Tropical Plant Biology最新文献

{"title":"Identification and Expression Analysis of Transcription Factors in Carallia Brachiata Genome","authors":"Hongmei Qiao","doi":"10.1007/s12042-024-09358-0","DOIUrl":"https://doi.org/10.1007/s12042-024-09358-0","url":null,"abstract":"<p>Transcription factors are important regulatory factors in gene expression. To explore the role of transcription factors in the adaptation of <i>Carallia brachiata</i> to its environment, this study identified the transcription factor family across the genome and analyzed their expression in eight tissues (roots, stems, leaves, flowers, ovules, fruits, seeds, embryos). The results showed that a total of 2322 transcription factor from 91 families were identified. They were significantly enriched in 12 pathways including plant signal transduction, circadian rthythm, MAPK signaling pathway-plant and plant-pathogen interaction etc. Most genes were involved in environmental information processing and environmental adaptation through signal transduction. The results of expression analysis showed 204 genes were tissue-specific. Genes that were responsible for the signal transduction of cytokinine, auxin, gibberellin, jasmonic acid, salicylic acid were mainly expressed in root, stem, leaf, flower, ovule and fruit while the genes that involve in ethylene and abscisic acid signal transduction were only expressed in seed and embryo. This study suggested that the transcription factors regulated different tissues of <i>C. brachiata</i> by participating in different hormone response pathways, so as to regulate plant growth and development.</p>","PeriodicalId":54356,"journal":{"name":"Tropical Plant Biology","volume":"49 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140565322","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":"Identification and Expression Profiles of Auxin-Related Gene Families Involved in Fiber Development in Jute (Corchorus capsularis)","authors":"Shaolian Jiang, Huawei Wei, Mengxin Huang, Lingling Zhuang, Jinping Huang, Haixiong Ma, Pingping Fang, Aifen Tao, Jianmin Qi, Jiantang Xu, Liwu Zhang","doi":"10.1007/s12042-024-09356-2","DOIUrl":"https://doi.org/10.1007/s12042-024-09356-2","url":null,"abstract":"<p>The <i>ARF</i> (Auxin response factor), <i>GH3</i> (Gretchen Hagen 3), and <i>Aux/IAA</i> (Auxin/indole-3-acetic acid) gene families are key components in auxin signaling pathway and function as regulators of growth in plants. However, this research is rarely reported in jute, which severely limits the understandings of mechanisms involved in fiber development. In this study, 13 <i>ARF</i>, 12 <i>GH3</i> and 20 <i>Aux/IAA</i> putative genes were identified in the whole genome of jute. Exon-intron structures revealed the high conservation among these auxin-related gene family members. Chromosomal localization and synteny analysis showed that segmental duplication contributed to the expansion of <i>CcARF</i>, <i>CcGH3</i> and <i>CcIAA</i> gene families. Phylogenetic and conserved motif analysis revealed that they have distinct functional and <i>CcARF</i>, <i>CcGH3</i> and <i>CcIAA</i>-specific domains, respectively. The expression pattern analysis based on RNA-seq and qRT-PCR indicated that 7 <i>CcARF</i>, 5 <i>CcGH3</i>, and 14 <i>CcIAA</i> genes showed higher expression in stem barks than leaves at the vigorous vegetative growth stage in an elite cultivar Huangma 179 with normal plant height, respectively, suggesting they might regulate the development of bast fiber. Moreover, the expression of 5 <i>CcARF</i>, 4 <i>CcGH3</i>, and 12 <i>CcIAA</i> genes was differentially expressed in stem barks of a typical GA₃ sensitive dwarf germplasm in comparison to Huangma 179. The cis-element analysis showed that promoters of 4 <i>CcARF</i>, 3 <i>CcGH3</i>, and 7 <i>CcIAA</i> genes had 1 to 3 cis-elements involved in gibberellin-responsiveness, giving a hint that they could respond to endogenous gibberellin accumulation in Huangma 179 and form a complicated network to regulate hormone regulatory network and plant height. This study provides useful information for functional analysis of <i>ARF</i>, <i>GH3</i>, and <i>Aux/IAA</i> genes, which would be taken as candidates for genetic improvement of bast fiber quality in jute.</p>","PeriodicalId":54356,"journal":{"name":"Tropical Plant Biology","volume":"1 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140565179","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":"Analysis of PIN Gene Family in Cymbidium ensifolium Revealed its Potential Function in Petal Development","authors":"Jiayi Chen, Peng Li, Longwei Xiong, Jinlan Lin, Liting Guo, Lu Yan, Tingting Huang, Ye Ai","doi":"10.1007/s12042-024-09357-1","DOIUrl":"https://doi.org/10.1007/s12042-024-09357-1","url":null,"abstract":"<p>The PIN (PIN-formed) proteins act as vital carriers, regulating auxin polar transport and playing a crucial role in plant growth and development. <i>Cymbidium ensifolium</i> (Orchidaceae) is a perennial herbaceous plant highly esteemed for its high ornamental value. The lotus-shape flowers of <i>C. ensifolium</i> are favored by consumers for their distinctive flower shape with shorter petals. To deepen our understanding of the members and characteristics of PIN gene family in <i>C. ensifolium</i>, this study performed genome-wide identification and analysis of <i>CePIN</i> members, including their physicochemical properties, protein and gene structures, conserved motifs, phylogenetic evolution, promoter components, and expression patterns. The results revealed a total of 16 PIN gene family members in the genome of <i>C. ensifolium</i>. Expression analysis demonstrated significant differential expression of all 16 <i>CePINs</i> across different tissues. Notably, a close correlation was observed between the expression of <i>CePIN1a</i> and <i>CePIN3</i> and the formation of lotus-shape flowers in <i>C. ensifolium</i>. These findings provide a foundational understanding for further exploration of <i>CePIN</i> functions and offer valuable insights for studying petal development in <i>C. ensifoliu</i>m.</p>","PeriodicalId":54356,"journal":{"name":"Tropical Plant Biology","volume":"1 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140565195","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":"Transcriptional Regulation of Biotic and Abiotic Stress Responses: Challenges and Potential Mechanism for Stress Tolerance and Chickpea Improvement","authors":"Nidhi Rai, Birinchi Kumar Sarma, Shashi Pandey Rai","doi":"10.1007/s12042-024-09354-4","DOIUrl":"https://doi.org/10.1007/s12042-024-09354-4","url":null,"abstract":"<p>The abiotic stress factors associated with climate change frequently enhance the severity of plant diseases, which have a detrimental impact on the growth and productivity of the various crops including legumes. After common beans, the chickpea (<i>Cicer spp.</i>) is the second most cultivated legume crop all over the world. They are susceptible to decreased productivity caused by the detrimental effects of several fungal and bacterial infections, which are regulated by environmental conditions. To understand crop growth, it is crucial to study how plants respond to infections in the presence/fluctuations of abiotic factors. However, to cope with these environmental changes, plants have developed a variety of specific signaling mechanisms for intracellular communications, leading to the initiation of complex defense systems of signal perception and signal transduction to induce/enhance defense responses. Various transcription factors (TFs), along with their cofactors and <i>cis</i>-regulatory elements, play a crucial role in plant defense mechanisms. Transcriptional control by TFs has a vital role in building plant defense mechanisms and related activities in response to viral and bacterial infections. However, the molecular mechanisms including the role of transcription factors (TFs) behind environmental cues are still little understood in chickpea. Therefore, the objective of this review is to outline the potential functions of key stress-responsive transcription factors (TFs), such as <i>WRKY, bHLH, bZIP, AP2/ERF</i>, and <i>MYB</i> gene families, in regulating defense-related genes and facilitating communication across the network of stress-responses during adverse conditions. Furthermore, understanding the function of transcription factors (TFs) could be advantageous in enhancing crop tolerance to develop stress-resistant chickpea cultivars utilizing advanced biotechnological techniques.</p>","PeriodicalId":54356,"journal":{"name":"Tropical Plant Biology","volume":"98 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140147493","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":"Understanding the Concept of Speed Breeding in Crop Improvement: Opportunities and Challenges Towards Global Food Security","authors":"Zafar Imam, Rafat Sultana, Rabiya Parveen, Swapnil, Digvijay Singh, Surabhi Sinha, Jyoti Prakash Sahoo","doi":"10.1007/s12042-024-09353-5","DOIUrl":"https://doi.org/10.1007/s12042-024-09353-5","url":null,"abstract":"<p>Considering fast-changing environment, emerging pathogens, and the imminent need to feed a global population that is predicted to increase to 9–10 billion people by the year 2050, plant breeders are faced with the challenge of exploring more efficient crop improvement strategies. The urgency to enhance crops under these conditions has become a paramount concern for scientists worldwide, as current crop enhancement projects progress at a pace insufficient to meet the growing food demand. Traditional breeding methods, which often take over 10 years to develop high-performing cultivars with desired traits, are proving to be inadequate. However, a new approach known as Speed breeding presents a game-changing opportunity for crop improvement in the face of a changing world offering the potential to significantly accelerate the development, marketing, and commercialization of improved plant varieties. Speed breeding, a methodology that manipulates temperature, light duration, and intensity to accelerate plant development, has emerged as a promising solution for achieving climate resilience, long-term yield, and nutritional security. Recent innovations in breeding technologies, including genotyping, marker-assisted selection (MAS), high throughput phenotyping, genomic selection (GS), overexpression/knock-down transgenic techniques, and genome editing, can be combined with speed breeding to achieve more precise and expedited outcomes in crop enhancement. This review explores the key opportunities and challenges associated with speed breeding to guide pre-breeding and breeding programs. To achieve more efficient outcomes in enhancing major food crops, this review highlights various alternative approaches and strategies adopted for speed breeding. Integrating speed breeding with existing technologies will be essential for future crop breeding success, and concerted efforts and ongoing research holds the potential to pave the way for a resilient and productive agricultural future.</p>","PeriodicalId":54356,"journal":{"name":"Tropical Plant Biology","volume":"32 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139679263","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":"Identification and Annotation of the 21 Novel Sugar Cane (Saccharum officinarum) MicroRNA Clusters and Their Significant Biological, Molecular and Cellular Targets","authors":"","doi":"10.1007/s12042-023-09352-y","DOIUrl":"https://doi.org/10.1007/s12042-023-09352-y","url":null,"abstract":"<h3>Abstract</h3> <p>MicroRNAs (miRNAs) are generated in a cell endogenously which have a nucleotide length of 18 to 26 and are also known as short non-protein coding RNAs. The majority of them are evolutionarily conserved in nature, suggesting a logical foundation for the anticipation of new miRNAs in association with their clusters in numerous plants. Considering this study, physical, bioinformatics and efficient methods are integrated to predict the fresh miRNA clusters along with their targets in sugar cane. In sugar cane, there were a total of 21 new miRNA clusters identified, which were linked to 15 miRNA families. These families are as 165a, 166b, 528a, 827, 2118, 2120b, 5168, 5564c, 5565g, 5568c, 6220, 6225, 6226, 6232a and 7540a. Multiple characteristics of such miRNA clusters, including web logo, phylogenetic tree and secondary structures have been developed. The minimal free energy (MFE) of the secondary structures has been attained and reported as well. In addition, mature miRNAs have been sought in stem section of the structure. Consequently, 115 miRNA targets were also found. These targets include substantial GO term which have important targets in the reproduction, DNA packaging, multicellular organismal process, gene expression, translation, transcription factors, protein binding, transporter activity, secretion, cell division, binding, growth &amp; development and aging. Hence, the achieved results of novel sugar cane miRNA clusters target several types of significant genes which help in managing the environment for sugar cane for better crop production.</p> <span> <h3>Graphical Abstract</h3> <p> <span> <span> <img alt=\"\" src=\"https://static-content.springer.com/image/MediaObjects/12042_2023_9352_Figa_HTML.png\"/> </span> </span></p> </span>","PeriodicalId":54356,"journal":{"name":"Tropical Plant Biology","volume":"28 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139668295","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, Phylogenetic and Expression Pattern Analysis of Fatty Acid Desaturase Genes in Castor (Ricinus communis L.)","authors":"Mengdi Sun, Jixing Zhang, Nan Wang, Xue Wei, Hong Fang, Xue Ding, Hui Xu, Xiumin Yu, Hongyan Huo, Ying Wu, Xiaoyu Wang","doi":"10.1007/s12042-023-09349-7","DOIUrl":"https://doi.org/10.1007/s12042-023-09349-7","url":null,"abstract":"<p>Fatty acid desaturase (FAD) plays a crucial role in plant growth, development, and stress response. The FADs have been identified and reported in diverse plants, but so far, the whole genome exploration and analysis of FADs in castor (<i>Ricinus communis</i> L.) have not been reported yet. In this study, the identification of the RcFADs was carried out using a sequence alignment method. The physicochemical properties, gene structure, protein motifs, evolution, as well as gene expression under cold stress and different tissues were analyzed. A total of 16 RcFADs in the castor genome were identified, which contained the TMEM189_B_domain (PF10520)/FA_desaturase (PF00487)/FA_desaturase_2 (PF03405) conserved domain. Phylogenetic analysis showed that RcFADs can be categorized into ω-3, ω-6, ADS/SLD/DES, FAD4, and FAB2 groups, indicating that the function of RcFADs may vary. RNA-Sequencing and real-time PCR showed that the expression of <i>RcFAD4</i> and <i>RcFAD8.1</i> were increased with the duration of cold treatments, indicating their involvement in cold adaptability of castor. Global expression profiles of the <i>RcFADs</i> in different tissues displayed diverse expression patterns, which suggested that these genes might play important roles in regulating different developmental and physiological processes in castor. This study provides valuable information for understanding the potential function of RcFADs in regulating the growth and development and abiotic stress responses in castor.</p>","PeriodicalId":54356,"journal":{"name":"Tropical Plant Biology","volume":"37 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138819072","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":"Influence of the Cellular Ultrastructure and Enzyme Activity of the Leaf Sheath on Spontaneous Defoliation in Sugarcane","authors":"Xin Hu, Tiantian Wang, Shaochun Liu, Jiawen Guo, Jingmei Dao, Xinxin Gao, Rudan Li, Gaoyuan Liu","doi":"10.1007/s12042-023-09351-z","DOIUrl":"https://doi.org/10.1007/s12042-023-09351-z","url":null,"abstract":"Abstract Spontaneous defoliation improves the harvesting efficiency and yield of sugarcane. Here, we investigated the ultrastructural changes and pectinase and cellulase activity in the third, fifth, and seventh leaf sheaths in four sugarcane varieties with varying spontaneous defoliation performance during maturation. At the early and middle stages of spontaneous defoliation, the cells in the abscission zones of the third, fifth, and seventh leaf sheaths were degrading. At the late stage, no complete organelles and hollow or broken spots in the cell walls were observed in the abscission zone cells of defoliation-prone varieties, while complete organelles and intact cell walls were present in the abscission zone cells at the same leaf positions in defoliation-resistant varieties. From the early to late stages, defoliation-prone varieties had higher pectinase activity in the abscission zones of the fifth and seventh leaf sheaths. At the early stage of defoliation, defoliation-prone varieties had significantly higher cellulase activity in the abscission zones of the third, fifth, and seventh leaf sheaths. Correlation analysis showed that the spontaneous defoliation rate was significantly positively correlated with pectinase activity in the leaf sheaths. In conclusion, the spontaneous defoliation of sugarcane was closely related to changes in cell morphology and pectinase activites in leaf sheaths.","PeriodicalId":54356,"journal":{"name":"Tropical Plant Biology","volume":"112 12","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135137819","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, Evolutionary and Expression Analyses of CrRLK1L Gene Family in Peanut (Arachis hypogaea L.)","authors":"Qinghua Qiao, Xuezhen Fu, Zhenxin Ren, Wei Qiao, Dong Xiao, Longfei He","doi":"10.1007/s12042-023-09350-0","DOIUrl":"https://doi.org/10.1007/s12042-023-09350-0","url":null,"abstract":"","PeriodicalId":54356,"journal":{"name":"Tropical Plant Biology","volume":" 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135242187","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":"Prospects of Marker-Assisted Recurrent Selection: Current Insights and Future Implications","authors":"Sarvamangala S Cholin, Chaitra C Kulkarni","doi":"10.1007/s12042-023-09348-8","DOIUrl":"https://doi.org/10.1007/s12042-023-09348-8","url":null,"abstract":"","PeriodicalId":54356,"journal":{"name":"Tropical Plant Biology","volume":"77 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136382227","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}