Trends Plant Sci , IF:18.313 , 2023 Aug doi: 10.1016/j.tplants.2023.07.006
A general concept of quantitative abiotic stress sensing.
Bielefeld University, Biochemistry and Physiology of Plants, W5-134, 33615 Bielefeld, Germany. Electronic address: karl-josef.dietz@uni-bielefeld.de.; Bielefeld University, Biochemistry and Physiology of Plants, W5-134, 33615 Bielefeld, Germany.
Plants often encounter stress in their environment. For appropriate responses to particular stressors, cells rely on sensory mechanisms that detect emerging stress. Considering sensor and signal amplification characteristics, a single sensor system hardly covers the entire stress range encountered by plants (e.g., salinity, drought, temperature stress). A dual system comprising stress-specific sensors and a general quantitative stress sensory system is proposed to enable the plant to optimize its response. The quantitative stress sensory system exploits the redox and reactive oxygen species (ROS) network by altering the oxidation and reduction rates of individual redox-active molecules under stress impact. The proposed mechanism of quantitative stress sensing also fits the requirement of dealing with multifactorial stress conditions.
PMID: 37591742
Genome Biol , IF:13.583 , 2023 Aug , V24 (1) : P194 doi: 10.1186/s13059-023-03032-6
Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem.
Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.; Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Wulumuqi, 830000, Xinjiang, China.; Department of Biosciences, Durham University, Durham, DH1 3LE, UK.; Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. xlzhang@mail.hzau.edu.cn.; Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. jsx@mail.hzau.edu.cn.
BACKGROUND: Somatic embryogenesis is a major process for plant regeneration. However, cell communication and the gene regulatory network responsible for cell reprogramming during somatic embryogenesis are still largely unclear. Recent advances in single-cell technologies enable us to explore the mechanism of plant regeneration at single-cell resolution. RESULTS: We generate a high-resolution single-cell transcriptomic landscape of hypocotyl tissue from the highly regenerable cotton genotype Jin668 and the recalcitrant TM-1. We identify nine putative cell clusters and 23 cluster-specific marker genes for both cultivars. We find that the primary vascular cell is the major cell type that undergoes cell fate transition in response to external stimulation. Further developmental trajectory and gene regulatory network analysis of these cell clusters reveals that a total of 41 hormone response-related genes, including LAX2, LAX1, and LOX3, exhibit different expression patterns in the primary xylem and cambium region of Jin668 and TM-1. We also identify novel genes, including CSEF, PIS1, AFB2, ATHB2, PLC2, and PLT3, that are involved in regeneration. We demonstrate that LAX2, LAX1 and LOX3 play important roles in callus proliferation and plant regeneration by CRISPR/Cas9 editing and overexpression assay. CONCLUSIONS: This study provides novel insights on the role of the regulatory network in cell fate transition and reprogramming during plant regeneration driven by somatic embryogenesis.
PMID: 37626404
New Phytol , IF:10.151 , 2023 Aug , V239 (3) : P992-1004 doi: 10.1111/nph.18788
A gene regulatory network in Arabidopsis roots reveals features and regulators of the plant response to elevated CO(2).
IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, 34000, Montpellier, France.; IMAG, Univ. Montpellier, CNRS, 34000, Montpellier, France.; Universite Paul-Valery-Montpellier 3, 34000, Montpellier, France.
The elevation of CO(2) in the atmosphere increases plant biomass but decreases their mineral content. The genetic and molecular bases of these effects remain mostly unknown, in particular in the root system, which is responsible for plant nutrient uptake. To gain knowledge about the effect of elevated CO(2) on plant growth and physiology, and to identify its regulatory in the roots, we analyzed genome expression in Arabidopsis roots through a combinatorial design with contrasted levels of CO(2) , nitrate, and iron. We demonstrated that elevated CO(2) has a modest effect on root genome expression under nutrient sufficiency, but by contrast leads to massive expression changes under nitrate or iron deficiencies. We demonstrated that elevated CO(2) negatively targets nitrate and iron starvation modules at the transcriptional level, associated with a reduction in high-affinity nitrate uptake. Finally, we inferred a gene regulatory network governing the root response to elevated CO(2) . This network allowed us to identify candidate transcription factors including MYB15, WOX11, and EDF3 which we experimentally validated for their role in the stimulation of growth by elevated CO(2) . Our approach identified key features and regulators of the plant response to elevated CO(2) , with the objective of developing crops resilient to climate change.
PMID: 36727308
Crit Rev Biotechnol , IF:8.429 , 2023 Dec , V43 (5) : P716-733 doi: 10.1080/07388551.2022.2058460
Systems seed biology to understand and manipulate rice grain quality and nutrition.
Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines.; Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.
PMID: 35723584
Sci Total Environ , IF:7.963 , 2023 Aug : P165800 doi: 10.1016/j.scitotenv.2023.165800
Designing an automatic pollen monitoring network for direct usage of observations to reconstruct the concentration fields.
Finnish Meteorological Institute, Erik Palmenin Aukio 1, 00560 Helsinki, Finland. Electronic address: Mikhail.sofiev@fmi.fi.; Center of Allergy & Environment (ZAUM), Member of the German Center for Lung Research (DZL), Technical University and Helmholtz Center, Munich, Germany.; Federal Office of Meteorology and Climatology MeteoSwiss, Chemin de l'Aerologie 1, 1530 Payerne, Switzerland.; Finnish Meteorological Institute, Erik Palmenin Aukio 1, 00560 Helsinki, Finland.; Faculty of Geography and Earth Sciences, University of Latvia, Rainis bvld 19, Riga LV-1586, Latvia.; University of Worcester, UK.; Institute of Allergology, Charite - Universitatsmedizin Berlin, Freie Universitat Berlin and Humboldt-Universitat zu Berlin, Berlin, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Allergology and Immunology, Berlin, Germany.; Department of Biology and Environmental Sciences, University of Gothenburg, Box 461, S-405 30 Gothenburg, Sweden.; Deutscher Wetterdienst, Berlin, Germany.; Institute of Public Health of the Republic of Slovenia, Slovenia.; School of Chemical Sciences, Dublin City University, Ireland.; Department of Botany, Ecology and Plant Physiology, Agrifood Campus of International Excellence CeiA3, University of Cordoba, Rabanales Campus, Celestino Mutis Building, E-14071 Cordoba, Spain; Andalusian Inter-University Institute for Earth System IISTA, University of Cordoba, Spain.; Faculty of Sciences, University of Porto and Earth Sciences Institute (ICT), Pole of the Faculty of Sciences, University of Porto, Portugal.; German Pollen Information Service Foundation (PID), Berlin, Germany.
We consider several approaches to a design of a regional-to-continent-scale automatic pollen monitoring network in Europe. Practical challenges related to the arrangement of such a network limit the range of possible solutions. A hierarchical network is discussed, highlighting the necessity of a few reference sites that follow an extended observations protocol and have corresponding capabilities. Several theoretically rigorous approaches to a network design have been developed so far. However, before starting the process, a network purpose, a criterion of its performance, and a concept of the data usage should be formalized. For atmospheric composition monitoring, developments follow one of the two concepts: a network for direct representation of concentration fields and a network for model-based data assimilation, inverse problem solution, and forecasting. The current paper demonstrates the first approach, whereas the inverse problems are considered in a follow-up paper. We discuss the approaches for the network design from theoretical and practical standpoints, formulate criteria for the network optimality, and consider practical constrains for an automatic pollen network. An application of the methodology is demonstrated for a prominent example of Germany's pollen monitoring network. The multi-step method includes (i) the network representativeness and (ii) redundancy evaluation followed by (iii) fidelity evaluation and improvement using synthetic data.
PMID: 37595925
Sci Total Environ , IF:7.963 , 2023 Sep , V892 : P164506 doi: 10.1016/j.scitotenv.2023.164506
Diversity of fungal microbiome obtained from plant rhizoplanes.
Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA.; Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA.; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.; Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA; Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA. Electronic address: dfrigirodrigues@uh.edu.
Microbial communities, and their ecological importance, have been investigated in several habitats. However, so far, most studies could not describe the closest microbial interactions and their functionalities. This study investigates the co-occurring interactions between fungi and bacteria in plant rhizoplanes and their potential functions. The partnerships were obtained using fungal-highway columns with four plant-based media. The fungi and associated microbiomes isolated from the columns were identified by sequencing the ITS (fungi) and 16S rRNA genes (bacteria). Statistical analyses including Exploratory Graph and Network Analysis were used to visualize the presence of underlying clusters in the microbial communities and evaluate the metabolic functions associated with the fungal microbiome (PICRUSt2). Our findings characterize the presence of both unique and complex bacterial communities associated with different fungi. The results showed that Bacillus was associated as exo-bacteria in 80 % of the fungi but occurred as putative endo-bacteria in 15 %. A shared core of putative endo-bacterial genera, potentially involved in the nitrogen cycle was found in 80 % of the isolated fungi. The comparison of potential metabolic functions of the putative endo- and exo-communities highlighted the potential essential factors to establish an endosymbiotic relationship, such as the loss of pathways associated with metabolites obtained from the host while maintaining pathways responsible for bacterial survival within the hypha.
PMID: 37295515
Genes Dis , IF:7.103 , 2023 Sep , V10 (5) : P2049-2063 doi: 10.1016/j.gendis.2022.09.009
The transcriptional regulators of virulence for Pseudomonas aeruginosa: Therapeutic opportunity and preventive potential of its clinical infections.
College of Plant Protection, Laboratory of Plant Immunity, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.; Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.; School of Pharmaceutical Sciences, Sun Yat-Sen University, University Town, Guangzhou, Guangdong 510006, China.; Tung Biomedical Sciences Centre, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.; Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guangdong 518057, China.
In Pseudomonas aeruginosa (P. aeruginosa), transcription factors (TFs) are important mediators in the genetic regulation of adaptability and pathogenicity to respond to multiple environmental stresses and host defences. The P. aeruginosa genome harbours 371 putative TFs; of these, about 70 have been shown to regulate virulence-associated phenotypes by binding to the promoters of their target genes. Over the past three decades, several techniques have been applied to identify TF binding sites on the P. aeruginosa genome, and an atlas of TF binding patterns has been mapped. The virulence-associated regulons of TFs show complex crosstalk in P. aeruginosa's regulatory network. In this review, we summarise the recent literature on TF regulatory networks involved in the quorum-sensing system, biofilm formation, pyocyanin synthesis, motility, the type III secretion system, the type VI secretion system, and oxidative stress responses. We discuss future perspectives that could provide insights and targets for preventing clinical infections caused by P. aeruginosa based on the global regulatory network of transcriptional regulators.
PMID: 37492705
J Exp Bot , IF:6.992 , 2023 Aug , V74 (15) : P4503-4519 doi: 10.1093/jxb/erad178
Deciphering transcriptional mechanisms of maize internodal elongation by regulatory network analysis.
State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing 100193, China.; North China Key Laboratory for Crop Germplasm Resources, Ministry of Education, State Key Laboratory of North China Crop Improvement and Regulation & College of Agronomy, Hebei Agricultural University, Baoding, Hebei 071001, China.; College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.
The lengths of the basal internodes is an important factor for lodging resistance of maize (Zea mays). In this study, foliar application of coronatine (COR) to 10 cultivars at the V8 growth stage had different suppression effects on the length of the eighth internode, with three being categorized as strong-inhibition cultivars (SC), five as moderate (MC), and two as weak (WC). RNA-sequencing of the eighth internode of the cultivars revealed a total of 7895 internode elongation-regulating genes, including 777 transcription factors (TFs). Genes related to the hormones cytokinin, gibberellin, auxin, and ethylene in the SC group were significantly down-regulated compared to WC, and more cell-cycle regulatory factors and cell wall-related genes showed significant changes, which severely inhibited internode elongation. In addition, we used EMSAs to explore the direct regulatory relationship between two important TFs, ZmABI7 and ZmMYB117, which regulate the cell cycle and cell wall modification by directly binding to the promoters of their target genes ZmCYC1, ZmCYC3, ZmCYC7, and ZmCPP1. The transcriptome reported in this study will provide a useful resource for studying maize internode development, with potential use for targeted genetic control of internode length to improve the lodging resistance of maize.
PMID: 37170764
J Exp Bot , IF:6.992 , 2023 Aug , V74 (14) : P3933-3950 doi: 10.1093/jxb/erad135
An evo-devo view of the gynoecium.
International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan.; Laboratorio de Genetica Molecular, Epigenetica, Desarrollo y Evolucion de Plantas, Instituto de Ecologia, Universidad Nacional Autonoma de Mexico, Ciudad Universitaria, Av. Universidad 3000, Coyoacan, Mexico DF 04510, Mexico.; Faculty of Advanced Science and Technology (FAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan.; Unidad de Genomica Avanzada (LANGEBIO), Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, Mexico.
The appearance of the flower marks a key event in the evolutionary history of plants. Among the four types of floral organs, the gynoecium represents the major adaptive advantage of the flower. The gynoecium is an enclosing structure that protects and facilitates the fertilization of the ovules, which then mature as seeds. Upon fertilization, in many species, the gynoecium itself eventually becomes the fruit, which contributes to the dispersal of the seeds. However, despite its importance and the recent advances in our understanding of the genetic regulatory network guiding early gynoecium development, many questions remain to be resolved regarding the extent of the conservation of the molecular mechanisms for gynoecium development among different taxa, and how these mechanisms give origin and diversification to the gynoecium. In this review, we compile the existing knowledge about the evolution, development, and molecular mechanisms involved in the origin and evolution of the gynoecium.
PMID: 37075814
Int J Biol Macromol , IF:6.953 , 2023 Aug , V246 : P125633 doi: 10.1016/j.ijbiomac.2023.125633
Morphology, sucrose metabolism and gene network reveal the molecular mechanism of seed fiber development in poplar.
State Key Laboratory for Efficient Production of Forest Resources, Key Laboratory of Silviculture and Conservation of the Ministry of Education, National Energy R&D Center for Non-food Biomass, Engineering Research Center for Carbon Sequestration and Sink Enhancement by Forestry and Grass of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.; State Key Laboratory for Efficient Production of Forest Resources, Key Laboratory of Silviculture and Conservation of the Ministry of Education, National Energy R&D Center for Non-food Biomass, Engineering Research Center for Carbon Sequestration and Sink Enhancement by Forestry and Grass of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China. Electronic address: zhongchen@bjfu.edu.cn.
Poplar is an important tree species for ecological protection, wood production, bioenergy and urban greening; it has been widely planted worldwide. However, the catkin fibers produced by female poplars can cause environmental pollution and safety hazards during spring. This study focused on Populus tomentosa, and revealed the sucrose metabolism regulatory mechanism of catkin fibers development from morphological, physiological and molecular aspects. Paraffin section suggested that poplar catkin fibers were not seed hairs and produced from the epidermal cells of funicle and placenta. Sucrose degradation via invertase and sucrose synthase played the dominant role during poplar catkin fibers development. The expression patterns revealed that sucrose metabolism-related genes played important roles during catkin fibers development. Y1H analysis indicated that there was a potential interaction between sucrose synthase 2 (PtoSUS2)/vacuolar invertase 3 (PtoVIN3) and trichome-regulating MYB transcription factors in poplar. Finally, the two key genes, PtoSUS2 and PtoVIN3, had roles in Arabidopsis trichome density, indicating that sucrose metabolism is important in poplar catkin fibers development. This study is not only helpful for clarifying the mechanism of sucrose regulation during trichome development in perennial woody plants, but also establishes a foundation to solve poplar catkin fibers pollution through genetic engineering methods.
PMID: 37406903
mSystems , IF:6.496 , 2023 Aug , V8 (4) : Pe0044023 doi: 10.1128/msystems.00440-23
Paired associated SARS-CoV-2 spike variable positions: a network analysis approach to emerging variants.
Department of Microbiology, Medical School, National and Kapodistrian University of Athens , Athens, Greece.; ELGO-Demeter, Plant Protection Division of Patras, Laboratory of Virology , Patras, Greece.; Department of Medicine, Stanford University , Stanford, California, USA.; Departments of Epidemiology and Population Health, Stanford University , Stanford, California, USA.; Department of Biomedical Data Science, Stanford University , Stanford, California, USA.; Department of Statistics, Stanford University , Stanford, California, USA.
Amino acids in variable positions of proteins may be correlated, with potential structural and functional implications. Here, we apply exact tests of independence in R x C contingency tables to examine noise-free associations between variable positions of the SARS-CoV-2 spike protein, using as a paradigm sequences from Greece deposited in GISAID (N = 6,683/1,078 full length) for the period 29 February 2020 to 26 April 2021 that essentially covers the first three pandemic waves. We examine the fate and complexity of these associations by network analysis, using associated positions (exact P /= 2) as links and the corresponding positions as nodes. We found a temporal linear increase of positional differences and a gradual expansion of the number of position associations over time, represented by a temporally evolving intricate web, resulting in a non-random complex network of 69 nodes and 252 links. Overconnected nodes corresponded to the most adapted variant positions in the population, suggesting a direct relation between network degree and position functional importance. Modular analysis revealed 25 k-cliques comprising 3 to 11 nodes. At different k-clique resolutions, one to four communities were formed, capturing epistatic associations of circulating variants (Alpha, Beta, B.1.1.318), but also Delta, which dominated the evolutionary landscape later in the pandemic. Cliques of aminoacidic positional associations tended to occur in single sequences, enabling the recognition of epistatic positions in real-world virus populations. Our findings provide a novel way of understanding epistatic relationships in viral proteins with potential applications in the design of virus control procedures. IMPORTANCE Paired positional associations of adapted amino acids in virus proteins may provide new insights for understanding virus evolution and variant formation. We investigated potential intramolecular relationships between variable SARS-CoV-2 spike positions by exact tests of independence in R x C contingency tables, having applied Average Product Correction (APC) to eliminate background noise. Associated positions (exact P /= 2) formed a non-random, epistatic network of 25 cliques and 1-4 communities at different clique resolutions, revealing evolutionary ties between variable positions of circulating variants and a predictive potential of previously unknown network positions. Cliques of different sizes represented theoretical combinations of changing residues in sequence space, allowing the identification of significant aminoacidic combinations in single sequences of real-world populations. Our analytic approach that links network structural aspects to mutational aminoacidic combinations in the spike sequence population offers a novel way to understand virus epidemiology and evolution.
PMID: 37432011
Food Res Int , IF:6.475 , 2023 Aug , V170 : P112950 doi: 10.1016/j.foodres.2023.112950
Aroma profiling of Shine Muscat grape provides detailed insights into the regulatory effect of gibberellic acid and N-(2-chloro-4-pyridinyl)-N-phenylurea applications on aroma quality.
Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, China.; Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.; Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, China. Electronic address: sdtalibo@163.com.; Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China. Electronic address: fruit@sjtu.edu.cn.
As plant growth regulators, gibberellic acid (GA(3)) and CPPU [forchlorfenuron, N-(2-chloro-4-pyridinyl)-N-phenylurea] are widely used in the production of table grapes. However, how these compounds regulate the aroma quality remains unclear. By measuring free and bound aroma compounds in Shine Muscat grapes from eight groups during whole growth period, GA(3) and CPPU were both found to significantly promote the synthesis of acyclic monoterpenes and (E)-2-hexenal, and double applications were found to further increase the aroma compound contents. On the other hand, GA(3) and CPPU obviously promoted the expansion of berries, and the effect of promoting the synthesis of aroma compounds was largely diminished. In conclusion, free compound concentrations in berry were almost unaffected by GA(3) and CPPU. From the perspective of aroma compounds, a highly concerted interplay was observed for terpenes, and bound compounds exhibited higher correlations than those of free compounds. In addition, 17 compounds could be used as markers that indicated the developmental timing of berries.
PMID: 37316003
Plant J , IF:6.417 , 2023 Sep , V115 (5) : P1408-1427 doi: 10.1111/tpj.16330
A very long chain fatty acid responsive transcription factor, MYB93, regulates lateral root development in Arabidopsis.
Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan.; Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 478-8501, Japan.; Department of Electrical and Electronic Engineering, Faculty of Science and Technology, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan.
Lateral roots (LRs) are critical to root system architecture development in plants. Although the molecular mechanisms by which auxin regulates LR development have been extensively studied, several additional regulatory systems are hypothesized to be involved. Recently, the regulatory role of very long chain fatty acids (VLCFAs) has been shown in LR development. Our analysis showed that LTPG1 and LTPG2, transporters of VLCFAs, are specifically expressed in the developing LR primordium (LRP), while the number of LRs is reduced in the ltpg1/ltpg2 double mutant. Moreover, late LRP development was hindered when the VLCFA levels were reduced by the VLCFA synthesis enzyme mutant, kcs1-5. However, the details of the regulatory mechanisms of LR development controlled by VLCFAs remain unknown. In this study, we propose a novel method to analyze the LRP development stages with high temporal resolution using a deep neural network and identify a VLCFA-responsive transcription factor, MYB93, via transcriptome analysis of kcs1-5. MYB93 showed a carbon chain length-specific expression response following treatment of VLCFAs. Furthermore, myb93 transcriptome analysis suggested that MYB93 regulated the expression of cell wall organization genes. In addition, we also found that LTPG1 and LTPG2 are involved in LR development through the formation of root cap cuticle, which is different from transcriptional regulation by VLCFAs. Our results suggest that VLCFA is a regulator of LRP development through transcription factor-mediated regulation of gene expression and the transportation of VLCFAs is also involved in LR development through root cap cuticle formation.
PMID: 37247130
Plant J , IF:6.417 , 2023 Aug , V115 (3) : P772-787 doi: 10.1111/tpj.16260
Gene expression and expression quantitative trait loci analyses uncover natural variations underlying the improvement of important agronomic traits during modern maize breeding.
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.; Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot, 010070, China.; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.; Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China.; HainanYazhou Bay Seed Lab, Sanya, 572025, China.; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
Maize (Zea mays L.) is a major staple crop worldwide, and during modern maize breeding, cultivars with increased tolerance to high-density planting and higher yield per plant have contributed significantly to the increased yield per unit land area. Systematically identifying key agronomic traits and their associated genomic changes during modern maize breeding remains a significant challenge because of the complexity of genetic regulation and the interactions of the various agronomic traits, with most of them being controlled by numerous small-effect quantitative trait loci (QTLs). Here, we performed phenotypic and gene expression analyses for a set of 137 elite inbred lines of maize from different breeding eras in China. We found four yield-related traits are significantly improved during modern maize breeding. Through gene-clustering analyses, we identified four groups of expressed genes with distinct trends of expression pattern change across the historical breeding eras. In combination with weighted gene co-expression network analysis, we identified several candidate genes regulating various plant architecture- and yield-related agronomic traits, such as ZmARF16, ZmARF34, ZmTCP40, ZmPIN7, ZmPYL10, ZmJMJ10, ZmARF1, ZmSWEET15b, ZmGLN6 and Zm00001d019150. Further, by combining expression quantitative trait loci (eQTLs) analyses, correlation coefficient analyses and population genetics, we identified a set of candidate genes that might have been under selection and contributed to the genetic improvement of various agronomic traits during modern maize breeding, including a number of known key regulators of plant architecture, flowering time and yield-related traits, such as ZmPIF3.3, ZAG1, ZFL2 and ZmBES1. Lastly, we validated the functional variations in GL15, ZmPHYB2 and ZmPYL10 that influence kernel row number, flowering time, plant height and ear height, respectively. Our results demonstrates the effectiveness of our combined approaches for uncovering key candidate regulatory genes and functional variation underlying the improvement of important agronomic traits during modern maize breeding, and provide a valuable genetic resource for the molecular breeding of maize cultivars with tolerance for high-density planting.
PMID: 37186341
Plant J , IF:6.417 , 2023 Aug , V115 (3) : P614-626 doi: 10.1111/tpj.16248
Co-expression network analysis of diverse wheat landraces reveals markers of early thermotolerance and a candidate master regulator of thermotolerance genes.
Department of Biology, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, YO10 5DD, UK.
Triticum aestivum L. (bread wheat) is a crop relied upon by billions of people around the world, as a major source of both income and calories. Rising global temperatures, however, pose a genuine threat to the livelihood of these people, as wheat growth and yields are extremely vulnerable to damage by heat stress. Here we present the YoGI wheat landrace panel, comprising 342 accessions that show remarkable phenotypic and genetic diversity thanks to their adaptation to different climates. We quantified the abundance of 110 790 transcripts from the panel and used these data to conduct weighted co-expression network analysis and to identify hub genes in modules associated with abiotic stress tolerance. We found that the expression of three hub genes, all heat-shock proteins (HSPs), were significantly correlated with early thermotolerance in a validation panel of landraces. These hub genes belong to the same module, with one (TraesCS4D01G207500.1) being a candidate master-regulator potentially controlling the expression of the other two hub genes, as well as a suite of other HSPs and heat-stress transcription factors (HSFs). In this work, therefore, we identify three validated hub genes, the expression of which can serve as markers of thermotolerance during early development, and suggest that TraesCS4D01G207500.1 is a potential master regulator of HSP and HSF expression - presenting the YoGI landrace panel as an invaluable tool for breeders wishing to determine and introduce novel alleles into modern varieties, for the production of climate-resilient crops.
PMID: 37077043
Plant J , IF:6.417 , 2023 Aug doi: 10.1111/tpj.16416
Organ-enriched gene expression during floral morphogenesis in wild barley.
Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.; Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan.; Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.; Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Jinan, 252100, China.
Floral morphology varies considerably between dicots and monocots. The ABCDE model explaining how floral organ development is controlled was formulated using core eudicots and applied to grass crops. Barley (Hordeum. vulgare) has unique floral morphogenesis. Wild barley (H. vulgare ssp. spontaneum), which is the immediate ancestor of cultivated barley (H. vulgare ssp. vulgare), contains a rich reservoir of genetic diversity. However, the wild barley genes involved in floral organ development are still relatively uncharacterized. In this study, we generated an organ-specific transcriptome atlas for wild barley floral organs. Genome-wide transcription profiles indicated that 22 838 protein-coding genes were expressed in at least one organ. These genes were grouped into seven clusters according to the similarities in their expression patterns. Moreover, 5619 genes exhibited organ-enriched expression, 677 of which were members of 47 transcription factor families. Gene ontology analyses suggested that the functions of the genes with organ-enriched expression influence the biological processes in floral organs. The co-expression regulatory network showed that the expression of 690 genes targeted by MADS-box proteins was highly positively correlated with the expression of ABCDE model genes during floral morphogenesis. Furthermore, the expression of 138 genes was specific to the wild barley OUH602 genome and not the Morex genome; most of these genes were highly expressed in the glume, awn, lemma, and palea. This study revealed the global gene expression patterns underlying floral morphogenesis in wild barley. On the basis of the study findings, a molecular mechanism controlling floral morphology in barley was proposed.
PMID: 37548103
Plant Physiol Biochem , IF:4.27 , 2023 Aug , V201 : P107920 doi: 10.1016/j.plaphy.2023.107920
Transcriptomic and genetic approaches reveal that the pipecolate biosynthesis pathway simultaneously regulates tomato fruit ripening and quality.
Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China; Department of Horticulture, Zhejiang University, Hangzhou, China.; Department of Horticulture, Zhejiang University, Hangzhou, China.; Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China; Department of Horticulture, Zhejiang University, Hangzhou, China. Electronic address: kaishi@zju.edu.cn.
Pipecolic acid (Pip) and N-hydroxypipecolic acid (NHP) have been found to accumulate during the ripening of multiple types of fruits; however, the function and mechanism of pipecolate pathway in fruits remain unclear. Here study was conducted on fruits produced by the model plant tomato, wherein the NHP biosynthesis-related genes, Slald1 and Slfmo1, were mutated. The results showed that the fruits of both the Slald1 and the Slfmo1 mutants exhibited a delayed onset of ripening, decreased fruit size, nutrition and flavor. Exogenous treatment with Pip and NHP promoted fruit ripening and improved fruit quality. Transcriptomic analysis combined with weighted gene co-expression network analysis revealed that the genes involved in the biosynthesis of amino acids, carbon metabolism, photosynthesis, starch and sucrose metabolism, flavonoid biosynthesis, and plant hormone signal transduction were affected by SlFMO1 gene mutation. Transcription factor prediction analysis revealed that the NAC and AP2/ERF-ERF family members are notably involved in the regulation pathway. Overall, our results suggest that the pipecolate biosynthesis pathway is involved in the simultaneous regulation of fruit ripening and quality and indicate that a regulatory mechanism at the transcriptional level exists. However, possible roles of endogenously synthesized Pip and NHP in these processes remain to be determined. The biosynthesis pathway genes SlALD1 and SlFMO1 may be potential breeding targets for promoting fruit ripening and improving fruit quality with concomitant yield increases.
PMID: 37527607
Plant Physiol Biochem , IF:4.27 , 2023 Aug , V201 : P107859 doi: 10.1016/j.plaphy.2023.107859
Natural variation in photosynthesis and water use efficiency of locally adapted Persian walnut populations under drought stress and recovery.
Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran. Electronic address: mm.arab@ut.ac.ir.; Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran. Electronic address: h_askari@sbu.ac.ir.; Photosynthesis Laboratory, Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran. Electronic address: aliniaeifard@ut.ac.ir.; Department of Agronomy, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran. Electronic address: mokhtassi@modares.ac.ir.; Department of Horticultural Sciences, Faculty of Agriculture, University of Vali-E-Asr, Rafsanjan, Iran. Electronic address: estaji1366@gmail.com.; Department of Horticulture, Faculty of Agriculture, University of Jiroft, Jiroft, Iran. Electronic address: m.hosseini@ujiroft.ac.ir.; Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran. Electronic address: sohrabi.s@lu.ac.ir.; Department of Plant Sciences, University of California, Davis, CA, 95616, USA. Electronic address: mbmesgaran@ucdavis.edu.; Department of Plant Sciences, University of California, Davis, CA, 95616, USA. Electronic address: caleslie@ucdavis.edu.; Department of Plant Sciences, University of California, Davis, CA, 95616, USA. Electronic address: pjbrown@ucdavis.edu.; Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran. Electronic address: kvahdati@ut.ac.ir.
Persian walnut is a drought-sensitive species with considerable genetic variation in the photosynthesis and water use efficiency of its populations, which is largely unexplored. Here, we aimed to elucidate changes in the efficiency of photosynthesis and water content using a diverse panel of 60 walnut families which were submitted to a progressive drought for 24 days, followed by two weeks of re-watering. Severe water-withholding reduced leaf relative water content (RWC) by 20%, net photosynthetic rate (P(n)) by 50%, stomatal conductance (g(s)) by 60%, intercellular CO(2) concentration (C(i)) by 30%, and transpiration rate (T(r)) by 50%, but improved water use efficiency (WUE) by 25%. Severe water-withholding also inhibited photosystem II functionality as indicated by reduced quantum yield of intersystem electron transport (phi(Eo)) and transfer of electrons per reaction center (ET(0)/RC), also enhanced accumulation of Q(A) (V(J)) resulted in the reduction of the photosynthetic performance (PI(ABS)) and maximal quantum yield of PSII (F(V)/F(M)); while elevated quantum yield of energy dissipation (phi(Do)), energy fluxes for absorption (ABS/RC) and dissipated energy flux (DI(0)/RC) in walnut families. Cluster analysis classified families into three main groups (tolerant, moderately tolerant, and sensitive), with the tolerant group from dry climates exhibiting lesser alterations in assessed parameters than the other groups. Multivariate analysis of phenotypic data demonstrated that RWC and biophysical parameters related to the chlorophyll fluorescence such as F(V)/F(M), phi(Eo), phi(Do), PI(ABS), ABS/RC, ET(0)/RC, and DI(0)/RC represent fast, robust and non-destructive biomarkers for walnut performance under drought stress. Finally, phenotype-environment association analysis showed significant correlation of some photosynthetic traits with geoclimatic factors, suggesting a key role of climate and geography in the adaptation of walnut to its habitat conditions.
PMID: 37406405
Plant Physiol Biochem , IF:4.27 , 2023 Aug , V201 : P107894 doi: 10.1016/j.plaphy.2023.107894
Molecular regulation of lipid metabolism in Suaeda salsa.
College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China; Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China.; College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.; Harbin Academy of Agricultural Science, Harbin, 150028, China.; Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China.; College of Food Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China. Electronic address: zhulei@byau.edu.cn.; College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China. Electronic address: xujingyu@byau.edu.cn.
Suaeda salsa is remarkable for its high oil content and abundant unsaturated fatty acids. In this study, the regulatory networks on fatty acid and lipid metabolism were constructed by combining the de novo transcriptome and lipidome data. Differentially expressed genes (DEGs) associated with lipids biosynthesis pathways were identified in the S. salsa transcriptome. DEGs involved in fatty acid and glycerolipids were generally up-regulated in leaf tissues. DEGs for TAG assembly were enriched in developing seeds, while DEGs in phospholipid metabolic pathways were enriched in root tissues. Polar lipids were extracted from S. salsa tissues and analyzed by lipidomics. The proportion of galactolipid MGDG was the highest in S. salsa leaves. The molar percentage of PG was high in the developing seeds, and the other main phospholipids had higher molar percentage in roots of S. salsa. The predominant C36:6 molecular species indicates that S. salsa is a typical 18:3 plant. The combined transcriptomic and lipidomic data revealed that different tissues of S. salsa were featured with DEGs associated with specific lipid metabolic pathways, therefore, represented unique lipid profiles. This study will be helpful on understanding lipid metabolism pathway and exploring the key genes involved in lipid synthesis in S. salsa.
PMID: 37482030
Plant Physiol Biochem , IF:4.27 , 2023 Aug , V201 : P107856 doi: 10.1016/j.plaphy.2023.107856
Integration of transcriptomic and metabolomic analysis unveils the response mechanism of sugar metabolism in Cyclocarya paliurus seedlings subjected to PEG-induced drought stress.
College of Forestry, Nanjing Forestry University, Nanjing, China.; College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.; College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China. Electronic address: fangsz@njfu.edu.cn.
Cyclocarya paliurus (Batal.) Iljinskaja is a multiple function tree species used for functional food and valued timber production. Carbohydrates, especially water-soluble carbohydrates, play an important role in osmotic protection, signal transduction and carbon storage. Under the circumstance of global climate change the abiotic stress would restrict the development of C. paliurus plantation, whereas there is few knowledge on the regulatory mechanisms of sugar metabolism under drought stress in C. paliurus. To investigate the drought response of C. paliurus at molecular level, we conducted an integrated analysis of transcriptomic and metabolomic of C. paliurus at three PEG-induced drought stress levels (0%: control; 15%: moderate drought; 25%: severe drought) in short term. Both moderate and severe drought treatments activated the chemical defense with lowering relative water content, and enhancing the contents of soluble protein, proline and malondialdehyde in the leaves. Meanwhile, alterations in the expression of differentially expressed genes and carbohydrate metabolism profiles were observed among the treatments. Weighted gene co-expression network analysis (WGCNA) showed 3 key modules, 8 structural genes (such as genes encoding beta-fructofuranosidase (INV), sucrose synthase (SUS), raffinose synthase (RS)) and 14 regulatory transcription factors were closely linked to sugar metabolism. Our results provided the foundation to understand the response mechanism of sugar metabolism in C. paliurus under drought stress, and would drive progress in breeding of drought-tolerant varieties and plantation development of the species.
PMID: 37354727
Environ Sci Pollut Res Int , IF:4.223 , 2023 Aug , V30 (37) : P86741-86761 doi: 10.1007/s11356-023-28663-x
Municipal solid waste compost: a comprehensive bibliometric data-driven review of 50 years of research and identification of future research themes.
Agronomy Section, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India.; Dairy Extension Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India.; Agronomy Section, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India. drdudi_rk@rediffmail.com.; Central Soil Salinity Research Institute, Karnal, Haryana, India.
This paper offers a thorough bibliometric review of the literature on municipal solid waste compost (MSWC), focusing on the past two decades. Using an extensive dataset of 827 documents, the research patterns are analyzed via the R-based Bibliometrix package, merging metadata from Web of Science and Scopus. The analysis reveals substantial global growth in MSWC research, with a particular surge in the last 20 years. Discipline-specific journals are the main publishers, while multidisciplinary environmental outlets gained more citations. The study identifies five major collaborative author clusters that dominate productivity and citation frequency. The thematic evolution over the past five decades shows a transition from waste disposal towards topics such as heavy metals, soil properties, and plant nutrition, with emerging themes like carbon sequestration, biochar, and microplastics signaling future research directions. Specifically, the field has experienced a 7.86% annual growth rate, with an average citation rate of 26.88 per article. The 827 publications emerged from 317 sources and 1910 authors, with an international co-authorship rate of 14.75%, reflecting the field's interdisciplinary character. Thirteen primary sources and twenty-two key authors were identified as major contributors. On the geographical front, Spain and Italy led with the most contributions and highest citation count, respectively. In terms of keywords, "heavy metals" and "sewage sludge" were the most recurrent, indicating the prevailing topics in MSWC research. This analysis hence provides key insights into the evolution and future trajectory of MSWC studies.
PMID: 37442933
G3 (Bethesda) , IF:3.154 , 2023 Aug doi: 10.1093/g3journal/jkad178
Cellular heterogeneity of the developing worker honey bee (Apis mellifera) pupa: a single cell transcriptomics analysis.
The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, UK, EH25 9RG.; Centre for Inflammation Research, University of Edinburgh, The Queen's Medical Research Institute, Edinburgh BioQuarter, Edinburgh, UK, EH16 4TJ.; Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK, EH4 2XU.; Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK, EH4 2XU.; Beebytes Analytics CIC, The Roslin Innovation Centre, The Charnock Bradley Building, University of Edinburgh, Easter Bush, Midlothian, UK, EH25 9RG.
It is estimated that animals pollinate 87.5% of flowering plants worldwide and that managed honey bees (Apis mellifera) account for 30-50% of this ecosystem service to agriculture. In addition to their important role as pollinators, honey bees are well-established insect models for studying learning and memory, behaviour, caste differentiation, epigenetic mechanisms, olfactory biology, sex determination and eusociality. Despite their importance to agriculture, knowledge of honey bee biology lags behind many other livestock species. In this study we have used scRNA-Seq to map cell types to different developmental stages of the worker honey bee (prepupa at day 11 and pupa at day 15), and sought to determine their gene expression signatures. To identify cell type populations, we examined the cell-to-cell network based on the similarity of the single-cells' transcriptomic profiles. Grouping similar cells together we identified 63 different cell clusters of which 17 clusters were identifiable at both stages. To determine genes associated with specific cell populations or with a particular biological process involved in honey bee development, we used gene co-expression analysis. We combined this analysis with literature mining, the honey bee protein atlas and Gene Ontology analysis to determine cell cluster identity. Of the cell clusters identified, 17 were related to the nervous system and sensory organs, 7 to the fat body, 19 to the cuticle, 5 to muscle, 4 to compound eye, 2 to midgut, 2 to hemocytes and 1 to malpighian tubule/pericardial nephrocyte. To our knowledge, this is the first whole single cell atlas of honey bees at any stage of development and demonstrates the potential for further work to investigate their biology at the cellular level.
PMID: 37548242
J Mol Evol , IF:2.395 , 2023 Aug , V91 (4) : P424-440 doi: 10.1007/s00239-023-10109-0
Phylogenetic and Evolutionary Analysis of Plant Small RNA 2'-O-Methyltransferase (HEN1) Protein Family.
Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, P.O. Box 74135-111, Jahrom, Islamic Republic of Iran. bheghrari@yahoo.com.; Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz, Islamic Republic of Iran.
HUA ENHANCER 1 (HEN1) is a pivotal mediator in protecting sRNAs from 3'-end uridylation and 3' to 5' exonuclease-mediated degradation in plants. Here, we investigated the pattern of the HEN1 protein family evolutionary history and possible relationships in the plant lineages using protein sequence analyses and conserved motifs composition, functional domain identification, architecture, and phylogenetic tree reconstruction and evolutionary history inference. According to our results, HEN1 protein sequences bear several highly conserved motifs in plant species retained during the evolution from their ancestor. However, several motifs are present only in Gymnosperms and Angiosperms. A similar trend showed for their domain architecture. At the same time, phylogenetic analysis revealed the grouping of the HEN1 proteins in the three main super clads. In addition, the Neighbor-net network analysis result provides some nodes have multiple parents indicating a few conflicting signals in the data, which is not the consequence of sampling error, the effect of the selected model, or the estimation method. By reconciling the protein and species tree, we considered the gene duplications in several given species and found 170 duplication events in the evolution of HEN1 in the plant lineages. According to our analysis, the main HEN1 superclass mostly showed orthologous sequences that illustrate the vertically transmitting of HEN1 to the main lines. However, in both orthologous and paralogs, we predicted insignificant structural deviations. Our analysis implies that small local structural changes that occur continuously during the folds can moderate the changes created in the sequence. According to our results, we proposed a hypothetical model and evolutionary trajectory for the HEN1 protein family in the plant kingdom.
PMID: 37191719