Plant Direct最新文献

{"title":"Metabolomics of related C3 and C4 Flaveria species indicate differences in the operation of photorespiration under fluctuating light.","authors":"Xinyu Fu, Urte Schlüter, Kaila Smith, Andreas P M Weber, Berkley J Walker","doi":"10.1002/pld3.70012","DOIUrl":"https://doi.org/10.1002/pld3.70012","url":null,"abstract":"<p><p>C₃ photosynthesis can be complemented with a C₄ carbon concentrating mechanism (CCM) to minimize photorespiratory losses. C₄ photosynthesis is often more efficient than C₃ under steady-state conditions. However, the C₄ CCM depends on inter-cellular metabolite concentration gradients, which must increase following increases in light intensity and could decrease rates of C₄ photosynthesis under fluctuating light. Additionally, incomplete flux through photorespiration could prove beneficial to C₄ assimilation during light induction of the CCM. Here, we compare metabolic profiles in the closely related C₃ <i>Flaveria robusta</i> and C₄ <i>Flaveria bidentis</i> during a light transient from low to high light to determine if these non-steady state accumulation patterns provide insight to the induction of the metabolite gradients needed to drive C4 intermediate transport and if there is incomplete cycling of photorespiratory intermediates. In these C₃ and C₄ species, metabolite steady-state pool sizes suggest that C₄ transport acids maintain concentration gradients across the bundle sheath and mesophyll cell types under these light fluctuations. However, there was incomplete flux through photorespiration in the C₄ <i>F. bidentis</i>, which could reduce photorespiratory CO₂ loss via glycine decarboxylation and help maintain higher rates of assimilation during following induction periods.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"8 10","pages":"e70012"},"PeriodicalIF":2.3,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11473189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142472889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection of damage caused by <i>Nezara viridula</i> on soybean using novel imaging approaches based on computed tomography and image color analysis.","authors":"Szilvia Gibicsár, Tamás Donkó, Dániel Fajtai, Sándor Keszthelyi","doi":"10.1002/pld3.70015","DOIUrl":"10.1002/pld3.70015","url":null,"abstract":"<p><p>Soybean (<i>Glycine max</i> L.) is an important leguminous plant, in which pests trigger significant damage every year. Important members of this community are insects with piercing-sucking mouthpart, especially the southern green stinkbug, <i>Nezara viridula</i> L.. This insect with its extraoral digestion causes visible alterations (morphological and color changes) in the seeds. We aimed to obtain precise information about the extent and nature of damage in soybeans caused by <i>N. viridula</i> using nondestructive imaging methods. Two infestation conditions were applied: one with controlled numbers of pests (six insects/15 pods) and another with naturally occurring pests (samples collected from the apical part of the plant and samples from whole plants). An intact control group was also included, resulting in four treatment groups. Seed samples were analyzed by computed tomography (CT) and image color analysis under laboratory conditions. According to our CT findings, the damage caused by <i>N. viridula</i> changed the radiodensity, volume, and shape (Solidity) of the soybean seeds during the pod-filling and maturing period. Radiodensity was significantly reduced in all three damaged categories compared to the intact sample; the mean radiodensity reduction range was 49-412 HU. The seed volume also decreased significantly (25%-80% decrease), with a threefold reduction for samples exposed to regulated damage compared to natural ones. The samples exposed to natural damage showed significant but minor reduction in solidity, while samples exposed to regulated damage showed a prominent decrease (~12%). Image color analysis showed that the damaged samples were well distinguishable, and the differences were statistically verifiable. The achieved data derived from our external and internal imaging approaches contribute to a better understanding of the internal chemical processes, and CT analysis helps to understand the alteration trends of the hidden structure of seeds caused by a pest. Our results can contribute to the development of a practically applicable system based on image analysis, which can identify lots damaged by insects.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"8 10","pages":"e70015"},"PeriodicalIF":2.3,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11464087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142392594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Systematic expression analysis of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 protein (CAP) superfamily in <i>Arabidopsis</i>.","authors":"Megumi Matsuzawa, Takumi Nakayama, Masa H Sato, Tomoko Hirano","doi":"10.1002/pld3.70003","DOIUrl":"10.1002/pld3.70003","url":null,"abstract":"<p><p>The Cysteine-rich secretory proteins (CRISPS), Antigen 5 (Ag5), and Pathogenesis-related 1 (PR-1) protein (CAP) superfamily members are found in multiple eukaryotic organisms, including yeasts, animals, and plants. Although one of the plant CAP family genes, <i>PR-1</i> is known to respond to pathogen infection in plants, the functions of other CAP family genes in <i>Arabidopsis</i> remain largely unknown. In this study, we conducted a comprehensive analysis of the similarities, loci, and expression patterns of 22 Arabidopsis CAP genes/proteins, providing a clue to elucidate their molecular functions. According to the promoter-β-glucuronidase (GUS) analysis, members of the <i>Arabidopsis</i> CAP family were expressed in various young tissues or organs, such as root and shoot meristems, reproductive tissues, and particularly at the lateral root initiation site before the formation of the lateral root primordium, with distinct expression specificity. In particular, <i>CAP51</i>, <i>CAP52</i>, and <i>CAP53</i> were specifically expressed in the cortical cells at the lateral root developing regions, suggesting that these genes may function in lateral root development. Thus, the expression patterns of Arabidopsis CAP family genes suggest that CAP family proteins may have certain function in the expressed organs or tissues in <i>Arabidopsis</i> plant.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"8 10","pages":"e70003"},"PeriodicalIF":2.3,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11464146/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dissecting the genetic architecture of sunflower disc diameter using genome-wide association study.","authors":"Yavuz Delen, Ravi V Mural, Semra Palali-Delen, Gen Xu, James C Schnable, Ismail Dweikat, Jinliang Yang","doi":"10.1002/pld3.70010","DOIUrl":"10.1002/pld3.70010","url":null,"abstract":"<p><p>Sunflower (<i>Helianthus annuus</i> L.) plays an essential role in meeting the demand for edible oil worldwide. The yield of sunflower seeds encompasses several component traits, including the disc diameter. Over three consecutive years, 2019, 2020, and 2022, we assessed phenotypic variation in disc diameter across a diverse set of sunflower accessions (N = 342) in replicated field trials. Upon aggregating the phenotypic data from multiple years, we estimated the broad sense heritability (<i>H</i> ²) of the disc diameter trait to be 0.88. A subset of N = 274 accessions was genotyped by using the tunable genotyping-by-sequencing (tGBS) method, resulting in 226,779 high-quality SNPs. Using these SNPs and the disc diameter phenotype, we conducted a genome-wide association study (GWAS) employing two statistical approaches: the mixed linear model (MLM) and the fixed and random model circulating probability unification (farmCPU). The MLM and farmCPU GWAS approaches identified 106 and 8 significant SNPs located close to 53 and 21 genes, respectively. The MLM analysis identified two significant peaks: a prominent signal on chromosome 10 and a relatively weaker signal on chromosome 16, both of which were also detected by farmCPU. The genetic loci associated with disc diameter, as well as the related candidate genes, present promising avenues for further functional validation and serve as a basis for sunflower oil yield improvement.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"8 10","pages":"e70010"},"PeriodicalIF":2.3,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11464090/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142392595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rating pome fruit quality traits using deep learning and image processing.","authors":"Nhan H Nguyen, Joseph Michaud, Rene Mogollon, Huiting Zhang, Heidi Hargarten, Rachel Leisso, Carolina A Torres, Loren Honaas, Stephen Ficklin","doi":"10.1002/pld3.70005","DOIUrl":"10.1002/pld3.70005","url":null,"abstract":"<p><p>Quality assessment of pome fruits (i.e. apples and pears) is used not only for determining the optimal harvest time but also for the progression of fruit-quality attributes during storage. Therefore, it is typical to repeatedly evaluate fruits during the course of a postharvest experiment. This evaluation often includes careful visual assessments of fruit for apparent defects and physiological symptoms. A general best practice for quality assessment is to rate fruit using the same individual rater or group of individual raters to reduce bias. However, such consistency across labs, facilities, and experiments is often not feasible or attainable. Moreover, while these visual assessments are critical empirical data, they are often coarse-grained and lack consistent objective criteria. Granny, is a tool designed for rating fruit using machine-learning and image-processing to address rater bias and improve resolution. Additionally, Granny supports backward compatibility by providing ratings compatible with long-established standards and references, promoting research program continuity. Current Granny ratings include starch content assessment, rating levels of peel defects, and peel color analyses. Integrative analyses enhanced by Granny's improved resolution and reduced bias, such as linking fruit outcomes to global scale -omics data, environmental changes, and other quantitative fruit quality metrics like soluble solids content and flesh firmness, will further enrich our understanding of fruit quality dynamics. Lastly, Granny is open-source and freely available.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"8 10","pages":"e70005"},"PeriodicalIF":2.3,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11461139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142392605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GABA promotes peroxisome proliferation in <i>Triticum monococcum</i> leaves.","authors":"Yunus Şahin, Taras Nazarov, Ercan Selçuk Ünlü, Andrei Smertenko, Nusret Zencrici","doi":"10.1002/pld3.70007","DOIUrl":"10.1002/pld3.70007","url":null,"abstract":"<p><p>Although peroxisomes are integral for both primary and secondary metabolism, how developmental changes affect activity of peroxisomes remains poorly understood. Here, we used published RNA-seq data to analyze the expression patterns of genes encoding 21 peroxisome metabolic pathways at successive developmental stages of <i>Zea mays</i> and <i>Oryza sativa</i>. Photorespiration was the most represented pathway in adult leaf relative to the juvenile stages. Components of reactive oxygen species (ROS)/reactive nitrogen species (RNS) metabolism, NADPH regeneration, and catabolism of polyamines were also enriched at later stages of leaf differentiation. The most commonly upregulated gene in differentiated leaves across all datasets of both species was <i>BETAINE ALANINE DEHYDROGENASE</i> (<i>BADH</i>). <i>BADH</i> functions in catabolism of polyamines where it converts 4-aminobutyraldehyde (ABAL) to 4-aminobutyrate (GABA). We tested the outcome of RNA-seq analysis by qRT-PCR in developing <i>Triticum monococcum</i> ssp. <i>monococcum</i> (Einkorn) seedlings. Consistent with the outcomes of RNA-seq analysis, transcription of <i>BADH</i> and <i>CATALASE3</i> (<i>CAT3</i>) were upregulated in older seedlings. CAT3 is an essential peroxisome biogenesis factor and a key enzyme of ROS homeostasis. Furthermore, exogenous application of GABA resulted in higher peroxisome abundance and transcriptional upregulation of <i>BADH</i> and a gene encoding another peroxisome biogenesis factor responsible for peroxisome fission, <i>PEROXIN11C</i> (<i>PEX11C</i>), in leaves. We propose that GABA contributes to regulation of peroxisome fission machinery during leaf differentiation.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"8 10","pages":"e70007"},"PeriodicalIF":2.3,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11452350/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142381507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Arabidopsis apoplast TET8 positively correlates to leaf senescence, and <i>tet3tet8</i> double mutants are delayed in leaf senescence.","authors":"Jayde A Zimmerman, Benjamin Verboonen, Andrew P Harrison Hanson, Luis R Arballo, Judy A Brusslan","doi":"10.1002/pld3.70006","DOIUrl":"10.1002/pld3.70006","url":null,"abstract":"<p><p>Extracellular vesicles (EVs) are membrane-bound exosomes secreted into the apoplast. Two distinct populations of EVs have been described in Arabidopsis: PEN1-associated and TET8-associated. We previously noted early leaf senescence in the <i>pen1</i> single and <i>pen1pen3</i> double mutant. Both PEN1 and PEN3 are abundant in EV proteomes suggesting that EVs might regulate leaf senescence in soil-grown plants. We observed that TET8 is more abundant in the apoplast of early senescing <i>pen1</i> and <i>pen1pen3</i> mutant rosettes and in older wild-type (WT) rosettes. The increase in apoplast TET8 in the <i>pen1</i> mutant did not correspond to increased <i>TET8</i> mRNA levels. In addition, apoplast TET8 was more abundant in the early leaf senescence <i>myb59</i> mutant, meaning the increase in apoplast TET8 protein during leaf senescence is not dependent on <i>pen1</i> or <i>pen3</i>. Genetic analysis showed a significant delay in leaf senescence in <i>tet3tet8</i> double mutants after 6 weeks of growth suggesting that these two tetraspanin paralogs operate additively and are positive regulators of leaf senescence. This is opposite of the effect of <i>pen1</i> and <i>pen1pen3</i> mutants that show early senescence and suggest PEN1 to be a negative regulator of leaf senescence. Our work provides initial support that apoplast-localized TET8 in combination with TET3 positively regulates age-related leaf senescence in soil-grown Arabidopsis plants.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"8 9","pages":"e70006"},"PeriodicalIF":2.3,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11422175/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142352546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering chemical diversity among five variants of <i>Abeliophyllum distichum</i> flowers through metabolomics analysis.","authors":"Yeong-Geun Lee, Jeong Eun Kwon, Won-Sil Choi, Nam-In Baek, Se Chan Kang","doi":"10.1002/pld3.616","DOIUrl":"https://doi.org/10.1002/pld3.616","url":null,"abstract":"<p><p><i>Abeliophyllum distichum</i> (Oleaceae), endemic to the Korean Peninsula and the sole member of its genus and species, possesses high scarcity value, escalating its importance under the Nagoya Protocol. Despite its significance, their metabolites and activities of <i>A. distichum</i> flowers remain unexplored. This study employs an integrated metabolomic approach utilizing NMR, LC/MS, GC/MS, and FTIR techniques to comprehensively analyze the metabolite profile of <i>A. distichum</i> flowers. By combining these methods, we identified 35 metabolites, 43 secondary metabolites, and 108 hydrophobic primary metabolites. Notably, distinct concentration patterns of these compounds were observed across five variants, classified based on morphological characteristics. Correlation analyses of primary and secondary metabolites unveiled varietal metabolic flux, providing insights into <i>A. distichum</i> flower metabolism. Additionally, the reconstruction of metabolic pathways based on dissimilarities in morphological traits elucidates variant-specific metabolic signatures. These findings not only enhance our understanding of chemical differences between varieties but also underscore the importance of considering varietal differences in future research and conservation efforts.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"8 9","pages":"e616"},"PeriodicalIF":2.3,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411454/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142293625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immunolocalization of hordein synthesis and transport in developing barley endosperm.","authors":"Gregory Tanner, Allison van de Meene, Anthony Bacic","doi":"10.1002/pld3.591","DOIUrl":"10.1002/pld3.591","url":null,"abstract":"<p><p>The spatial accumulation of hordeins in the developing endosperm of barley grains was examined by immunofluorescence microscopy (immunolight microscopy [iLM]) and immunoelectron microscopy (iEM) to establish the timing and subcellular pattern of hordein synthesis and deposition. The pattern seen for hordeins was compared to other abundant grain proteins, such as serpin Z4 and lipid transfer protein 1 (LTP1). Hordein accumulates throughout grain development, from 6 to 37 days post-anthesis (DPA). In contrast, serpin Z4 was present at 6 DPA, but the greatest synthesis and accumulation occurred during the middle of seed development, from 15 to 30 DPA. LTP1 accumulated later in seed development, from 15 to 30 DPA. Hordeins accumulated within the lumen of the endoplasmic reticulum (ER), were exocytosed from the ER membrane, and accumulated in protein bodies, which then fused either with the protein storage vacuoles or with other protein bodies, which also later fused with the protein storage vacuoles. iEM showed hordein, and LTP1 appeared not to traverse the Golgi apparatus (GA). Hordein, LTP1, and serpin Z4 colocalized to the same protein bodies and were co-transported to the protein storage vacuole in the same protein bodies. It is likely that this represents a general transport mechanism common to storage proteins in developing grains.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"8 9","pages":"e591"},"PeriodicalIF":2.3,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11377179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of light regimes on circadian gene co‐expression networks in Arabidopsis thaliana","authors":"Quentin Rivière, Virginie Raskin, Romário de Melo, Stéphanie Boutet, Massimiliano Corso, Matthieu Defrance, Alex A. R. Webb, Nathalie Verbruggen, Armand D. Anoman","doi":"10.1002/pld3.70001","DOIUrl":"https://doi.org/10.1002/pld3.70001","url":null,"abstract":"Light/dark (LD) cycles are responsible for oscillations in gene expression, which modulate several aspects of plant physiology. Those oscillations can persist under constant conditions due to regulation by the circadian oscillator. The response of the transcriptome to light regimes is dynamic and allows plants to adapt rapidly to changing environmental conditions. We compared the transcriptome of Arabidopsis under LD and constant light (LL) for 3 days and identified different gene co‐expression networks in the two light regimes. Our studies yielded unforeseen insights into circadian regulation. Intuitively, we anticipated that gene clusters regulated by the circadian oscillator would display oscillations under LD cycles. However, we found transcripts encoding components of the flavonoid metabolism pathway that were rhythmic in LL but not in LD. We also discovered that the expressions of many stress‐related genes were significantly increased during the dark period in LD relative to the subjective night in LL, whereas the expression of these genes in the light period was similar. The nocturnal pattern of these stress‐related gene expressions suggested a form of “skotoprotection.” The transcriptomics data were made available in a web application named <jats:italic>Cyclath</jats:italic>, which we believe will be a useful tool to contribute to a better understanding of the impact of light regimes on plants.","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"180 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142224049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}