Displaying publications 1 - 20 of 92 in total

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  1. Khaliq G, Ali S, Ejaz S, Abdi G, Faqir Y, Ma J, et al.
    Front Plant Sci, 2023;14:1233477.
    PMID: 38034576 DOI: 10.3389/fpls.2023.1233477
    The effect of γ-aminobutyric acid (GABA) treatment at two concentrations (1 mM or 5 mM) on papaya fruit stored at 4°C and 80%-90% relative humidity for 5 weeks was investigated. The application of GABA at 5 mM apparently inhibited chilling injury, internal browning, electrolyte leakage, malondialdehyde (MDA), hydrogen peroxide (H2O2), polyphenol oxidase (PPO), phospholipase D (PLD), and lipoxygenase (LOX) activities of papaya fruit. Fruit treated with 5 mM GABA enhanced the activities of ascorbate peroxidase (APX), catalase (CAT), glutathione reductase (GR), superoxide dismutase (SOD), glutamate decarboxylase (GAD), and phenylalanine ammonia-lyase (PAL). In addition, GABA treatment significantly displayed higher levels of proline, endogenous GABA accumulation, phenolic contents, and total antioxidant activity than the nontreated papaya. The results suggested that GABA treatment may be a useful approach to improving the chilling tolerance of papaya fruit by reducing oxidative stress and enhancing the defense system.
  2. Remali J, Sahidin I, Aizat WM
    Front Plant Sci, 2022;13:809497.
    PMID: 35463410 DOI: 10.3389/fpls.2022.809497
    Xanthones are secondary metabolites rich in structural diversity and possess a broad array of pharmacological properties, such as antitumor, antidiabetic, and anti-microbes. These aromatic compounds are found in higher plants, such as Clusiaceae, Hypericaceae, and Gentianaceae, yet their biosynthetic pathways have not been comprehensively updated especially within the last decade (up to 2021). In this review, plant xanthone biosynthesis is detailed to illuminate their intricacies and differences between species. The pathway initially involves the shikimate pathway, either through L-phenylalanine-dependent or -independent pathway, that later forms an intermediate benzophenone, 2,3',4,6-tetrahydoxybenzophenone. This is followed by a regioselective intramolecular mediated oxidative coupling to form xanthone ring compounds, 1,3,5-trihydroxyxanthone (1,3,5-THX) or 1,3,7-THX, the core precursors for xanthones in most plants. Recent evidence has shed some lights onto the enzymes and reactions involved in this xanthone pathway. In particular, several biosynthetic enzymes have been characterized at both biochemical and molecular levels from various organisms including Hypericum spp., Centaurium erythraea and Garcinia mangostana. Proposed pathways for a plethora of other downstream xanthone derivatives including swertianolin and gambogic acid (derived from 1,3,5-THX) as well as gentisin, hyperixanthone A, α-mangostin, and mangiferin (derived from 1,3,7-THX) have also been thoroughly covered. This review reports one of the most complete xanthone pathways in plants. In the future, the information collected here will be a valuable resource for a more directed molecular works in xanthone-producing plants as well as in synthetic biology application.
  3. Wan Abdullah WMAN, Saidi NB, Yusof MT, Wee CY, Loh HS, Ong-Abdullah J, et al.
    Front Plant Sci, 2021;12:769855.
    PMID: 35095950 DOI: 10.3389/fpls.2021.769855
    Fusarium oxysporum f. sp. cubense tropical race 4 (FocTR4) is a destructive necrotrophic fungal pathogen afflicting global banana production. Infection process involves the activation of programmed cell death (PCD). In this study, seven Musa acuminata vacuolar processing enzyme (MaVPE1-MaVPE7) genes associated with PCD were successfully identified. Phylogenetic analysis and tissue-specific expression categorized these MaVPEs into the seed and vegetative types. FocTR4 infection induced the majority of MaVPE expressions in the susceptible cultivar "Berangan" as compared to the resistant cultivar "Jari Buaya." Consistently, upon FocTR4 infection, high caspase-1 activity was detected in the susceptible cultivar, while low level of caspase-1 activity was recorded in the resistant cultivar. Furthermore, inhibition of MaVPE activities via caspase-1 inhibitor in the susceptible cultivar reduced tonoplast rupture, decreased lesion formation, and enhanced stress tolerance against FocTR4 infection. Additionally, the Arabidopsis VPE-null mutant exhibited higher tolerance to FocTR4 infection, indicated by reduced sporulation rate, low levels of H2O2 content, and high levels of cell viability. Comparative proteomic profiling analysis revealed increase in the abundance of cysteine proteinase in the inoculated susceptible cultivar, as opposed to cysteine proteinase inhibitors in the resistant cultivar. In conclusion, the increase in vacuolar processing enzyme (VPE)-mediated PCD played a crucial role in modulating susceptibility response during compatible interaction, which facilitated FocTR4 colonization in the host.
  4. Plissonneau C, Benevenuto J, Mohd-Assaad N, Fouché S, Hartmann FE, Croll D
    Front Plant Sci, 2017;8:119.
    PMID: 28217138 DOI: 10.3389/fpls.2017.00119
    Epidemics caused by fungal plant pathogens pose a major threat to agro-ecosystems and impact global food security. High-throughput sequencing enabled major advances in understanding how pathogens cause disease on crops. Hundreds of fungal genomes are now available and analyzing these genomes highlighted the key role of effector genes in disease. Effectors are small secreted proteins that enhance infection by manipulating host metabolism. Fungal genomes carry 100s of putative effector genes, but the lack of homology among effector genes, even for closely related species, challenges evolutionary and functional analyses. Furthermore, effector genes are often found in rapidly evolving chromosome compartments which are difficult to assemble. We review how population and comparative genomics toolsets can be combined to address these challenges. We highlight studies that associated genome-scale polymorphisms with pathogen lifestyles and adaptation to different environments. We show how genome-wide association studies can be used to identify effectors and other pathogenicity-related genes underlying rapid adaptation. We also discuss how the compartmentalization of fungal genomes into core and accessory regions shapes the evolution of effector genes. We argue that an understanding of genome evolution provides important insight into the trajectory of host-pathogen co-evolution.
  5. Rosli MAF, Mediani A, Azizan KA, Baharum SN, Goh HH
    Front Plant Sci, 2021;12:655004.
    PMID: 33968110 DOI: 10.3389/fpls.2021.655004
    Hybridization is key to the evolution and diversity of plants in nature. Nepenthaceae comprises a family of diverse tropical carnivorous pitcher plant species with extensive hybridization. However, there is no study to date on the metabolite expression of hybrids in this family. We performed a non-targeted metabolomics analysis of the pitchers of two Nepenthes species with different dietary habits, namely, the semi-detritivorous N. ampullaria and carnivorous N. rafflesiana with their hybrid (N. × hookeriana) for a comparative study. The whole-pitcher samples were extracted in methanol:chloroform:water (3:1:1) via sonication-assisted extraction and analyzed using ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS) followed by data analysis to profile chemical compositions. A total of 1,441 metabolite features were profiled from the three species in which 43.3% of features in the hybrid samples were not found in either of its parents. The partial least squares discriminant analysis (PLS-DA) found 324 metabolite features with variable in projection (VIP) values greater than one in which 55 features were statistically significant. This showed that the hybrid is closer to N. rafflesiana, which is consistent to the previous study on gene and protein expressions. A total of 105 metabolites were putatively identified with manual searches using public metabolite databases. Phenols were detected to be the most abundant secondary metabolites due to a high flavonoid content, especially in N. rafflesiana. The most abundant feature 476.3s:449.102 was found to be the most significant VIP for distinguishing between the three species as a chemical marker. This is the first study comparing metabolites in the carnivory organs of different Nepenthes species with comprehensive profiling and putative identification. The differential metabolite compositions in the pitchers of different species might have ecological implications with the hybrid showing intermediate phenotype between the parents as well as manifesting unique metabolites. However, there is no clear evidence of metabolites related to the differences in dietary habits between the hybrid and the two parent species.
  6. Zulkapli MM, Ab Ghani NS, Ting TY, Aizat WM, Goh HH
    Front Plant Sci, 2020;11:625507.
    PMID: 33552113 DOI: 10.3389/fpls.2020.625507
    Nepenthes is a genus comprising carnivorous tropical pitcher plants that have evolved trapping organs at the tip of their leaves for nutrient acquisition from insect trapping. Recent studies have applied proteomics approaches to identify proteins in the pitcher fluids for better understanding the carnivory mechanism, but protein identification is hindered by limited species-specific transcriptomes for Nepenthes. In this study, the proteomics informed by transcriptomics (PIT) approach was utilized to identify and compare proteins in the pitcher fluids of Nepenthes ampullaria, Nepenthes rafflesiana, and their hybrid Nepenthes × hookeriana through PacBio isoform sequencing (Iso-Seq) and liquid chromatography-mass spectrometry (LC-MS) proteomic profiling. We generated full-length transcriptomes from all three species of 80,791 consensus isoforms with an average length of 1,692 bp as a reference for protein identification. The comparative analysis found that transcripts and proteins identified in the hybrid N. × hookeriana were more resembling N. rafflesiana, both of which are insectivorous compared with omnivorous N. ampullaria that can derive nutrients from leaf litters. Previously reported hydrolytic proteins were detected, including proteases, glucanases, chitinases, phosphatases, nucleases, peroxidases, lipid transfer protein, thaumatin-like protein, pathogenesis-related protein, and disease resistance proteins. Many new proteins with diverse predicted functions were also identified, such as amylase, invertase, catalase, kinases, ligases, synthases, esterases, transferases, transporters, and transcription factors. Despite the discovery of a few unique enzymes in N. ampullaria, we found no strong evidence of adaptive evolution to produce endogenous enzymes for the breakdown of leaf litter. A more complete picture of digestive fluid protein composition in this study provides important insights on the molecular physiology of pitchers and carnivory mechanism of Nepenthes species with distinct dietary habits.
  7. Jaffar NS, Jawan R, Chong KP
    Front Plant Sci, 2022;13:1047945.
    PMID: 36714743 DOI: 10.3389/fpls.2022.1047945
    The microbial diseases cause significant damage in agriculture, resulting in major yield and quality losses. To control microbiological damage and promote plant growth, a number of chemical control agents such as pesticides, herbicides, and insecticides are available. However, the rising prevalence of chemical control agents has led to unintended consequences for agricultural quality, environmental devastation, and human health. Chemical agents are not naturally broken down by microbes and can be found in the soil and environment long after natural decomposition has occurred. As an alternative to chemical agents, biocontrol agents are employed to manage phytopathogens. Interest in lactic acid bacteria (LAB) research as another class of potentially useful bacteria against phytopathogens has increased in recent years. Due to the high level of biosafety, they possess and the processes they employ to stimulate plant growth, LAB is increasingly being recognized as a viable option. This paper will review the available information on the antagonistic and plant-promoting capabilities of LAB and its mechanisms of action as well as its limitation as BCA. This review aimed at underlining the benefits and inputs from LAB as potential alternatives to chemical usage in sustaining crop productivity.
  8. Ting HM, Cheah BH, Chen YC, Yeh PM, Cheng CP, Yeo FKS, et al.
    Front Plant Sci, 2020;11:257.
    PMID: 32211010 DOI: 10.3389/fpls.2020.00257
    Glucosinolates are defense-related secondary metabolites found in Brassicaceae. When Brassicaceae come under attack, glucosinolates are hydrolyzed into different forms of glucosinolate hydrolysis products (GHPs). Among the GHPs, isothiocyanates are the most comprehensively characterized defensive compounds, whereas the functional study of nitriles, another group of GHP, is still limited. Therefore, this study investigates whether 3-butenenitrile (3BN), a nitrile, can trigger the signaling pathways involved in the regulation of defense responses in Arabidopsis thaliana against biotic stresses. Briefly, the methodology is divided into three stages, (i) evaluate the physiological and biochemical effects of exogenous 3BN treatment on Arabidopsis, (ii) determine the metabolites involved in 3BN-mediated defense responses in Arabidopsis, and (iii) assess whether a 3BN treatment can enhance the disease tolerance of Arabidopsis against necrotrophic pathogens. As a result, a 2.5 mM 3BN treatment caused lesion formation in Arabidopsis Columbia (Col-0) plants, a process found to be modulated by nitric oxide (NO). Metabolite profiling revealed an increased production of soluble sugars, Krebs cycle associated carboxylic acids and amino acids in Arabidopsis upon a 2.5 mM 3BN treatment, presumably via NO action. Primary metabolites such as sugars and amino acids are known to be crucial components in modulating plant defense responses. Furthermore, exposure to 2.0 mM 3BN treatment began to increase the production of salicylic acid (SA) and jasmonic acid (JA) phytohormones in Arabidopsis Col-0 plants in the absence of lesion formation. The production of SA and JA in nitrate reductase loss-of function mutant (nia1nia2) plants was also induced by the 3BN treatments, with a greater induction for JA. The SA concentration in nia1nia2 plants was lower than in Col-0 plants, confirming the previously reported role of NO in controlling SA production in Arabidopsis. A 2.0 mM 3BN treatment prior to pathogen assays effectively alleviated the leaf lesion symptom of Arabidopsis Col-0 plants caused by Pectobacterium carotovorum ssp. carotovorum and Botrytis cinerea and reduced the pathogen growth on leaves. The findings of this study demonstrate that 3BN can elicit defense response pathways in Arabidopsis, which potentially involves a coordinated crosstalk between NO and phytohormone signaling.
  9. Govender NT, Mahmood M, Seman IA, Wong MY
    Front Plant Sci, 2017;8:1395.
    PMID: 28861093 DOI: 10.3389/fpls.2017.01395
    Basal stem rot, caused by the basidiomycete fungus, Ganoderma boninense, is an economically devastating disease in Malaysia. Our study investigated the changes in lignin content and composition along with activity and expression of the phenylpropanoid pathway enzymes and genes in oil palm root tissues during G. boninense infection. We sampled control (non-inoculated) and infected (inoculated) seedlings at seven time points [1, 2, 3, 4, 8, and 12 weeks post-inoculation (wpi)] in a randomized design. The expression profiles of phenylalanine ammonia lyase (PAL), cinnamyl alcohol dehydrogenase (CAD), and peroxidase (POD) genes were monitored at 1, 2, and 3 wpi using real-time quantitative polymerase chain reaction. Seedlings at 4, 8, and 12 wpi were screened for lignin content, lignin composition, enzyme activities (PAL, CAD, and POD), growth (weight and height), and disease severity (DS). Gene expression analysis demonstrated up-regulation of PAL, CAD, and POD genes in the infected seedlings, relative to the control seedlings at 1, 2, and 3 wpi. At 2 and 3 wpi, CAD showed highest transcript levels compared to PAL and POD. DS increased progressively throughout sampling, with 5, 34, and 69% at 4, 8, and 12 wpi, respectively. Fresh weight and height of the infected seedlings were significantly lower compared to the control seedlings at 8 and 12 wpi. Lignin content of the infected seedlings at 4 wpi was significantly higher than the control seedlings, remained elicited with no change at 8 wpi, and then collapsed with a significant reduction at 12 wpi. The nitrobenzene oxidation products of oil palm root lignin yielded both syringyl and guaiacyl monomers. Accumulation of lignin in the infected seedlings was in parallel to increased syringyl monomers, at 4 and 8 wpi. The activities of PAL and CAD enzymes in the infected seedlings at DS = 5-34% were significantly higher than the control seedlings and thereafter collapsed at DS = 69%.
  10. Burgess AJ, Retkute R, Preston SP, Jensen OE, Pound MP, Pridmore TP, et al.
    Front Plant Sci, 2016;7:1392.
    PMID: 27708654
    Physical perturbation of a plant canopy brought about by wind is a ubiquitous phenomenon and yet its biological importance has often been overlooked. This is partly due to the complexity of the issue at hand: wind-induced movement (or mechanical excitation) is a stochastic process which is difficult to measure and quantify; plant motion is dependent upon canopy architectural features which, until recently, were difficult to accurately represent and model in 3-dimensions; light patterning throughout a canopy is difficult to compute at high-resolutions, especially when confounded by other environmental variables. Recent studies have reinforced the expectation that canopy architecture is a strong determinant of productivity and yield; however, links between the architectural properties of the plant and its mechanical properties, particularly its response to wind, are relatively unknown. As a result, biologically relevant data relating canopy architecture, light- dynamics, and short-scale photosynthetic responses in the canopy setting are scarce. Here, we hypothesize that wind-induced movement will have large consequences for the photosynthetic productivity of our crops due to its influence on light patterning. To address this issue, in this study we combined high resolution 3D reconstructions of a plant canopy with a simple representation of canopy perturbation as a result of wind using solid body rotation in order to explore the potential effects on light patterning, interception, and photosynthetic productivity. We looked at two different scenarios: firstly a constant distortion where a rice canopy was subject to a permanent distortion throughout the whole day; and secondly, a dynamic distortion, where the canopy was distorted in incremental steps between two extremes at set time points in the day. We find that mechanical canopy excitation substantially alters light dynamics; light distribution and modeled canopy carbon gain. We then discuss methods required for accurate modeling of mechanical canopy excitation (here coined the 4-dimensional plant) and some associated biological and applied implications of such techniques. We hypothesize that biomechanical plant properties are a specific adaptation to achieve wind-induced photosynthetic enhancement and we outline how traits facilitating canopy excitation could be used as a route for improving crop yield.
  11. Jamil IN, Remali J, Azizan KA, Nor Muhammad NA, Arita M, Goh HH, et al.
    Front Plant Sci, 2020;11:944.
    PMID: 32754171 DOI: 10.3389/fpls.2020.00944
    Across all facets of biology, the rapid progress in high-throughput data generation has enabled us to perform multi-omics systems biology research. Transcriptomics, proteomics, and metabolomics data can answer targeted biological questions regarding the expression of transcripts, proteins, and metabolites, independently, but a systematic multi-omics integration (MOI) can comprehensively assimilate, annotate, and model these large data sets. Previous MOI studies and reviews have detailed its usage and practicality on various organisms including human, animals, microbes, and plants. Plants are especially challenging due to large poorly annotated genomes, multi-organelles, and diverse secondary metabolites. Hence, constructive and methodological guidelines on how to perform MOI for plants are needed, particularly for researchers newly embarking on this topic. In this review, we thoroughly classify multi-omics studies on plants and verify workflows to ensure successful omics integration with accurate data representation. We also propose three levels of MOI, namely element-based (level 1), pathway-based (level 2), and mathematical-based integration (level 3). These MOI levels are described in relation to recent publications and tools, to highlight their practicality and function. The drawbacks and limitations of these MOI are also discussed for future improvement toward more amenable strategies in plant systems biology.
  12. Ikram NK, Zhan X, Pan XW, King BC, Simonsen HT
    Front Plant Sci, 2015;6:129.
    PMID: 25852702 DOI: 10.3389/fpls.2015.00129
    Plants biosynthesize a great diversity of biologically active small molecules of interest for fragrances, flavors, and pharmaceuticals. Among specialized metabolites, terpenoids represent the greatest molecular diversity. Many terpenoids are very complex, and total chemical synthesis often requires many steps and difficult chemical reactions, resulting in a low final yield or incorrect stereochemistry. Several drug candidates with terpene skeletons are difficult to obtain by chemical synthesis due to their large number of chiral centers. Thus, biological production remains the preferred method for industrial production for many of these compounds. However, because these chemicals are often found in low abundance in the native plant, or are produced in plants which are difficult to cultivate, there is great interest in engineering increased production or expression of the biosynthetic pathways in heterologous hosts. Although there are many examples of successful engineering of microbes such as yeast or bacteria to produce these compounds, this often requires extensive changes to the host organism's metabolism. Optimization of plant gene expression, post-translational protein modifications, subcellular localization, and other factors often present challenges. To address the future demand for natural products used as drugs, new platforms are being established that are better suited for heterologous production of plant metabolites. Specifically, direct metabolic engineering of plants can provide effective heterologous expression for production of valuable plant-derived natural products. In this review, our primary focus is on small terpenoids and we discuss the benefits of plant expression platforms and provide several successful examples of stable production of small terpenoids in plants.
  13. Nie Y, Lau SYL, Tan X, Lu X, Liu S, Tahvanainen T, et al.
    Front Plant Sci, 2022;13:974251.
    PMID: 36160957 DOI: 10.3389/fpls.2022.974251
    Melting permafrost mounds in subarctic palsa mires are thawing under climate warming and have become a substantial source of N2O emissions. However, mechanistic insights into the permafrost thaw-induced N2O emissions in these unique habitats remain elusive. We demonstrated that N2O emission potential in palsa bogs was driven by the bacterial residents of two dominant Sphagnum mosses especially of Sphagnum capillifolium (SC) in the subarctic palsa bog, which responded to endogenous and exogenous Sphagnum factors such as secondary metabolites, nitrogen and carbon sources, temperature, and pH. SC's high N2O emission activity was linked with two classes of distinctive hyperactive N2O emitters, including Pseudomonas sp. and Enterobacteriaceae bacteria, whose hyperactive N2O emitting capability was characterized to be dominantly pH-responsive. As the nosZ gene-harboring emitter, Pseudomonas sp. SC-H2 reached a high level of N2O emissions that increased significantly with increasing pH. For emitters lacking the nosZ gene, an Enterobacteriaceae bacterium SC-L1 was more adaptive to natural acidic conditions, and N2O emissions also increased with pH. Our study revealed previously unknown hyperactive N2O emitters in Sphagnum capillifolium found in melting palsa mound environments, and provided novel insights into SC-associated N2O emissions.
  14. Sgamma T, Masiero E, Mali P, Mahat M, Slater A
    Front Plant Sci, 2018;9:1828.
    PMID: 30619401 DOI: 10.3389/fpls.2018.01828
    Herbal medicines are used globally for their health benefits as an alternative therapy method to modern medicines. The market for herbal products has increased rapidly over the last few decades, but this has in turn increased the opportunities for malpractices such as contamination or substitution of products with alternative plant species. In the 1990s, a series of severe renal disease cases were reported in Belgium associated with weight loss treatment, in which the active species Stephania tetrandra was found to be substituted with Aristolochia fangchi. A. fangchi contains toxic aristolochic acids, which have been linked to kidney failure, as well as cancers of the urinary tract. Because of these known toxicities, herbal medicines containing these compounds, or potentially contaminated by these plants, have been restricted or banned in some countries, but they are still available via the internet and in alternate formulations. In this study, a DNA based method based on quantitative real-time PCR (qPCR) was tested to detect and distinguish Aristolochia subg. Siphisia (Duch.) O.C.Schmidt species from a range of medicinal plants that could potentially be contaminated with Aristolochia material. Specific primers were designed to confirm that Aristolochia subg. Siphisia can be detected, even in small amounts, if it is present in the products, fulfilling the aim of offering a simple, cheaper and faster solution than the chemical methods. A synthetic gBlock template containing the primer sequences was used as a reference standard to calibrate the qPCR assay and to estimate the copy number of a target gene per sample. Generic primers covering the conserved 5.8S rRNA coding region were used as internal control to verify DNA quality and also as a reference gene for relative quantitation. To cope with potentially degraded DNA, all qPCR primer sets were designed to generate PCR products of under 100 bp allowing detection and quantification of A. fangchi gBlock even when mixed with S. tetrandra gBlock in different ratios. All proportions of Aristolochia, from 100 to 2%, were detected. Using standards, associating the copy number to each start quantity, the detection limit was calculated and set to about 50 copies.
  15. Lau WC, Rafii MY, Ismail MR, Puteh A, Latif MA, Ramli A
    Front Plant Sci, 2015;6:832.
    PMID: 26528304 DOI: 10.3389/fpls.2015.00832
    After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers' preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated.
  16. Tan B, Li Y, Liu T, Tan X, He Y, You X, et al.
    Front Plant Sci, 2021;12:691651.
    PMID: 34456936 DOI: 10.3389/fpls.2021.691651
    As natural agroecology deteriorates, controlled environment agriculture (CEA) systems become the backup support for coping with future resource consumption and potential food crises. Compared with natural agroecology, most of the environmental parameters of the CEA system rely on manual management. Such a system is dependent and fragile and prone to degradation, which includes harmful bacteria proliferation and productivity decline. Proper water management is significant for constructing a stabilized rhizosphere microenvironment. It has been proved that water is an efficient tool for changing the availability of nutrients, plant physiological processes, and microbial communities within. However, for CEA issues, relevant research is lacking at present. The article reviews the interactive mechanism between water management and rhizosphere microenvironments from the perspectives of physicochemical properties, physiological processes, and microbiology in CEA systems. We presented a synthesis of relevant research on water-root-microbes interplay, which aimed to provide detailed references to the conceptualization, research, diagnosis, and troubleshooting for CEA systems, and attempted to give suggestions for the construction of a high-tech artificial agricultural ecology.
  17. Nawae W, Naktang C, Charoensri S, U-Thoomporn S, Narong N, Chusri O, et al.
    Front Plant Sci, 2023;14:1137077.
    PMID: 36875624 DOI: 10.3389/fpls.2023.1137077
    Durian (Durio zibethinus), which yields the fruit known as the "King of Fruits," is an important economic crop in Southeast Asia. Several durian cultivars have been developed in this region. In this study, we resequenced the genomes of three popular durian cultivars in Thailand, including Kradumthong (KD), Monthong (MT), and Puangmanee (PM) to investigate genetic diversities of cultivated durians. KD, MT, and PM genome assemblies were 832.7, 762.6, and 821.6 Mb, and their annotations covered 95.7, 92.4, and 92.7% of the embryophyta core proteins, respectively. We constructed the draft durian pangenome and analyzed comparative genomes with related species in Malvales. Long terminal repeat (LTR) sequences and protein families in durian genomes had slower evolution rates than that in cotton genomes. However, protein families with transcriptional regulation function and protein phosphorylation function involved in abiotic and biotic stress responses appeared to evolve faster in durians. The analyses of phylogenetic relationships, copy number variations (CNVs), and presence/absence variations (PAVs) suggested that the genome evolution of Thai durians was different from that of the Malaysian durian, Musang King (MK). Among the three newly sequenced genomes, the PAV and CNV profiles of disease resistance genes and the expressions of methylesterase inhibitor domain containing genes involved in flowering and fruit maturation in MT were different from those in KD and PM. These genome assemblies and their analyses provide valuable resources to gain a better understanding of the genetic diversity of cultivated durians, which may be useful for the future development of new durian cultivars.
  18. Singh D, Lawrence K, Marker S, Bhattacharjee I, Lawrence R, Choudhary R, et al.
    Front Plant Sci, 2023;14:1017652.
    PMID: 36968405 DOI: 10.3389/fpls.2023.1017652
    INTRODUCTION: Foxtail millet (Setaria italica L. beauv) is an important crop in underdeveloped countries; however, yield levels are low. The use of varied germplasm in a breeding approach is critical for increasing productivity. Foxtail millet can be cultivated effectively in a wide range of environmental circumstances but it is best suited to hot and dry climates.

    METHODS: In the current study, multivariant traits were used to define 50 genotypes in the first year and 10 genotypes in the second year. The phenotypic correlations among all traits in the entire germplasm were assessed, and the data acquired for all quantitative characters were subjected to analysis of variance for augmented block design. Furthermore, WINDOWS STAT statistical software was used to carry out a principal component analysis (PCA). The presence of substantial variations in most symptoms was shown by analysis of variance.

    RESULTS: Genotypic coefficient of variation (GCV) projections for grain yields were the highest, followed by panicle lengths and biological yields. Plant height and leaf length had the highest PCV estimates, followed by leaf width. Low GCV and phenotypic coefficient of variation (PCV) were measured as leaf length and 50% flowering in days. According to the PCV study, direct selection based on characters, panicle weight, test weight, and straw weight had a high and positive effect on grain yield per plant in both the rainy and summer seasons, indicating the true relationship between these characters and grain yield per plant, which aids indirect selection for these traits and thus improves grain yield per plant. Variability in foxtail millet germplasm enables plant breeders to effectively select appropriate donor lines for foxtail millet genetic improvement.

    DISCUSSION: Based on the average performance of genotypes considered superior in terms of grain yield components under Prayagraj agroclimatic conditions, the best five genotypes were: Kangni-7 (GS62), Kangni-1 (G5-14), Kangni-6 (GS-55), Kangni-5 (GS-389), and Kangni-4 (GS-368).

  19. Wan Zakaria WN, Loke KK, Zulkapli MM, Mohd Salleh F', Goh HH, Mohd Noor N
    Front Plant Sci, 2015;6:1229.
    PMID: 26793209 DOI: 10.3389/fpls.2015.01229
  20. Zhang Y, Jiang K, Chen S, Wang L, Zhang X, Xu W, et al.
    Front Plant Sci, 2023;14:1234729.
    PMID: 37885663 DOI: 10.3389/fpls.2023.1234729
    RATIONALE: Ganoderma lucidum (G. lucidum) is a popular medicinal fungus that has been used in traditional medicine for decades, with its provenance influencing its medicinal and commercial worth. The amount of active ingredients and the price of G. lucidum from different origins vary significantly; hence, fraudulent labeling is common. Reliable techniques for G. lucidum geographic verification are urgently required to safeguard the interests of consumers, producers, and honest dealers. A stable isotope is widely acknowledged as a useful traceability technique and could be developed to confirm the geographical origin of G. lucidum.

    METHODS: G. lucidum samples from various sources and in varying stages were identified by using δ 13C, δD, δ 18O, δ 15N, C, and N contents combined with chemometric tools. Chemometric approaches, including PCA, OPLS-DA, PLS, and FLDA models, were applied to the obtained data. The established models were used to trace the origin of G. lucidum from various sources or track various stages of G. lucidum.

    RESULTS: In the stage model, the δ 13C, δD, δ 18O, δ 15N, C, and N contents were considered meaningful variables to identify various stages of G. lucidum (bud development, growth, and maturing) using PCA and OPLS-DA and the findings were validated by the PLS model rather than by only four variables (δ 13C, δD, δ 18O, and δ 15N). In the origin model, only four variables, namely δ 13C, δD, δ 18O, and δ 15N, were used. PCA divided G. lucidum samples into four clusters: A (Zhejiang), B (Anhui), C (Jilin), and D (Fujian). The OPLS-DA model could be used to classify the origin of G. lucidum. The model was validated by other test samples (Pseudostellaria heterophylla), and the external test (G. lucidum) by PLS and FLDA models demonstrated external verification accuracy of up to 100%.

    CONCLUSION: C, H, O, and N stable isotopes and C and N contents combined with chemometric techniques demonstrated considerable potential in the geographic authentication of G. lucidum, providing a promising method to identify stages of G. lucidum.

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