Monocot Species Research Articles

CLAW: An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data.

Chloroplasts are photosynthetic organelles in algal and plant cells that contain their own genome. Chloroplast genomes are commonly used in evolutionary studies and taxonomic identification and are increasingly becoming a target for crop improvement studies. As DNA sequencing becomes more affordable, researchers are collecting vast swathes of high-quality whole-genome sequence data from laboratory and field settings alike. Whole tissue read libraries sequenced with the primary goal of understanding the nuclear genome will inadvertently contain many reads derived from the chloroplast genome. These whole-genome, whole-tissue read libraries can additionally be used to assemble chloroplast genomes with little to no extra cost. While several tools exist that make use of short-read second generation and third-generation long-read sequencing data for chloroplast genome assembly, these tools may have complex installation steps, inadequate error reporting, poor expandability, and/or lack scalability. Here, we present CLAW (Chloroplast Long-read Assembly Workflow), an easy to install, customise, and use Snakemake tool to assemble chloroplast genomes from chloroplast long-reads found in whole-genome read libraries (https://github.com/aaronphillips7493/CLAW). Using 19 publicly available reference chloroplast genome assemblies and long-read libraries from algal, monocot and eudicot species, we show that CLAW can rapidly produce chloroplast genome assemblies with high similarity to the reference assemblies. CLAW was designed such that users have complete control over parameterisation, allowing individuals to optimise CLAW to their specific use cases. We expect that CLAW will provide researchers (with varying levels of bioinformatics expertise) with an additional resource useful for contributing to the growing number of publicly available chloroplast genome assemblies.

Development and application of an inexpensive open-source dendrometer for detecting xylem water potential and radial stem growth at high spatial and temporal resolution.

There is currently a need for inexpensive, continuous, non-destructive water potential measurements at high temporal resolution (<1min). We describe here the development and testing of an entirely open-source dendrometer that, when combined with periodic Scholander pressure chamber measurements, provides sub-minute resolution estimates of water potential when placed on tissues exhibiting little or no secondary growth (petioles, monocotyledon stems). The dendrometer can also be used to measure radial growth of stems and branches when placed on dicotyledon and gymnosperm species. The dendrometer can be interfaced directly with a computer in real time in the lab or greenhouse, or connected to a datalogger for long periods of use in the field on batteries. We tested this device on a herbaceous dicotyledon (Helianthus annuus) (petioles and stems) and a monocotyledon (Zea mays) species (stems) for 1 week during dehydration and re-watering treatments under laboratory conditions. We also demonstrated the ability of the device to record branch and trunk diameter variation of a woody dicotyledon (Rhus typhina) in the field. Under laboratory conditions, we compared our device (hereafter 'contact' dendrometer) with modified versions of another open-source dendrometer (the 'optical' dendrometer). Overall, contact and optical dendrometers were well aligned with one another, with Pearson correlation coefficients ranging from 0.77 to 0.97. Both dendrometer devices were well aligned with direct measurements of xylem water potential, with calibration curves exhibiting significant non-linearity, especially at water potentials near the point of incipient plasmolysis, with pseudo R2 values (Efron) ranging from 0.89 to 0.99. Overall, both dendrometers were comparable and provided sufficient resolution to detect subtle differences in stem water potential (ca. 50 kPa) resulting from light-induced changes in transpiration, vapour pressure deficit and drying/wetting soils. All hardware designs, alternative configurations, software and build instructions for the contact dendrometers are provided.

Tricetin and Tricin: An Overview of the Chemistry, Sources, Contents, and Pharmacological Properties of these Flavones

In this overview, information on the chemistry, sources, contents, and pharmacological properties of two flavones, namely, tricetin (TCT) and tricin (TC), is updated. TCT occurs mainly in honey and pollen of plant species belonging to the genus Eucalyptus of the family Myrtaceae. TC is found in monocotyledon species of the family Poaceae, occurring mainly in cereal crops such as oats, barley, rice, wheat, and corn, and in bamboo species. The chemical structure of TCT contains two hydroxyl (OH) groups at C5 and C7 of ring A and three OH groups at C3’, C4’, and C5’ of ring B, with no methoxy (OCH3) groups. TC has two OH groups at C5 and C7 of ring A, two OCH3 groups at C3’ and C5’, and one OH group at C4’ of ring B, i.e., at both sides of the C4’ OH group. This renders greater bioavailability, higher metabolic stability, and better intestinal absorption to TC than TCT. In this overview, TCT and TC have eight and seven studies on anti-cancer properties, and 14 and 31 studies on other pharmacological properties, respectively. Both flavones are equally strong in terms of cytotoxicity towards cancer cells. With greater bioavailability, higher metabolic stability, and better intestinal absorption, the other pharmacological properties of TC are stronger than TCT, but not for anti-cancer properties.

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution.

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.

Exploring Aegilops caudata: A Comprehensive Study of the CslF6 Gene and β-Glucan.

In the quest for sustainable and nutritious food sources, exploration of ancient grains and wild relatives of cultivated cereals has gained attention. Aegilops caudata, a wild wheatgrass species, stands out as a promising genetic resource due to its potential for crop enhancement and intriguing nutritional properties. This manuscript investigates the CslF6 gene sequence and protein structure of Aegilops caudata, employing comparative analysis with other grass species to identify potential differences impacting β-glucan content. The study involves comprehensive isolation and characterization of the CslF6 gene in Ae. caudata, utilizing genomic sequence analysis, protein structure prediction, and comparative genomics. Comparisons with sequences from diverse monocots reveal evolutionary relationships, highlighting high identities with wheat genomes. Specific amino acid motifs in the CslF6 enzyme sequence, particularly those proximal to key catalytic motifs, exhibit variations among monocot species. These differences likely contribute to alterations in β-glucan composition, notably impacting the DP3:DP4 ratio, which is crucial for understanding and modulating the final β-glucan content. The study positions Ae. caudata uniquely within the evolutionary landscape of CslF6 among monocots, suggesting potential genetic divergence or unique functional adaptations within this species. Overall, this investigation enriches our understanding of β-glucan biosynthesis, shedding light on the role of specific amino acid residues in modulating enzymatic activity and polysaccharide composition.

Computational analysis of the AP2/ERF family in crops genome

BackgroundThe Apetala 2/ethylene-responsive factor family has diverse functions that enhance development and torment resistance in the plant genome. In variation, the ethylene-responsive factor (ERF) family of TF’s genes is extensive in the crop genome. Generally, the plant-specific ethylene-responsive factor family may divided by the dehydration-responsive element-binding (DREB) subfamily. So, the AP2/ERF super-family demonstrated the repeated AP2 domain during growth. The sole AP2 domain function represents abiotic stress resistance. Also, the AP2 with B3 domain enhances during the replication of brassinosteroid.ObjectiveThe study objective is to investigate the Apetala 2/ethylene-responsive factor family in a model organism of the Arabidopsis thaliana for comparative analysis towards Solanum lycopersicum (Tomato), Brassica juncea (Indian and Chinese mustard), Zea mays L. (Maize) and Oryza sativa (Indian and Japanese Rice). So, examinations of the large AP2/ERF super-family are mandatory to explore the Apetala 2 (AP2) family, ERF family, DREB subfamily, and RAV family involved during growth and abiotic stress stimuli in crops.MethodsTherefore, perform bioinformatics and computational methods to the current knowledge of the Apetala 2/ethylene-responsive factor family and their subfamilies in the crop genome. This method may be valuable for functional analysis of particular genes and their families in the plant genome.ResultsObservation data provided evidence of the Apetala 2/ethylene-responsive factor (AP2/ERF) super-family and their sub-family present in Arabidopsis thaliana (Dicots) and compared with Solanum lycopersicum (Dicots), Brassica juncea (Dicots), Zea mays L. (Monocots) and Oryza sativa (Monocots). Also, remarks genes in Oryza sativa. This report upgraded the Apetala 2/ethylene-responsive factor (AP2/ERF) family in the crop genome. So, the analysis documented the conserved domain, motifs, and phylogenetic tree towards Dicots and Monocots species. Those outcomes will be valuable for future studies of the defensive Apetala 2/ethylene-responsive factor family in crops.ConclusionTherefore, the study concluded that the several species-specific TF genes in the Apetala 2/ethylene-responsive factor (AP2/ERF) family in Arabidopsis thaliana and compared with crop-species of Solanum lycopersicum, Brassica juncea, Zea mays L. and Oryza sativa. Those plant-specific genes regulate during growth and abiotic stress control in plants.

Selective herbicide safening in dicot plants: a case study in Arabidopsis.

Safeners are agrochemicals co-applied with herbicides that facilitate selective control of weeds by protecting monocot crops from chemical injury through enhancing the expression of detoxifying enzymes such as glutathione transferases (GSTs). Even though the application of safeners causes the induction of genes encoding GSTs in model dicots such as Arabidopsis thaliana, safeners do not protect broadleaf crops from herbicide injury. In this study, we proposed that the localized induction of Arabidopsis GSTs and the fundamental differences in their detoxifying activity between dicot and monocot species, underpin the failure of safeners to protect Arabidopsis from herbicide toxicity. Using the herbicide safener, isoxadifen-ethyl, we showed that three tau (U) family GSTs namely AtGSTU7, AtGSTU19 and AtGSTU24 were induced with different magnitude by isoxadifen treatment in root and rosette tissues. The higher magnitude of inducibility of these AtGSTUs in the root tissues coincided with the enhanced metabolism of flufenacet, a herbicide that is active in root tissue, protecting Arabidopsis plants from chemical injury. Assay of the recombinant enzyme activities and the significant reduction in flufenacet metabolism determined in the T-DNA insertion mutant of AtGSTU7 (gstu7) in Arabidopsis plants identified an important function for AtGSTU7 protein in flufenacet detoxification. In-silico structural modeling of AtGSTU7, suggested the unique high activity of this enzyme toward flufenacet was due to a less constrained active site compared to AtGSTU19 and AtGSTU24. We demonstrate here that it is possible to induce herbicide detoxification in dicotyledonous plants by safener treatment, albeit with this activity being restricted to very specific combinations of herbicide chemistry, and the localized induction of enzymes with specific detoxifying activities.

Towards a true conservation zero tillage system: “A proposed solution based on computer vision to herbicide resistance.”

The Zero Tillage (ZT) or Non-Tillage system constitutes an agricultural production approach designed for improved soil conservation, reduced fossil fuel usage, mitigation of waterway pollution, water and wind erosion, and addressing soil compaction, among other objectives. In this way, ZT promises more sustainable agriculture. However, current ZT production systems depend on herbicide applications for weed control. The use of herbicides with the same modes of action over many years has led to numerous resistant weed species, which end up threatening the success of the herbicide weed control and, consequently, the overall success of the ZT system. Being able to automatically detect and classify weed species directly under the sprayer during the chemical application is an alternative to control populations of weeds since it would allow selecting the herbicide and dose for those particular species. This study, conducted over 15 years in commercial fields utilizing Zero Tillage (ZT) management, examined various ground covers intrinsic to the ZT system originating from previous crops or residues post-harvest. ZT features a broad spectrum of contexts due to the complexity of different ground cover types, which challenge computer vision techniques. The assessment focused on the automatic detection and classification of among the most problematic monocotyledonous and dicotyledonous weed species in the province of Cordoba in Argentina, with the objective of enabling a more targeted and selective approach to their control. These are Amaranthus palmeri, Echinochloa crus-galli, Eleusine indica, Parietaria debilis and Conyza sumatrensis. Additionally, some species belong to the same botanical families with several morphological resemblances that defy vision algorithms. This work proceeded through a machine learning approach applied to computer vision features such as SIFT (scale-invariant feature transform), K-means (clustering), and Bag of Features over the Support Vector Machine for classification. The results showed an accuracy between 89 % and 98 % over the species, allowing a significant reduction of herbicide while applying the adequate active ingredient. Moreover, virtual binary maps from weed patches are devised to be implemented through ISOBUS protocol. Thus the current research contributes significantly to the issue of controlling populations of weeds in the ZT agriculture system.

The expression of lignin biosynthesis genes during plant development and effects of downregulated cinnamyl alcohol dehydrogenase (CAD) gene in bahiagrass (Paspalum notatum Flügge)

AbstractBahiagrass (Paspalum notatum Flügge) is a warm‐season grass where high lignin content limits its forage quality, negatively affecting animal performance. To create a new breeding method by genome editing, isolation and characterization of lignin biosynthesis genes and identification of their molecular relationships are essential. The caffeic acid O‐methyltransferase (COMT) and cinnamyl alcohol dehydrogenase (CAD) cDNA clones were isolated from bahiagrass, and their protein sequences showed high similarity to other C4 monocot species through phylogenetic analysis. Gene expression analysis of phenylalanine ammonia‐lyase (PAL), COMT and CAD, involved in crucial stages of lignin biosynthesis and lignin content, was conducted at different plant developmental stages. The highest gene expression levels of these genes were observed in the vegetative (V) and early reproductive stages, while the lignin content increased until the middle reproductive stage and remained constant thereafter. Additionally, to further understand the molecular relationships in lignin biosynthesis, the effect of CAD downregulation was analyzed in transgenic bahiagrass lines introduced with sorghum CAD antisense and RNAi vector obtained from a previous report. This led to a reduced lignin content and affected the expression of PAL and COMT working upstream of CAD. In the V stage, PAL expression was lower in transgenic lines compared to wild type (WT), while COMT expression showed no significant differences. However, PAL and COMT expression of transgenic lines in the middle reproductive stage (R2) was significantly higher than in the WT. These findings suggest that the downregulation of CAD gene expression affects PAL and COMT expression and induces a feedback system in the R2 stage. Lignin content influenced the phenotype of the transgenic plants with significantly reduced lignin, exhibiting a dwarf phenotype with shorter plant heights. The findings of this study can be applied to genome editing for the development of practical new breeding materials with improved digestibility in bahiagrass.

A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes).

Commelinales belongs to the commelinids clade, which also comprises Poales that includes the most important monocot species, such as rice, wheat, and maize. No reference genome of Commelinales is currently available. Water hyacinth (Pontederia crassipes or Eichhornia crassipes), a member of Commelinales, is one of the devastating aquatic weeds, although it is also grown as an ornamental and medical plant. Here, we present a chromosome-scale reference genome of the tetraploid water hyacinth with a total length of 1.22 Gb (over 95% of the estimated size) across 8 pseudochromosome pairs. With the representative genomes, we reconstructed a phylogeny of the commelinids, which supported Zingiberales and Commelinales being sister lineages of Arecales and shed lights on the controversial relationship of the orders. We also reconstructed ancestral karyotypes of the commelinids clade and confirmed the ancient commelinids genome having 8 chromosomes but not 5 as previously reported. Gene family analysis revealed contraction of disease-resistance genes during polyploidization of water hyacinth, likely a result of fitness requirement for its role as a weed. Genetic diversity analysis using 9 water hyacinth lines from 3 continents (South America, Asia, and Europe) revealed very closely related nuclear genomes and almost identical chloroplast genomes of the materials, as well as provided clues about the global dispersal of water hyacinth. The genomic resources of P. crassipes reported here contribute a crucial missing link of the commelinids species and offer novel insights into their phylogeny.

Phylogenomics of Plant NLR Immune Receptors to Identify Functionally Conserved Sequence Motifs.

In recent years, the increase in genome sequencing across diverse plant species has provided a significant advantage for phylogenomics studies, allowing the analysis of one of the most diverse gene families in plants: nucleotide-binding leucine-rich repeat receptors (NLRs). However, due to the sequence diversity of the NLR gene family, identifying key molecular features and functionally conserved sequence patterns is challenging through multiple sequence alignment. Here, we present a step-by-step protocol for a computational pipeline designed to identify evolutionarily conserved motifs in plant NLR proteins. In this protocol, we use a large-scale NLR dataset, including 1,862 NLR genes annotated from monocot and dicot species, to predict conserved sequence motifs, such as the MADA and EDVID motifs, within the coiled-coil (CC)-NLR subfamily. Our pipeline can be applied to identify molecular signatures that have remained conserved in the gene family over evolutionary time across plant species. Key features • Phylogenomics analysis of plant NLR immune receptor family. • Identification of functionally conserved sequence patterns among plant NLRs.

THE YIELD OF ANJASMORO CULTIVARS SOYBEAN [Glycine max (L.) Merrill] WITH COMPOST TREATMENT FROM TOBACCO OR SOURSOP LEAVES AND ITS WEED CONDITIONS

One of the important problems in soybean production is the weed growth. This study was conducted to observe the growth of weeds in the growth of soybean plants that are given compost. Anjasmoro soybean varieties were planted in Surakarta, on April 14, 2020. There are four types of treatment, namely given compost fertilizer made from tobacco leaves, soursop leaves, a mixture of tobacco leaves and soursop, and without fertilizer. Weeds were allowed to grow together with soybeans in 15 polybags, per treatment. Observation and identification of weeds were carried out twice, 4 weeks after planting and at harvest time. The results found 9 kinds of weeds consisting of 5 species of Monocots and 4 types of Dicotiles. The total wet weight of weeds was every treatment: 1,539 grams, while the wet weight of the soybean crop at harvest was 858.4 grams. Wet weed weight in the control treatment was 284,8 grams. The wet weight of weeds in soybean plants was the largest mixture fertilizer treatment that is 514,8 grams. The number of pods ranges from 17 to 26. The sum of seeds per soybean plant in giving mixed compost is at most 98 grains. Mixed fertilizer treatment can increase the yield of Anjasmoro soybean, although weed growth up.

Automatic annotation of the bHLH gene family in plants

BackgroundThe bHLH transcription factor family is named after the basic helix-loop-helix (bHLH) domain that is a characteristic element of their members. Understanding the function and characteristics of this family is important for the examination of a wide range of functions. As the availability of genome sequences and transcriptome assemblies has increased significantly, the need for automated solutions that provide reliable functional annotations is emphasised.ResultsA phylogenetic approach was adapted for the automatic identification and functional annotation of the bHLH transcription factor family. The bHLH_annotator, designed for the automated functional annotation of bHLHs, was implemented in Python3. Sequences of bHLHs described in literature were collected to represent the full diversity of bHLH sequences. Previously described orthologs form the basis for the functional annotation assignment to candidates which are also screened for bHLH-specific motifs. The pipeline was successfully deployed on the two Arabidopsis thaliana accessions Col-0 and Nd-1, the monocot species Dioscorea dumetorum, and a transcriptome assembly of Croton tiglium. Depending on the applied search parameters for the initial candidates in the pipeline, species-specific candidates or members of the bHLH family which experienced domain loss can be identified.ConclusionsThe bHLH_annotator allows a detailed and systematic investigation of the bHLH family in land plant species and classifies candidates based on bHLH-specific characteristics, which distinguishes the pipeline from other established functional annotation tools. This provides the basis for the functional annotation of the bHLH family in land plants and the systematic examination of a wide range of functions regulated by this transcription factor family.

Genome-Wide Identification of Callose Synthase Family Genes and Their Expression Analysis in Floral Bud Development and Hormonal Responses in Prunus mume.

Callose is an important polysaccharide composed of beta-1,3-glucans and is widely implicated in plant development and defense responses. Callose synthesis is mainly catalyzed by a family of callose synthases, also known as glucan synthase-like (GSL) enzymes. Despite the fact that GSL family genes were studied in a few plant species, their functional roles have not been fully understood in woody perennials. In this study, we identified total of 84 GSL genes in seven plant species and classified them into six phylogenetic clades. An evolutionary analysis revealed different modes of duplication driving the expansion of GSL family genes in monocot and dicot species, with strong purifying selection constraining the protein evolution. We further examined the gene structure, protein sequences, and physiochemical properties of 11 GSL enzymes in Prunus mume and observed strong sequence conservation within the functional domain of PmGSL proteins. However, the exon-intron distribution and protein motif composition are less conservative among PmGSL genes. With a promoter analysis, we detected abundant hormonal responsive cis-acting elements and we inferred the putative transcription factors regulating PmGSLs. To further understand the function of GSL family genes, we analyzed their expression patterns across different tissues, and during the process of floral bud development, pathogen infection, and hormonal responses in Prunus species and identified multiple GSL gene members possibly implicated in the callose deposition associated with bud dormancy cycling, pathogen infection, and hormone signaling. In summary, our study provides a comprehensive understanding of GSL family genes in Prunus species and has laid the foundation for future functional research of callose synthase genes in perennial trees.

How Does Sustainable Management Practices Affect Weed Flora and Tuber Yield of Potato Crop in Mediterranean Environment?

AbstractIntensive potato cultivation affects weed species composition by selecting dominant and competitive weeds that represent a constraint of potato productivity. Field experiments were conducted during 2015 and 2016 growing seasons to examine the effects of soil tillage (plowing (PL), spading (SM), sub soiling (SS)) and fertilizer source (mineral (Min) and organic (Org)) on potato yield and weed community under Mediterranean environment. A randomized complete block design with three replications was adopted. Weed density and biomass were measured at the potato harvesting time. Weed density was highest in SS, intermediate in SM, and lowest in PL (43.8, 40.3, and 28.8 plants m−2). Similar trend was observed in weed biomass. Weed density and biomass were higher in Org than Min (42.1 vs. 36.4 plants m−2 and 129.6 vs. 117.9 g m−2, respectively). Perennial, monocot, and dicot weed species were the most abundant in subsoiling (13.1, 9.3 and 34.5 plants m−2). Density of perennial and dicot species were higher in Org than Min. Monocots were mostly linked with Min, while dicots were mainly associated with Org. Although tuber yield was higher in PL and Min (481.9 and 627.5 g m−2 of DM), it was affected by growing season and might be associated to SM and Org. Although the study shows that increased weed biodiversity in the system, achieved with more sustainable practices, proves to be an obstacle to potato production, the adoption of spading machine applied in combination with mineral and organic fertilizers could be a valid alternative to plowing. Further studies are required to develop sustainable agricultural techniques able to improve the competitive capacity of crops and reduce the selection of dominant weed species.

Exploring bundle bamboo split technique in bending dendrocalamus asper for landscape structure

Bamboo is one of the fastest-growing natural construction materials and is locally available in most developing countries, including South America, Africa, and Asia. Bamboo is a “green gold” plant in the tropical forest. It is a fast-growing monocotyledon species belonging to the Gramineae family (Bambusoideae) and requires a short time for re-production. Bamboo’s physical strength provides builders from ancient times until today an opportunity to use bamboo as a natural and sustainable construction material for building houses and structures. Due to its capability to bend, bamboo is the most preferred material in vernacular construction and lately in Southeast Asia countries which borne new trend in building design. The built-environment professionals, namely landscape architects, architects, and engineers in Malaysia, still lack knowledge of bamboo, especially on bending capabilities, as one of the sustainable construction materials. Less concern was given to researching the capabilities of bamboo’s ability to bend, even though its strength is more than steel and provides various design opportunities compared to other sustainable materials. Different types of bamboo present different strength capacities. Therefore, the aims of this research is to compare and determine their strength capacity, bending criteria and species suitability for design and construction in Malaysia. This paper collects published literature on experimental studies on the different methods of Hot and Cold Bending Methods which allow bamboo to bend to suit designer needs and concentrate on Malaysian Dendrocalamus asper (Buluh Betung), which considered as tough and durable species, as the primary construction material for landscape structures. Bundle Bamboo Split (BBS), identified as one of the bending techniques adopted for an experimental project, using BBS of 0.8m radius, produces a prototype for a landscape structure. The findings indicate observation of works by a team of craftsmen trained by an expert in bamboo construction who used to produce bamboo structures from Bali, Indonesia, highlighted tools and procedures in bamboo construction. In short, this paper will also enhance the use of bamboo as an accessible, durable, creative and sustainable construction material that represents the local identity of Tropical Malaysia Landscape Architecture.

Boron deficiency responses in maize (Zea mays L.) roots

AbstractBackgroundBoron (B) is an essential micronutrient for plants. Dicot plants respond to insufficient B supply by altering root architecture and root hair growth. How root systems of rather low‐B demanding monocot species such as maize (Zea mays L.) respond to B deficiency in terra has not been experimentally resolved, yet.AimsThe study aims to investigate root responses and their physiological consequences under B deficiency during the vegetative growth of maize.MethodsB73 wild‐type (WT) maize and its root hairless rth3 mutant were grown under varying B supply conditions in soil columns and in an automated root phenotyping facility. Biomass data, root system architecture traits, the mineral elemental composition and molecular B‐deficiency responses were quantified.ResultsThough having very low leaf B concentrations, no major growth deficit, apart from chlorotic stripes on leaves, was recorded on maize root and shoot development, with or without root hairs, on B‐deficient conditions. Although leaf B concentration of the rth3 mutant is significantly lower under B‐deficient and under B‐surplus conditions compared to the WT, the rth3 mutant neither developed a larger total root length, more fine roots nor displayed a higher expression of B uptake transporters as compensatory adaptations.ConclusionsStrikingly, maize plants did neither react with an inhibited root growth nor by a compensatory root foraging behaviour to severe B‐deficient in terra growth conditions. This is rather atypical for plants. The performance and altered leaf B concentrations of rth3 mutants may be biased by secondary effects, such as an overall reduced root growth.

Blocking miR528 function promotes tillering and regrowth in switchgrass.

MiRNAs have been reported to be the key regulators involving a wide range of biological processes in diverse plant species, but their functions in switchgrass, an important biofuel and forage crop, are largely unknown. Here, we reported the novel function of miR528, which has expanded to four copies in switchgrass, in controlling biomass trait of tillering number and regrowth rate after mowing. Blocking miR528 activity by expressing short tandem target mimic (STTM) increased tiller number and regrowth rate after mowing. The quadruple pvmir528 mutant lines derived from genome editing also showed such improved traits. Degradome and RNA-seq analysis, combined with in situ hybridization assay revealed that up-regulation of two miR528 targets coding for Cu/Zn-SOD enzymes, might be responsible for the improved traits of tillering and regrowth in pvmir528 mutant. Additionally, natural variations in the miR528-SOD interaction exist in C3 and C4 monocot species, implying the distinct regulatory strength of the miR528-SOD module during monocot evolution. Overall, our data illuminated a novel role of miR528 in controlling biomass traits and provided a new target for genetic manipulation-mediated crop improvement.

Modulation of warm temperature-sensitive growth using a phytochrome B dark reversion variant, phyB[G515E], in Arabidopsis and rice

IntroductionAmbient temperature-induced hypocotyl elongation in Arabidopsis seedlings is sensed by the epidermis-localized phytochrome B (phyB) and transduced into auxin biosynthesis via a basic helix-loop-helix transcription factor, phytochrome-interacting factor 4 (PIF4). Once synthesized, auxin travels down from the cotyledons to the hypocotyl, triggering hypocotyl cell elongation. Thus, the phyB–PIF4 module involved in thermosensing and signal transduction is a potential genetic target for engineering warm temperature-insensitive plants. ObjectivesThis study aims to manipulate warm temperature-induced elongation of plants at the post-translational level using phyB variants with dark reversion, the expression of which is subjected to heat stress. MethodsThe thermosensitive growth response of Arabidopsis was manipulated by expressing the single amino acid substitution variant of phyB (phyB[G515E]), which exhibited a lower dark reversion rate than wild-type phyB. Other variants with slow (phyB[G564E]) or rapid (phyB[S584F]) dark reversion or light insensitivity (phyB[G767R]) were also included in this study for comparison. Warming-induced transient expression of phyB variants was achieved using heat shock-inducible promoters. Arabidopsis PHYB[G515E] and PHYB[G564E] were also constitutively expressed in rice in an attempt to manipulate the heat sensitivity of a monocotyledonous plant species. ResultsAt an elevated temperature, Arabidopsis seedlings transiently expressing PHYB[G515E] under the control of a heat shock-inducible promoter exhibited shorter hypocotyls than those expressing PHYB and other PHYB variant genes. This warm temperature-insensitive growth was related to the lowered PIF4 and auxin responses. In addition, transgenic rice seedlings expressing Arabidopsis PHYB[G515E] and PHYB[G564E] showed warm temperature-insensitive shoot growth. ConclusionTransient expression of phyB variants with altered dark reversion rates could serve as an effective optogenetic technique for manipulating PIF4–auxin-mediated thermomorphogenic responses in plants.

The Past, Present, and Future of Wheat Dwarf Virus Management-A Review.

Wheat dwarf disease (WDD) is an important disease of monocotyledonous species, including economically important cereals. The causative pathogen, wheat dwarf virus (WDV), is persistently transmitted mainly by the leafhopper Psammotettix alienus and can lead to high yield losses. Due to climate change, the periods of vector activity increased, and the vectors have spread to new habitats, leading to an increased importance of WDV in large parts of Europe. In the light of integrated pest management, cultivation practices and the use of resistant/tolerant host plants are currently the only effective methods to control WDV. However, knowledge of the pathosystem and epidemiology of WDD is limited, and the few known sources of genetic tolerance indicate that further research is needed. Considering the economic importance of WDD and its likely increasing relevance in the coming decades, this study provides a comprehensive compilation of knowledge on the most important aspects with information on the causal virus, its vector, symptoms, host range, and control strategies. In addition, the current status of genetic and breeding efforts to control and manage this disease in wheat will be discussed, as this is crucial to effectively manage the disease under changing environmental conditions and minimize impending yield losses.