, and ZF-HD) through machine-learning models for the detection of TF targets across different tissues and stages by combining tsCUT&Tag, ATAC-seq, and expression profiling. This dynamic regulome demonstrates the distinct binding specificity and co-factors for these homeobox subfamilies, indicative of functional divergence between and within them. Furthermore, we assemble a SAM dynamic regulome, illustrating potential functional mechanisms associated with plant architecture. Lastly, we generate a wox13a mutant that provides evidence that WOX13A directly regulates Gn1 expression to modulate plant height, validating the regulome of SAM-related homeobox genes. Conclusions The SAM-related homeobox transcription-factor regulome presents an unprecedented opportunity to dissect the molecular mechanisms governing SAM maintenance and development, thereby advancing our understanding of maize growth and shoot architecture.

Plants use light as a resource and signal. Photons within the 400–700 nm waveband are considered photosynthetically active. Far‐red photons (FR, 700–800 nm) are used by plants to detect nearby vegetation and elicit the shade avoidance syndrome. In addition, FR photons have also been shown to contribute to photosynthesis, but knowledge about these dual effects remains scarce. Here, we study shoot‐architectural and photosynthetic responses to supplemental FR light during the photoperiod in several rice varieties. We observed that FR enrichment only mildly affected the rice transcriptome and shoot architecture as compared to established model species, whereas leaf formation, tillering and biomass accumulation were clearly promoted. Consistent with this growth promotion, we found that CO2‐fixation in supplemental FR was strongly enhanced, especially in plants acclimated to FR‐enriched conditions as compared to control conditions. This growth promotion dominates the effects of FR photons on shoot development and architecture. When substituting FR enrichment with an end‐of‐day FR pulse, this prevented photosynthesis‐promoting effects and elicited shade avoidance responses. We conclude that FR photons can have a dual role, where effects depend on the environmental context: in addition to being an environmental signal, they are also a potent source of harvestable energy. Summary statement: The ratio of red: far‐red (FR) light is monitored by phytochrome photoreceptors as a cue for neighbour proximity, and a drop in this ratio plants elicit so‐called shade avoidance responses. Here we show in a number of rice varieties that FR enrichment triggers only marginal shade avoidance but contributes significantly to leaf‐level photosynthesis and whole‐plant biomass accumulation. [ABSTRACT FROM AUTHOR]

Transcription factors in coordination with phytohormones form an intricate regulatory network modulating vital cellular mechanisms like development, growth and senescence in plants. In this study, we have functionally characterized the transcription factor OsNAC121 by developing gene silencing and overexpressing transgenic rice plants, followed by detailed analyses of the plant architecture. Transgenic lines exhibited remodelling in crown root development, lateral root structure and density, tiller height and number, panicle and grain morphologies, underpinning the imbalanced auxin: cytokinin ratio due to perturbed auxin transportation. Application of cytokinin, auxin and abscisic acid increased OsNAC121 gene expression nearly 17-, 6- and 91-folds, respectively. qRT-PCR results showed differential expressions of auxin and cytokinin pathway genes, implying their altered levels. A 47-fold higher expression level of OsNAC121 during milky stage in untransformed rice, compared to 14-day old shoot tissue, suggests its crucial role in grain filling; as evidenced by a large number of undeveloped grains produced by the gene silenced lines. Crippled gravitropic response by the transgenic plants indicates their impaired auxin transport. Bioinformatics revealed that OsNAC121 interacts with co-repressor (TOPLESS) proteins and forms a part of the inhibitor complex OsIAA10, an essential core component of auxin signalling pathway. Therefore, OsNAC121 emerges as an important regulator of various aspects of plant architecture through modulation of crosstalk between auxin and cytokinin, altering their concentration gradient in the meristematic zones, and consequently modifying different plant organogenesis processes.Key message: Analyses of gene silencing and overexpression lines unveil the role of rice transcription factor OsNAC121 in root system architecture, tiller height and number as well as panicle and grain morphologies, which are modulated by auxin-cytokinin homeostasis. [ABSTRACT FROM AUTHOR]

Abstract Background In soybeans, faster canopy coverage (CC) is a highly desirable trait but a fully covered canopy is unfavorable to light interception at lower levels in the canopy with most of the incident radiation intercepted at the top of the canopy. Shoot architecture that influences CC is well studied in crops such as maize and wheat, and altering architectural traits has resulted in enhanced yield. However, in soybeans the study of shoot architecture has not been as extensive. Results This study revealed significant differences in CC among the selected soybean accessions. The rate of CC was found to decrease at the beginning of the reproductive stage (R1) followed by an increase during the R2-R3 stages. Most of the accessions in the study achieved maximum rate of CC between R2-R3 stages. We measured Light interception (LI), defined here as the ratio of Photosynthetically Active Radiation (PAR) transmitted through the canopy to the incoming PAR or the radiation above the canopy. LI was found to be significantly correlated with CC parameters, highlighting the relationship between canopy structure and light interception. The study also explored the impact of plant shape on LI and CO2 assimilation. Plant shape was characterized into distinct quantifiable parameters and by modeling the impact of plant shape on LI and CO2 assimilation, we found that plants with broad and flat shapes at the top maybe more photosynthetically efficient at low light levels, while conical shapes were likely more advantageous when light was abundant. Shoot architecture of plants in this study was described in terms of whole plant, branching and leaf-related traits. There was significant variation for the shoot architecture traits between different accessions, displaying high reliability. We found that that several shoot architecture traits such as plant height, and leaf and internode-related traits strongly influenced CC and LI. Conclusion In conclusion, this study provides insight into the relationship between soybean shoot architecture, canopy coverage, and light interception. It demonstrates that novel shoot architecture traits we have defined here are genetically variable, impact CC and LI and contribute to our understanding of soybean morphology. Correlations between different architecture traits, CC and LI suggest that it is possible to optimize soybean growth without compromising on light transmission within the soybean canopy. In addition, the study underscores the utility of integrating low-cost 2D phenotyping as a practical and cost-effective alternative to more time-intensive 3D or high-tech low-throughput methods. This approach offers a feasible means of studying basic shoot architecture traits at the field level, facilitating a broader and efficient assessment of plant morphology.

Background: In soybeans, faster canopy coverage (CC) is a highly desirable trait but a fully covered canopy is unfavorable to light interception at lower levels in the canopy with most of the incident radiation intercepted at the top of the canopy. Shoot architecture that influences CC is well studied in crops such as maize and wheat, and altering architectural traits has resulted in enhanced yield. However, in soybeans the study of shoot architecture has not been as extensive. Results: This study revealed significant differences in CC among the selected soybean accessions. The rate of CC was found to decrease at the beginning of the reproductive stage (R1) followed by an increase during the R2-R3 stages. Most of the accessions in the study achieved maximum rate of CC between R2-R3 stages. We measured Light interception (LI), defined here as the ratio of Photosynthetically Active Radiation (PAR) transmitted through the canopy to the incoming PAR or the radiation above the canopy. LI was found to be significantly correlated with CC parameters, highlighting the relationship between canopy structure and light interception. The study also explored the impact of plant shape on LI and CO2 assimilation. Plant shape was characterized into distinct quantifiable parameters and by modeling the impact of plant shape on LI and CO2 assimilation, we found that plants with broad and flat shapes at the top maybe more photosynthetically efficient at low light levels, while conical shapes were likely more advantageous when light was abundant. Shoot architecture of plants in this study was described in terms of whole plant, branching and leaf-related traits. There was significant variation for the shoot architecture traits between different accessions, displaying high reliability. We found that that several shoot architecture traits such as plant height, and leaf and internode-related traits strongly influenced CC and LI. Conclusion: In conclusion, this study provides insight into the relationship between soybean shoot architecture, canopy coverage, and light interception. It demonstrates that novel shoot architecture traits we have defined here are genetically variable, impact CC and LI and contribute to our understanding of soybean morphology. Correlations between different architecture traits, CC and LI suggest that it is possible to optimize soybean growth without compromising on light transmission within the soybean canopy. In addition, the study underscores the utility of integrating low-cost 2D phenotyping as a practical and cost-effective alternative to more time-intensive 3D or high-tech low-throughput methods. This approach offers a feasible means of studying basic shoot architecture traits at the field level, facilitating a broader and efficient assessment of plant morphology. [ABSTRACT FROM AUTHOR]

Shoot architecture in maize is critical since it determines resource use, impacts wind and rain damage tolerance, and affects yield stability. Quantifying the diversity among inbred lines in heterosis breeding is essential, especially when describing germplasm resources. However, traditional geometric description methods oversimplify shoot architecture and ignore the plant’s overall architecture, making it difficult to reflect and illustrate diversity. This study presents a new method to describe maize shoot architecture and quantifies its diversity by combining computer vision algorithms and persistent homology. Our results reveal that persistent homology can capture key characteristics of shoot architecture in maize and other details often overlooked by traditional geometric analysis. Based on this method, the morphological diversity of shoot architecture can be mined (quantified), and the main shoot architecture types can be obtained. Consequently, this method can easily describe the diversity of shoot architecture in many maize materials.

In higher plants, the shoot apical meristem produces lateral organs in a regular spacing (phyllotaxy) and timing (plastochron). The molecular analysis of mutants associated with phyllotaxy and plastochron would increase our understanding of the mechanism of shoot architecture formation. In this study, we identified mutant mnd8ynp5 that shows an increased rate of leaf emergence and a larger number of nodes in combination with a dwarfed growth habit from an EMS-treated population of the elite barley cultivar Yangnongpi 5. Using a map-based cloning strategy, the mnd8 gene was narrowed down to a 6.7-kb genomic interval on the long arm of chromosome 5H. Sequence analysis revealed that a C to T single-nucleotide mutation occurred at the first exon (position 953) of HORVU5Hr1G118820, leading to an alanine (Ala) to valine (Val) substitution at the 318th amino acid site. Next, HORVU5Hr1G118820 was defined as the candidate gene of MND8 encoding 514 amino acids and containing two multidrug and toxic compound extrusion (MATE) domains. It is highly homologous to maize Bige1 and has a conserved function in the regulation of plant development by controlling the leaf initiation rate. Examination of modern barely varieties showed that Hap-1 was the dominant haplotype and was selected in barley breeding around the world. Collectively, our results indicated that mnd8ynp5 is a novel allele of the HORVU5Hr1G118820 gene that is possibly responsible for the shortened plastochron and many noded dwarf phenotype in barley.

Societal Impact Statement: Rice farming is transitioning from transplanting rice seedlings towards the less labour‐intensive and less water‐demanding method of directly seeding rice. This, however, is accompanied by increased weed proliferation. To tackle this issue, this study seeks to identify how the crop itself can better suppress weeds, with a focus on light competition via shading. Using a rice diversity panel, traits were identified that contribute to enhanced shading capacity, and these traits were encapsulated into a single shading capacity metric. This was followed by the identification of the genetic loci underpinning variation in the core traits. The identified haplotypes can be used in breeding programmes to improve weed suppression by rice, thus contributing to sustainable agriculture. Summary: In modern rice farming, one of the major constraints is weed proliferation and the entailed ecological impact of herbicide application. This requires increased weed competitiveness in current rice varieties, achieved via enhanced shade casting to limit the growth of shade‐sensitive weeds.To identify traits that increase rice shading capacity, we exhaustively phenotyped a rice diversity panel of 344 varieties at an early vegetative stage. A genome‐wide association study (GWAS) revealed genetic loci underlying variation in canopy architecture traits linked with shading capacity.The screen shows considerable natural variation in shoot architecture for 13 examined traits, of which shading potential is mostly determined by projected shoot area, number of leaves, culm height and canopy solidity. The shading rank, a metric based on these core traits, identifies varieties with the highest shading potential. Five genetic loci were found to be associated with canopy architecture, shading potential and early vigour.Identification of traits contributing to shading capacity and underlying allelic variation will serve future genomic‐assisted breeding programmes. Implementing the presented genetic resources for increased shading and weed competitiveness in rice breeding will make its farming less dependent on herbicides and contribute towards more environmentally sustainable agriculture. [ABSTRACT FROM AUTHOR]

Phytohormones play a central role in plant development and environmental responses. Auxin is a classical hormone that is required for organ formation, tissue patterning, and defense responses. Auxin pathways have been extensively studied across numerous land plant lineages, including bryophytes and eudicots. In contrast, our understanding of the roles of auxin in maize morphogenesis and immune responses is limited. Here, we review evidence for auxin-mediated processes in maize and describe promising areas for future research in the auxin field. Several recent transcriptomic and genetic studies have demonstrated that auxin is a key influencer of both vegetative and reproductive development in maize (namely roots, leaves, and kernels). Auxin signaling has been implicated in both maize shoot architecture and immune responses through genetic and molecular analyses of the conserved co-repressor RAMOSA ENHANCER LOCUS2. Polar auxin transport is linked to maize drought responses, root growth, shoot formation, and leaf morphogenesis. Notably, maize has been a key system for delineating auxin biosynthetic pathways and offers many opportunities for future investigations on auxin metabolism. In addition, crosstalk between auxin and other phytohormones has been uncovered through gene expression studies and is important for leaf and root development in maize. Collectively these studies point to auxin as a cornerstone for maize biology that could be leveraged for improved crop resilience and yield. [ABSTRACT FROM AUTHOR]

Cereals are a group of grasses cultivated by humans for their grain. It is from these cereal grains that the majority of all calories consumed by humans are derived. The production of these grains is the result of the development of a series of hierarchical reproductive structures that form the distinct shoot architecture of the grasses. Being spatiotemporally complex, the coordination of grass shoot development is tightly controlled by a network of genes and signals, including the key phytohormone auxin. Hormonal manipulation has therefore been identified as a promising potential approach to increasing cereal crop yields and therefore ultimately global food security. Recent work translating the substantial body of auxin research from model plants into cereal crop species is revealing the contribution of auxin biosynthesis, transport, and signalling to the development of grass shoot architecture. This review discusses this still-maturing knowledge base and examines the possibility that changes in auxin biology could have been a causative agent in the evolution of differences in shoot architecture between key grass species, or could underpin the future selective breeding of cereal crops. [ABSTRACT FROM AUTHOR]

Plants are capable of regulating their shoot architecture in response to diverse internal and external environments. The circadian clock is an adaptive mechanism that integrates information from internal and ambient conditions to help plants cope with recurring environmental fluctuations. Despite the current understanding of plant circadian clock and genetic framework underlying plant shoot architecture, the intricate connection between these two adaptive mechanisms remains largely unclear. In this study, we elucidated how the core clock gene LUX ARRHYTHMO (LUX) regulates shoot architecture in the model legume plant Medicago truncatula. We show that mtlux mutant displays increased main stem height, reduced lateral shoot length, and decreased the number of lateral branches and biomass yield. Gene expression analysis revealed that MtLUX regulated shoot architecture by repressing the expression of strigolactone receptor MtD14 and MtTB1/MtTCP1A, a TCP gene that functions centrally in modulating shoot architecture. In vivo and in vitro experiments showed that MtLUX directly binds to a cis-element in the promoter of MtTB1/MtTCP1A, suggesting that MtLUX regulates branching by rhythmically suppressing MtTB1/MtTCP1A. This work demonstrates the regulatory effect of the circadian clock on shoot architecture, offering a new understanding underlying the genetic basis towards the flexibility of plant shoot architecture.

Plant architecture develops post-embryonically and emerges from a dialogue between the developmental signals and environmental cues. Length and branching of the vegetative and reproductive tissues were the focus of improvement of plant performance from the early days of plant breeding. Current breeding priorities are changing, as we need to prioritize plant productivity under increasingly challenging environmental conditions. While it has been widely recognized that plant architecture changes in response to the environment, its contribution to plant productivity in the changing climate remains to be fully explored. This review will summarize prior discoveries of genetic control of plant architecture traits and their effect on plant performance under environmental stress. We review new tools in phenotyping that will guide future discoveries of genes contributing to plant architecture, its plasticity, and its contributions to stress resilience. Subsequently, we provide a perspective into how integrating the study of new species, modern phenotyping techniques, and modeling can lead to discovering new genetic targets underlying the plasticity of plant architecture and stress resilience. Altogether, this review provides a new perspective on the plasticity of plant architecture and how it can be harnessed for increased performance under environmental stress.

Plant architecture develops post-embryonically and emerges from a dialogue between the developmental signals and environmental cues. Length and branching of the vegetative and reproductive tissues were the focus of improvement of plant performance from the early days of plant breeding. Current breeding priorities are changing, as we need to prioritize plant productivity under increasingly challenging environmental conditions. While it has been widely recognized that plant architecture changes in response to the environment, its contribution to plant productivity in the changing climate remains to be fully explored. This review will summarize prior discoveries of genetic control of plant architecture traits and their effect on plant performance under environmental stress. We review new tools in phenotyping that will guide future discoveries of genes contributing to plant architecture, its plasticity, and its contributions to stress resilience. Subsequently, we provide a perspective into how integrating the study of new species, modern phenotyping techniques, and modeling can lead to discovering new genetic targets underlying the plasticity of plant architecture and stress resilience. Altogether, this review provides a new perspective on the plasticity of plant architecture and how it can be harnessed for increased performance under environmental stress.

Summary: Plants have adapted to different environmental niches by fine‐tuning the developmental factors working together to regulate traits. Variations in the developmental factors result in a wide range of quantitative variations in these traits that helped plants survive better. The major developmental pathways affecting plant architecture are also under the control of such pathways. Most notable are the CLAVATA‐WUSCHEL pathway regulating shoot apical meristem fate, GID1‐DELLA module influencing plant height and tillering, LAZY1‐TAC1 module controlling branch/tiller angle and the TFL1‐FT determining the floral fate in plants. Allelic variants of these key regulators selected during domestication shaped the crops the way we know them today. There is immense yield potential in the 'ideal plant architecture' of a crop. With the available genome‐editing techniques, possibilities are not restricted to naturally occurring variations. Using a transient reprogramming system, one can screen the effect of several developmental gene expressions in novel ecosystems to identify the best targets. We can use the plant's fine‐tuning mechanism for customizing crops to specific environments. The process of crop domestication can be accelerated with a proper understanding of these developmental pathways. It is time to step forward towards the next‐generation molecular breeding for restructuring plant types in crops ensuring yield stability. [ABSTRACT FROM AUTHOR]

Leaf development underlies crop growth and productivity and has been a major target of crop domestication and improvement. However, most genes controlling leaf development in barley remain unknown. We identified a dwarf and liguleless (dl) mutant derived by ethylmethane sulfonate mutagenesis. The dl mutant showed dramatic changes in shoot architecture compared with wild-type (Yangnongpi 5) plants. Besides lacking ligules, the dl mutant showed much shorter plant height (28 cm) than Yangnongpi 5 (78 cm). By map-based cloning, the dl gene was localized to a 56.58-kb genomic interval on the long arm of chromosome 7. A C-to-T single-nucleotide substitution was identified at exon position 790, and is a functional mutation resulting in a proline-to-serine substitution at the 264th amino acid residue of HORVU7Hr1G106960. Consequently, HORVU7Hr1G106960 was identified as the DL gene, encoding 269 amino acids and containing the Arabidopsis LSH1 and Oryza G1 (ALOG) domain. DL is highly similar to rice OsG1-LIKE 1/2 (OsG1L1/2) and sorghum AWN1/AWN1-10 at the amino acid level. Although the dl mutant allele showed no expression changes in selected tissues by real-time PCR, we propose HORVU7Hr1G106960 as a candidate gene conferring the dwarf and liguleless phenotype in barley.

Higher plants generate new leaves from shoot meristems throughout their vegetative lifespan. The tempo of leaf initiation is dynamically regulated by physiological cues, but little is known about the underlying genetic signaling pathways that coordinate this rate. Two maize (Zea mays) mutants, terminal ear1 (te1) and phytochrome B1;phytochrome B2 (phyB1;phyB2), oppositely affect leaf initiation rates and total leaf number at the flowering time: te1 mutants make leaves faster whereas phyB1;phyB2 mutants make leaves slower than wild-type plants. To test whether PhyB1, PhyB2, and TE1 act in overlapping or distinct pathways to regulate leaf initiation, we crossed te1 and phyB1;phyB2 created an F2 population segregating for these three mutations and quantified various phenotypes among the resulting genotypes, including leaf number, leaf initiation rate, plant height, leaf length, leaf width, number of juvenile leaves, stalk diameter, and dry shoot biomass. Leaf number and initiation rate in phyB1;phyB2;te1 plants fell between the extremes of the two parents, suggesting an additive genetic interaction between te1 and phyB1;phyB2 rather than epistasis. Therefore, we conclude that PhyB1, PhyB2, and TE1 likely control leaf initiation through distinct signaling pathways. [ABSTRACT FROM AUTHOR]

SUMMARY: Gravitropism guides growth to shape plant architecture above and below ground. Mutations in LAZY1 impair stem gravitropism and cause less upright inflorescence branches (wider angles). The LAZY1 protein resides at the plasma membrane and in the nucleus. The plasma membrane pool is necessary and sufficient for setting branch angles. To investigate the molecular mechanism of LAZY1 function, we screened for LAZY1‐interacting proteins in yeast. We identified BRXL4, a shoot‐specific protein related to BREVIS RADIX. The BRXL4‐LAZY1 interaction occurred at the plasma membrane in plant cells, and not detectably in the nucleus. Mutations in the C‐terminus of LAZY1, but not other conserved regions, prevented the interaction. Opposite to lazy1, brxl4 mutants displayed faster gravitropism and more upright branches. Overexpressing BRXL4 produced strong lazy1 phenotypes. The apparent negative regulation of LAZY1 function is consistent with BRXL4 reducing LAZY1 expression or the amount of LAZY1 at the plasma membrane. Measurements indicated that both are true. LAZY1 mRNA was three‐fold more abundant in brxl4 mutants and almost undetectable in BRXL4 overexpressors. Plasma membrane LAZY1 was higher and nuclear LAZY1 lower in brxl4 mutants compared with the wild type. To explain these results, we suggest that BRXL4 reduces the amount of LAZY1 at the plasma membrane where it functions in gravity signaling and promotes LAZY1 accumulation in the nucleus where it reduces LAZY1 expression, possibly by suppressing its own transcription. This explanation of how BRXL4 negatively regulates LAZY1 suggests ways to modify shoot system architecture for practical purposes. [ABSTRACT FROM AUTHOR]

Long‐lived perennial plants optimize their shoot architecture by responding to seasonal cues. The main strategy used by plants of temperate and boreal regions with respect to surviving the extremely unfavourable conditions of winter comprises the protection of their apical and lateral meristematic tissues. This involves myriads of transcriptional, translational and metabolic changes in the plants because shoot architecture is controlled by multiple pathways that regulate processes such as bud formation and flowering, small RNAs, environmental factors (especially light quality, photoperiod and temperature), hormones, and sugars. Recent studies have begun to reveal how these pathways are recruited for the seasonal adaptation and regulation of shoot architecture in perennial plants, including the role of a regulatory module consisting of antagonistic players terminal flower 1 (TFL1) and like‐ap1 (LAP1) in the hybrid aspen. Here, we review recent progress in our understanding of the genetic control of shoot architecture in perennials compared to in annuals. [ABSTRACT FROM AUTHOR]

In recent years, 3D imaging became an increasingly popular screening modality for high-throughput plant phenotyping. The 3D scans provide a rich source of information about architectural plant organization which cannot always be derived from multi-view projection 2D images. On the other hand, 3D scanning is associated with a principle inaccuracy by assessment of geometrically complex plant structures, for example, due the loss of geometrical information on reflective, shadowed, inclined and/or curved leaf surfaces. Here, we aim to quantitatively assess the impact of geometrical inaccuracies in 3D plant data on phenotypic descriptors of four different shoot architectures, including tomato, maize, cucumber, and arabidopsis. For this purpose, virtual laser scanning of synthetic models of these four plant species was used. This approach was applied to simulate different scenarios of 3D model perturbation, as well as the principle loss of geometrical information in shadowed plant regions. Our experimental results show that different plant traits exhibit different and, in general, plant type specific dependency on the level of geometrical perturbations. However, some phenotypic traits are tendentially more or less correlated with the degree of geometrical inaccuracies in assessing 3D plant architecture. In particular, integrative traits, such as plant area, volume, and physiologically important light absorption show stronger correlation with the effectively visible plant area than linear shoot traits, such as total plant height and width crossover different scenarios of geometrical perturbation. Our study addresses an important question of reliability and accuracy of 3D plant measurements and provides solution suggestions for consistent quantitative analysis and interpretation of imperfect data by combining measurement results with computational simulation of synthetic plant models. [ABSTRACT FROM AUTHOR]

Argonaute (AGO) proteins are the core components of the RNA-induced silencing complexes (RISC) in the cytoplasm and nucleus, and are necessary for the development of plant shoot meristem, which gives rise to the above-ground plant body. In this study, we identified 23 Phyllostachys edulis AGO genes (PhAGOs) that were distributed unequally on the 14 unmapped scaffolds. Gene collinearity and phylogeny analysis showed that the innovation of PhAGO genes was mainly due to dispersed duplication and whole-genome duplication, which resulted in the enlarged PhAGO family. PhAGO genes were expressed in a temporal-spatial expression pattern, and they encoded proteins differently localized in the cytoplasm and/or nucleus. Overexpression of the PhAGO2 and PhAGO4 genes increased the number of tillers or leaves in Oryza sativa and affected the shoot architecture of Arabidopsis thaliana. These results provided insight into the fact that PhAGO genes play important roles in plant development. • The innovation of PhAGO genes were mainly due to dispersed and whole-genome duplication. • PhAGOs with temporal-spatial expression pattern were distributed unequally on the 14 unmapped scaffolds of moso bamboo. • Ectopic expression of PhAGO2 and PhAGO4 affected the shoot architecture of Oryza sativa and Arabidopsis thaliana. [ABSTRACT FROM AUTHOR]

Abstract Background Shoot architecture is fundamentally crucial to crop growth and productivity. As a key component of shoot architecture, plant height is known to be controlled by both genetic and environmental factors, though specific details remain scarce. Results In this study, 308 representative soybean lines from a core collection and 168 F9 soybean progeny were planted at distinct field sites. The results demonstrated the presence of significant genotype × environment interaction (G × E) effects on traits associated with plant height in a natural soybean population. In total, 19 loci containing 51 QTLs (quantitative trait locus) for plant height were identified across four environments, with 23, 13 and 15 being QTLs for SH (shoot height), SNN (stem node number) and AIL (average internode length), respectively. Significant LOD ranging from 2.50 to 16.46 explained 2.80–26.10% of phenotypic variation. Intriguingly, only two loci, Loc11 and Loc19–1, containing 20 QTLs, were simultaneously detected across all environments. Results from Pearson correlation analysis and PCA (principal component analysis) revealed that each of the five agro-meteorological factors and four soil properties significantly affected soybean plant height traits, and that the corresponding QTLs had additive effects. Among significant environmental factors, AD (average day-length), AMaT (average maximum temperature), pH, and AN (available nitrogen) had the largest impacts on soybean plant height. Therefore, in spite of uncontrollable agro-meteorological factors, soybean shoot architecture might be remolded through combined efforts to produce superior soybean genetic materials while also optimizing soil properties. Conclusions Overall, the comprehensive set of relationships outlined herein among environment factors, soybean genotypes and QTLs in effects on plant height opens new avenues to explore in work aiming to increase soybean yield through improvements in shoot architecture.

Soybean (Glycine max [L.] Merr.) serves as a major source of protein and oil for humans and animals. Shoot architecture, the spatial arrangement of a plant's above-ground organs, strongly affects crop yield and is therefore a critical agronomic trait. Unlike wheat and rice crops that have greatly benefitted from the Green Revolution, soybean yield has not changed significantly in the past six decades owing to its unique shoot architecture. Soybean is a pod-bearing crop with pods adhered to the nodes, and variation in shoot architecture traits, such as plant height, node number, branch number and number of seeds per pod, directly affects the number of pods and seeds per plant, thereby determining yield. In this review, we summarize the relationship between soybean yield and these major components of shoot architecture. We also describe the latest advances in identifying the genes and molecular mechanisms underlying soybean shoot architecture and discuss possible directions and approaches for breeding new soybean varieties with ideal shoot architecture and improved yield., (© 2024 John Wiley & Sons Ltd.)

Cytokinin (CK) is a key plant hormone, but one whose effects are often misunderstood, partly due to reliance on older data from before the molecular genetic age of plant science. In this mini-review, we examine the role of CK in controlling the reproductive shoot architecture of flowering plants. We begin with a long overdue re-examination of the role of CK in shoot branching, and discuss the relatively paucity of genetic evidence that CK does play a major role in this process. We then examine the role of CK in determining the number of inflorescences, flowers, fruit and seed that plants initiate during reproductive development, and how these are arranged in space and time. The genetic evidence for a major role of CK in controlling these processes is much clearer, and CK has profound effects in boosting the size and number of most reproductive structures. Conversely, the attenuation of CK levels during the reproductive phase likely contributes to reduced organ size seen later in flowering, and the ultimate arrest of inflorescence meristems during end-of-flowering. We finish by discussing how this information can potentially be used to improve crop yields., (© 2024 The Author(s).)

Strigolactone acts with other plant hormones to influence shoot architecture by suppressing axiliary bud outgrowth. The exogenous application of synthetic analogues of strigolactone, such as GR24, have been investigated as a way to manage plant architecture in a number of crops. In this study we test whether GR24 can be used to supress bud outgrowth in clonal propagules of tea tree (Melaleuca alternifolia) in order to retain a “single stem” form desirable for machine planting. GR24 was applied to decapitated rooted cuttings of tea tree at two rates (0.5 mg L-1 and 1.5 mg L-1), with and without auxin. By 21 days post-treatment, GR24 at both rates had significantly (p

Strigolactone acts with other plant hormones to influence shoot architecture by suppressing axillary bud outgrowth. The exogenous application of synthetic analogues of strigolactone, such as GR24, have been investigated as a way to manage plant architecture in a number of crops. In this study we test whether GR24 can be used to supress bud outgrowth in clonal propagules of tea tree (Melaleuca alternifolia) in order to retain a "single stem" form desirable for machine planting. GR24 was applied to decapitated rooted cuttings of tea tree at two rates (0.5 mg L-1 and 1.5 mg L-1), with and without auxin. By 21 days post treatment, GR24 at both rates had significantly (p<0.05), reduced the mean number of axillary buds (5.7±0.4 and 5.5±0.3 buds respectively) compared to decapitated untreated control plants (8.9±0.6 buds). Suppression of buds was significantly higher again when auxin was applied in conjunction with GR24. Nonetheless, no exogenous hormone treatment was as effective at suppressing bud outgrowth as the apical dominance that occurred in intact control plants (1.1±0.4 buds). [ABSTRACT FROM AUTHOR]

Edamame is a type of green, vegetable soybean and improving shoot architecture traits for edamame is important for breeding of high-yield varieties by decreasing potential loss due to harvesting. In this study, we use digital imaging technology and computer vision algorithms to characterize major traits of shoot architecture for edamame. Using a population of edamame PIs, we seek to identify underlying genetic control of different shoot architecture traits. We found significant variations in the shoot architecture of the edamame lines including long-skinny and candle stick-like structures. To quantify the similarity and differences of branching patterns between these edamame varieties, we applied a topological measurement called persistent homology. Persistent homology uses algebraic geometry algorithms to measure the structural similarities between complex shapes. We found intriguing relationships between the topological features of branching networks and pod numbers in our plant population, suggesting combination of multiple topological features contribute to the overall pod numbers on a plant. We also identified potential candidate genes including a lateral organ boundary gene family protein and a MADS-box gene that are associated with the pod numbers. This research provides insight into the genetic regulation of shoot architecture traits and can be used to further develop edamame varieties that are better adapted to mechanical harvesting.

Shoot branching is a pivotal process during plant growth and development, and is antagonistically orchestrated by auxin and sugars. In contrast to extensive investigations on hormonal regulatory networks, our current knowledge on the role of sugar signalling pathways in bud outgrowth is scarce. Based on a comprehensive stepwise strategy, we investigated the role of glycolysis/the tricarboxylic acid (TCA) cycle and the oxidative pentose phosphate pathway (OPPP) in the control of bud outgrowth. We demonstrated that these pathways are necessary for bud outgrowth promotion upon plant decapitation and in response to sugar availability. They are also targets of the antagonistic crosstalk between auxin and sugar availability. The two pathways act synergistically to down-regulate the expression of BRC1 , a conserved inhibitor of shoot branching. Using Rosa calluses stably transformed with GFP-fused promoter sequences of RhBRC1 (pRhBRC1), glycolysis/TCA cycle and the OPPP were found to repress the transcriptional activity of pRhBRC1 cooperatively. Glycolysis/TCA cycle- and OPPP-dependent regulations involve the –1973/–1611 bp and –1206/–709 bp regions of pRhBRC1 , respectively. Our findings indicate that glycolysis/TCA cycle and the OPPP are integrative parts of shoot branching control and can link endogenous factors to the developmental programme of bud outgrowth, likely through two distinct mechanisms. [ABSTRACT FROM AUTHOR]

The control of apical dominance involves auxin, strigolactones (SLs), cytokinins (CKs), and sugars, but the mechanistic controls of this regulatory network are not fully understood. Here, we show that brassinosteroid (BR) promotes bud outgrowth in tomato through the direct transcriptional regulation of BRANCHED1 (BRC1) by the BR signaling component BRASSINAZOLE-RESISTANT1 (BZR1). Attenuated responses to the removal of the apical bud, the inhibition of auxin, SLs or gibberellin synthesis, or treatment with CK and sucrose, were observed in bud outgrowth and the levels of BRC1 transcripts in the BR-deficient or bzr1 mutants. Furthermore, the accumulation of BR and the dephosphorylated form of BZR1 were increased by apical bud removal, inhibition of auxin, and SLs synthesis or treatment with CK and sucrose. These responses were decreased in the DELLA-deficient mutant. In addition, CK accumulation was inhibited by auxin and SLs, and decreased in the DELLA-deficient mutant, but it was increased in response to sucrose treatment. CK promoted BR synthesis in axillary buds through the action of the type-B response regulator, RR10. Our results demonstrate that BR signaling integrates multiple pathways that control shoot branching. Local BR signaling in axillary buds is therefore a potential target for shaping plant architecture. [ABSTRACT FROM AUTHOR]

Edamame is a type of green, vegetable soybean and improving shoot architecture traits for edamame is important for breeding of high-yield varieties by decreasing potential loss due to harvesting. In this study, we use digital imaging technology and computer vision algorithms to characterize major traits of shoot architecture for edamame. Using a population of edamame PIs, we seek to identify underlying genetic control of different shoot architecture traits. We found significant variations in the shoot architecture of the edamame lines including long-skinny and candle stick-like structures. To quantify the similarity and differences of branching patterns between these edamame varieties, we applied a topological measurement called persistent homology. Persistent homology uses algebraic geometry algorithms to measure the structural similarities between complex shapes. We found intriguing relationships between the topological features of branching networks and pod numbers in our plant population, suggesting combination of multiple topological features contribute to the overall pod numbers on a plant. We also identified potential candidate genes including a lateral organ boundary gene family protein and a MADS-box gene that are associated with the pod numbers. This research provides insight into the genetic regulation of shoot architecture traits and can be used to further develop edamame varieties that are better adapted to mechanical harvesting. [ABSTRACT FROM AUTHOR]

More than 1.1 billion tonnes of maize grain were harvested across 197 million hectares in 2019 (FAOSTAT 2020). The vast global productivity of maize is largely driven by denser planting practices, higher yield potential per area of land, and increased yield potential per plant. Shoot architecture, the three-dimensional structural arrangement of the above-ground plant body, is critical to maize grain yield and biomass. Structure of the shoot is integral to all aspects of modern agronomic practices. Here, the developmental genetics of the maize vegetative shoot is reviewed. Plant architecture is ultimately determined by meristem activity, developmental patterning, and growth. The following topics are discussed: shoot apical meristem, leaf architecture, axillary meristem and shoot branching, and intercalary meristem and stem activity. Where possible, classical and current studies in maize developmental genetics, as well as recent advances leveraged by "-omics" analyses, are highlighted within these sections. [ABSTRACT FROM AUTHOR]

Background: Shoot architecture is fundamentally crucial to crop growth and productivity. As a key component of shoot architecture, plant height is known to be controlled by both genetic and environmental factors, though specific details remain scarce. Results: In this study, 308 representative soybean lines from a core collection and 168 F9 soybean progeny were planted at distinct field sites. The results demonstrated the presence of significant genotype × environment interaction (G × E) effects on traits associated with plant height in a natural soybean population. In total, 19 loci containing 51 QTLs (quantitative trait locus) for plant height were identified across four environments, with 23, 13 and 15 being QTLs for SH (shoot height), SNN (stem node number) and AIL (average internode length), respectively. Significant LOD ranging from 2.50 to 16.46 explained 2.80–26.10% of phenotypic variation. Intriguingly, only two loci, Loc11 and Loc19–1, containing 20 QTLs, were simultaneously detected across all environments. Results from Pearson correlation analysis and PCA (principal component analysis) revealed that each of the five agro-meteorological factors and four soil properties significantly affected soybean plant height traits, and that the corresponding QTLs had additive effects. Among significant environmental factors, AD (average day-length), AMaT (average maximum temperature), pH, and AN (available nitrogen) had the largest impacts on soybean plant height. Therefore, in spite of uncontrollable agro-meteorological factors, soybean shoot architecture might be remolded through combined efforts to produce superior soybean genetic materials while also optimizing soil properties. Conclusions: Overall, the comprehensive set of relationships outlined herein among environment factors, soybean genotypes and QTLs in effects on plant height opens new avenues to explore in work aiming to increase soybean yield through improvements in shoot architecture. [ABSTRACT FROM AUTHOR]

Summary: Polycarpic perennials maintain vegetative growth after flowering. PERPETUAL FLOWERING 1 (PEP1), the orthologue of FLOWERING LOCUS C (FLC) in Arabis alpina regulates flowering and contributes to polycarpy in a vernalisation‐dependent pathway. pep1 mutants do not require vernalisation to flower and have reduced return to vegetative growth as all of their axillary branches become reproductive.To identify additional genes that regulate flowering and contribute to perennial traits we performed an enhancer screen of pep1. Using mapping‐by‐sequencing, we cloned a mutant (enhancer of pep1‐055, eop055), performed transcriptome analysis and physiologically characterised the role it plays on perennial traits in an introgression line carrying the eop055 mutation and a functional PEP1 wild‐type allele.eop055 flowers earlier than pep1 and carries a lesion in the A. alpina orthologue of the APETALA2 (AP2)‐like gene, TARGET OF EAT2 (AaTOE2). AaTOE2 is a floral repressor and acts upstream of SQUAMOSA PROMOTER‐BINDING PROTEIN‐LIKE 5 (AaSPL5). In the wild‐type background, which requires cold treatment to flower, AaTOE2 regulates the age‐dependent response to vernalisation. In addition, AaTOE2 ensures the maintenance of vegetative growth by delaying axillary meristem initiation and repressing flowering of axillary buds before and during cold exposure.We conclude that AaTOE2 is instrumental in fine tuning different developmental traits in the perennial life cycle of A. alpina. [ABSTRACT FROM AUTHOR]

Summary: Perennials have a complex shoot architecture with axillary meristems organized in zones of differential bud activity and fate. This includes zones of buds maintained dormant for multiple seasons and used as reservoirs for potential growth in case of damage. The shoot of Arabis alpina, a perennial relative of Arabidopsis thaliana, consists of a zone of dormant buds placed between subapical vegetative and basal flowering branches. This shoot architecture is shaped after exposure to prolonged cold, required for flowering.To understand how vernalization ensures the maintenance of dormant buds, we performed physiological and transcriptome studies, followed the spatiotemporal changes of auxin, and generated transgenic plants.Our results demonstrate that the complex shoot architecture in A. alpina is shaped by its flowering behavior, specifically the initiation of inflorescences during cold treatment and rapid flowering after subsequent exposure to growth‐promoting conditions. Dormant buds are already formed before cold treatment. However, dormancy in these buds is enhanced during, and stably maintained after, vernalization by a BRC1‐dependent mechanism. Post‐vernalization, stable maintenance of dormant buds is correlated with increased auxin response, transport, and endogenous indole‐3‐acetic acid levels in the stem.Here, we provide a functional link between flowering and the maintenance of dormant buds in perennials. [ABSTRACT FROM AUTHOR]

Shoot architecture is critical for optimizing plant adaptation and productivity. In contrast with annuals, branching in perennials native to temperate and boreal regions must be coordinated with seasonal growth cycles. How branching is coordinated with seasonal growth is poorly understood. We identified key components of the genetic network that controls branching and its regulation by seasonal cues in the model tree hybrid aspen. Our results demonstrate that branching and its control by seasonal cues is mediated by mutually antagonistic action of aspen orthologs of the flowering regulators TERMINAL FLOWER 1 (TFL1) and APETALA1 (LIKE APETALA 1/LAP1). LAP1 promotes branching through local action in axillary buds. LAP1 acts in a cytokinin-dependent manner, stimulating expression of the cellcycle regulator AIL1 and suppressing BRANCHED1 expression to promote branching. Short photoperiod and low temperature, the major seasonal cues heralding winter, suppress branching by simultaneous activation of TFL1 and repression of the LAP1 pathway. Our results thus reveal the genetic network mediating control of branching and its regulation by environmental cues facilitating integration of branching with seasonal growth control in perennial trees. [ABSTRACT FROM AUTHOR]

Summary: To optimize shoot growth and structure of cereals, we need to understand the genetic components controlling initiation and elongation. While measuring total shoot growth at high throughput using 2D imaging has progressed, recovering the 3D shoot structure of small grain cereals at a large scale is still challenging. Here, we present a method for measuring defined individual leaves of cereals, such as wheat and barley, using few images. Plant shoot modelling over time was used to measure the initiation and elongation of leaves in a bi‐parental barley mapping population under low and high soil salinity. We detected quantitative trait loci (QTL) related to shoot growth per se, using both simple 2D total shoot measurements and our approach of measuring individual leaves. In addition, we detected QTL specific to leaf elongation and not to total shoot size. Of particular importance was the detection of a QTL on chromosome 3H specific to the early responses of leaf elongation to salt stress, a locus that could not be detected without the computer vision tools developed in this study. Significance Statement: To dissect overall shoot growth in small grain cereals, a computer vision‐based approach was developed for the measurement of individual leaves, which requires only few input images, making image acquisition fast and high throughput. The applicability of this approach is shown by mapping QTL for leaf elongation in a barley mapping population in response to salinity. [ABSTRACT FROM AUTHOR]

Carrot is a globally important crop, yet efficient and accurate methods for quantifying its most important agronomic traits are lacking. To address this problem, we developed an automated image analysis platform that extracts components of size and shape for carrot shoots and roots, which are necessary to advance carrot breeding and genetics. This method reliably measured variation in shoot size and shape, petiole number, petiole length, and petiole width as evidenced by high correlations with hundreds of manual measurements. Similarly, root length and biomass were accurately measured from the images. This platform also quantified shoot and root shapes in terms of principal components, which do not have traditional, manually measurable equivalents. We applied the pipeline in a study of a six-parent diallel population and an F2 mapping population consisting of 316 individuals. We found high levels of repeatability within a growing environment, with low to moderate repeatability across environments. We also observed co-localization of quantitative trait loci for shoot and root characteristics on chromosomes 1, 2, and 7, suggesting these traits are controlled by genetic linkage and/or pleiotropy. By increasing the number of individuals and phenotypes that can be reliably quantified, the development of a rapid, automated image analysis pipeline to measure carrot shoot and root morphology will expand the scope and scale of breeding and genetic studies.

Carrot is a globally important crop, yet efficient and accurate methods for quantifying its most important agronomic traits are lacking. To address this problem, we developed an automated image analysis platform that extracts components of size and shape for carrot shoots and roots, which are necessary to advance carrot breeding and genetics. This method reliably measured variation in shoot size and shape, petiole number, petiole length, and petiole width as evidenced by high correlations with hundreds of manual measurements. Similarly, root length and biomass were accurately measured from the images. This platform also quantified shoot and root shapes in terms of principal components, which do not have traditional, manually measurable equivalents. We applied the pipeline in a study of a six-parent diallel population and an F2 mapping population consisting of 316 individuals. We found high levels of repeatability within a growing environment, with low to moderate repeatability across environments. We also observed co-localization of quantitative trait loci for shoot and root characteristics on chromosomes 1, 2, and 7, suggesting these traits are controlled by genetic linkage and/or pleiotropy. By increasing the number of individuals and phenotypes that can be reliably quantified, the development of a rapid, automated image analysis pipeline to measure carrot shoot and root morphology will expand the scope and scale of breeding and genetic studies. [ABSTRACT FROM AUTHOR]

Plant shoot systems give rise to characteristic above-ground plant architectures. Shoots are formed from axillary meristems and buds, whose growth and development is modulated by systemic and local signals. These cues convey information about nutrient and water availability, light quality, sink/source organ activity and other variables that determine the timeliness and competence to maintain development of new shoots. This information is translated into a local response, in meristems and buds, of growth or quiescence. Although some key genes involved in the onset of bud latency have been identified, the gene regulatory networks (GRNs) controlled by these genes are not well defined. Moreover, it has not been determined whether bud dormancy induced by environmental cues, such as a low red-to-far-red light ratio, shares genetic mechanisms with bud latency induced by other causes, such as apical dominance or a short-day photoperiod. Furthermore, the evolution and conservation of these GRNs throughout angiosperms is not well established. We have reanalyzed public transcriptomic datasets that compare quiescent and active axillary buds of Arabidopsis, with datasets of axillary buds of the woody species Vitis vinifera (grapevine) and apical buds of Populus tremula x Populus alba (poplar) during the bud growth-to-dormancy transition. Our aim was to identify potentially common GRNs induced during the process that leads to bud para-, eco- and endodormancy. In Arabidopsis buds that are entering eco- or paradormancy, we have identified four induced interrelated GRNs that correspond to a carbon (C) starvation syndrome, typical of tissues undergoing low C supply. This response is also detectable in poplar and grapevine buds before and during the transition to dormancy. In all eukaryotes, C-limiting conditions are coupled to growth arrest and latency like that observed in dormant axillary buds. Bud dormancy might thus be partly a consequence of the underlying C starvation syndrome triggered by environmental and endogenous cues that anticipate or signal conditions unfavorable for sustained shoot growth.

Grasses possess basal and aerial axillary buds. Previous studies have largely focused on basal bud (tiller) formation but scarcely touched on aerial buds, which may lead to aerial branch development., Genotypes with and without aerial buds were identified in switchgrass ( Panicum virgatum), a dedicated bioenergy crop. Bud development was characterized using scanning electron microscopy. Microarray, RNA-seq and quantitative reverse transcription polymerase chain reaction ( RT-qPCR) were used to identify regulators of bud formation. Gene function was characterized by down-regulation and overexpression., Overexpression of miR156 induced aerial bud formation in switchgrass. Various analyses revealed that SQUAMOSA PROMOTER BINDING PROTEIN LIKE4 ( SPL4), one of the miR156 targets, directly regulated aerial axillary bud initiation. Down-regulation of SPL4 promoted aerial bud formation and increased basal buds, while overexpression of SPL4 seriously suppressed bud formation and tillering. RNA-seq and RT- qPCR identified potential downstream genes of SPL4., Unlike all previously reported genes acting as activators of basal bud initiation, SPL4 acts as a suppressor for the formation of both aerial and basal buds. The miR156- SPL4 module predominantly regulates aerial bud initiation and partially controls basal bud formation. Genetic manipulation of SPL4 led to altered plant architecture with increased branching, enhanced regrowth after cutting and improved biomass yield. [ABSTRACT FROM AUTHOR]

Plant shoot systems give rise to characteristic above-ground plant architectures. Shoots are formed from axillary meristems and buds, whose growth and development is modulated by systemic and local signals. These cues convey information about nutrient and water availability, light quality, sink/source organ activity and other variables that determine the timeliness and competence to maintain development of new shoots. This information is translated into a local response, in meristems and buds, of growth or quiescence. Although some key genes involved in the onset of bud latency have been identified, the gene regulatory networks (GRNs) controlled by these genes are not well defined. Moreover, it has not been determined whether bud dormancy induced by environmental cues, such as a low red-to-far-red light ratio, shares genetic mechanisms with bud latency induced by other causes, such as apical dominance or a short-day photoperiod. Furthermore, the evolution and conservation of these GRNs throughout angiosperms is not well established. We have reanalyzed public transcriptomic datasets that compare quiescent and active axillary buds of Arabidopsis, with datasets of axillary buds of the woody species Vitis vinifera (grapevine) and apical buds of Populus tremula x Populus alba (poplar) during the bud growth-to-dormancy transition. Our aim was to identify potentially common GRNs induced during the process that leads to bud para-, eco- and endodormancy. In Arabidopsis buds that are entering eco- or paradormancy, we have identified four induced interrelated GRNs that correspond to a carbon (C) starvation syndrome, typical of tissues undergoing low C supply. This response is also detectable in poplar and grapevine buds before and during the transition to dormancy. In all eukaryotes, C-limiting conditions are coupled to growth arrest and latency like that observed in dormant axillary buds. Bud dormancy might thus be partly a consequence of the underlying C starvation syndrome triggered by environmental and endogenous cues that anticipate or signal conditions unfavorable for sustained shoot growth. [ABSTRACT FROM AUTHOR]

Strigolactones (SLs) are important intrinsic growth regulators that control plant architecture by coordinating shoot and root development. Recent studies demonstrate that SL signals act via targeting the degradation protein DWARF53 (D53) family of chaperonin-like proteins. This process requires DWARF14 (D14) as strigolactones signal receptor and DWARF3 (D3) forming Skp-Cullin-F-box (SCF) complex as ubiquitin E3 ligase. Although the interactions of these signal components can be expected, where and how the SLs signalling occur within cells in a tissue-specific manner is still uncertain. In this study, we characterize a rice high-tillering dwarf mutant, ext.-M1B, displaying resistance to synthetic strigolactone mixture rac-GR24. Through genetic analysis, we find that ext.-M1B is a new allelic mutant of D3 with a nucleotide mutation resulting in a truncated protein of wide-type D3. We demonstrate that the mutation affects neither gene expression level nor the protein sub-cellular localization, whereas it disrupts the perception of SLs signal in ext.-M1B mutant. Moreover, we find that overexpression of D3 in wild type background causes no significant phenotype, but suppression of D3 by RNA interfering results in a clear phenocopy of SL mutants. By expressing fluorescent D3 fusion protein in rice, we first show that D3 is stable consistently in the nucleus with or without strigolactone treatment. Taken together, our data indicates that D3 encoding an F-box protein in nucleus, as a stable signal component response to strigolactone regulating rice shoot architecture. [ABSTRACT FROM AUTHOR]

In apple, the first-order branch of a tree has a characteristic architecture constituting three shoot types: bourses (rosettes), bourse shoots, and vegetative shoots. Its overall architecture as well as that of each shoot thus determines the distribution of sources (leaves) and sinks (fruits) and could have an influence on the amount of sugar allocated to fruits. Knowledge of architecture, in particular the position and area of leaves helps to quantify source strength. In order to reconstruct this initial architecture, rules equipped with allometric relations could be used: these allow predicting model parameters that are difficult to measure from simple traits that can be determined easily, non-destructively and directly in the orchard. Once such allometric relations are established they can be used routinely to recreate initial structures. Models based on allometric relations have been established in this study in order to predict the leaf areas of the three different shoot types of three apple cultivars with different branch architectures: "Fuji," "Ariane," and "Rome Beauty." The allometric relations derived from experimental data allowed us to model the total shoot leaf area as well as the individual leaf area for each leaf rank, for each shoot type and each genotype. This was achieved using two easily measurable input variables: total leaf number per shoot and the length of the biggest leaf on the shoot. The models were tested using a different data set, and they were able to accurately predict leaf area of all shoot types and genotypes. Additional focus on internode lengths on spurs contributed to refine the models. [ABSTRACT FROM AUTHOR]

Three varieties of Bidens pilosa are recorded in Taiwan, among them only B. pilosa var. radiata is considered an invasive plant, while B. pilosa var. minor and B. pilosa var. pilosa are naturalized in Taiwan. To identify traits making var. radiata spreading faster than the other two varieties in sympatric areas, we grew these three varieties in summer and in fall and compared their morphology and traits related to growth. We found that all three varieties grew faster in summer than in fall and var. radiata grew faster and accumulated more biomass than the other two varieties in summer but not in fall. Further analysis revealed that the proportion of shoot biomass allocating to axillary shoots might contribute to the aforementioned differences. Shoots of all three varieties were capable of producing adventitious roots. However, the growing angle of the lowest axillary shoots was significantly more horizontal in var. radiata than in the other two varieties and the secondary axillary shoots were only found in var. radiata. Accordingly, the axillary shoots of var. radiata would have greater opportunity to contact soil, produce adventitious roots and generate ramets than those of var. minor and var. pilosa. We concluded that more biomass allocating to axillary shoots and more horizontally-oriented axillary shoots were important traits contributing to the faster growth and better clonal growth potential of B. pilosa var. radiata than the other two varieties in Taiwan. [ABSTRACT FROM AUTHOR]