Plant Biotechnology Reports最新文献

{"title":"Exploring secondary structures within the nuclear ribosomal DNA internal transcribed spacers (nr DNA ITS) for enhanced phylogenetic insights in Medicago sativa (alfalfa)","authors":"M. Alp Furan, Gulistan Genli, Mehtap Yıldız, Hyeon-Jin Sun","doi":"10.1007/s11816-024-00915-3","DOIUrl":"https://doi.org/10.1007/s11816-024-00915-3","url":null,"abstract":"<p>ITS sections, which are situated inside the ribosomal DNA operon, are recognized for their high levels of diversity and slow rate of evolution, which makes them important for plant phylogenetic studies. The objective of this work is to use the internal transcribed spacer (ITS) regions of 18 alfalfa (<i>Medicago sativa</i>) genotypes/varieties to determine their genetic relationships and to verify possible genetic markers for variety identification and classification. This has been done by validating the secondary structures of the ITS regions and observing the effects of the relationships among the lowest energy state, the total number of possible secondary structure hairpins, and (GC) content. The results indicated that the length of the ITS sequences varied between 426 and 629 nucleotides and that the G + C content of the ITS region varied between 46.6 and 50%. In this study, the analysis of molecular variance (AMOVA) was used to validate the effectiveness of configuration analysis and revealed that fluctuations in the data accounted for a substantial amount of the observed total variance. Moreover, 94 percent of the genotypes analyzed exhibited a significant degree of variety. This shows that a large fraction of the observed variation is likely attributable to genetic variables. Population four, comprising Bilensoy80, Emily, Quin, Vendor, and Felicia, had the highest degree of heterozygosity at 68.8%, whereas population two, including Gozlu1, Prosementi, Nimet and Local (Van), had the lowest level at 37.5%. The original Shannon’s approach as an unbiased estimator employed in population genetics research validated the differences among alfalfa genotypes with the AMOVA analysis results of this study. Individual differences were found to be 59%, whereas population differences were found to be 41%. There have been a few ITS studies on <i>Medicago sativa</i> that have utilized ITS as a phylogenetic marker to estimate connections and define new taxonomic categories (e.g., tribes). However, our research also includes an analysis of the secondary structure of these sequences and the results of this study imply that ITS sequence and secondary structure data can be utilized to understand the intraspecific genetic makeup of different alfalfa varieties.</p>","PeriodicalId":20216,"journal":{"name":"Plant Biotechnology Reports","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141614676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sorghum-encoded microRNAs: current status and future prospects","authors":"Rekha Yadav, Chandra Pal Singh","doi":"10.1007/s11816-024-00914-4","DOIUrl":"https://doi.org/10.1007/s11816-024-00914-4","url":null,"abstract":"<p>Sorghum (<i>Sorghum bicolor</i> (L.) Moench) is an annual or short-term perennial plant belonging to the economically important family Poaceae. Sorghum, a C4 crop, has multiple uses like food, fodder, forage, and also as a biofuel feedstock. With an ability to thrive under harsh environmental conditions and adaptability to diverse climates and soils, sorghum has a long history of cultivation in the semi-arid tropics of Africa, Asia, and Latin America. Gene regulation plays an important role in adaptability to adverse environmental conditions. MicroRNAs (miRNAs) are one of the classes of small non-coding RNAs that have emerged as a key regulators of gene expression. These small RNAs are profoundly present in all higher eukaryotes including plants. These are involved in regulating the intrinsic normal growth of cells and the development of organisms as well as in maintaining the integrity of genomes. In plants, miRNAs have been functionally implicated in abiotic stress tolerance, flower development, root development, grain size determination, yield, and immune responses. Several miRNAs have been reported in sorghum, and the potential functions of some miRNAs have been characterized. Here, in this review, an overview of sorghum-encoded miRNAs is provided. The potential known and putative functions of these miRNAs are critically discussed. In addition, the possible methods for employing miRNAs as a tool for sorghum improvement are also suggested. The present review will help us to understand the miRNA functions in sorghum and underlying regulatory gene networks which have applications to design effective methods to achieve desired traits.</p>","PeriodicalId":20216,"journal":{"name":"Plant Biotechnology Reports","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141610921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and expression analysis of the SOD gene family under biotic and abiotic stresses in sweet orange","authors":"Xulin Li, Ke Wen, Tuo Yin, Chaoying Chen, Ling Zhu, Xiuyao Yang, Yinqiang Zi, Ke Zhao, Jiaming Zhang, Hanyao Zhang","doi":"10.1007/s11816-024-00913-5","DOIUrl":"https://doi.org/10.1007/s11816-024-00913-5","url":null,"abstract":"<p>Superoxide dismutase (SOD) protects plants from biotic and abiotic stress-induced reactive oxygen species toxicity and is extensively involved in plant growth and development. As the most widely cultivated and productive citrus fruit in the world, sweet oranges are susceptible to biotic and abiotic stresses during growth, affecting their yield and quality. However, the <i>SOD</i> gene family has not been identified in sweet oranges. Therefore, in this study, the sweet orange <i>SOD</i> gene family was systematically identified using bioinformatics methods, and a total of 15 sweet orange <i>SOD</i> (<i>CsSOD</i>) genes were identified and categorized into three subfamilies, Cu/Zn–SOD, Fe–SOD, and Mn–SOD, based on the results of the phylogenetic tree. Further analysis of gene structure and conserved motifs revealed that the motifs and exon and intron structures of <i>CsSOD</i> genes in the same subfamily were relatively identical, with only minor differences. In addition, we predicted hormone-related, light-response-related, and defense-related cis-acting elements in the promoters 2 kb upstream of the <i>CsSOD</i> genes. Transcriptome data analysis revealed that <i>SOD</i> genes were expressed under both abiotic and abiotic stresses, and the expression levels of some of the genes varied significantly. This study provides a basis for further understanding the biologic properties and functions of the <i>SOD</i> gene family in sweet oranges and provides a vital foundation for the study of sweet oranges under biotic and abiotic stresses.</p>","PeriodicalId":20216,"journal":{"name":"Plant Biotechnology Reports","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141574154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exogenous methyl jasmonate mediates tolerance of heat stress in Korean fir (Abies koreana)","authors":"Da Young Lee, Da Young Park, Hyeong Cheol Park","doi":"10.1007/s11816-024-00912-6","DOIUrl":"https://doi.org/10.1007/s11816-024-00912-6","url":null,"abstract":"<p>Heat stress is a major environmental stress that affects the growth and development of plants. Korean fir (<i>Abies koreana</i>), a rare species endemic to South Korea, is sensitive to global climate change. The effect of exogenous methyl jasmonate (MeJA) on heat stress tolerance was, therefore, investigated in this species. During heat stress, the expression levels of eight genes (<i>AkNAC19, AkMPK6, AkERF4, AkEFP, AkNAC2, AkbHLH, AkHSP17.6</i>, and <i>AkMYB123</i>) were assessed in needles of <i>A. koreana</i> following treatment with 0, 0.1, 1.0, or 2.0 mM MeJA. Optimal upregulation of expression of most genes was observed 24 h post-treatment with 2.0 mM MeJA. Similar results were obtained when gene expression was analyzed 1, 2, 4, and 8 days post-treatment with 2.0 mM MeJA. Under heat stress conditions, plants treated with 2.0 mM MeJA initially showed a rapid decline in electrolyte leakage and higher chlorophyll content after 28 days of heat stress; however, opposite trends were observed in untreated plants, indicating that MeJA mediated tolerance to heat stress. Higher levels of expression of <i>AkERF4, AkNAC2</i>, and <i>AkHSP17.6</i> were observed in MeJA-treated needles than in untreated needles, indicating these genes were strongly associated with MeJA-mediated heat tolerance. Therefore, these results suggest that the ability of Korean fir to tolerate abiotic stress is associated with endogenous MeJA synthesis or signaling, and identifies <i>AkERF4</i>, <i>AkNAC2</i>, and <i>AkHSP17.6</i> as potential candidates for genes involved in the stress-tolerance mechanism.</p>","PeriodicalId":20216,"journal":{"name":"Plant Biotechnology Reports","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141509101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Green biotherapeutics: overcoming challenges in plant-based expression platforms","authors":"Rishabh Rajkumar Jadhav, Deepa Khare","doi":"10.1007/s11816-024-00910-8","DOIUrl":"https://doi.org/10.1007/s11816-024-00910-8","url":null,"abstract":"<p>Plant-based expression platforms offer a promising avenue to produce biotherapeutics due to their scalability, cost-effectiveness, and potential for complex protein expression. However, the widespread adoption of these platforms faces significant challenges. This review provides an overview of the current landscape of plant-based expression systems, highlighting their advantages and limitations. Regulatory hurdles, concerns about product purity and consistency, technical limitations, and economic considerations are discussed as major obstacles to the utilization of plant-based platforms. Strategies for overcoming these challenges, including advancements in genetic engineering, optimization of protein expression, post-translational modification and quality, and implementation of stringent quality control measures, are explored. Case studies and success stories illustrate the feasibility and potential of plant-based expression platforms for commercial production. Future perspectives and opportunities for collaboration between academia, industry, and regulatory agencies are also discussed. Ultimately, this review aims to provide insights into the potential of plant-based expression platforms and the path forward to harness their full potential in the production of green biotherapeutics.</p>","PeriodicalId":20216,"journal":{"name":"Plant Biotechnology Reports","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141509102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment of elite pepper breeding lines using molecular markers","authors":"E. Ekbiç, Ceylan Özlem Okay","doi":"10.1007/s11816-024-00911-7","DOIUrl":"https://doi.org/10.1007/s11816-024-00911-7","url":null,"abstract":"","PeriodicalId":20216,"journal":{"name":"Plant Biotechnology Reports","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141356743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating photosynthetic evolution and the feasibility of inducing C4 syndrome in C3 plants","authors":"Nidhi S. Mukundan, Kapaettu Satyamoorthy, Vidhu Sankar Babu","doi":"10.1007/s11816-024-00908-2","DOIUrl":"https://doi.org/10.1007/s11816-024-00908-2","url":null,"abstract":"","PeriodicalId":20216,"journal":{"name":"Plant Biotechnology Reports","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141386163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nitric oxide mediated growth enhancement of tomato under salinity stress","authors":"Watheq Natiq Jumaah, Rizwana Begum Syed Nabi, Nkulu Kabange Rolly, Teferi Alem Adamu, Rupesh Tayade, Nay Chi Aye, Adil Hussain, Byung-Wook Yun","doi":"10.1007/s11816-024-00909-1","DOIUrl":"https://doi.org/10.1007/s11816-024-00909-1","url":null,"abstract":"<p>Salinity is a major problem for agricultural production throughout the world significantly limiting crop production. Here, we evaluated the effect of different concentrations of nitric oxide (NO) growth and development of five different tomato cultivars under salt stress induced by different concentrations of sodium chloride (NaCl). Results showed that germination was significantly reduced by the salt-stress treatments in a dose-dependent manner, where germination was significantly reduced by 75 mM NaCl but completely suppressed by 100 mM NaCl. Pre-treatment of seeds with 0.001 mM sodium nitroprusside (SNP) as a NO donor for 8 h not only accelerated the germination rate but also significantly improved the growth of seedlings under salt stress induced by 50 mM NaCl as compared to the salt-stressed plants not treated with SNP. Real-time PCR analysis showed that SNP treatment decreased the expression of antioxidant gene <i>SlGRX1</i> after 6 and 12 h of the treatment but increased after 24 and 48 h. On the other hand, the expression of <i>SlAPX1</i> was reduced at all time points, indicating a reactive oxygen species (ROS)-scavenging effect of the SNP treatment via <i>GRX1</i> transcript accumulation. This suggests that NO plays a vital role in seed germination and early plant development. It is, therefore, concluded that exogenous NO treatment of tomato seeds can improve seed germination and plant growth under saline conditions.</p>","PeriodicalId":20216,"journal":{"name":"Plant Biotechnology Reports","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141253485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioactivity assessment of high potency arachidin mixture from large-scale peanut hairy root culture medium","authors":"Phadtraphorn Chayjarung, Kanjana Wongkrajang, Chanyanut Pankaew, Chonnikan Tothong, Wannakan Poonsap, Pakwuan Wongshaya, Siriwat Kucharoenphaibul, Anupan Kongbangkerd, Apinun Limmongkon","doi":"10.1007/s11816-024-00907-3","DOIUrl":"https://doi.org/10.1007/s11816-024-00907-3","url":null,"abstract":"<p>Peanut hairy root culture serves as a potent tool for producing valuable prenylated stilbenoids. A significant amount of chitosan (CHT), methyl jasmonate (MeJA), and methyl-β-cyclodextrin (CD) was used to elicit hairy roots in a bioreactor, which were later subjected to freeze-drying and extracted with acetone. The group Gr.4, obtained from the first-column chromatography and consisting of partially purified mixed arachidin, exhibited the highest antioxidant activity, measuring 3,067.53 ± 176.98 µmole Trolox/g crude extract. Moreover, when examining the antimicrobial activity, the partially purified Gr.4 showed the lowest minimum inhibition concentration (MIC) values against <i>Staphylococcus aureus, Salmonella</i> Typhimurium, <i>Escherichia coli</i>, and <i>Candida albicans</i>, with values of 31, 63, 125, and 78 µg/ml, respectively. Furthermore, the DNA nicking assay using the Fenton reaction demonstrated the DNA damage effect when plasmid DNA was exposed to concentrations of 25–100 µg/ml of partially purified Gr.4. Additionally, the scanning electron microscopy (SEM) results revealed irregularities and abnormalities in all tested microbial cells after treatment with 2xMIC of partially purified Gr.4. The enhanced activity exhibited by mixed arachidin compounds compared to the crude extract indicates a high potency of mixed arachidin. Moreover, the simplicity of isolation and purification suggests that the mixed arachidin compounds could be a preferable alternative for further applications as effective compounds rather than using them in individually purified forms.</p>","PeriodicalId":20216,"journal":{"name":"Plant Biotechnology Reports","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141190636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular identification and characterization of iris yellow spot virus (IYSV) and garlic virus X (GVX) infecting Allium species","authors":"Muhammad Usman Shahid, Abid Riaz, Tahira Shafique, Mayasar I. Al-zaban, Diaa Abd El-Moneim, Sheikh Mansoor, Yong Suk Hung, Hyeon-Jin Sun","doi":"10.1007/s11816-024-00905-5","DOIUrl":"https://doi.org/10.1007/s11816-024-00905-5","url":null,"abstract":"<p><i>Allium</i> species, such as Onion (<i>Allium cepa</i> L.) and garlic (<i>Allium sativum</i> L.), have been cultivated worldwide for centuries due to its enormous medicinal uses as well as for cooking practices. A large number of RNA viruses have been known to cause significant yield losses and also adversely affect the quality of <i>Allium</i> species. Among them, iris yellow spot virus (IYSV) and associated garlic virus X (GVX) from tospovirus family cause huge number of yield losses in onion and garlic crop. The disease due to IYSV and GVX was recorded in different locations on the basis of their characteristic symptoms. Experiments revealed that IYSV has the ability to transmit mechanically in a very efficient manner while the dispersal of GVX was only limited through its vector as compared to mechanical transmission. The disease incidence of IYSV on onion was reported about 80% while 2% of GVX was reported on garlic by mechanical transmission. Result revealed that IYSV is more viruliferous and has the ability to transmit more efficiently on onion as compared to GVX on garlic. PCR amplified IYSV samples of approximately 800 base pairs (bps) product using specific primer targeting coat protein (Cp) region, whereas no amplicon was detected for GVX infected samples. Phylogenetic analyses of 2 isolates RP13PK and RP27PK have shown 99.3% homogeneity with isolate DQ233469 as compared to remaining isolates. Therefore, the findings indicate that IYSV is a highly variable virus, undergoing rapid evolution in the region, necessitating vigilant monitoring and effective management. The outcomes imply that greater caution is required for controlling IYSV compared to GVX. Disease management strategies should be formulated with careful consideration of the swift evolution patterns exhibited by IYSV.</p>","PeriodicalId":20216,"journal":{"name":"Plant Biotechnology Reports","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141190561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}