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Chen Z, Chen F, Qin Y, Wang L, Jia R, Zhao J, Lin K, Zhang Y. Genome-wide identification and analysis of expression patterns of the ABC1K gene family members in Medicago sativa. FRONTIERS IN PLANT SCIENCE 2024; 15:1486525. [PMID: 39654960 PMCID: PMC11625579 DOI: 10.3389/fpls.2024.1486525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Accepted: 11/06/2024] [Indexed: 12/12/2024]
Abstract
The ABC1K (activity of bc1 complex kinase) atypical protein kinase family regulates diverse physiological functions in plants, including the development, growth, and response of plants to various stress stimuli. However, to date, only a few members of the alfalfa (Medicago sativa) ABC1K gene family have been identified, which severely limits the exploration of the functional mechanism of alfalfa ABC1K. Here, we identified 22 ABC1K genes from the alfalfa genome and categorized them into four types on the basis of phylogenetic analysis results and gene structure. We then characterized the physical and biochemical properties, chromosomal location, subcellular localization, cis-regulatory elements, and conserved motifs of these genes. Transcript profiling analysis confirmed that MsABC1Ks were widely expressed in various alfalfa tissues, with tissue-specific expression. We also found that salt and drought conditions significantly regulated MsABC1K gene expression, thus indicating that MsABC1K genes perform critical functions in alfalfa's response to abiotic stress. In summary, the findings of our study serve as an important basis to enhance the stress resistance of alfalfa and provide valuable insights to better comprehend the functions of the MsABC1K gene family.
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Affiliation(s)
- Zhengqiang Chen
- Key Laboratory of Biohazard Monitoring, Green Prevention and Control for Artificial Grassland, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Fangqi Chen
- Key Laboratory of Biohazard Monitoring, Green Prevention and Control for Artificial Grassland, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot, China
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yaxuan Qin
- Key Laboratory of Biohazard Monitoring, Green Prevention and Control for Artificial Grassland, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot, China
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Le Wang
- Key Laboratory of Biohazard Monitoring, Green Prevention and Control for Artificial Grassland, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Ruifang Jia
- Key Laboratory of Biohazard Monitoring, Green Prevention and Control for Artificial Grassland, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Jun Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Kejian Lin
- Key Laboratory of Biohazard Monitoring, Green Prevention and Control for Artificial Grassland, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yuanyuan Zhang
- Key Laboratory of Biohazard Monitoring, Green Prevention and Control for Artificial Grassland, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot, China
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Guo Y, Shang X, Ma L, Cao Y. RNA-Binding Protein-Mediated Alternative Splicing Regulates Abiotic Stress Responses in Plants. Int J Mol Sci 2024; 25:10548. [PMID: 39408875 PMCID: PMC11477454 DOI: 10.3390/ijms251910548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 09/28/2024] [Accepted: 09/29/2024] [Indexed: 10/20/2024] Open
Abstract
The alternative splicing of pre-mRNA generates distinct mRNA variants from a pre-mRNA, thereby modulating a gene's function. The splicing of pre-mRNA depends on splice sites and regulatory elements in pre-mRNA, as well as the snRNA and proteins that recognize these sequences. Among these, RNA-binding proteins (RBPs) are the primary regulators of pre-mRNA splicing and play a critical role in the regulation of alternative splicing by recognizing the elements in pre-mRNA. However, little is known about the function of RBPs in stress response in plants. Here, we summarized the RBPs involved in the alternative splicing of pre-mRNA and their recognizing elements in pre-mRNA, and the recent advance in the role of RBP-mediated alternative splicing in response to abiotic stresses in plants. This review proposes that the regulation of pre-mRNA alternative splicing by RBPs is an important way for plants to adapt to abiotic stresses, and the regulation of alternative splicing by RBPs is a promising direction for crop breeding.
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Affiliation(s)
| | | | | | - Ying Cao
- College of Life Sciences, Capital Normal University, Beijing 100048, China; (Y.G.); (X.S.); (L.M.)
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Zi Y, Zhang M, Yang X, Zhao K, Yin T, Wen K, Li X, Liu X, Zhang H. Identification of the sweet orange (Citrus sinensis) bHLH gene family and the role of CsbHLH55 and CsbHLH87 in regulating salt stress. THE PLANT GENOME 2024; 17:e20502. [PMID: 39215542 DOI: 10.1002/tpg2.20502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/01/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
Salt stress is one of the primary environmental stresses limiting plant growth and production and adversely affecting the growth, development, yield, and fruit quality of Citrus sinensis. bHLH (basic helix-loop-helix) genes are involved in many bioregulatory processes in plants, including growth and development, phytohormone signaling, defense responses, and biosynthesis of specific metabolites. In this study, by bioinformatics methods, 120 CsbHLHgenes were identified, and phylogenetic analysis classified them into 18 subfamilies that were unevenly distributed on nine chromosomes. The cis-acting elements of the CsbHLH genes were mainly hormone-related cis-acting elements. Seventeen CsbHLH genes exhibited significant differences in expression under salt stress. Six CsbHLH genes with significant differences in expression were randomly selected for quantitative real-time polymerase chain reaction (qRT-PCR) validation. The qRT-PCR results showed a strong correlation with the transcriptome data. Phytohormones such as jasmonic acid (JA) are essential for biotic and abiotic stress responses in plants, and CsbHLH55 and CsbHLH87 are considered candidate target genes for sweet orange MYC2 transcription factors involved in the JA signaling pathway. These genes are the main downstream effectors in the JA signaling pathway and can be activated to participate in the JA signaling pathway. Activation of the JA signaling pathway inhibits the production of reactive oxygen species and improves the salt tolerance of sweet orange plants. The CsbHLH55 and CsbHLH87 genes could be candidate genes for breeding new transgenic salt-resistant varieties of sweet orange.
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Affiliation(s)
- Yinqiang Zi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Mengjie Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Xiuyao Yang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Ke Zhao
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Tuo Yin
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Ke Wen
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Xulin Li
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Xiaozhen Liu
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
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Hanif S, Farooq S, Kiani MZ, Zia M. Surface modified ZnO NPs by betaine and proline build up tomato plants against drought stress and increase fruit nutritional quality. CHEMOSPHERE 2024; 362:142671. [PMID: 38906183 DOI: 10.1016/j.chemosphere.2024.142671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/08/2024] [Accepted: 06/19/2024] [Indexed: 06/23/2024]
Abstract
Drought stress is a serious challenge for global food production. Nanofertilizers and nanocomposites cope with such environmental stresses and also increase nutritional contents of fruits. An in vitro experiment was designed to use Zinc Oxide Nanoparticles (ZnO NPs) primed with Proline and Betaine (ZnOP and ZnOBt NPs) at 50 and 100 mg/kg soil against drought stress in Tomato (Solanum lycopersicum) plants. Plant morphological, biochemical, and fruit nutritional quality were accessed. Maximum plant height was observed under the treatment of ZnOP50 (1.09 m) and ZnO 100 (1.06 m). ZnOP and ZnOBt also improved the chlorophyll content up to 86% and 87.16%, respectively. Application of ZnOP NPs also demonstrated maximum tomato yield (204 g tomato/plant) followed by ZnO NPs and ZnOBt NPs. Nanocomposites decreased phenolics and flavonoids contents in drought stressed plants demonstrating the mitigation of oxidative stress. Nanofertilizer also increased the concentration of phenolics and flavonoids in fruits that increased the nutritional contents. Furthermore a significant accumulation of betaine, proline, and lycopene in fruits on nanocomposite treatment made it nutritional and healthy. Lycopene content increased up to 2.01% and 1.23% in presence of ZnOP50 and ZnOP100, respectively. These outcomes validate that drought stress in plant can be reduced by accumulation of different phytochemicals and quenching oxidative stress. The study deems that nano zinc carrying osmoregulators can greatly reduce the negative effects of drought stress and increase nutritional quality of tomato fruits.
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Affiliation(s)
- Saad Hanif
- Department of Biotechnology, Quaid-i-Azam University Islamabad Pakistan, 45320, Pakistan
| | - Snovia Farooq
- Department of Biotechnology, Quaid-i-Azam University Islamabad Pakistan, 45320, Pakistan
| | - Misbah Zeb Kiani
- Department of Biotechnology, Quaid-i-Azam University Islamabad Pakistan, 45320, Pakistan
| | - Muhammad Zia
- Department of Biotechnology, Quaid-i-Azam University Islamabad Pakistan, 45320, Pakistan.
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Ma H, Pei J, Zhuo J, Tang Q, Hou D, Lin X. The CONSTANS-LIKE gene PeCOL13 regulates flowering through intron-retained alternative splicing in Phyllostachys edulis. Int J Biol Macromol 2024; 274:133393. [PMID: 38917922 DOI: 10.1016/j.ijbiomac.2024.133393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/14/2024] [Accepted: 06/22/2024] [Indexed: 06/27/2024]
Abstract
Woody bamboo exhibits a unique flowering characteristic with a lengthy flowering cycle, often followed by death. In many plant species, alternative splicing (AS) is a common phenomenon involved in controlling flowering. In this study, a PeCOL13 gene in moso bamboo (Phyllostachys edulis) was characterized. It produced two isoforms: PeCOL13α and PeCOL13β, due to an intron-retained AS. The PeCOL13α expressed in the vegetative phase and the reproductive phase, but the PeCOL13β didn't express during the vegetative phase and showed only a weak expression from F1 to F3 during the reproductive phase. Overexpression of PeCOL13α in rice (Oryza sativa) resulted in a delayed heading time through inhibiting the expressions of Hd3a, OsFTL1, and Ehd1 and activating the expressions of Ghd7 and RCN1. However, the PeCOL13β-overexpressed rice didn't show any significant differences in flowering compared with wild-type (WT), and the expressions of downstream flowering genes had no notable changes. Further analysis revealed that both PeCOL13α and PeCOL13β can bind to the PeFT promoter. Meanwhile, PeCOL13α can inhibit the transcription of PeFT, but PeCOL13β showed no effect. When PeCOL13α and PeCOL13β coexist, the inhibitory effect of PeCOL13α on PeFT transcription was weakened by PeCOL13β. This study provides new insights into the mechanism of bamboo flowering research.
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Affiliation(s)
- Hongjia Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin' an 311300, China; Bamboo Industry Institute, Zhejiang A&F University, Lin' an 311300, China
| | - Jialong Pei
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin' an 311300, China; Bamboo Industry Institute, Zhejiang A&F University, Lin' an 311300, China
| | - Juan Zhuo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin' an 311300, China; Bamboo Industry Institute, Zhejiang A&F University, Lin' an 311300, China
| | - Qingyun Tang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin' an 311300, China; Bamboo Industry Institute, Zhejiang A&F University, Lin' an 311300, China
| | - Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin' an 311300, China; Bamboo Industry Institute, Zhejiang A&F University, Lin' an 311300, China.
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin' an 311300, China; Bamboo Industry Institute, Zhejiang A&F University, Lin' an 311300, China.
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Zhang W, Wang H, Guo Y, Hao X, Li Y, He W, Zhao X, Cai S, Song X. Functional Validation of Different Alternative Splicing Variants of the Chrysanthemum lavandulifolium ClNUM1 Gene in Tobacco. Curr Issues Mol Biol 2024; 46:5242-5256. [PMID: 38920986 PMCID: PMC11201747 DOI: 10.3390/cimb46060314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/27/2024] Open
Abstract
The Asteraceae are widely distributed throughout the world, with diverse functions and large genomes. Many of these genes remain undiscovered and unstudied. In this study, we discovered a new gene ClNUM1 in Chrysanthemum lavandulifolium and studied its function. In this study, bioinformatics, RT-qPCR, paraffin sectioning, and tobacco transgenics were utilized to bioinformatically analyze and functionally study the three variable splice variants of the unknown gene ClNUM1 cloned from C. lavandulifolium. The results showed that ClNUM1.1 and ClNUM1.2 had selective 3' splicing and selective 5' splicing, and ClNUM1.3 had selective 5' splicing. When the corresponding transgenic tobacco plants were subjected to abiotic stress treatment, in the tobacco seedlings, the ClNUM1.1 gene and the ClNUM1.2 gene enhanced salt and low-temperature tolerance and the ClNUM1.3 gene enhanced low-temperature tolerance; in mature tobacco plants, the ClNUM1.1 gene was able to enhance salt and low-temperature tolerance, and the ClNUM1.2 and ClNUM1.3 genes were able to enhance low-temperature tolerance. In summary, there are differences in the functions of the different splice variants and the different seedling stages of transgenic tobacco, but all of them enhanced the resistance of tobacco to a certain extent. The analysis and functional characterization of the ClNUM1 gene provided new potential genes and research directions for abiotic resistance breeding in Chrysanthemum.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xuebin Song
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (W.Z.); (H.W.); (Y.G.); (X.H.); (Y.L.); (W.H.); (X.Z.); (S.C.)
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7
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Muhammad T, Yang T, Wang B, Yang H, Tuerdiyusufu D, Wang J, Yu Q. Comprehensive genomic characterization and expression analysis of calreticulin gene family in tomato. FRONTIERS IN PLANT SCIENCE 2024; 15:1397765. [PMID: 38711609 PMCID: PMC11070585 DOI: 10.3389/fpls.2024.1397765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024]
Abstract
Calreticulin (CRT) is a calcium-binding endoplasmic reticulum (ER) protein that has been identified for multiple cellular processes, including protein folding, regulation of gene expression, calcium (Ca2+) storage and signaling, regeneration, and stress responses. However, the lack of information about this protein family in tomato species highlights the importance of functional characterization. In the current study, 21 CRTs were identified in four tomato species using the most recent genomic data and performed comprehensive bioinformatics and SlCRT expression in various tissues and treatments. In the bioinformatics analysis, we described the physiochemical properties, phylogeny, subcellular positions, chromosomal location, promoter analysis, gene structure, motif distribution, protein structure and protein interaction. The phylogenetic analysis classified the CRTs into three groups, consensus with the gene architecture and conserved motif analyses. Protein structure analysis revealed that the calreticulin domain is highly conserved among different tomato species and phylogenetic groups. The cis-acting elements and protein interaction analysis indicate that CRTs are involved in various developmental and stress response mechanisms. The cultivated and wild tomato species exhibited similar gene mapping on chromosomes, and synteny analysis proposed that segmental duplication plays an important role in the evolution of the CRTs family with negative selection pressure. RNA-seq data analysis showed that SlCRTs were differentially expressed in different tissues, signifying the role of calreticulin genes in tomato growth and development. qRT-PCR expression profiling showed that all SlCRTs except SlCRT5 were upregulated under PEG (polyethylene glycol) induced drought stress and abscisic acid (ABA) treatment and SlCRT2 and SlCRT3 were upregulated under salt stress. Overall, the results of the study provide information for further investigation of the functional characterization of the CRT genes in tomato.
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Affiliation(s)
- Tayeb Muhammad
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Tao Yang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Baike Wang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Haitao Yang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Diliaremu Tuerdiyusufu
- College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi, China
| | - Juan Wang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Qinghui Yu
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
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Liu T, Wang Q, Li Y, Chen Y, Jia B, Zhang J, Guo W, Li FY. Bio-organic fertilizer facilitated phytoremediation of heavy metal(loid)s-contaminated saline soil by mediating the plant-soil-rhizomicrobiota interactions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171278. [PMID: 38417528 DOI: 10.1016/j.scitotenv.2024.171278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/11/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Bio-organic fertilizer (BOF) was effective to promote the phytoremediation efficiency of heavy metal(loid)s-contaminated saline soil (HCSS) by improving rhizosphere soil properties, especially microbiome. However, there existed unclear impacts of BOF on plant metabolome and plant-driven manipulation on rhizosphere soil microbiota in HCSS, which were pivotal contributors to stress defense of plants trapped in adverse conditions. Here, a pot experiment was conducted to explore the mechanisms of BOF in improving alfalfa (Medicago sativa)-performing phytoremediation of HCSS. BOF application significantly increased the biomass (150.87-401.58 %) to support the augments of accumulation regarding heavy metal(loid)s (87.50 %-410.54 %) and salts (38.27 %-271.04 %) in alfalfa. BOF promoted nutrients and aggregates stability but declined pH of rhizosphere soil, accompanied by the boosts of rhizomicrobiota including increased activity, reshaped community structure, enriched plant growth promoting rhizobacteria (Blastococcus, Modestobacter, Actinophytocola, Bacillus, and Streptomyces), strengthened mycorrhizal symbiosis (Leohumicola, Funneliformis, and unclassified_f_Ceratobasidiaceae), optimized co-occurrence networks, and beneficial shift of keystones. The conjoint analysis of plant metabolome and physiological indices confirmed that BOF reprogrammed the metabolic processes (synthesis, catabolism, and long-distance transport of amino acid, lipid, carbohydrate, phytohormone, stress-resistant secondary metabolites, etc) and physiological functions (energy supply, photosynthesis, plant immunity, nutrients assimilation, etc) that are associated intimately. The consortium of root metabolome, soil metabolome, and soil microbiome revealed that BOF facilitated the exudation of metabolites correlated with rhizomicrobiota (structure, biomarker, and keystone) and rhizosphere oxidative status, e.g., fatty acyls, phenols, coumarins, phenylpropanoids, highlighting the plant-driven regulation on rhizosphere soil microbes and environment. By compiling various results and omics data, it was concluded that BOF favored the adaptation and phytoremediation efficiency of alfalfa by mediating the plant-soil-rhizomicrobiota interactions. The results would deepen understanding of the mechanisms by which BOF improved phytoremediation of HCSS, and provide theoretical guidance to soil amelioration and BOF application.
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Affiliation(s)
- Tai Liu
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Qian Wang
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Yongchao Li
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Yunong Chen
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Bingbing Jia
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Jingxia Zhang
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Wei Guo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China.
| | - Frank Yonghong Li
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
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9
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Jiao N, Xu J, Wang Y, Li D, Chen F, Chen Y, Chen J. Genome-wide characterization of post-transcriptional processes related to wood formation in Dalbergia odorifera. BMC Genomics 2024; 25:372. [PMID: 38627613 PMCID: PMC11022335 DOI: 10.1186/s12864-024-10300-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Alternative polyadenylation (APA), alternative splicing (AS), and long non-coding RNAs (lncRNAs) play regulatory roles in post-transcriptional processes in plants. However, little is known about their involvement in xylem development in Dalbergia odorifera, a valuable rosewood species with medicinal and commercial significance. We addressed this by conducting Isoform Sequencing (Iso-Seq) using PacBio's SMRT technology and combined it with RNA-seq analysis (RNA sequencing on Illumina platform) after collecting xylem samples from the transition zone and the sapwood of D. odorifera. RESULTS We identified 14,938 full-length transcripts, including 9,830 novel isoforms, which has updated the D. odorifera genome annotation. Our analysis has revealed that 4,164 genes undergo APA, whereas 3,084 genes encounter AS. We have also annotated 118 lncRNAs. Furthermore, RNA-seq analysis identified 170 differential alternative splicing (DAS) events, 344 genes with differential APA site usage (DE-APA), and 6 differentially expressed lncRNAs in the transition zone when compared to the sapwood. AS, APA, and lncRNAs are differentially regulated during xylem development. Differentially expressed APA genes were enriched for terpenoid and flavonoid metabolism, indicating their role in the heartwood formation. Additionally, DE-APA genes were associated with cell wall biosynthesis and terpenoid metabolism, implying an APA's role in wood formation. A DAS gene (involved in chalcone accumulation) with a significantly greater inclusion of the last exon in the transition zone than in the sapwood was identified. We also found that differentially expressed lncRNAs targeted the genes related to terpene synthesis. CONCLUSIONS This study enhances our understanding of the molecular regulatory mechanisms underlying wood formation in D. odorifera, and provides valuable genetic resources and insights for its molecular-assisted breeding.
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Affiliation(s)
- Nanbo Jiao
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China
| | - Jieru Xu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China
| | - Yue Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China
| | - Dunxi Li
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Feifei Chen
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Yu Chen
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Jinhui Chen
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China.
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China.
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Rajendran S, Kang YM, Yang IB, Eo HB, Baek KL, Jang S, Eybishitz A, Kim HC, Je BI, Park SJ, Kim CM. Functional characterization of plant specific Indeterminate Domain (IDD) transcription factors in tomato (Solanum lycopersicum L.). Sci Rep 2024; 14:8015. [PMID: 38580719 PMCID: PMC10997639 DOI: 10.1038/s41598-024-58903-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/04/2024] [Indexed: 04/07/2024] Open
Abstract
Plant-specific transcription factors (TFs) are responsible for regulating the genes involved in the development of plant-specific organs and response systems for adaptation to terrestrial environments. This includes the development of efficient water transport systems, efficient reproductive organs, and the ability to withstand the effects of terrestrial factors, such as UV radiation, temperature fluctuations, and soil-related stress factors, and evolutionary advantages over land predators. In rice and Arabidopsis, INDETERMINATE DOMAIN (IDD) TFs are plant-specific TFs with crucial functions, such as development, reproduction, and stress response. However, in tomatoes, IDD TFs remain uncharacterized. Here, we examined the presence, distribution, structure, characteristics, and expression patterns of SlIDDs. Database searches, multiple alignments, and motif alignments suggested that 24 TFs were related to Arabidopsis IDDs. 18 IDDs had two characteristic C2H2 domains and two C2HC domains in their coding regions. Expression analyses suggest that some IDDs exhibit multi-stress responsive properties and can respond to specific stress conditions, while others can respond to multiple stress conditions in shoots and roots, either in a tissue-specific or universal manner. Moreover, co-expression database analyses suggested potential interaction partners within IDD family and other proteins. This study functionally characterized SlIDDs, which can be studied using molecular and bioinformatics methods for crop improvement.
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Affiliation(s)
- Sujeevan Rajendran
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Yu Mi Kang
- Department of Horticultural and Life Science, Pusan National University, Milyang, 50463, Korea
| | - In Been Yang
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Hye Bhin Eo
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Kyung Lyung Baek
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Seonghoe Jang
- World Vegetable Center Korea Office (WKO), Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Assaf Eybishitz
- World Vegetable Center, P.O. Box 42, Tainan, 74199, Shanhua, Taiwan
| | - Ho Cheol Kim
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Byeong Il Je
- Department of Horticultural and Life Science, Pusan National University, Milyang, 50463, Korea
| | - Soon Ju Park
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
| | - Chul Min Kim
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea.
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11
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Tarasov SS, Krutova EK. Dynamics of the Activity of Antioxidant Enzymes and the Expression of the Genes Encoding Them in Wheat after Exposure to Ultrasound. BIOL BULL+ 2024; 51:346-357. [DOI: 10.1134/s1062359023605323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 01/04/2025]
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12
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Punzo P, Suede Cigliano R, Aversano R, Grillo S, Batelli G. Determination of Differential Alternative Splicing Under Stress Conditions. Methods Mol Biol 2024; 2832:67-79. [PMID: 38869788 DOI: 10.1007/978-1-0716-3973-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Alternative splicing (AS) is an important mechanism contributing to stress-induced regulation of gene expression and proteome diversity. Massive sequencing technologies allow the identification of transcripts generated via stress-responsive AS, potentially important for adaptation to stress conditions. Several bioinformatics tools have been developed to identify differentially expressed alternative splicing events/transcripts from RNA-sequencing results. This chapter describes a detailed protocol for differential alternative splicing analysis using the rMATS tool. In addition, we provide guidelines for validation of the detected splice variants by qRT-PCR based on the obtained output files.
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Affiliation(s)
- Paola Punzo
- CNR Institute of Biosciences and Bioresources, Research Division Portici, Portici, Italy
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy
| | | | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy
| | - Stefania Grillo
- CNR Institute of Biosciences and Bioresources, Research Division Portici, Portici, Italy
| | - Giorgia Batelli
- CNR Institute of Biosciences and Bioresources, Research Division Portici, Portici, Italy.
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13
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Yao P, Zhang C, Qin T, Liu Y, Liu Z, Xie X, Bai J, Sun C, Bi Z. Comprehensive Analysis of GH3 Gene Family in Potato and Functional Characterization of StGH3.3 under Drought Stress. Int J Mol Sci 2023; 24:15122. [PMID: 37894803 PMCID: PMC10606756 DOI: 10.3390/ijms242015122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
As an important hormone response gene, Gretchen Hagen 3 (GH3) maintains hormonal homeostasis by conjugating excess auxin with amino acids during plant stress-related signaling pathways. GH3 genes have been characterized in many plant species, but they are rarely reported in potato. Here, 19 StGH3 genes were isolated and characterized. Phylogenetic analysis indicated that StGH3s were divided into two categories (group I and group III). Analyses of gene structure and motif composition showed that the members of a specific StGH3 subfamily are relatively conserved. Collinearity analysis of StGH3 genes in potato and other plants laid a foundation for further exploring the evolutionary characteristics of the StGH3 genes. Promoter analysis showed that most StGH3 promoters contained hormone and abiotic stress response elements. Multiple transcriptome studies indicated that some StGH3 genes were responsive to ABA, water deficits, and salt treatments. Moreover, qRT-PCR analysis indicated that StGH3 genes could be induced by phytohormones (ABA, SA, and MeJA) and abiotic stresses (water deficit, high salt, and low temperature), although with different patterns. Furthermore, transgenic tobacco with transient overexpression of the StGH3.3 gene showed positive regulation in response to water deficits by increasing proline accumulation and reducing the leaf water loss rate. These results suggested that StGH3 genes may be involved in the response to abiotic stress through hormonal signal pathways. Overall, this study provides useful insights into the evolution and function of StGH3s and lays a foundation for further study on the molecular mechanisms of StGH3s in the regulation of potato drought resistance.
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Affiliation(s)
- Panfeng Yao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
| | - Chunli Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Tianyuan Qin
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
| | - Xiaofei Xie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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14
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Wang J, Sun L, Zhang H, Jiao B, Wang H, Zhou S. Transcriptome analysis during vernalization in wheat (Triticum aestivum L.). BMC Genom Data 2023; 24:43. [PMID: 37563565 PMCID: PMC10416481 DOI: 10.1186/s12863-023-01144-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Vernalization, as a vital process in the life cycle of winter cereal, has important effects on floral organ formation and flowering time. Many morphological changes together with molecular changes occur during the vernalization period. Here, we used transcriptome sequencing to analyze the transcriptomic changes in wheat leaves before, during and after vernalization using the winter wheat cultivar 'Shiluan02-1'. RESULTS A total of 16,370 differentially expressed genes were obtained across different vernalization periods. Gene Ontology enrichment analysis revealed that photoperiodism, photoprotection, photosynthesis, lipid transport and biosynthetic process, and chlorophyll metabolic process were closely related to vernalization. In addition, AP2/ERF, C2H2, bHLH, WRKY, MYB, MYB-related, and NAC transcription factors were significantly enriched during vernalization, and the transcription factor expression patterns suggested the intricate regulation of transcription factor modules in plant vernalization pathways. Analysis of gene expression patterns of the MADS-box transcription factor genes showed different expression patterns during vernalization phases, among which VERNALIZATION1 (VRN1) genes were found to gradually increase during vernalization periods from V0 to V35, while decline in the V42 phase, then increase after vernalization. The Tavrt-2 gene cooperated with Tavrn1 to regulate flowering induced by vernalization, and its expression level was rapidly increased by vernalization but declined in the V42 phase and then increased after vernalization. Some genes from the ICE-CBF-COR pathway were also identified, and additional analysis indicated that some key genes related to phytohormone biosynthesis and signal transduction were enriched during the vernalization period, such as gibberellic acid, ethylene, abscisic acid and jasmonic acid biosynthesis and signaling pathway genes. CONCLUSIONS Our study provides valuable molecular information for future studies on wheat vernalization regulation and also serves as an excellent reference for future wheat breeding.
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Affiliation(s)
- Jiao Wang
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, China
| | - Lei Sun
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, China
| | - Hongwei Zhang
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, China
| | - Bo Jiao
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, China
| | - Haibo Wang
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, China
| | - Shuo Zhou
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, China.
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15
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Zheng J, Wen S, Yu Z, Luo K, Rong J, Ding M. Alternative Splicing during Fiber Development in G. hirsutum. Int J Mol Sci 2023; 24:11812. [PMID: 37511571 PMCID: PMC10380772 DOI: 10.3390/ijms241411812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Cotton is a valuable cash crop in many countries. Cotton fiber is a trichome that develops from a single epidermal cell and serves as an excellent model for understanding cell differentiation and other life processes. Alternative splicing (AS) of genes is a common post-transcriptional regulatory process in plants that is essential for plant growth and development. The process of AS during cotton fiber formation, on the other hand, is mainly unknown. A substantial number of multi-exon genes were discovered to be alternatively spliced during cotton fiber formation in this study, accounting for 23.31% of the total number of genes in Gossypium hirsutum. Retention intron (RI) is not necessarily the most common AS type, indicating that AS genes and processes during fiber development are very temporal and tissue-specific. When compared to fiber samples, AS is more prevalent at the fiber initiation stages and in the ovule, indicating that development stages and tissues use different AS strategies. Genes involved in fiber development have gone through stage-specific AS, demonstrating that AS regulates cotton fiber development. Furthermore, AS can be regulated by trans-regulation elements such as splicing factor and cis-regulation elements such as gene length, exon numbers, and GC content, particularly at exon-intron junction sites. Our findings also suggest that increased DNA methylation may aid in the efficiency of AS, and that gene body methylation is key in AS control. Finally, our research will provide useful information about the roles of AS during the cotton fiber development process.
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Affiliation(s)
- Jing Zheng
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Shuhan Wen
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Zhipeng Yu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Keyan Luo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Mingquan Ding
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
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16
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Sampedro-Guerrero J, Vives-Peris V, Gomez-Cadenas A, Clausell-Terol C. Efficient strategies for controlled release of nanoencapsulated phytohormones to improve plant stress tolerance. PLANT METHODS 2023; 19:47. [PMID: 37189192 PMCID: PMC10184380 DOI: 10.1186/s13007-023-01025-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/06/2023] [Indexed: 05/17/2023]
Abstract
Climate change due to different human activities is causing adverse environmental conditions and uncontrolled extreme weather events. These harsh conditions are directly affecting the crop areas, and consequently, their yield (both in quantity and quality) is often impaired. It is essential to seek new advanced technologies to allow plants to tolerate environmental stresses and maintain their normal growth and development. Treatments performed with exogenous phytohormones stand out because they mitigate the negative effects of stress and promote the growth rate of plants. However, the technical limitations in field application, the putative side effects, and the difficulty in determining the correct dose, limit their widespread use. Nanoencapsulated systems have attracted attention because they allow a controlled delivery of active compounds and for their protection with eco-friendly shell biomaterials. Encapsulation is in continuous evolution due to the development and improvement of new techniques economically affordable and environmentally friendly, as well as new biomaterials with high affinity to carry and coat bioactive compounds. Despite their potential as an efficient alternative to phytohormone treatments, encapsulation systems remain relatively unexplored to date. This review aims to emphasize the potential of phytohormone treatments as a means of enhancing plant stress tolerance, with a specific focus on the benefits that can be gained through the improved exogenous application of these treatments using encapsulation techniques. Moreover, the main encapsulation techniques, shell materials and recent work on plants treated with encapsulated phytohormones have been compiled.
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Affiliation(s)
- Jimmy Sampedro-Guerrero
- Departamento de Biología, Bioquímica y Ciencias Naturales, Universitat Jaume I, 12071, Castelló de la Plana, Castellón, Spain
| | - Vicente Vives-Peris
- Departamento de Biología, Bioquímica y Ciencias Naturales, Universitat Jaume I, 12071, Castelló de la Plana, Castellón, Spain
| | - Aurelio Gomez-Cadenas
- Departamento de Biología, Bioquímica y Ciencias Naturales, Universitat Jaume I, 12071, Castelló de la Plana, Castellón, Spain.
| | - Carolina Clausell-Terol
- Departamento de Ingeniería Química, Instituto Universitario de Tecnología Cerámica, Universitat Jaume I, 12071, Castelló de la Plana, Castellón, Spain.
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17
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Huang Y, Jiao Y, Yang S, Mao D, Wang F, Chen L, Liang M. SiNCED1, a 9-cis-epoxycarotenoid dioxygenase gene in Setaria italica, is involved in drought tolerance and seed germination in transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1121809. [PMID: 36968367 PMCID: PMC10034083 DOI: 10.3389/fpls.2023.1121809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Foxtail millet (Setaria italica L.) is a vital cereal food crop with promising development and utilization potential because of its outstanding ability to resist drought stress. However, the molecular mechanisms underlying its drought stress resistance remain unclear. In this study, we aimed to elucidate the molecular function of a 9-cis-epoxycarotenoid dioxygenase gene, SiNCED1, in the drought stress response of foxtail millet. Expression pattern analysis showed that SiNCED1 expression was significantly induced by abscisic acid (ABA), osmotic stress, and salt stress. Furthermore, ectopic overexpression of SiNCED1 could enhance drought stress resistance by elevating endogenous ABA levels and promoting stomatal closure. Transcript analysis indicated that SiNCED1 modulated ABA-related stress responsive gene expression. In addition, we found that ectopic expression of SiNCED1 delayed seed germination under normal and abiotic stress conditions. Taken together, our results show that SiNCED1 plays a positive role in the drought tolerance and seed dormancy of foxtail millet by modulating ABA biosynthesis. In conclusion, this study revealed that SiNCED1 is an important candidate gene for the improvement of drought stress tolerance in foxtail millet and could be beneficial in the breeding and investigation of drought tolerance in other agronomic crops.
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Affiliation(s)
- Yuan Huang
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
- College of Life Science, Hunan Normal University, Changsha, China
| | - Yang Jiao
- College of Life Science, Hunan Normal University, Changsha, China
| | - Sha Yang
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Dandan Mao
- College of Life Science, Hunan Normal University, Changsha, China
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
| | - Feng Wang
- College of Life Science, Hunan Normal University, Changsha, China
| | - Liangbi Chen
- College of Life Science, Hunan Normal University, Changsha, China
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
| | - Manzhong Liang
- College of Life Science, Hunan Normal University, Changsha, China
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
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18
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Boulanger HG, Guo W, Monteiro LDFR, Calixto CPG. Co-expression network of heat-response transcripts: A glimpse into how splicing factors impact rice basal thermotolerance. Front Mol Biosci 2023; 10:1122201. [PMID: 36818043 PMCID: PMC9932781 DOI: 10.3389/fmolb.2023.1122201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
To identify novel solutions to improve rice yield under rising temperatures, molecular components of thermotolerance must be better understood. Alternative splicing (AS) is a major post-transcriptional mechanism impacting plant tolerance against stresses, including heat stress (HS). AS is largely regulated by splicing factors (SFs) and recent studies have shown their involvement in temperature response. However, little is known about the splicing networks between SFs and AS transcripts in the HS response. To expand this knowledge, we constructed a co-expression network based on a publicly available RNA-seq dataset that explored rice basal thermotolerance over a time-course. Our analyses suggest that the HS-dependent control of the abundance of specific transcripts coding for SFs might explain the widespread, coordinated, complex, and delicate AS regulation of critical genes during a plant's inherent response to extreme temperatures. AS changes in these critical genes might affect many aspects of plant biology, from organellar functions to cell death, providing relevant regulatory candidates for future functional studies of basal thermotolerance.
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Affiliation(s)
- Hadrien Georges Boulanger
- Université Paris-Saclay, Gif-sur-Yvette, France,École Nationale Supérieure d'Informatique pour l'Industrie et l’Entreprise, Evry-Courcouronnes, France,Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Wenbin Guo
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | | | - Cristiane Paula Gomes Calixto
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil,*Correspondence: Cristiane Paula Gomes Calixto,
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19
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Yang T, Tian M, Gao T, Wang C, Wang X, Chen C, Yang W. Genome-wide transcriptomic analysis identifies candidate genes involved in jasmonic acid-mediated salt tolerance of alfalfa. PeerJ 2023; 11:e15324. [PMID: 37168537 PMCID: PMC10166079 DOI: 10.7717/peerj.15324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/10/2023] [Indexed: 05/13/2023] Open
Abstract
Soil salinity imposes a major threat to plant growth and agricultural productivity. Despite being one of the most common fodder crops in saline locations, alfalfa is vulnerable to salt stress. Jasmonic acid (JA) is a phytohormone that influences plant response to abiotic stimuli such as salt stress. However, key genes and pathways by which JA-mediated salt tolerance of alfalfa are little known. A comprehensive transcriptome analysis was performed to elucidate the underlying molecular mechanisms of JA-mediated salt tolerance. The transcripts regulated by salt (S) compared to control (C) and JA+salt (JS) compared to C were investigated. Venn diagram and expression pattern of DEGs indicated that JS further altered a series of genes expression regulated by salt treatment, implying the roles of JA in priming salt tolerance. Enrichment analysis revealed that DEGs exclusively regulated by JS treatment belonged to primary or secondary metabolism, respiratory electron transport chain, and oxidative stress resistance. Alternatively, splicing (AS) was induced by salt alone or JA combined treatment, with skipped exon (SE) events predominately. DEGs undergo exon skipping involving some enriched items mentioned above and transcription factors. Finally, the gene expressions were validated using quantitative polymerase chain reaction (qPCR), which produced results that agreed with the sequencing results. Taken together, these findings suggest that JA modulates the expression of genes related to energy supply and antioxidant capacity at both the transcriptional and post-transcriptional levels, possibly through the involvement of transcription factors and AS events.
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Affiliation(s)
- Tianhui Yang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Mei Tian
- Institute of Horticultural Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Ting Gao
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Chuan Wang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Xiaochun Wang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Caijin Chen
- Branch Institute of Guyuan, Ningxia Academy of Agriculture and Forestry Sciences, Guyuan, Ningxia, China
| | - Weidi Yang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
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20
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Abdel-Aziz HMM, Benavides-Mendoza A, Rizwan M, Seleiman MF. Editorial: Nanofertilizers and abiotic stress tolerance in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1154113. [PMID: 37089660 PMCID: PMC10119583 DOI: 10.3389/fpls.2023.1154113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/28/2023] [Indexed: 05/03/2023]
Affiliation(s)
- Heba M. M. Abdel-Aziz
- Botany Department, Faculty of Science, Mansoura University, Mansoura, Egypt
- *Correspondence: Heba M. M. Abdel-Aziz,
| | | | - Muhammad Rizwan
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Mahmoud F. Seleiman
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
- Department of Crop Sciences, Faculty of Agriculture, Menoufia University, Shibin El-Kom, Egypt
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Wang Y, Fan J, Wu X, Guan L, Li C, Gu T, Li Y, Ding J. Genome-Wide Characterization and Expression Profiling of HD-Zip Genes in ABA-Mediated Processes in Fragaria vesca. PLANTS (BASEL, SWITZERLAND) 2022; 11:3367. [PMID: 36501406 PMCID: PMC9737017 DOI: 10.3390/plants11233367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Members of homeodomain-leucine zipper (HD-Zip) transcription factors can play their roles by modulating abscisic acid (ABA) signaling in Arabidopsis. So far, our knowledge of the functions of HD-Zips in woodland strawberries (Fragaria vesca), a model plant for studying ABA-mediated fruit ripening, is limited. Here, we identified a total of 31 HD-Zip genes (FveHDZ1-31) in F. vesca, and classified them into four subfamilies (I to IV). Promoter analyses show that the ABA-responsive element, ABRE, is prevalent in the promoters of subfamily I and II FveHDZs. RT-qPCR results demonstrate that 10 of the 14 investigated FveHDZs were consistently >1.5-fold up-regulated or down-regulated in expression in response to exogenous ABA, dehydration, and ABA-induced senescence in leaves. Five of the six consistently up-regulated genes are from subfamily I and II. Thereinto, FveHDZ4, and 20 also exhibited significantly enhanced expression along with increased ABA content during fruit ripening. In yeast one-hybrid assays, FveHDZ4 proteins could bind the promoter of an ABA signaling gene FvePP2C6. Collectively, our results strongly support that the FveHDZs, particularly those from subfamilies I and II, are involved in the ABA-mediated processes in F. vesca, providing a basis for further functional characterization of the HD-Zips in strawberry and other plants.
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Affiliation(s)
- Yong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Junmiao Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Xinjie Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Ling Guan
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Chun Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Tingting Gu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269, USA
| | - Jing Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
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22
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Comprehensive Identification and Functional Analysis of Stress-Associated Protein (SAP) Genes in Osmotic Stress in Maize. Int J Mol Sci 2022; 23:ijms232214010. [PMID: 36430489 PMCID: PMC9692755 DOI: 10.3390/ijms232214010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Stress-associated proteins (SAPs) are a kind of zinc finger protein with an A20/AN1 domain and contribute to plants' adaption to various abiotic and biological stimuli. However, little is known about the SAP genes in maize (Zea mays L.). In the present study, the SAP genes were identified from the maize genome. Subsequently, the protein properties, gene structure and duplication, chromosomal location, and cis-acting elements were analyzed by bioinformatic methods. Finally, their expression profiles under osmotic stresses, including drought and salinity, as well as ABA, and overexpression in Saccharomyces cerevisiae W303a cells, were performed to uncover the potential function. The results showed that a total of 10 SAP genes were identified and named ZmSAP1 to ZmSAP10 in maize, which was unevenly distributed on six of the ten maize chromosomes. The ZmSAP1, ZmSAP4, ZmSAP5, ZmSAP6, ZmSAP7, ZmSAP8 and ZmSAP10 had an A20 domain at N terminus and AN1 domain at C terminus, respectively. Only ZmSAP2 possessed a single AN1 domain at the N terminus. ZmSAP3 and ZmSAP9 both contained two AN1 domains without an A20 domain. Most ZmSAP genes lost introns and had abundant stress- and hormone-responsive cis-elements in their promoter region. The results of quantitative real-time PCR showed that all ZmSAP genes were regulated by drought and saline stresses, as well as ABA induction. Moreover, heterologous expression of ZmSAP2 and ZmSAP7 significantly improved the saline tolerance of yeast cells. The study provides insights into further underlying the function of ZmSAPs in regulating stress response in maize.
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23
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Sperotto RA, Hrmova M, Graether SP, Timmers LFSM. Editorial: Structural bioinformatics and biophysical approaches for understanding the plant responses to biotic and abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1012584. [PMID: 36161033 PMCID: PMC9507305 DOI: 10.3389/fpls.2022.1012584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Raul A. Sperotto
- Graduate Program in Biotechnology, University of Taquari Valley – Univates, Lajeado, Brazil
- Graduate Program in Plant Physiology, Federal University of Pelotas, Pelotas, Brazil
| | - Maria Hrmova
- Faculty of Sciences, Engineering and Technology, University of Adelaide, Adelaide, SA, Australia
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Steffen P. Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Luis Fernando S. M. Timmers
- Graduate Program in Biotechnology, University of Taquari Valley – Univates, Lajeado, Brazil
- Graduate Program in Medical Sciences, University of Taquari Valley – Univates, Lajeado, Brazil
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24
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Advances in the Molecular Mechanisms of Abscisic Acid and Gibberellins Functions in Plants 2.0. Int J Mol Sci 2022; 23:ijms23158524. [PMID: 35955659 PMCID: PMC9368775 DOI: 10.3390/ijms23158524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 07/27/2022] [Indexed: 02/05/2023] Open
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