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Regulatory mechanisms of the LBD40 transcription factor in Arabidopsis thaliana somatic embryogenesis 拟南芥体细胞胚胎发生中 LBD40 转录因子的调控机制
IF 3 3区 生物学
Plant Direct Pub Date : 2023-12-06 DOI: 10.1002/pld3.547
Sanjay Joshi, Kristine Hill, Manohar Chakrabarti, Sharyn E. Perry
{"title":"Regulatory mechanisms of the LBD40 transcription factor in Arabidopsis thaliana somatic embryogenesis","authors":"Sanjay Joshi, Kristine Hill, Manohar Chakrabarti, Sharyn E. Perry","doi":"10.1002/pld3.547","DOIUrl":"https://doi.org/10.1002/pld3.547","url":null,"abstract":"Somatic embryogenesis (SE) is a process by which an embryo is derived from somatic tissue. Transcription factors (TFs) have been identified that control this process. One such TF that promotes SE is AGAMOUS-like 15 (AGL15). Prior work has shown that AGL15 can both induce and repress gene expression. One way this type of dual function TF works is via protein interactions, so a yeast 2-hybrid (Y2H) screen was undertaken. One intriguing protein with which AGL15 interacted in Y2H was LBD40. LBD40 encodes a LATERAL ORGAN BOUNDARIES (LOB)-domain TF that is unique to plants and is primarily expressed during seed development. Here, we confirm the AGL15-LBD40 interaction by quantitative assays and <i>in planta</i> co-immunoprecipation. We also document a role for LBD40, and the closely related protein LBD41, in supporting SE. To determine downstream genes potentially controlled by LBD40, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) was used. More than 400 binding regions for LBD40 were consistently found genome-wide. To determine genes responsive to LBD40/41 accumulation, RNA-seq analysis of transcriptomes of wild-type control and loss-of-function <i>lbd40/lbd41</i> was performed. Combining these datasets provides insight into genes directly and indirectly controlled by these LOB domain TFs. The gene ontology (GO) enrichment analysis of these regulated genes showed an overrepresentation of biological processes that are associated with SE, further indicating the importance of LBD40 in SE. This work provides insight into SE, a poorly understood, but essential process to generate transgenic plants to meet agricultural demands or test gene function. This manuscript reports on experiments to understand the role that LDB40, a TF, plays in support of SE by investigating genes directly and indirectly controlled by LBD40 and examining physical and genetic interactions with other TFs active in SE. We uncover targets of LBD40 and an interacting TF of the MADS family and investigate targets involvement in SE.","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"32 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138580150","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}
引用次数: 0
Conserved cellular patterning in the mesophyll of rice leaves. 水稻叶片中叶的细胞模式保持不变。
IF 2.3 3区 生物学
Plant Direct Pub Date : 2023-12-04 eCollection Date: 2023-12-01 DOI: 10.1002/pld3.549
Jen Sloan, Saranrat Wang, Qi Yang Ngai, Yi Xiao, Jodie Armand, Matthew J Wilson, Xin-Guang Zhu, Andrew J Fleming
{"title":"Conserved cellular patterning in the mesophyll of rice leaves.","authors":"Jen Sloan, Saranrat Wang, Qi Yang Ngai, Yi Xiao, Jodie Armand, Matthew J Wilson, Xin-Guang Zhu, Andrew J Fleming","doi":"10.1002/pld3.549","DOIUrl":"10.1002/pld3.549","url":null,"abstract":"<p><p>The mesophyll cells of grass leaves, such as rice, are traditionally viewed as displaying a relatively uniform pattern, in contrast to the clear distinctions of palisade and spongy layers in typical eudicot leaves. This quantitative analysis of mesophyll cell size and shape in rice leaves reveals that there is an inherent pattern in which cells in the middle layer of the mesophyll are larger and less circular and have a distinct orientation of their long axis compared to mesophyll cells in other layers. Moreover, this pattern was observed in a range of rice cultivars and species. The significance of this pattern with relation to potential photosynthetic function and the implication of the widespread use of middle layer mesophyll cells as typical of the rice leaf have been investigated and discussed.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"7 12","pages":"e549"},"PeriodicalIF":2.3,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10695703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138488302","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}
引用次数: 0
Photosynthetically active radiation is required for seedling growth promotion by volcanic dacitic tuff breccia (Azomite). 火山英安质凝灰岩角砾岩(Azomite)促进幼苗生长需要光合有效辐射。
IF 2.3 3区 生物学
Plant Direct Pub Date : 2023-12-01 DOI: 10.1002/pld3.537
Kent F McCue, Elijah Mehlferber, Robert Reed, Alexis Ortiz, Jon Ferrel, Rajnish Khanna
{"title":"Photosynthetically active radiation is required for seedling growth promotion by volcanic dacitic tuff breccia (Azomite).","authors":"Kent F McCue, Elijah Mehlferber, Robert Reed, Alexis Ortiz, Jon Ferrel, Rajnish Khanna","doi":"10.1002/pld3.537","DOIUrl":"10.1002/pld3.537","url":null,"abstract":"<p><p>A plant's growth and development are shaped by its genome and the capacity to negotiate its environment for access to light, water, and nutrients. There is a vital need to understand the interactions between the plant, its physical environment, and the fertilizers used in agriculture. In this study, a commercially available volcanic ash fertilizer, Azomite®, characterized as dacitic (rhyolitic) tuff breccia, was tested for its effect on promoting early seedling vigor. Early growth and photomorphogenesis processes are well studied in Arabidopsis. Seedling assays under different light conditions were used to dissect the underlying mechanisms involved. These assays are well established and can be translated to agriculturally important crop plants. The volcanic ash fertilizer was tested at different concentrations on seedlings grown on basic media lacking sucrose either in continuous darkness (Dc), continuous Red (Rc), Far-Red (FRc), or White Light (WLc). Micronutrients in the volcanic ash significantly increased seedling growth under Rc and WLc, but not under Dc and FRc, indicating that photosynthetically active radiation was required for the observed growth increase. Furthermore, red-light photoreceptor mutant, <i>phyB-9</i>, lacked the growth response, and higher amount of fertilizer reduced growth in all conditions tested. These data suggest that light triggers the ability of the seedling to utilize micronutrients in volcanic ash in a dose-dependent manner. The methods described here can be used to establish mechanisms of activity of various nutrient inputs and, coupled with whole-genome expression profiling, can lead to better insights into optimizing nutrient field applications to improve crop production.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"7 12","pages":"e537"},"PeriodicalIF":2.3,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10690473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138478394","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}
引用次数: 0
Identification and preliminary characterization of conserved uncharacterized proteins from Chlamydomonas reinhardtii, Arabidopsis thaliana, and Setaria viridis. reinhardtii衣藻、拟南芥和蛇尾草中未鉴定的保守蛋白的鉴定和初步鉴定。
IF 3 3区 生物学
Plant Direct Pub Date : 2023-12-01 DOI: 10.1002/pld3.527
Eric P Knoshaug, Peipei Sun, Ambarish Nag, Huong Nguyen, Erin M Mattoon, Ningning Zhang, Jian Liu, Chen Chen, Jianlin Cheng, Ru Zhang, Peter St John, James Umen
{"title":"Identification and preliminary characterization of conserved uncharacterized proteins from <i>Chlamydomonas reinhardtii</i>, <i>Arabidopsis thaliana</i>, and <i>Setaria viridis</i>.","authors":"Eric P Knoshaug, Peipei Sun, Ambarish Nag, Huong Nguyen, Erin M Mattoon, Ningning Zhang, Jian Liu, Chen Chen, Jianlin Cheng, Ru Zhang, Peter St John, James Umen","doi":"10.1002/pld3.527","DOIUrl":"10.1002/pld3.527","url":null,"abstract":"<p><p>The rapid accumulation of sequenced plant genomes in the past decade has outpaced the still difficult problem of genome-wide protein-coding gene annotation. A substantial fraction of protein-coding genes in all plant genomes are poorly annotated or unannotated and remain functionally uncharacterized. We identified unannotated proteins in three model organisms representing distinct branches of the green lineage (Viridiplantae): <i>Arabidopsis thaliana</i> (eudicot), <i>Setaria viridis</i> (monocot), and <i>Chlamydomonas reinhardtii</i> (Chlorophyte alga). Using similarity searching, we identified a subset of unannotated proteins that were conserved between these species and defined them as Deep Green proteins. Bioinformatic, genomic, and structural predictions were performed to begin classifying Deep Green genes and proteins. Compared to whole proteomes for each species, the Deep Green set was enriched for proteins with predicted chloroplast targeting signals predictive of photosynthetic or plastid functions, a result that was consistent with enrichment for daylight phase diurnal expression patterning. Structural predictions using AlphaFold and comparisons to known structures showed that a significant proportion of Deep Green proteins may possess novel folds. Though only available for three organisms, the Deep Green genes and proteins provide a starting resource of high-value targets for further investigation of potentially new protein structures and functions conserved across the green lineage.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"7 12","pages":"e527"},"PeriodicalIF":3.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10690477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138478393","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}
引用次数: 0
Dissecting genomic regions and underlying sheath blight resistance traits in rice (Oryza sativa L.) using a genome-wide association study. 利用全基因组关联研究剖析水稻(Oryza sativa L.)的基因组区域和潜在的抗纹枯病性状。
IF 2.3 3区 生物学
Plant Direct Pub Date : 2023-11-23 eCollection Date: 2023-11-01 DOI: 10.1002/pld3.540
R Naveenkumar, Annamalai Anandan, Seenichamy Rathinam Prabhukarthikeyan, Anumalla Mahender, Ganesan Sangeetha, Shyam Saran Vaish, Pawan Kumar Singh, Waseem Hussain, Jauhar Ali
{"title":"Dissecting genomic regions and underlying sheath blight resistance traits in rice (<i>Oryza sativa</i> L.) using a genome-wide association study.","authors":"R Naveenkumar, Annamalai Anandan, Seenichamy Rathinam Prabhukarthikeyan, Anumalla Mahender, Ganesan Sangeetha, Shyam Saran Vaish, Pawan Kumar Singh, Waseem Hussain, Jauhar Ali","doi":"10.1002/pld3.540","DOIUrl":"10.1002/pld3.540","url":null,"abstract":"<p><p>The productivity of rice is greatly affected by the infection of the plant pathogenic fungus <i>Rhizoctonia solani</i>, which causes a significant grain yield reduction globally. There exist a limited number of rice accessions that are available to develop sheath blight resistance (ShB). Our objective was to identify a good source of the ShB resistance, understand the heritability, and trait interactions, and identify the genomic regions for ShB resistance traits by genome-wide association studies (GWAS). In the present study, a set of 330 traditional landraces and improved rice varieties were evaluated for ShB resistance and created a core panel of 192 accessions used in the GWAS. This panel provides a more considerable amount of genetic variance and found a significant phenotypic variation among the panel of rice accessions for all the agro-morphological and disease-resistance traits over the seasons. The infection rate of ShB and disease reaction were calculated as percent disease index (PDI) and area under the disease progress curve (AUDPC). The correlation analysis showed a significant positive association between PDIs and AUPDC and a negative association between PDI and plant height, flag leaf length, and grain yield. The panel was genotyped with 133 SSR microsatellite markers, resulting in a genome coverage of 314.83 Mb, and the average distance between markers is 2.53 Mb. By employing GLM and MLM (Q + K) models, 30 marker-trait associations (MTAs) were identified with targeted traits over the seasons. Among these QTLs, eight were found to be novel and located on 2, 4, 8, 10, and 12 chromosomes, which explained the phenotypic variation ranging from 5% to 15%. With the GWAS approach, six candidate genes were identified. Os05t0566400, Os08t0155900, and Os09t0567300 were found to be associated with defense mechanisms against ShB. These findings provided insights into the novel donors of IC283139, IC 277248, Sivappuchithirai Kar, and Bowalia. The promising genomic regions on 10 of 12 chromosomes associated with ShB would be useful in developing rice varieties with durable disease resistance.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"7 11","pages":"e540"},"PeriodicalIF":2.3,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10667636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138462123","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}
引用次数: 0
Interactions with microbial consortia have variable effects in organic carbon and production of exometabolites among genotypes of Populus trichocarpa. 不同基因型的毛杨与微生物群落的相互作用对有机碳和外代谢产物的产生有不同的影响。
IF 2.3 3区 生物学
Plant Direct Pub Date : 2023-11-21 eCollection Date: 2023-11-01 DOI: 10.1002/pld3.544
Alyssa A Carrell, Miranda Clark, Sara Jawdy, Wellington Muchero, Gladys Alexandre, Jesse L Labbé, Tomás A Rush
{"title":"Interactions with microbial consortia have variable effects in organic carbon and production of exometabolites among genotypes of <i>Populus trichocarpa</i>.","authors":"Alyssa A Carrell, Miranda Clark, Sara Jawdy, Wellington Muchero, Gladys Alexandre, Jesse L Labbé, Tomás A Rush","doi":"10.1002/pld3.544","DOIUrl":"10.1002/pld3.544","url":null,"abstract":"<p><p>Poplar is a short-rotation woody crop frequently studied for its significance as a sustainable bioenergy source. The successful establishment of a poplar plantation partially depends on its rhizosphere-a dynamic zone governed by complex interactions between plant roots and a plethora of commensal, mutualistic, symbiotic, or pathogenic microbes that shape plant fitness. In an exploratory endeavor, we investigated the effects of a consortium consisting of ectomycorrhizal fungi and a beneficial <i>Pseudomonas</i> sp. strain GM41 on plant growth (including height, stem girth, leaf, and root growth) and as well as growth rate over time, across four <i>Populus trichocarpa</i> genotypes. Additionally, we compared the level of total organic carbon and plant exometabolite profiles across different poplar genotypes in the presence of the microbial consortium. These data revealed no significant difference in plant growth parameters between the treatments and the control across four different poplar genotypes at 7 weeks post-inoculation. However, total organic carbon and exometabolite profiles were significantly different between the genotypes and the treatments. These findings suggest that this microbial consortium has the potential to trigger early signaling responses in poplar, influencing its metabolism in ways crucial for later developmental processes and stress tolerance.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"7 11","pages":"e544"},"PeriodicalIF":2.3,"publicationDate":"2023-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10660807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138462135","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}
引用次数: 0
Effect of ethylene pretreatment on tomato plant responses to salt, drought, and waterlogging stress. 乙烯预处理对番茄植株盐、旱、涝胁迫响应的影响
IF 2.3 3区 生物学
Plant Direct Pub Date : 2023-11-17 eCollection Date: 2023-11-01 DOI: 10.1002/pld3.548
Petar Mohorović, Batist Geldhof, Kristof Holsteens, Marilien Rinia, Johan Ceusters, Bram Van de Poel
{"title":"Effect of ethylene pretreatment on tomato plant responses to salt, drought, and waterlogging stress.","authors":"Petar Mohorović, Batist Geldhof, Kristof Holsteens, Marilien Rinia, Johan Ceusters, Bram Van de Poel","doi":"10.1002/pld3.548","DOIUrl":"10.1002/pld3.548","url":null,"abstract":"<p><p>Salinity, drought, and waterlogging are common environmental stresses that negatively impact plant growth, development, and productivity. One of the responses to abiotic stresses is the production of the phytohormone ethylene, which induces different coping mechanisms that help plants resist or tolerate stress. In this study, we investigated if an ethylene pretreatment can aid plants in activating stress-coping responses prior to the onset of salt, drought, and waterlogging stress. Therefore, we measured real-time transpiration and CO<sub>2</sub> assimilation rates and the impact on biomass during and after 3 days of abiotic stress. Our results showed that an ethylene pretreatment of 1 ppm for 4 h did not significantly influence the negative effects of waterlogging stress, while plants were more sensitive to salt stress as reflected by enhanced water losses due to a higher transpiration rate. However, when exposed to drought stress, an ethylene pretreatment resulted in reduced transpiration rates, reducing water loss during drought stress. Overall, our findings indicate that pretreating tomato plants with ethylene can potentially regulate their responses during the forthcoming stress period, but optimization of the ethylene pre-treatment duration, timing, and dose is needed. Furthermore, it remains tested if the effect is related to the stress duration and severity and whether an ethylene pretreatment has a net positive or negative effect on plant vigor during stress recovery. Further investigations are needed to elucidate the mode of action of how ethylene priming impacts subsequent stress responses.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"7 11","pages":"e548"},"PeriodicalIF":2.3,"publicationDate":"2023-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10654692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138462133","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}
引用次数: 0
Functional analysis of Salix purpurea genes support roles for ARR17 and GATA15 as master regulators of sex determination. 杨柳性别决定主要调控因子ARR17和GATA15的功能分析。
IF 2.3 3区 生物学
Plant Direct Pub Date : 2023-11-15 eCollection Date: 2023-11-01 DOI: 10.1002/pld3.546
Brennan Hyden, Dana L Carper, Paul E Abraham, Guoliang Yuan, Tao Yao, Leo Baumgart, Yu Zhang, Cindy Chen, Ronan O'Malley, Jin-Gui Chen, Xiaohan Yang, Robert L Hettich, Gerald A Tuskan, Lawrence B Smart
{"title":"Functional analysis of <i>Salix purpurea</i> genes support roles for <i>ARR17</i> and <i>GATA15</i> as master regulators of sex determination.","authors":"Brennan Hyden, Dana L Carper, Paul E Abraham, Guoliang Yuan, Tao Yao, Leo Baumgart, Yu Zhang, Cindy Chen, Ronan O'Malley, Jin-Gui Chen, Xiaohan Yang, Robert L Hettich, Gerald A Tuskan, Lawrence B Smart","doi":"10.1002/pld3.546","DOIUrl":"10.1002/pld3.546","url":null,"abstract":"<p><p>The Salicaceae family is of growing interest in the study of dioecy in plants because the sex determination region (SDR) has been shown to be highly dynamic, with differing locations and heterogametic systems between species. Without the ability to transform and regenerate <i>Salix</i> in tissue culture, previous studies investigating the mechanisms regulating sex in the genus <i>Salix</i> have been limited to genome resequencing and differential gene expression, which are mostly descriptive in nature, and functional validation of candidate sex determination genes has not yet been conducted. Here, we used Arabidopsis to functionally characterize a suite of previously identified candidate genes involved in sex determination and sex dimorphism in the bioenergy shrub willow <i>Salix purpurea</i>. Six candidate master regulator genes for sex determination were heterologously expressed in Arabidopsis, followed by floral proteome analysis. In addition, 11 transcription factors with predicted roles in mediating sex dimorphism downstream of the SDR were tested using DAP-Seq in both male and female <i>S. purpurea</i> DNA. The results of this study provide further evidence to support models for the roles of <i>ARR17</i> and <i>GATA15</i> as master regulator genes of sex determination in <i>S. purpurea</i>, contributing to a regulatory system that is notably different from that of its sister genus <i>Populus</i>. Evidence was also obtained for the roles of two transcription factors, an <i>AP2</i>/<i>ERF</i> family gene and a homeodomain-like transcription factor, in downstream regulation of sex dimorphism.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"7 11","pages":"e3546"},"PeriodicalIF":2.3,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10651977/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138462134","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}
引用次数: 0
Genome-wide identification and expression analysis of Na+/H+antiporter (NHX) genes in tomato under salt stress. 盐胁迫下番茄Na+/H+反转运蛋白(NHX)基因的全基因组鉴定及表达分析
IF 2.3 3区 生物学
Plant Direct Pub Date : 2023-11-13 eCollection Date: 2023-11-01 DOI: 10.1002/pld3.543
Erman Cavusoglu, Ugur Sari, Iskender Tiryaki
{"title":"Genome-wide identification and expression analysis of <i>Na</i><sup>+</sup>/<i>H</i><sup>+</sup><i>antiporter</i> (<i>NHX</i>) genes in tomato under salt stress.","authors":"Erman Cavusoglu, Ugur Sari, Iskender Tiryaki","doi":"10.1002/pld3.543","DOIUrl":"10.1002/pld3.543","url":null,"abstract":"<p><p>Plant <i>Na</i> <sup>+</sup>/<i>H</i> <sup>+</sup> <i>antiporter</i> (<i>NHX</i>) genes enhance salt tolerance by preventing excessive Na<sup>+</sup> accumulation in the cytosol through partitioning of Na<sup>+</sup> ions into vacuoles or extracellular transport across the plasma membrane. However, there is limited detailed information regarding the salt stress responsive <i>SlNHX</i>s in the most recent tomato genome. We investigated the role of this gene family's expression patterns in the open flower tissues under salt shock in <i>Solanum lycopersicum</i> using a genome-wide approach. A total of seven putative <i>SlNHX</i> genes located on chromosomes 1, 4, 6, and 10 were identified, but no ortholog of the <i>NHX5</i> gene was identified in the tomato genome. Phylogenetic analysis revealed that these genes are divided into three different groups. SlNHX proteins with 10-12 transmembrane domains were hypothetically localized in vacuoles or cell membranes. Promoter analysis revealed that <i>SlNHX6</i> and <i>SlNHX8</i> are involved with the stress-related MeJA hormone in response to salt stress signaling. The structural motif analysis of SlNHX1, -2, -3, -4, and -6 proteins showed that they have highly conserved amiloride binding sites. The protein-protein network revealed that SlNHX7 and SlNHX8 interact physically with Salt Overly Sensitive (SOS) pathway proteins. Transcriptome analysis demonstrated that the <i>SlNHX2</i> and <i>SlNHX6</i> genes were substantially expressed in the open flower tissues. Moreover, quantitative PCR analysis indicated that all <i>SlNHX</i> genes, particularly <i>SlNHX6</i> and <i>SlNHX8</i>, are significantly upregulated by salt shock in the open flower tissues. Our results provide an updated framework for future genetic research and development of breeding strategies against salt stress in the tomato.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"7 11","pages":"e543"},"PeriodicalIF":2.3,"publicationDate":"2023-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10641485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"107592073","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}
引用次数: 0
Metabolomic, photoprotective, and photosynthetic acclimatory responses to post-flowering drought in sorghum. 高粱花后干旱对代谢组学、光保护和光合适应的响应。
IF 2.3 3区 生物学
Plant Direct Pub Date : 2023-11-13 eCollection Date: 2023-11-01 DOI: 10.1002/pld3.545
Christopher R Baker, Dhruv Patel-Tupper, Benjamin J Cole, Lindsey G Ching, Oliver Dautermann, Armen C Kelikian, Cayci Allison, Julie Pedraza, Julie Sievert, Aivett Bilbao, Joon-Yong Lee, Young-Mo Kim, Jennifer E Kyle, Kent J Bloodsworth, Vanessa Paurus, Kim K Hixson, Robert Hutmacher, Jeffery Dahlberg, Peggy G Lemaux, Krishna K Niyogi
{"title":"Metabolomic, photoprotective, and photosynthetic acclimatory responses to post-flowering drought in sorghum.","authors":"Christopher R Baker, Dhruv Patel-Tupper, Benjamin J Cole, Lindsey G Ching, Oliver Dautermann, Armen C Kelikian, Cayci Allison, Julie Pedraza, Julie Sievert, Aivett Bilbao, Joon-Yong Lee, Young-Mo Kim, Jennifer E Kyle, Kent J Bloodsworth, Vanessa Paurus, Kim K Hixson, Robert Hutmacher, Jeffery Dahlberg, Peggy G Lemaux, Krishna K Niyogi","doi":"10.1002/pld3.545","DOIUrl":"10.1002/pld3.545","url":null,"abstract":"<p><p>Climate change is globally affecting rainfall patterns, necessitating the improvement of drought tolerance in crops. <i>Sorghum bicolor</i> is a relatively drought-tolerant cereal. Functional stay-green sorghum genotypes can maintain green leaf area and efficient grain filling during terminal post-flowering water deprivation, a period of ~10 weeks. To obtain molecular insights into these characteristics, two drought-tolerant genotypes, BTx642 and RTx430, were grown in replicated control and terminal post-flowering drought field plots in California's Central Valley. Photosynthetic, photoprotective, and water dynamics traits were quantified and correlated with metabolomic data collected from leaves, stems, and roots at multiple timepoints during control and drought conditions. Physiological and metabolomic data were then compared to longitudinal RNA sequencing data collected from these two genotypes. The unique metabolic and transcriptomic response to post-flowering drought in sorghum supports a role for the metabolite galactinol in controlling photosynthetic activity through regulating stomatal closure in post-flowering drought. Additionally, in the functional stay-green genotype BTx642, photoprotective responses were specifically induced in post-flowering drought, supporting a role for photoprotection in the molecular response associated with the functional stay-green trait. From these insights, new pathways are identified that can be targeted to maximize yields under growth conditions with limited water.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":"7 11","pages":"e545"},"PeriodicalIF":2.3,"publicationDate":"2023-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10641490/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"107592074","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}
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