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Bhardwaj E, Pokhriyal E, Jain A, Lal M, Khari M, Jalan K, Das S. The non-canonically organized members of MIR395 gene family in Brassica juncea are associated with developmentally regulated, sulfate-stress responsive bidirectional promoters that exhibit orientation-dependent differential transcriptional activity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 348:112214. [PMID: 39127349 DOI: 10.1016/j.plantsci.2024.112214] [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: 04/26/2024] [Revised: 07/02/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024]
Abstract
Several MICRORNA genes belonging to same family or different families are often found in homologous or non-homologous clusters. Among the various classes, head-to-head arranged genes form one of the largest categories of non-canonically organized genes. Such head-to-head arranged, non-canonically organized genes possibly share cis-regulatory region with the intergenic sequence having the potential to function as bi-directional promoter (BDP). The transcriptional regulation of head-to-head arranged genes, especially with bidirectional promoters, remains an enigma. In the past, bidirectional promoters have been characterized for a small set of protein-coding gene pairs in plants; however, to the best of our knowledge, no such study has been carried so far for MICRORNA genes. The present study thus functionally characterizes bidirectional promoters associated with members of MIR395 family, which is evolutionary conserved and is most frequently occurring cluster across plant kingdom. In Arabidopsis thaliana, the MIR395 gene family contains six members with two head-to-head arranged gene pairs- MIR395A-B and MIR395E-F. This organization was found to be conserved at seven loci for MIR395A-B, and eleven loci for MIR395E-F in five Brassica sps. Sequence analysis of the putative bidirectional promoters revealed variation in length, GC content and distribution of strict TATA-box. Comparatively higher level of conservation at both the ends of the bidirectional promoters, corresponding to ca. 250 bp upstream of 5'end of the respective MIRNA precursor, was observed. These conserved regions harbour several abiotic stress (nutrient, salt, drought) and hormone (ABA, ethylene) responsive cis-motifs. Functional characterization of putative bidirectional promoters associated with MIR395A-B and MIR395E-F from Arabidopsis and their respective orthologs from Brassica juncea (Bj_A08 MIR395A-B, Bj_B03 MIR395A-B, Bj_A07.1 MIR395E-F and Bj_A07.2 MIR395E-F) was carried out using a dual-reporter vector with β-glucuronidase (GUS) and Green Fluorescent Protein (GFP). Analysis of transcriptional regulation of the two reporter genes - GUS and GFP during developmental stages confirmed their bidirectional nature. Orientation-dependent differential reporter activity indicated asymmetric nature of the promoters. Comparison of the reporter activity amongst orthologs, paralogs and homeologs revealed regulatory diversification, an outcome expected in polyploid genomes. Interestingly, reporter gene activities driven by selected bidirectional promoters were also observed in anther and siliques apart vegetative tissues indicating role of miR395 in anther and fruit development. Finally, we evaluated the activity of reporter genes driven under transcriptional regulation of bidirectional promoters under normal and sulfate-deprived conditions which revealed asymmetric inducibility under sulfate-starvation, in agreement with the known role of miR395 in sulfate homeostasis.
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Affiliation(s)
- Ekta Bhardwaj
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Ekta Pokhriyal
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Aditi Jain
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Mukund Lal
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Megha Khari
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Komal Jalan
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi 110007, India.
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Yuan J, Wang X, Qu S, Shen T, Li M, Zhu L. The roles of miR156 in abiotic and biotic stresses in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108150. [PMID: 37922645 DOI: 10.1016/j.plaphy.2023.108150] [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: 08/02/2023] [Revised: 10/09/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
MicroRNAs (miRNAs), known as a kind of non-coding RNA, can negatively regulate its target genes. To date, the roles of various miRNAs in plant development and resistance to abiotic and biotic stresses have been widely explored. The present review summarized and discussed the functions of miR156 or miR156-SPL module in abiotic and biotic stresses, such as drought, salt, heat, cold stress, UV-B radiation, heavy mental hazards, nutritional starvation, as well as plant viruses, plant diseases, etc. Based on this, the regulation of miR156-involved stress tolerance was better understood, thus, it would be much easier for plant biologists to carry out suitable strategies to help plants suffer from unfavorable living environments.
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Affiliation(s)
- Jing Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xi Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shengtao Qu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tian Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lingcheng Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Samynathan R, Venkidasamy B, Shanmugam A, Ramalingam S, Thiruvengadam M. Functional role of microRNA in the regulation of biotic and abiotic stress in agronomic plants. Front Genet 2023; 14:1272446. [PMID: 37886688 PMCID: PMC10597799 DOI: 10.3389/fgene.2023.1272446] [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: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
The increasing demand for food is the result of an increasing population. It is crucial to enhance crop yield for sustainable production. Recently, microRNAs (miRNAs) have gained importance because of their involvement in crop productivity by regulating gene transcription in numerous biological processes, such as growth, development and abiotic and biotic stresses. miRNAs are small, non-coding RNA involved in numerous other biological functions in a plant that range from genomic integrity, metabolism, growth, and development to environmental stress response, which collectively influence the agronomic traits of the crop species. Additionally, miRNA families associated with various agronomic properties are conserved across diverse plant species. The miRNA adaptive responses enhance the plants to survive environmental stresses, such as drought, salinity, cold, and heat conditions, as well as biotic stresses, such as pathogens and insect pests. Thus, understanding the detailed mechanism of the potential response of miRNAs during stress response is necessary to promote the agronomic traits of crops. In this review, we updated the details of the functional aspects of miRNAs as potential regulators of various stress-related responses in agronomic plants.
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Affiliation(s)
- Ramkumar Samynathan
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Baskar Venkidasamy
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Ashokraj Shanmugam
- Plant Physiology and Biotechnology Division, UPASI Tea Research Foundation, Coimbatore, Tamil Nadu, India
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Lab, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, Republic of Korea
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Pasandideh Arjmand M, Samizadeh Lahiji H, Mohsenzadeh Golfazani M, Biglouei MH. Evaluation of protein's interaction and the regulatory network of some drought-responsive genes in Canola under drought and re-watering conditions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1085-1102. [PMID: 37829706 PMCID: PMC10564702 DOI: 10.1007/s12298-023-01345-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 10/14/2023]
Abstract
Drought stress is one of the most important environmental stresses that severely limits the growth and yield of Canola. The re-watering can compensate for the damage caused by drought stress. Investigation of protein's interaction of genes involved in important drought-responsive pathways and their regulatory network by microRNAs (miRNAs) under drought and re-watering conditions are helpful approaches to discovering drought-stress tolerance and recovery mechanisms. In this study, the protein's interaction and functional enrichment analyses of glycolysis, pentose phosphate, glyoxylate cycle, fatty acid biosynthesis, heat shock factor main genes, and the regulatory network of key genes by miRNAs were investigated by in silico analysis. Then, the relative expression of key genes and their related miRNAs were investigated in tolerant and susceptible genotypes of Canola under drought and re-watering conditions by Real-time PCR technique. The bna-miR156b/c/g, bna-miR395d/e/f, bna-miR396a, and all the studied key genes except HSFA1E and PK showed changes in expression levels in one or both genotypes after re-watering. The PPC1 and HSFB2B expression decreased, whereas the MLS and CAC3 expression increased in both genotypes under re-watering treatment after drought stress. It could cause the regulation of oxaloacetate production, the increase of the glyoxylate cycle, lipid biosynthesis, and the reduction of the negative regulation of HSFs under re-watering conditions. It seems that PPC1, G6PD2, MLS, CAC3, and HSFB2B were involved in the recovery mechanisms after drought stress of Canola. They were regulated by drought-responsive miRNAs to respond appropriately to drought stress. Therefore, regulating these genes could be important in plant recovery mechanisms. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01345-1.
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Affiliation(s)
- Maryam Pasandideh Arjmand
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | | | | | - Mohammad Hassan Biglouei
- Department of Water Engineering, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
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Morsi NAA, Hashem OSM, El-Hady MAA, Abd-Elkrem YM, El-temsah ME, Galal EG, Gad KI, Boudiar R, Silvar C, El-Hendawy S, Mansour E, Abdelkader MA. Assessing Drought Tolerance of Newly Developed Tissue-Cultured Canola Genotypes under Varying Irrigation Regimes. AGRONOMY 2023; 13:836. [DOI: 10.3390/agronomy13030836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Drought is a major abiotic stress that greatly affects canola growth, production, and quality. Moreover, water scarcity is projected to be more severe and frequent as a result of climate change, in particular in arid environments. Thereupon, developing drought-tolerant and high-yielding canola genotypes has become more critical to sustaining its production and ensuring global food security with the continuing population growth. In the present study, ten canola genotypes comprising six developed tissue-cultured canola genotypes, two exotic genotypes, and two commercial cultivars were evaluated under four irrigation regimes. The applied irrigation regimes were well-watered (100% crop evapotranspiration, ETc), mild drought (80% ETc), moderate drought (60% ETc), and severe drought (40% ETc) conditions. Drought-stress treatments (80, 60, and 40% ETc) gradually reduced the chlorophyll content, relative water content, flowering time, days to maturity, plant height, number of pods, number of branches, seed yield, and oil percentage, and increased proline, phenolic, anthocyanin, and glycine betaine contents. The evaluated genotypes exhibited varied responses to drought-stress conditions. The developed tissue-cultured genotypes T2, T3, and T1, as well as exotic genotype Torpe, possessed the highest performance in all evaluated parameters and surpassed the other tested genotypes under water-deficit conditions. Overall, our findings elicited the superiority of certain newly developed tissue-cultured genotypes and exotic ones compared with commercial cultivars, which could be exploited in canola breeding under water-deficit conditions.
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Affiliation(s)
- Nahid A. A. Morsi
- Cell Research Department (CRD), Field Crops Research Institute (FCRI), Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Omnia S. M. Hashem
- Crop Physiology Research Department, Field Crops Research Institute (FCRI), Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Mohamed A. Abd El-Hady
- Agronomy Department, Faculty of Agriculture, Ain Shams University, Hadayek Shoubra, P.O. Box 68, Cairo 11241, Egypt
| | - Yasser M. Abd-Elkrem
- Agronomy Department, Faculty of Agriculture, Ain Shams University, Hadayek Shoubra, P.O. Box 68, Cairo 11241, Egypt
| | - Mohamed E. El-temsah
- Agronomy Department, Faculty of Agriculture, Ain Shams University, Hadayek Shoubra, P.O. Box 68, Cairo 11241, Egypt
| | - Elhussin G. Galal
- Wheat Research Department, Field Crops Research Institute (FCRI), Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Khaled I. Gad
- Wheat Research Department, Field Crops Research Institute (FCRI), Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Ridha Boudiar
- Biotechnology Research Center—C.R.Bt Constantine, UV 03, P.O. Box E73, Nouvelle Ville Ali Mendjeli, Constantine 25016, Algeria
| | - Cristina Silvar
- Grupo de Investigación en Bioloxía Evolutiva, CICA—Centro Interdisciplinar de Química e Bioloxía, Universidade da Coruña, 15071 A Coruña, Spain
| | - Salah El-Hendawy
- Department of Plant Production, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Elsayed Mansour
- Department of Crop Science, Faculty of Agriculture, Zagazig University, Zagazig 44519, Egypt
| | - Mohamed A. Abdelkader
- Agronomy Department, Faculty of Agriculture, Ain Shams University, Hadayek Shoubra, P.O. Box 68, Cairo 11241, Egypt
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Sarwar R, Li L, Yu J, Zhang Y, Geng R, Meng Q, Zhu K, Tan XL. Functional Characterization of the Cystine-Rich-Receptor-like Kinases ( CRKs) and Their Expression Response to Sclerotinia sclerotiorum and Abiotic Stresses in Brassica napus. Int J Mol Sci 2022; 24:ijms24010511. [PMID: 36613954 PMCID: PMC9820174 DOI: 10.3390/ijms24010511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/24/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022] Open
Abstract
Cysteine-rich receptor-like kinases (CRKs) are transmembrane proteins that bind to the calcium ion to regulate stress-signaling and plant development-related pathways, as indicated by several pieces of evidence. However, the CRK gene family hasn’t been inadequately examined in Brassica napus. In our study, 27 members of the CRK gene family were identified in Brassica napus, which are categorized into three phylogenetic groups and display synteny relationship to the Arabidopsis thaliana orthologs. All the CRK genes contain highly conserved N-terminal PKINASE domain; however, the distribution of motifs and gene structure were variable conserved. The functional divergence analysis between BnaCRK groups indicates a shift in evolutionary rate after duplication events, demonstrating that BnaCRKs might direct a specific function. RNA-Seq datasets and quantitative real-time PCR (qRT-PCR) exhibit the complex expression profile of the BnaCRKs in plant tissues under multiple stresses. Nevertheless, BnaA06CRK6-1 and BnaA08CRK8 from group B were perceived to play a predominant role in the Brassica napus stress signaling pathway in response to drought, salinity, and Sclerotinia sclerotiorum infection. Insights gained from this study improve our knowledge about the Brassica napus CRK gene family and provide a basis for enhancing the quality of rapeseed.
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Affiliation(s)
- Rehman Sarwar
- School of Food Science and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Lei Li
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Jiang Yu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Yijie Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Rui Geng
- School of Food Science and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Qingfeng Meng
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Keming Zhu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Xiao-Li Tan
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
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7
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Islam W, Idrees A, Waheed A, Zeng F. Plant responses to drought stress: microRNAs in action. ENVIRONMENTAL RESEARCH 2022; 215:114282. [PMID: 36122702 DOI: 10.1016/j.envres.2022.114282] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Drought is common in most regions of the world, and it has a significant impact on plant growth and development. Plants, on the other hand, have evolved their own defense systems to deal with the extreme weather. The reprogramming of gene expression by microRNAs (miRNAs) is one of these defense mechanisms. miRNAs are short noncoding RNAs that have emerged as key post-transcriptional gene regulators in a variety of species. Drought stress modulates the expression of certain miRNAs that are functionally conserved across plant species. These characteristics imply that miRNA-based genetic changes might improve drought resistance in plants. This study highlights current knowledge of plant miRNA biogenesis, regulatory mechanisms and their role in drought stress responses. miRNAs functions and their adaptations by plants during drought stress has also been explained that can be exploited to promote drought-resistance among economically important crops.
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Affiliation(s)
- Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Atif Idrees
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Abdul Waheed
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Li J, Li Y, Wang R, Fu J, Zhou X, Fang Y, Wang Y, Liu Y. Multiple Functions of MiRNAs in Brassica napus L. Life (Basel) 2022; 12:1811. [PMID: 36362967 PMCID: PMC9694376 DOI: 10.3390/life12111811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/04/2022] [Accepted: 11/06/2022] [Indexed: 09/05/2023] Open
Abstract
The worldwide climate changes every year due to global warming, waterlogging, drought, salinity, pests, and pathogens, impeding crop productivity. Brassica napus is one of the most important oil crops in the world, and rapeseed oil is considered one of the most health-beneficial edible vegetable oils. Recently, miRNAs have been found and confirmed to control the expression of targets under disruptive environmental conditions. The mechanism is through the formation of the silencing complex that mediates post-transcriptional gene silencing, which pairs the target mRNA and target cleavage and/or translation inhibition. However, the functional role of miRNAs and targets in B. napus is still not clarified. This review focuses on the current knowledge of miRNAs concerning development regulation and biotic and abiotic stress responses in B. napus. Moreover, more strategies for miRNA manipulation in plants are discussed, along with future perspectives, and the enormous amount of transcriptome data available provides cues for miRNA functions in B. napus. Finally, the construction of the miRNA regulatory network can lead to the significant development of climate change-tolerant B. napus through miRNA manipulation.
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Affiliation(s)
- Jian Li
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou 221121, China
| | - Yangyang Li
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou 221121, China
| | - Rongyuan Wang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou 221121, China
| | - Jiangyan Fu
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou 221121, China
| | - Xinxing Zhou
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou 221121, China
| | - Yujie Fang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Yaju Liu
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou 221121, China
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Sarwar R, Geng R, Li L, Shan Y, Zhu KM, Wang J, Tan XL. Genome-Wide Prediction, Functional Divergence, and Characterization of Stress-Responsive BZR Transcription Factors in B. napus. FRONTIERS IN PLANT SCIENCE 2022; 12:790655. [PMID: 35058951 PMCID: PMC8764130 DOI: 10.3389/fpls.2021.790655] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/01/2021] [Indexed: 05/12/2023]
Abstract
BRASSINAZOLE RESISTANT (BZR) are transcriptional factors that bind to the DNA of targeted genes to regulate several plant growth and physiological processes in response to abiotic and biotic stresses. However, information on such genes in Brassica napus is minimal. Furthermore, the new reference Brassica napus genome offers an excellent opportunity to systematically characterize this gene family in B. napus. In our study, 21 BnaBZR genes were distributed across 19 chromosomes of B. napus and clustered into four subgroups based on Arabidopsis thaliana orthologs. Functional divergence analysis among these groups evident the shifting of evolutionary rate after the duplication events. In terms of structural analysis, the BnaBZR genes within each subgroup are highly conserved but are distinctive within groups. Organ-specific expression analyses of BnaBZR genes using RNA-seq data and quantitative real-time polymerase chain reaction (qRT-PCR) revealed complex expression patterns in plant tissues during stress conditions. In which genes belonging to subgroups III and IV were identified to play central roles in plant tolerance to salt, drought, and Sclerotinia sclerotiorum stress. The insights from this study enrich our understanding of the B. napus BZR gene family and lay a foundation for future research in improving rape seed environmental adaptability.
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Affiliation(s)
- Rehman Sarwar
- School of Food Science and Biological Engineering, Jiangsu University, Zhenjiang, China
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Rui Geng
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Lei Li
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Yue Shan
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ke-Ming Zhu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Jin Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiao-Li Tan
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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10
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Um T, Choi J, Park T, Chung PJ, Jung SE, Shim JS, Kim YS, Choi I, Park SC, Oh S, Seo JS, Kim J. Rice microRNA171f/SCL6 module enhances drought tolerance by regulation of flavonoid biosynthesis genes. PLANT DIRECT 2022; 6:e374. [PMID: 35028494 PMCID: PMC8743358 DOI: 10.1002/pld3.374] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 12/08/2021] [Indexed: 05/27/2023]
Abstract
Plants have evolved sophisticated defense systems to enhance drought tolerance. These include the microRNA (miRNA) group of small noncoding RNAs that act as post-transcriptional regulators; however, details of the mechanisms by which they confer drought tolerance are not well understood. Here, we show that osa-MIR171f, a member of osa-MIR171 gene family, is mainly expressed in response to drought stress and regulates the transcript levels of SCARECROW-LIKE6-I (SCL6-I) and SCL6-II in rice (Oryza sativa). The SCL6 genes are known to be involved in shoot branching and flag leaf morphology. Osa-MIR171f-overexpressing (osa-MIR171f-OE) transgenic plants showed reduced drought symptoms compared with non-transgenic (NT) control plants under both field drought and polyethylene glycol (PEG)-mediated dehydration stress conditions. Transcriptome analysis of osa-MIR171f-OE plants and osa-mir171f-knockout (K/O) lines generated by clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) revealed that osa-mature-miR171a-f (osa-miR171) regulates the expression of flavonoid biosynthesis genes, consequently leading to drought tolerance. This upregulation in the osa-MIR171f-OE plants, which did not occur in NT control plants, was observed under both normal and drought conditions. Our findings indicate that osa-miR171 plays a role in drought tolerance by regulating SCL6-I and SCL6-II transcript levels.
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Affiliation(s)
- Taeyoung Um
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangSouth Korea
- Agriculture and Life Sciences Research InstituteKangwon National UniversityChuncheonSouth Korea
| | - Joohee Choi
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangSouth Korea
- Novel Food DivisionNational Institute of Food and Drug Safety EvaluationCheongjuSouth Korea
| | - Taehyeon Park
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangSouth Korea
| | - Pil Joong Chung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangSouth Korea
| | - Se Eun Jung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangSouth Korea
| | - Jae Sung Shim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangSouth Korea
- School of Biological Sciences and TechnologyChonnam National UniversityGwangjuSouth Korea
| | - Youn Shic Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangSouth Korea
- Agriculture and Life Sciences Research InstituteKangwon National UniversityChuncheonSouth Korea
| | - Ik‐Young Choi
- Department of Agricultural and life industryKangwon National UniversityChuncheonSouth Korea
| | - Soo Chul Park
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangSouth Korea
- Department of Agricultural Biotechnology, National Academy of Agricultural ScienceRural Development AdministrationJeonjuSouth Korea
| | - Se‐Jun Oh
- LaSemilla Co. LtdPyeongchangSouth Korea
| | - Jun Sung Seo
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangSouth Korea
| | - Ju‐Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangSouth Korea
- LaSemilla Co. LtdPyeongchangSouth Korea
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11
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Kourani M, Mohareb F, Rezwan FI, Anastasiadi M, Hammond JP. Genetic and Physiological Responses to Heat Stress in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:832147. [PMID: 35449889 PMCID: PMC9016328 DOI: 10.3389/fpls.2022.832147] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/04/2022] [Indexed: 05/07/2023]
Abstract
Given the current rise in global temperatures, heat stress has become a major abiotic challenge affecting the growth and development of various crops and reducing their productivity. Brassica napus, the second largest source of vegetable oil worldwide, experiences a drastic reduction in seed yield and quality in response to heat. This review outlines the latest research that explores the genetic and physiological impact of heat stress on different developmental stages of B. napus with a special attention to the reproductive stages of floral progression, organogenesis, and post flowering. Several studies have shown that extreme temperature fluctuations during these crucial periods have detrimental effects on the plant and often leading to impaired growth and reduced seed production. The underlying mechanisms of heat stress adaptations and associated key regulatory genes are discussed. Furthermore, an overview and the implications of the polyploidy nature of B. napus and the regulatory role of alternative splicing in forming a priming-induced heat-stress memory are presented. New insights into the dynamics of epigenetic modifications during heat stress are discussed. Interestingly, while such studies are scarce in B. napus, opposite trends in expression of key genetic and epigenetic components have been identified in different species and in cultivars within the same species under various abiotic stresses, suggesting a complex role of these genes and their regulation in heat stress tolerance mechanisms. Additionally, omics-based studies are discussed with emphasis on the transcriptome, proteome and metabolome of B. napus, to gain a systems level understanding of how heat stress alters its yield and quality traits. The combination of omics approaches has revealed crucial interactions and regulatory networks taking part in the complex machinery of heat stress tolerance. We identify key knowledge gaps regarding the impact of heat stress on B. napus during its yield determining reproductive stages, where in-depth analysis of this subject is still needed. A deeper knowledge of heat stress response components and mechanisms in tissue specific models would serve as a stepping-stone to gaining insights into the regulation of thermotolerance that takes place in this important crop species and support future breeding of heat tolerant crops.
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Affiliation(s)
- Mariam Kourani
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - Fady Mohareb
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
- *Correspondence: Fady Mohareb,
| | - Faisal I. Rezwan
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - Maria Anastasiadi
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - John P. Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
- John P. Hammond,
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12
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Zeeshan M, Qiu CW, Naz S, Cao F, Wu F. Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars. Int J Mol Sci 2021; 22:ijms222212556. [PMID: 34830438 PMCID: PMC8621374 DOI: 10.3390/ijms222212556] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 01/16/2023] Open
Abstract
Salinity is a serious environmental issue. It has a substantial effect on crop yield, as many crop species are sensitive to salinity due to climate change, and it impact is continuing to increase. Plant microRNAs (miRNAs) contribute to salinity stress response in bread wheat. However, the underlying molecular mechanisms by which miRNAs confer salt tolerance in wheat are unclear. We conducted a genome-wide discovery study using Illumina high throughput sequencing and comprehensive in silico analysis to obtain insight into the underlying mechanisms by which small RNAs confer tolerance to salinity in roots of two contrasting wheat cvv., namely Suntop (salt-tolerant) and Sunmate (salt-sensitive). A total of 191 microRNAs were identified in both cultivars, consisting of 110 known miRNAs and 81 novel miRNAs; 181 miRNAs were shared between the two cultivars. The known miRNAs belonged to 35 families consisted of 23 conserved and 12 unique families. Salinity stress induced 43 and 75 miRNAs in Suntop and Sunmate, respectively. Among them, 14 and 29 known and novel miRNAs were expressed in Suntop and 37 and 38 in Sunmate. In silico analysis revealed 861 putative target mRNAs for the 75 known miRNAs and 52 putative target mRNAs for the 15 candidate novel miRNAs. Furthermore, seven miRNAs including tae-miR156, tae-miR160, tae-miR171a-b, tae-miR319, tae-miR159a-b, tae-miR9657 and novel-mir59 that regulate auxin responsive-factor, SPL, SCL6, PCF5, R2R3 MYB, and CBL-CIPK, respectively, were predicted to contribute to salt tolerance in Suntop. This information helps further our understanding of how the molecular mechanisms of salt tolerance are mediated by miRNAs and may facilitate the genetic improvement of wheat cultivars.
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Affiliation(s)
- Muhammad Zeeshan
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (M.Z.); (C.-W.Q.); (S.N.); (F.C.)
- Key Laboratory of Crop Cultivation and Tillage, Agricultural College of Guangxi University, Nanning 530004, China
| | - Cheng-Wei Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (M.Z.); (C.-W.Q.); (S.N.); (F.C.)
| | - Shama Naz
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (M.Z.); (C.-W.Q.); (S.N.); (F.C.)
| | - Fangbin Cao
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (M.Z.); (C.-W.Q.); (S.N.); (F.C.)
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (M.Z.); (C.-W.Q.); (S.N.); (F.C.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel./Fax: +86-571-8898-2827
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13
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Wang C, Tian M, Zhang Y. Characterization of microRNAs involved in asymbiotic germination of Bletilla striata (Orchidaceae) seeds. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:163-173. [PMID: 34358730 DOI: 10.1016/j.plaphy.2021.07.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Orchids are distributed worldwide, and some species have considerable economic value. Orchid seeds are minute in size, simple in structure, and deficient in nutrient reserves. Asymbiotic seed germination is an important propagation strategy for orchids. MicroRNAs (miRNAs) play an essential role in seed germination. However, few studies have examined miRNAs involved in seed germination in orchids. Here, we conducted comparative small RNA sequencing at five stages to characterize the miRNAs involved in asymbiotic seed germination in Bletilla striata. A total of 253 known and 125 novel miRNAs were identified. Of them, 71 known and 29 novel miRNAs showed distinct expression among the five stages. Quantitative PCR revealed negative correlations of expression between differentially expressed miRNAs (DE miRNAs) and their targets. Function annotation and enrichment analyses of the targets of DE miRNAs between adjacent stages indicate that miRNA-target regulations are involved in many important processes during germination, such as signaling, biosynthesis, and transport of plant hormones. Twenty-two miRNAs were inferred to participate in plant hormone-related processes. The contents of abscisic acid, gibberellin A3, indole-3-acetic acid, jasmonic acid, trans zeatin riboside, and N6-(Δ2-isopentenyl) adenine varied significantly among the five stages. Nine tested plant hormone-related miRNAs and their targets exhibited significant correlations with at least one plant hormone. 5'-RLM-RACE validated that a transcript encoding auxin response factor was cleaved by Bst-miR160e as predicted. For the first time, we characterized miRNAs associated with the asymbiotic seed germination of an orchid species, which will help understand the miRNA-mediated regulatory mechanism of seed germination in orchids.
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Affiliation(s)
- Caixia Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China.
| | - Min Tian
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Ying Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
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14
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Zhao G, Cheng P, Zhang T, Abdalmegeed D, Xu S, Shen W. Hydrogen-rich water prepared by ammonia borane can enhance rapeseed (Brassica napus L.) seedlings tolerance against salinity, drought or cadmium. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112640. [PMID: 34392154 DOI: 10.1016/j.ecoenv.2021.112640] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 05/04/2023]
Abstract
Hydrogen agriculture is recently recognized as an emerging and promising approach for low-carbon society. Since shorter retention time for hydrogen gas (H2) in conventional electrolytically produced hydrogen-rich water (HRW) limits its application, seeking a more suitable method to produce and maintain H2 level in HRW for longer time remain a challenge for scientific community. To solve above problems, we compared and concluded that the H2 in HRW prepared by ammonia borane (NH3·BH3) could meet above requirement. The biological effects of HRW prepared by NH3·BH3 were further evaluated in seedlings of rapeseed, the most important crop for producing vegetable oil worldwide. Under our experimental conditions, 2 mg/L NH3·BH3-prepared HRW could confer 3-day-old hydroponic seedlings tolerance against 150 mM sodium chloride (NaCl), 20% polyethylene glycol (PEG; w/v), or 100 μM CdCl2 stress, and intensify endogenous nitric oxide (NO) accumulation under above stresses. The alleviation of seedlings growth stunt was confirmed by reducing cell death and reestablishing redox homeostasis. Reconstructing ion homeostasis, increasing proline content, and reducing Cd accumulation were accordingly observed. Above responses were sensitive to the removal of endogenous NO with its scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethyl-imidazoline-1-1-oxyl-3-oxide (cPTIO; 100 μM), reflecting the requirement of NO functioning in the regulation of plant physiology achieved by NH3·BH3-prepared HRW. The application of 1 mM tungstate, an inhibitor of nitrate reductase (NR; an important NO synthetic enzyme), showed the similar blocking responses in the phenotype, suggesting that NR might be the major source of NO involved in above H2 actions. Together, these results revealed that HRW prepared by NH3·BH3 could enhance rapeseed seedlings tolerance against abiotic stress, thus opening a new window for the application of H2 in agricultural production.
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Affiliation(s)
- Gan Zhao
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengfei Cheng
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Tong Zhang
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Dyaaaldin Abdalmegeed
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Sheng Xu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Wenbiao Shen
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; Center of Hydrogen Science, Shanghai Jiao Tong University, Shanghai 200240, China.
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15
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Regmi R, Newman TE, Kamphuis LG, Derbyshire MC. fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen. BMC PLANT BIOLOGY 2021; 21:366. [PMID: 34380425 PMCID: PMC8356391 DOI: 10.1186/s12870-021-03148-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/27/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Small RNAs are short non-coding RNAs that are key gene regulators controlling various biological processes in eukaryotes. Plants may regulate discrete sets of sRNAs in response to pathogen attack. Sclerotinia sclerotiorum is an economically important pathogen affecting hundreds of plant species, including the economically important oilseed B. napus. However, there are limited studies on how regulation of sRNAs occurs in the S. sclerotiorum and B. napus pathosystem. RESULTS We identified different classes of sRNAs from B. napus using high throughput sequencing of replicated mock and infected samples at 24 h post-inoculation (HPI). Overall, 3999 sRNA loci were highly expressed, of which 730 were significantly upregulated during infection. These 730 up-regulated sRNAs targeted 64 genes, including disease resistance proteins and transcriptional regulators. A total of 73 conserved miRNA families were identified in our dataset. Degradome sequencing identified 2124 cleaved mRNA products from these miRNAs from combined mock and infected samples. Among these, 50 genes were specific to infection. Altogether, 20 conserved miRNAs were differentially expressed and 8 transcripts were cleaved by the differentially expressed miRNAs miR159, miR5139, and miR390, suggesting they may have a role in the S. sclerotiorum response. A miR1885-triggered disease resistance gene-derived secondary sRNA locus was also identified and verified with degradome sequencing. We also found further evidence for silencing of a plant immunity related ethylene response factor gene by a novel sRNA using 5'-RACE and RT-qPCR. CONCLUSIONS The findings in this study expand the framework for understanding the molecular mechanisms of the S. sclerotiorum and B. napus pathosystem at the sRNA level.
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Affiliation(s)
- Roshan Regmi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Floreat, WA, 6014, Australia.
| | - Toby E Newman
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Floreat, WA, 6014, Australia
| | - Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
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Su W, Raza A, Zeng L, Gao A, Lv Y, Ding X, Cheng Y, Zou X. Genome-wide analysis and expression patterns of lipid phospholipid phospholipase gene family in Brassica napus L. BMC Genomics 2021; 22:548. [PMID: 34273948 PMCID: PMC8286584 DOI: 10.1186/s12864-021-07862-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/25/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Lipid phosphate phosphatases (LPP) are critical for regulating the production and degradation of phosphatidic acid (PA), an essential signaling molecule under stress conditions. Thus far, the LPP family genes have not been reported in rapeseed (Brassica napus L.). RESULTS In this study, a genome-wide analysis was carried out to identify LPP family genes in rapeseed that respond to different stress conditions. Eleven BnLPPs genes were identified in the rapeseed genome. Based on phylogenetic and synteny analysis, BnLPPs were classified into four groups (Group I-Group IV). Gene structure and conserved motif analysis showed that similar intron/exon and motifs patterns occur in the same group. By evaluating cis-elements in the promoters, we recognized six hormone- and seven stress-responsive elements. Further, six putative miRNAs were identified targeting three BnLPP genes. Gene ontology analysis disclosed that BnLPP genes were closely associated with phosphatase/hydrolase activity, membrane parts, phosphorus metabolic process, and dephosphorylation. The qRT-PCR based expression profiles of BnLPP genes varied in different tissues/organs. Likewise, several gene expression were significantly up-regulated under NaCl, PEG, cold, ABA, GA, IAA, and KT treatments. CONCLUSIONS This is the first report to describe the comprehensive genome-wide analysis of the rapeseed LPP gene family. We identified different phytohormones and abiotic stress-associated genes that could help in enlightening the plant tolerance against phytohormones and abiotic stresses. The findings unlocked new gaps for the functional verification of the BnLPP gene family during stresses, leading to rapeseed improvement.
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Affiliation(s)
- Wei Su
- Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture, 430062, Wuhan, Hubei, China
| | - Ali Raza
- Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture, 430062, Wuhan, Hubei, China
| | - Liu Zeng
- Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture, 430062, Wuhan, Hubei, China
| | - Ang Gao
- Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture, 430062, Wuhan, Hubei, China
| | - Yan Lv
- Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture, 430062, Wuhan, Hubei, China
| | - Xiaoyu Ding
- Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture, 430062, Wuhan, Hubei, China
| | - Yong Cheng
- Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture, 430062, Wuhan, Hubei, China
| | - Xiling Zou
- Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture, 430062, Wuhan, Hubei, China.
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17
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Liu W, Li S, Zhang C, Jin F, Li W, Li X. Identification of Candidate Genes for Drought Tolerance at Maize Seedlings Using Genome-Wide Association. IRANIAN JOURNAL OF BIOTECHNOLOGY 2021; 19:e2637. [PMID: 34825009 PMCID: PMC8590722 DOI: 10.30498/ijb.2021.209324.2637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Drought stress is a serious threat that limit maize growth and production. OBJECTIVES The assessment tolerance level of maize by measuring changes in the main biochemical and physiological indicators under drought stress. MATERIAL AND METHODS We performed a genome-wide association analysis of biochemical and physiological indicators using an elite association panel. RESULTS The results revealed that eight significant SNPs (p<0.05/N) located in eight genes that are distributed on different chromosomes were associated with drought resistance indices under drought stress. Among these genes, four genes were linked via the associated SNPs with drought-resistance indices of the malondialdehyde activity (MDA), three genes were linked with drought resistance indexes of the superoxide dismutase activity (SOD), and one gene was linked with drought resistance indexes of relative conductivity (REC). The candidate genes functioned as transcription factors, enzymes, and transporters, which included trehalase, the AP2/EREB160 transcription factor, and glutathione S-transferase and also encoded a gene of unknown function. These genes may be directly or indirectly involved in drought resistance. The expression levels of ZmEREB160 responded to ABA and drought stress. CONCLUSIONS These results provided good information to understand the genetic basis of variation in drought resistance indices of biochemical and physiological indicators during drought stress.
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Affiliation(s)
- Wenping Liu
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, Jilin, China
| | - Shufang Li
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, Jilin, China
| | - Chunxiao Zhang
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, Jilin, China
| | - Fengxue Jin
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, Jilin, China
| | - Wanjun Li
- Taonan Research Center, Jilin Academy of Agricultural Sciences, Taonan 137100, Jilin, China
| | - Xiaohui Li
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, Jilin, China
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18
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Jin T, Sun Y, Shan Z, He J, Wang N, Gai J, Li Y. Natural variation in the promoter of GsERD15B affects salt tolerance in soybean. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1155-1169. [PMID: 33368860 PMCID: PMC8196659 DOI: 10.1111/pbi.13536] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 05/24/2023]
Abstract
Salt stress has detrimental effects on crop growth and yield, and the area of salt-affected land is increasing. Soybean is a major source of vegetable protein, oil and feed, but considered as a salt-sensitive crop. Cultivated soybean (Glycine max) is domesticated from wild soybean (G. soja) but lost considerable amount of genetic diversity during the artificial selection. Therefore, it is important to exploit the gene pool of wild soybean. In this study, we identified 34 salt-tolerant accessions from wild soybean germplasm and found that a 7-bp insertion/deletion (InDel) in the promoter of GsERD15B (early responsive to dehydration 15B) significantly affects the salt tolerance of soybean. GsERD15B encodes a protein with transcriptional activation function and contains a PAM2 domain to mediate its interaction with poly(A)-binding (PAB) proteins. The 7-bp deletion in GsERD15B promoter enhanced the salt tolerance of soybean, with increased up-regulation of GsERD15B, two GmPAB genes, the known stress-related genes including GmABI1, GmABI2, GmbZIP1, GmP5CS, GmCAT4, GmPIP1:6, GmMYB84 and GmSOS1 in response to salt stress. We propose that natural variation in GsERD15B promoter affects soybean salt tolerance, and overexpression of GsERD15B enhanced salt tolerance probably by increasing the expression levels of genes related to ABA-signalling, proline content, catalase peroxidase, dehydration response and cation transport.
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Affiliation(s)
- Ting Jin
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNational Center for Soybean ImprovementKey Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Yangyang Sun
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNational Center for Soybean ImprovementKey Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Zhong Shan
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNational Center for Soybean ImprovementKey Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Jianbo He
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNational Center for Soybean ImprovementKey Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Ning Wang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNational Center for Soybean ImprovementKey Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNational Center for Soybean ImprovementKey Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNational Center for Soybean ImprovementKey Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
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19
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Cheng X, He Q, Tang S, Wang H, Zhang X, Lv M, Liu H, Gao Q, Zhou Y, Wang Q, Man X, Liu J, Huang R, Wang H, Chen T, Liu J. The miR172/IDS1 signaling module confers salt tolerance through maintaining ROS homeostasis in cereal crops. THE NEW PHYTOLOGIST 2021; 230:1017-1033. [PMID: 33462818 DOI: 10.1111/nph.17211] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/10/2021] [Indexed: 05/14/2023]
Abstract
Salt stress triggers the overdose accumulation of reactive oxygen species (ROS) in crop plants, leading to severe oxidative damage to living tissues. MicroRNAs (miRNAs) act as master regulators orchestrating the stress responsive regulatory networks as well as salt tolerance. However, the fundamental roles of miRNAs in modulating salt tolerance in cereal crops, especially in salt-triggered ROS scavenging remain largely unknown. Through small RNA sequencing, a salt-responsive miRNA, miR172 was identified in rice. Further, by generating the miR172-overexpression or MIR172 gene loss-of-function mutant lines, the biological significance of miR172 and its downstream signaling pathways related to salt tolerance were defined. We demonstrated that miR172 is a positive regulator of salt tolerance in both rice and wheat. More interestingly, miR172a and miR172b, but not miR172c or miR172d are involved in salt stress response, emphasizing the functional differentiation within miR172 family members. Further evidence uncovers a novel miR172/IDS1 regulatory module that functions as a crucial molecular rheostat in maintaining ROS homeostasis during salt stress, mainly through balancing the expression of a group of ROS-scavenging genes. Our findings establish a direct molecular link between miRNAs and detoxification response in cereal crops for improving salt tolerance.
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Affiliation(s)
- Xiliu Cheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haoran Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Center, Beijing, 100193, China
| | - Xiangxiang Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mingjie Lv
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huafeng Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qian Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yue Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qi Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinyu Man
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rongfeng Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Agricultural Science and Technology Center, Chengdu, 610213, China
| | - Tao Chen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Center, Beijing, 100193, China
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20
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Xue X, Jiao F, Xu H, Jiao Q, Zhang X, Zhang Y, Du S, Xi M, Wang A, Chen J, Wang M. The role of RNA-binding protein, microRNA and alternative splicing in seed germination: a field need to be discovered. BMC PLANT BIOLOGY 2021; 21:194. [PMID: 33882821 PMCID: PMC8061022 DOI: 10.1186/s12870-021-02966-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 04/07/2021] [Indexed: 05/20/2023]
Abstract
Seed germination is the process through which a quiescent organ reactivates its metabolism culminating with the resumption cell divisions. It is usually the growth of a plant contained within a seed and results in the formation of a seedling. Post-transcriptional regulation plays an important role in gene expression. In cells, post-transcriptional regulation is mediated by many factors, such as RNA-binding proteins, microRNAs, and the spliceosome. This review provides an overview of the relationship between seed germination and post-transcriptional regulation. It addresses the relationship between seed germination and RNA-binding proteins, microRNAs and alternative splicing. This presentation of the current state of the knowledge will promote new investigations into the relevance of the interactions between seed germination and post-transcriptional regulation in plants.
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Affiliation(s)
- Xiaofei Xue
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Fuchao Jiao
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
- Dryland-Technology Key Laboratory of Shandong Province, Qingdao Agricultural, Qingdao, 266109, China
| | - Haicheng Xu
- Administrative Committee of Yellow River Delta Agri-High-Tech Industry Demonstration Zone, Dongying, 257347, China
| | - Qiqing Jiao
- Shandong Institute of Pomology, Tai'an, 271000, China
| | - Xin Zhang
- Jinan Fruit Research Institute, All China Federation of Supply and Marketing Co-operatives, Jinan, 250000, China
| | - Yong Zhang
- Shandong Academy of Agricultural Sciences, Jinan, 250000, China
| | - Shangyi Du
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Menghan Xi
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Aiguo Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jingtang Chen
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
- Dryland-Technology Key Laboratory of Shandong Province, Qingdao Agricultural, Qingdao, 266109, China
| | - Ming Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China.
- Dryland-Technology Key Laboratory of Shandong Province, Qingdao Agricultural, Qingdao, 266109, China.
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21
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Chaudhary S, Grover A, Sharma PC. MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops. Life (Basel) 2021; 11:life11040289. [PMID: 33800690 PMCID: PMC8066829 DOI: 10.3390/life11040289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.
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Affiliation(s)
- Saurabh Chaudhary
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
- Correspondence: (S.C.); (P.C.S.)
| | - Atul Grover
- Defence Institute of Bio-Energy Research, Defence Research and Development Organisation (DRDO), Haldwani 263139, India;
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi 110078, India
- Correspondence: (S.C.); (P.C.S.)
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22
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Xu T, Zhang L, Yang Z, Wei Y, Dong T. Identification and Functional Characterization of Plant MiRNA Under Salt Stress Shed Light on Salinity Resistance Improvement Through MiRNA Manipulation in Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:665439. [PMID: 34220888 PMCID: PMC8247772 DOI: 10.3389/fpls.2021.665439] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/29/2021] [Indexed: 05/07/2023]
Abstract
Salinity, as a major environmental stressor, limits plant growth, development, and crop yield remarkably. However, plants evolve their own defense systems in response to salt stress. Recently, microRNA (miRNA) has been broadly studied and considered to be an important regulator of the plant salt-stress response at the post-transcription level. In this review, we have summarized the recent research progress on the identification, functional characterization, and regulatory mechanism of miRNA involved in salt stress, have discussed the emerging manipulation of miRNA to improve crop salt resistance, and have provided future direction for plant miRNA study under salt stress, suggesting that the salinity resistance of crops could be improved by the manipulation of microRNA.
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Affiliation(s)
- Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- *Correspondence: Tao Xu,
| | - Long Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Zhengmei Yang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Yiliang Wei
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Tingting Dong,
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23
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Eshkiki EM, Hajiahmadi Z, Abedi A, Kordrostami M, Jacquard C. In Silico Analyses of Autophagy-Related Genes in Rapeseed ( Brassica napus L.) under Different Abiotic Stresses and in Various Tissues. PLANTS 2020; 9:plants9101393. [PMID: 33092180 PMCID: PMC7594038 DOI: 10.3390/plants9101393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/21/2022]
Abstract
The autophagy-related genes (ATGs) play important roles in plant growth and response to environmental stresses. Brassica napus (B. napus) is among the most important oilseed crops, but ATGs are largely unknown in this species. Therefore, a genome-wide analysis of the B. napus ATG gene family (BnATGs) was performed. One hundred and twenty-seven ATGs were determined due to the B. napus genome, which belongs to 20 main groups. Segmental duplication occurred more than the tandem duplication in BnATGs. Ka/Ks for the most duplicated pair genes were less than one, which indicated that the negative selection occurred to maintain their function during the evolution of B. napus plants. Based on the results, BnATGs are involved in various developmental processes and respond to biotic and abiotic stresses. One hundred and seven miRNA molecules are involved in the post-transcriptional regulation of 41 BnATGs. In general, 127 simple sequence repeat marker (SSR) loci were also detected in BnATGs. Based on the RNA-seq data, the highest expression in root and silique was related to BnVTI12e, while in shoot and seed, it was BnATG8p. The expression patterns of the most BnATGs were significantly up-regulated or down-regulated responding to dehydration, salinity, abscisic acid, and cold. This research provides information that can detect candidate genes for genetic manipulation in B. napus.
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Affiliation(s)
- Elham Mehri Eshkiki
- Department of Agricultural Biotechnology, Payame Noor University (PNU), Tehran P.O. Box 19395-4697, Iran;
| | - Zahra Hajiahmadi
- Department of Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht P.O. Box 41635-1314, Iran; (Z.H.); (A.A.)
| | - Amin Abedi
- Department of Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht P.O. Box 41635-1314, Iran; (Z.H.); (A.A.)
| | - Mojtaba Kordrostami
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj P.O. Box 31485498, Iran;
| | - Cédric Jacquard
- Resistance Induction and Bioprotection of Plants Unit (RIBP)—EA4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Moulin de la Housse, CEDEX 2, BP 1039, 51687 Reims, France
- Correspondence: ; Tel.: +33-3-26-91-34-36
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24
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Xia H, Yu S, Kong D, Xiong J, Ma X, Chen L, Luo L. Temporal responses of conserved miRNAs to drought and their associations with drought tolerance and productivity in rice. BMC Genomics 2020; 21:232. [PMID: 32171232 PMCID: PMC7071783 DOI: 10.1186/s12864-020-6646-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/04/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Plant miRNAs play crucial roles in responses to drought and developmental processes. It is essential to understand the association of miRNAs with drought-tolerance (DT), as well as their impacts on growth, development, and reproduction (GDP). This will facilitate our utilization of rice miRNAs in breeding. RESULTS In this study, we investigated the time course of miRNA responses to a long-term drought among six rice genotypes by high-throughput sequencing. In total, 354 conserved miRNAs were drought responsive, representing obvious genotype- and stage-dependent patterns. The drought-responsive miRNAs (DRMs) formed complex regulatory network via their coexpression and direct/indirect impacts on the rice transcriptome. Based on correlation analyses, 211 DRMs were predicted to be associated with DT and/or GDP. Noticeably, 14.2% DRMs were inversely correlated with DT and GDP. In addition, 9 pairs of mature miRNAs, each derived from the same pre-miRNAs, were predicted to have opposite roles in regulating DT and GDP. This suggests a potential yield penalty if an inappropriate miRNA/pre-miRNA is utilized. miRNAs have profound impacts on the rice transcriptome reflected by great number of correlated drought-responsive genes. By regulating these genes, a miRNA could activate diverse biological processes and metabolic pathways to adapt to drought and have an influence on its GDP. CONCLUSION Based on the temporal pattern of miRNAs in response to drought, we have described the complex network between DRMs. Potential associations of DRMs with DT and/or GDP were disclosed. This knowledge provides valuable information for a better understanding in the roles of miRNAs play in rice DT and/or GDP, which can facilitate our utilization of miRNA in breeding.
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Affiliation(s)
- Hui Xia
- Shanghai Agrobiological Gene Center, Shanghai, China.
| | - Shunwu Yu
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Deyan Kong
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Jie Xiong
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Xiaosong Ma
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Liang Chen
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, China.
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25
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Hou G, Du C, Gao H, Liu S, Sun W, Lu H, Kang J, Xie Y, Ma D, Wang C. Identification of microRNAs in developing wheat grain that are potentially involved in regulating grain characteristics and the response to nitrogen levels. BMC PLANT BIOLOGY 2020; 20:87. [PMID: 32103721 PMCID: PMC7045451 DOI: 10.1186/s12870-020-2296-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/20/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) play crucial roles in the regulation of plant development and growth, but little information is available concerning their roles during grain development under different nitrogen (N) application levels. Our objective was to identify miRNAs related to the regulation of grain characteristics and the response to different N fertilizer conditions. RESULTS A total of 79 miRNAs (46 known and 33 novel miRNAs) were identified that showed significant differential expression during grain development under both high nitrogen (HN) and low nitrogen (LN) treatments. The miRNAs that were significantly upregulated early in grain development target genes involved mainly in cell differentiation, auxin-activated signaling, and transcription, which may be associated with grain size; miRNAs abundant in the middle and later stages target genes mainly involved in carbohydrate and nitrogen metabolism, transport, and kinase activity and may be associated with grain filling. Additionally, we identified 50 miRNAs (22 known and 28 novel miRNAs), of which 11, 9, and 39 were differentially expressed between the HN and LN libraries at 7, 17, and 27 days after anthesis (DAA). The miRNAs that were differentially expressed in response to nitrogen conditions target genes involved mainly in carbohydrate and nitrogen metabolism, the defense response, and transport as well as genes that encode ubiquitin ligase. Only one novel miRNA (PC-5p-2614_215) was significantly upregulated in response to LN treatment at all three stages, and 21 miRNAs showed significant differential expression between HN and LN conditions only at 27 DAA. We therefore propose a model for target gene regulation by miRNAs during grain development with N-responsive patterns. CONCLUSIONS The potential targets of the identified miRNAs are related to various biological processes, such as carbohydrate/nitrogen metabolism, transcription, cellular differentiation, transport, and defense. Our results indicate that miRNA-mediated networks, via posttranscriptional regulation, play crucial roles in grain development and the N response, which determine wheat grain weight and quality. Our study provides useful information for future research of regulatory mechanisms that focus on improving grain yield and quality.
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Affiliation(s)
- Gege Hou
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chenyang Du
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Honghuan Gao
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Sujun Liu
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wan Sun
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongfang Lu
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Juan Kang
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yingxin Xie
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dongyun Ma
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China.
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Chenyang Wang
- College of Agronomy/National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou, 450002, China.
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
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26
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Lohani N, Jain D, Singh MB, Bhalla PL. Engineering Multiple Abiotic Stress Tolerance in Canola, Brassica napus. FRONTIERS IN PLANT SCIENCE 2020; 11:3. [PMID: 32161602 PMCID: PMC7052498 DOI: 10.3389/fpls.2020.00003] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/03/2020] [Indexed: 05/22/2023]
Abstract
Impacts of climate change like global warming, drought, flooding, and other extreme events are posing severe challenges to global crop production. Contribution of Brassica napus towards the oilseed industry makes it an essential component of international trade and agroeconomics. Consequences from increasing occurrences of multiple abiotic stresses on this crop are leading to agroeconomic losses making it vital to endow B. napus crop with an ability to survive and maintain yield when faced with simultaneous exposure to multiple abiotic stresses. For an improved understanding of the stress sensing machinery, there is a need for analyzing regulatory pathways of multiple stress-responsive genes and other regulatory elements such as non-coding RNAs. However, our understanding of these pathways and their interactions in B. napus is far from complete. This review outlines the current knowledge of stress-responsive genes and their role in imparting multiple stress tolerance in B. napus. Analysis of network cross-talk through omics data mining is now making it possible to unravel the underlying complexity required for stress sensing and signaling in plants. Novel biotechnological approaches such as transgene-free genome editing and utilization of nanoparticles as gene delivery tools are also discussed. These can contribute to providing solutions for developing climate change resilient B. napus varieties with reduced regulatory limitations. The potential ability of synthetic biology to engineer and modify networks through fine-tuning of stress regulatory elements for plant responses to stress adaption is also highlighted.
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Affiliation(s)
| | | | | | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
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27
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Kang T, Yu CY, Liu Y, Song WM, Bao Y, Guo XT, Li B, Zhang HX. Subtly Manipulated Expression of ZmmiR156 in Tobacco Improves Drought and Salt Tolerance Without Changing the Architecture of Transgenic Plants. FRONTIERS IN PLANT SCIENCE 2020; 10:1664. [PMID: 31998347 PMCID: PMC6965348 DOI: 10.3389/fpls.2019.01664] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 11/26/2019] [Indexed: 05/23/2023]
Abstract
Plants in the juvenile state are more tolerant to adverse conditions. Constitutive expression of MicroRNA156 (miR156) prolonged the juvenile phase and increased resistance to abiotic stress, but also affected the architecture of transgenic plants. In this study, we investigated the possibility of subtle manipulation of miR156 expression in flowering plants, with the goal to increase tolerance to abiotic stress without altering the normal growth and development of transgenic plants. Transgenic tobacco plants expressing ZmmiR156 from maize were generated, driven either by the cauliflower mosaic virus (CaMV) 35S promoter or the stress-inducible ZmRab17 promoter. Expression of ZmmiR156 led to improved drought and salt tolerance in both 35S::MIR156 and Rab17::MIR156 transgenic plants, as shown by more vigorous growth, greater biomass production and higher antioxidant enzyme expression after a long period of drought or salt treatment, when compared to wild type and transgenic vector control plants. However, constitutive expression of ZmmiR156 also resulted in retarded growth, increased branching and delayed flowering of transgenic plants. These undesirable developmental changes could be mitigated by using the stress-inducible ZmRab17 promoter. Furthermore, under drought or salt stress conditions, expression of ZmmiR156 reduced the transcript level of NtSPL2 and NtSPL9, the genes potentially targeted by ZmmiR156, as well as that of CP1, CP2, and SAG12, the senescence-associated genes in tobacco. Collectively, our results indicate that ZmmiR156 can be temporally manipulated for the genetic improvement of plants resistant to various abiotic stresses.
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Affiliation(s)
- Tao Kang
- College of Agriculture, Ludong University, Yantai, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chun-Yan Yu
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
| | - Yue Liu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Wei-Meng Song
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Bao
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Tong Guo
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
| | - Bei Li
- College of Agriculture, Ludong University, Yantai, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
| | - Hong-Xia Zhang
- College of Agriculture, Ludong University, Yantai, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), Yantai, China
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28
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Ahmed W, Xia Y, Li R, Bai G, Siddique KHM, Guo P. Non-coding RNAs: Functional roles in the regulation of stress response in Brassica crops. Genomics 2019; 112:1419-1424. [PMID: 31430515 DOI: 10.1016/j.ygeno.2019.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 07/03/2019] [Accepted: 08/16/2019] [Indexed: 12/22/2022]
Abstract
Brassica crops face a combination of different abiotic and biotic stresses in the field that can reduce plant growth and development by affecting biochemical and morpho-physiological processes. Emerging evidence suggests that non-coding RNAs (ncRNAs), especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), play a significant role in the modulation of gene expression in response to plant stresses. Recent advances in computational and experimental approaches are of great interest for identifying and functionally characterizing ncRNAs. While progress in this field is limited, numerous ncRNAs involved in the regulation of gene expression in response to stress have been reported in Brassica. In this review, we summarize the modes of action and functions of stress-related miRNAs and lncRNAs in Brassica as well as the approaches used to identify ncRNAs.
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Affiliation(s)
- Waqas Ahmed
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Guihua Bai
- United States Department of Agriculture - Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas 66506, United States
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, LB 5005, Perth, WA 6001, Australia
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China.
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29
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Wei L, Yang B, Jian H, Zhang A, Liu R, Zhu Y, Ma J, Shi X, Wang R, Li J, Xu X. Genome-wide identification and characterization of Gretchen Hagen3 ( GH3) family genes in Brassica napus. Genome 2019; 62:597-608. [PMID: 31271724 DOI: 10.1139/gen-2018-0161] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The hormone auxin is involved in many biological processes throughout a plant's lifecycle. However, genes in the GH3 (Gretchen Hagen3) family, one of the three major auxin-responsive gene families, have not yet been identified in oilseed rape (Brassica napus). In this study, we identified 63 BnaGH3 genes in oilseed rape using homology searches. We analyzed the chromosome locations, gene structures, and phylogenetic relationships of the BnaGH3 genes, as well as the cis-elements in their promoters. Most BnaGH3 genes are located on chromosomes A03, A09, C02, C03, and C09, each with 4-7 members. In addition, we analyzed the expression patterns of BnaGH3 genes in seven tissues by transcriptome sequencing and quantitative RT-PCR analysis of plants under exogenous IAA treatment. The BnaGH3 genes showed different expression patterns in various tissues. BnaA.GH3.2-1 and BnaC.GH3.2-1 were expressed in the seed and seed coat during development and in response to IAA treatment. These results shed light on the possible roles of the GH3 gene family in oilseed rape.
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Affiliation(s)
- Lijuan Wei
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China
| | - Bo Yang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China
| | - Hongju Jian
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China.,Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China
| | - Aoxiang Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China.,Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China
| | - Ruiying Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China.,Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China
| | - Yan Zhu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China.,Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China
| | - Jinqi Ma
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China.,Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China
| | - Xiangtian Shi
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China.,Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China
| | - Rui Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China.,Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China.,Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China.,Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China
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High-throughput sequencing and differential expression analysis of miRNAs in response to Brassinosteroid treatment in Arabidopsis thaliana. Funct Integr Genomics 2019; 19:597-615. [PMID: 30783808 DOI: 10.1007/s10142-019-00668-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/05/2019] [Accepted: 02/07/2019] [Indexed: 10/27/2022]
Abstract
Brassinosteroids are a class of phytohormones that play crucial roles in improving stress tolerance in plants. Many biochemical and physiological changes in response to abiotic stress are related to regulation of gene expression and accumulation of associated proteins. MicroRNAs (miRNAs) are class of small non-coding RNAs that regulate gene expression post-transcriptionally. Roles of these regulatory RNAs in brassinosteroid (BR) signalling have however remained elusive. In this study using high-throughput small RNA sequencing method, we present a comprehensive compilation of BR-induced differentially expressed microRNAs in root and shoots of Arabidopsis thaliana seedlings. We identified 229 known miRNAs belonging to 102 families and 27 novel miRNAs that express in response to exogenous BR treatment. Out of 102 families, miRNAs belonging to known 48 families and out of 27 novel miRNAs, 23 were observed to be differentially expressed in response to BR treatment. Among the conserved miRNAs, all members of miR169 were observed to be downregulated in both shoot and root samples. While, auxin-responsive factors were predicted to be direct targets of some novel miRNAs that are upregulated in shoots and suppressed in roots. The BR-responsive tissue-specific miRNome characterized in this study can be used as a starting point by investigators for functional validation studies that will shed light on the underlying molecular mechanism of BR-mediated stress tolerance at the level of post-transcriptional gene regulation.
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31
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Associating transcriptional regulation for rapid germination of rapeseed (Brassica napus L.) under low temperature stress through weighted gene co-expression network analysis. Sci Rep 2019; 9:55. [PMID: 30635606 PMCID: PMC6329770 DOI: 10.1038/s41598-018-37099-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 12/03/2018] [Indexed: 12/23/2022] Open
Abstract
Slow germination speed caused by low temperature stress intensifies the risk posed by adverse environmental factors, contributing to low germination rate and reduced production of rapeseed. The purpose of this study was to understand the transcriptional regulation mechanism for rapid germination of rapeseed. The results showed that seed components and size do not determine the seed germination speed. Different temporal transcriptomic profiles were generated under normal and low temperature conditions in genotypes with fast and slow germination speeds. Using weight gene co-expression network analysis, 37 823 genes were clustered into 15 modules with different expression patterns. There were 10 233 and 9111 differentially expressed genes found to follow persistent tendency of up- and down-regulation, respectively, which provided the conditions necessary for germination. Hub genes in the continuous up-regulation module were associated with phytohormone regulation, signal transduction, the pentose phosphate pathway, and lipolytic metabolism. Hub genes in the continuous down-regulation module were involved in ubiquitin-mediated proteolysis. Through pairwise comparisons, 1551 specific upregulated DEGs were identified for the fast germination speed genotype under low temperature stress. These DEGs were mainly enriched in RNA synthesis and degradation metabolisms, signal transduction, and defense systems. Transcription factors, including WRKY, bZIP, EFR, MYB, B3, DREB, NAC, and ERF, are associated with low temperature stress in the fast germination genotype. The aquaporin NIP5 and late embryogenesis abundant (LEA) protein genes contributed to the water uptake and transport under low temperature stress during seed germination. The ethylene/H2O2-mediated signal pathway plays an important role in cell wall loosening and embryo extension during germination. The ROS-scavenging system, including catalase, aldehyde dehydrogenase, and glutathione S-transferase, was also upregulated to alleviate ROS toxicity in the fast germinating genotype under low temperature stress. These findings should be useful for molecular assisted screening and breeding of fast germination speed genotypes for rapeseed.
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Jian H, Zhang A, Ma J, Wang T, Yang B, Shuang LS, Liu M, Li J, Xu X, Paterson AH, Liu L. Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L. BMC Genomics 2019; 20:21. [PMID: 30626329 PMCID: PMC6325782 DOI: 10.1186/s12864-018-5356-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/09/2018] [Indexed: 01/10/2023] Open
Abstract
Background Optimum flowering time is a key agronomic trait in Brassica napus. To investigate the genetic architecture and genetic regulation of flowering time in this important crop, we conducted quantitative trait loci (QTL) analysis of flowering time in a recombinant inbred line (RIL) population, including lines with extreme differences in flowering time, in six environments, along with RNA-Seq analysis. Results We detected 27 QTLs distributed on eight chromosomes among six environments, including one major QTL on chromosome C02 that explained 11–25% of the phenotypic variation and was stably detected in all six environments. RNA-Seq analysis revealed 105 flowering time-related differentially expressed genes (DEGs) that play roles in the circadian clock/photoperiod, autonomous pathway, and hormone and vernalization pathways. We focused on DEGs related to the regulation of flowering time, especially DEGs in QTL regions. Conclusions We identified 45 flowering time-related genes in these QTL regions, eight of which are DEGs, including key flowering time genes PSEUDO RESPONSE REGULATOR 7 (PRR7) and FY (located in a major QTL region on C02). These findings provide insights into the genetic architecture of flowering time in B. napus. Electronic supplementary material The online version of this article (10.1186/s12864-018-5356-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongju Jian
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China.,Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Aoxiang Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Jinqi Ma
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Tengyue Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Bo Yang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Lan Shuan Shuang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Min Liu
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA.
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China.
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Zhang Y, Zhang Q, Hao L, Wang S, Wang S, Zhang W, Xu C, Yu Y, Li T. A novel miRNA negatively regulates resistance to Glomerella leaf spot by suppressing expression of an NBS gene in apple. HORTICULTURE RESEARCH 2019; 6:93. [PMID: 31645951 PMCID: PMC6804642 DOI: 10.1038/s41438-019-0175-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/13/2019] [Accepted: 06/15/2019] [Indexed: 05/07/2023]
Abstract
Glomerella leaf spot (GLS) of apple (Malus×domestica Borkh.), caused by Glomerella cingulata, is an emerging fungal epidemic threatening the apple industry. Little is known about the molecular mechanism underlying resistance to this devastating fungus. In this study, high-throughput sequencing technology was used to identify microRNAs (miRNAs) involved in GLS resistance in apple. We focused on miRNAs that target genes related to disease and found that expression of a novel miRNA, Md-miRln20, was higher in susceptible apple varieties than in resistant ones. Furthermore, its target gene Md-TN1-GLS exhibited the opposite expression pattern, which suggested that the expression levels of Md-miRln20 and its target gene are closely related to apple resistance to GLS. Furthermore, downregulation of Md-miRln20 in susceptible apple leaves resulted in upregulation of Md-TN1-GLS and reduced the disease incidence. Conversely, overexpression of Md-miRln20 in resistant apple leaves suppressed Md-TN1-GLS expression, with increased disease incidence. We demonstrated that Md-miRln20 negatively regulates resistance to GLS by suppressing Md-TN1-GLS expression and showed, for the first time, a crucial role for miRNA in response to GLS in apple.
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Affiliation(s)
- Yi Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Qiulei Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Li Hao
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Shengnan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Shengyuan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Wenna Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Chaoran Xu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Yunfei Yu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
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Jian H, Ma J, Wei L, Liu P, Zhang A, Yang B, Li J, Xu X, Liu L. Integrated mRNA, sRNA, and degradome sequencing reveal oilseed rape complex responses to Sclerotinia sclerotiorum (Lib.) infection. Sci Rep 2018; 8:10987. [PMID: 30030454 PMCID: PMC6054686 DOI: 10.1038/s41598-018-29365-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/10/2018] [Indexed: 11/23/2022] Open
Abstract
Sclerotinia stem rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is a devastating disease resulting in yield losses and decreases in seed quality in oilseed rape (Brassica napus) worldwide. However, the molecular mechanisms underlying the response of oilseed rape to S. sclerotiorum infection at the transcriptional and post-transcriptional levels are poorly understood. Here, we used an integrated omics approach (transcriptome, sRNAome, and degradome sequencing) on the Illumina platform to compare the RNA expression and post-transcriptional profiles of oilseed rape plants inoculated or not with S. sclerotiorum. In total, 7,065 differentially expressed genes (DEGs) compared with the mock-inoculated control at 48 hours post inoculation were identified. These DEGs were associated with protein kinases, signal transduction, transcription factors, hormones, pathogenesis-related proteins, secondary metabolism, and transport. In the sRNA-Seq analysis, 77 known and 176 novel miRNAs were identified; however, only 10 known and 41 novel miRNAs were differentially expressed between the samples inoculated or not with S. sclerotiorum. Degradome sequencing predicted 80 cleavage sites with 64 miRNAs. Integrated mRNA, sRNA and degradome sequencing analysis reveal oilseed rape complex responses to S. sclerotiorum infection. This study provides a global view of miRNA and mRNA expression profiles in oilseed rape following S. sclerotiorum infection.
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Affiliation(s)
- Hongju Jian
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, P. R. China
| | - Jinqi Ma
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, P. R. China
| | - Lijuan Wei
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, P. R. China
| | - Pu Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, P. R. China
| | - Aoxiang Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, P. R. China
| | - Bo Yang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, P. R. China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, P. R. China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, P. R. China
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, P. R. China.
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Shokri-Gharelo R, Noparvar PM. Molecular response of canola to salt stress: insights on tolerance mechanisms. PeerJ 2018; 6:e4822. [PMID: 29844974 PMCID: PMC5969047 DOI: 10.7717/peerj.4822] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/02/2018] [Indexed: 01/16/2023] Open
Abstract
Canola (Brassica napus L.) is widely cultivated around the world for the production of edible oils and biodiesel fuel. Despite many canola varieties being described as ‘salt-tolerant’, plant yield and growth decline drastically with increasing salinity. Although many studies have resulted in better understanding of the many important salt-response mechanisms that control salt signaling in plants, detoxification of ions, and synthesis of protective metabolites, the engineering of salt-tolerant crops has only progressed slowly. Genetic engineering has been considered as an efficient method for improving the salt tolerance of canola but there are many unknown or little-known aspects regarding canola response to salinity stress at the cellular and molecular level. In order to develop highly salt-tolerant canola, it is essential to improve knowledge of the salt-tolerance mechanisms, especially the key components of the plant salt-response network. In this review, we focus on studies of the molecular response of canola to salinity to unravel the different pieces of the salt response puzzle. The paper includes a comprehensive review of the latest studies, particularly of proteomic and transcriptomic analysis, including the most recently identified canola tolerance components under salt stress, and suggests what researchers should focus on in future studies.
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Affiliation(s)
- Reza Shokri-Gharelo
- Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, Iran
| | - Pouya Motie Noparvar
- Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, Iran.,Young Researchers and Elite Club, Islamic Azad University, Tabriz, Iran
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Jian H, Yang B, Zhang A, Ma J, Ding Y, Chen Z, Li J, Xu X, Liu L. Genome-Wide Identification of MicroRNAs in Response to Cadmium Stress in Oilseed Rape ( Brassica napus L.) Using High-Throughput Sequencing. Int J Mol Sci 2018; 19:ijms19051431. [PMID: 29748489 PMCID: PMC5983666 DOI: 10.3390/ijms19051431] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/29/2018] [Accepted: 05/07/2018] [Indexed: 02/03/2023] Open
Abstract
MicroRNAs (miRNAs) have important roles in regulating stress-response genes in plants. However, identification of miRNAs and the corresponding target genes that are induced in response to cadmium (Cd) stress in Brassica napus remains limited. In the current study, we sequenced three small-RNA libraries from B. napus after 0 days, 1 days, and 3 days of Cd treatment. In total, 44 known miRNAs (belonging to 27 families) and 103 novel miRNAs were identified. A comprehensive analysis of miRNA expression profiles found 39 differentially expressed miRNAs between control and Cd-treated plants; 13 differentially expressed miRNAs were confirmed by qRT-PCR. Characterization of the corresponding target genes indicated functions in processes including transcription factor regulation, biotic stress response, ion homeostasis, and secondary metabolism. Furthermore, we propose a hypothetical model of the Cd-response mechanism in B. napus. Combined with qRT-PCR confirmation, our data suggested that miRNAs were involved in the regulations of TFs, biotic stress defense, ion homeostasis and secondary metabolism synthesis to respond Cd stress in B. napus.
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Affiliation(s)
- Hongju Jian
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Bo Yang
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Aoxiang Zhang
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Jinqi Ma
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Yiran Ding
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Zhiyou Chen
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Jiana Li
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Xinfu Xu
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
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37
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Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species. Sci Rep 2018; 8:4960. [PMID: 29563515 PMCID: PMC5862966 DOI: 10.1038/s41598-018-23334-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/09/2018] [Indexed: 01/13/2023] Open
Abstract
Non-coding RNA (ncRNA) is abundant in plant genomes, but is poorly described with unknown functionality in most species. Using whole genome RNA sequencing, we identified 1885, 1910 and 1299 lncRNAs and 186, 157 and 161 miRNAs at the whole genome level in the three Brassica species B. napus, B. oleracea and B. rapa, respectively. The lncRNA sequences were divergent between the three Brassica species. One quarter of lncRNAs were located in tandem repeat (TR) region. The expression of both lncRNAs and miRNAs was strongly biased towards the A rather than the C subgenome in B. napus, unlike mRNA expression. miRNAs in genic regions had higher average expression than miRNAs in non-genic regions in B. napus and B. oleracea. We provide a comprehensive reference for the distribution, functionality and interactions of lncRNAs and miRNAs in Brassica.
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39
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Yang Y, Guo Y. Elucidating the molecular mechanisms mediating plant salt-stress responses. THE NEW PHYTOLOGIST 2018; 217:523-539. [PMID: 29205383 DOI: 10.1111/nph.14920] [Citation(s) in RCA: 657] [Impact Index Per Article: 109.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/11/2017] [Indexed: 05/18/2023]
Abstract
Contents Summary 523 I. Introduction 523 II. Sensing salt stress 524 III. Ion homeostasis regulation 524 IV. Metabolite and cell activity responses to salt stress 527 V. Conclusions and perspectives 532 Acknowledgements 533 References 533 SUMMARY: Excess soluble salts in soil (saline soils) are harmful to most plants. Salt imposes osmotic, ionic, and secondary stresses on plants. Over the past two decades, many determinants of salt tolerance and their regulatory mechanisms have been identified and characterized using molecular genetics and genomics approaches. This review describes recent progress in deciphering the mechanisms controlling ion homeostasis, cell activity responses, and epigenetic regulation in plants under salt stress. Finally, we highlight research areas that require further research to reveal new determinants of salt tolerance in plants.
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Affiliation(s)
- Yongqing Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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40
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Deng Y, Ma W. Metformin inhibits HaCaT cell viability via the miR-21/PTEN/Akt signaling pathway. Mol Med Rep 2017; 17:4062-4066. [PMID: 29286158 DOI: 10.3892/mmr.2017.8364] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 06/26/2017] [Indexed: 11/06/2022] Open
Abstract
Substantial preclinical evidence has indicated out a direct anti‑proliferation effect of metformin on various solid tumors; however, further and more detailed exploration into its molecular mechanism remains to be performed. The present study aimed to investigate the effect of metformin on cell viability and its underlying mechanism, in the cultured human skin keratinocyte cell line, HaCaT. In addition, it aimed to clarify the role of the microRNA-21(miR-21)/phosphatase and tensin homolog (PTEN)/AKT serine/threonine kinase 1 (Akt) signaling pathway, which has been hypothesized to be involved in the molecular mechanism of this drug. Cell Counting Kit‑8 assays were used to assess the impact of metformin on cell viability; reverse transcription‑quantitative polymerase chain reaction was used to quantify the expression of miR‑21; western blotting was used to monitor the expression level of PTEN and Akt proteins. In addition, miR‑21 expression levels were artificially manipulated in HaCaT cells using a miR‑21 inhibitor in order to observe the subsequent expression changes of miR‑21 targets and alterations in cell viability. The results indicated that metformin suppressed HaCaT cell growth in a dose‑ and time‑dependent manner (P<0.05). Metformin treatment downregulated miR‑21 expression (t=‑8.903, P<0.05). Following transfection with the miR‑21 inhibitor, HaCaT cell growth was significantly slower than in the control groups (P<0.05). In addition, reduced miR‑21 levels results in significantly increased PTEN protein expression levels and reduced Akt protein expression levels compared with control (P<0.05). Metformin was, therefore, concluded to inhibit HaCaT cell growth in a time‑and dose‑dependent manner, and the miR‑21/PTEN/Akt signaling pathway may serve a crucial role in the molecular mechanism of metformin's effect on HaCaT cells. Therefore the present study presents an advanced insight into the potential inhibitory effect of metformin on tumor cells.
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Affiliation(s)
- Yue Deng
- Hypertension Center of Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100006, P.R. China
| | - Weiyuan Ma
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
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Xing L, Zhu M, Zhang M, Li W, Jiang H, Zou J, Wang L, Xu M. High-Throughput Sequencing of Small RNA Transcriptomes in Maize Kernel Identifies miRNAs Involved in Embryo and Endosperm Development. Genes (Basel) 2017; 8:genes8120385. [PMID: 29240690 PMCID: PMC5748703 DOI: 10.3390/genes8120385] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/07/2017] [Accepted: 12/07/2017] [Indexed: 12/17/2022] Open
Abstract
Maize kernel development is a complex biological process that involves the temporal and spatial expression of many genes and fine gene regulation at a transcriptional and post-transcriptional level, and microRNAs (miRNAs) play vital roles during this process. To gain insight into miRNA-mediated regulation of maize kernel development, a deep-sequencing technique was used to investigate the dynamic expression of miRNAs in the embryo and endosperm at three developmental stages in B73. By miRNA transcriptomic analysis, we characterized 132 known miRNAs and six novel miRNAs in developing maize kernel, among which, 15 and 14 miRNAs were commonly differentially expressed between the embryo and endosperm at 9 days after pollination (DAP), 15 DAP and 20 DAP respectively. Conserved miRNA families such as miR159, miR160, miR166, miR390, miR319, miR528 and miR529 were highly expressed in developing embryos; miR164, miR171, miR393 and miR2118 were highly expressed in developing endosperm. Genes targeted by those highly expressed miRNAs were found to be largely related to a regulation category, including the transcription, macromolecule biosynthetic and metabolic process in the embryo as well as the vitamin biosynthetic and metabolic process in the endosperm. Quantitative reverse transcription-PCR (qRT-PCR) analysis showed that these miRNAs displayed a negative correlation with the levels of their corresponding target genes. Importantly, our findings revealed that members of the miR169 family were highly and dynamically expressed in the developing kernel, which will help to exploit new players functioning in maize kernel development.
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Affiliation(s)
- Lijuan Xing
- Biotechnology Research Institute, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Ming Zhu
- Biotechnology Research Institute, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Min Zhang
- Biotechnology Research Institute, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Wenzong Li
- Biotechnology Research Institute, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Haiyang Jiang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Junjie Zou
- Biotechnology Research Institute, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Lei Wang
- Biotechnology Research Institute, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Miaoyun Xu
- Biotechnology Research Institute, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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42
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Zhang G, Zhang M, Zhao Z, Ren Y, Li Q, Wang W. Wheat TaPUB1 modulates plant drought stress resistance by improving antioxidant capability. Sci Rep 2017; 7:7549. [PMID: 28790447 PMCID: PMC5548723 DOI: 10.1038/s41598-017-08181-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/10/2017] [Indexed: 01/29/2023] Open
Abstract
E3 ligases play significant roles in plant stress tolerance by targeting specific substrate proteins for post-translational modification. In a previous study, we cloned TaPUB1 from Triticum aestivum L., which encodes a U-box E3 ligase. Real-time polymerase chain reaction revealed that the gene was up-regulated under drought stress. To investigate the function of TaPUB1 in the response of plants to drought, we generated transgenic Nicotiana benthamiana (N. benthamiana) plants constitutively expressing TaPUB1 under the CaMV35S promoter. Compared to wild type (WT), the transgenic plants had higher germination and seedling survival rates as well as higher photosynthetic rate and water retention, suggesting that the overexpression of TaPUB1 enhanced the drought tolerance of the TaPUB1 overexpressing (OE) plants. Moreover, less accumulation of reactive oxygen species (ROS) and stronger antioxidant capacity were detected in the OE plants than in the WT plants. To characterize the mechanisms involved, methyl viologen (MV) was used to induce oxidative stress conditions and we identified the functions of this gene in the plant tolerance to oxidative stress. Our results suggest that TaPUB1 positively modulates plant drought stress resistance potential by improving their antioxidant capacity.
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Affiliation(s)
- Guangqiang Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, P.R. China
| | - Meng Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, P.R. China
- Collaborative Innovation Center, Jining Medical University, Jining, Shandong, 272067, P.R. China
| | - Zhongxian Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, P.R. China
| | - Yuanqing Ren
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, P.R. China
| | - Qinxue Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, P.R. China
| | - Wei Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, P.R. China.
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Feng JL, Yang ZJ, Chen SP, El-Kassaby YA, Chen H. High throughput sequencing of small RNAs reveals dynamic microRNAs expression of lipid metabolism during Camellia oleifera and C. meiocarpa seed natural drying. BMC Genomics 2017; 18:546. [PMID: 28728593 PMCID: PMC5520325 DOI: 10.1186/s12864-017-3923-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/04/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Camellia species are ancient oilseed plants with a history of cultivation over two thousand years. Prior to oil extraction, natural seed drying is often practiced, a process affecting fatty acid quality and quantity. MicroRNAs (miRNA) of lipid metabolism associated with camellia seed natural drying are unexplored. To obtain insight into the function of miRNAs in lipid metabolism during natural drying, Illumina sequencing of C. oleifera and C. meiocarpa small-RNA was conducted. RESULTS A total of 274 candidate miRNAs were identified and 3733 target unigenes were annotated by performing a BLASTX. Through integrated GO and KEGG function annotation, 23 miRNA regulating 131 target genes were identified as lipid metabolism, regulating fatty acid biosynthesis, accumulation and catabolism. We observed one, two, and four miRNAs of lipid metabolism which were specially expressed in C. Meiocarpa, C. oleifera, and the two species collectively, respectively. At 30% moisture contents, C. meiocarpa and C. oleifer produced nine and eight significant differentially expressed miRNAs, respectively, with high fatty acid synthesis and accumulation activities. Across the two species, 12 significant differentially expressed miRNAs were identified at the 50% moisture content. CONCLUSIONS Sequencing of small-RNA revealed the presence of 23 miRNAs regulating lipid metabolism in camellia seed during natural drying and permitted comparative miRNA profiles between C. Meiocarpa and C. oleifera. Furthermore, this study successfully identified the best drying environment at which the quantity and quality of lipid in camellia seed are at its maximum.
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Affiliation(s)
- Jin-Ling Feng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhi-Jian Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shi-Pin Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
| | - Hui Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Chen Z, Yuan Y, Fu D, Shen C, Yang Y. Identification and Expression Profiling of the Auxin Response Factors in Dendrobium officinale under Abiotic Stresses. Int J Mol Sci 2017; 18:E927. [PMID: 28471373 PMCID: PMC5454840 DOI: 10.3390/ijms18050927] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/24/2017] [Accepted: 04/25/2017] [Indexed: 01/18/2023] Open
Abstract
Auxin response factor (ARF) proteins play roles in plant responses to diverse environmental stresses by binding specifically to the auxin response element in the promoters of target genes. Using our latest public Dendrobium transcriptomes, a comprehensive characterization and analysis of 14 DnARF genes were performed. Three selected DnARFs, including DnARF1, DnARF4, and DnARF6, were confirmed to be nuclear proteins according to their transient expression in epidermal cells of Nicotiana benthamiana leaves. Furthermore, the transcription activation abilities of DnARF1, DnARF4, and DnARF6 were tested in a yeast system. Our data showed that DnARF6 is a transcriptional activator in Dendrobium officinale. To uncover the basic information of DnARF gene responses to abiotic stresses, we analyzed their expression patterns under various hormones and abiotic treatments. Based on our data, several hormones and significant stress responsive DnARF genes have been identified. Since auxin and ARF genes have been identified in many plant species, our data is imperative to reveal the function of ARF mediated auxin signaling in the adaptation to the challenging Dendrobium environment.
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Affiliation(s)
- Zhehao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
| | - Ye Yuan
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
| | - Di Fu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China.
| | - Yanjun Yang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China.
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Wang K, Dantec C, Lemaire P, Onuma TA, Nishida H. Genome-wide survey of miRNAs and their evolutionary history in the ascidian, Halocynthia roretzi. BMC Genomics 2017; 18:314. [PMID: 28427349 PMCID: PMC5399378 DOI: 10.1186/s12864-017-3707-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/12/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND miRNAs play essential roles in the modulation of cellular functions via degradation and/or translation attenuation of target mRNAs. They have been surveyed in a single ascidian genus, Ciona. Recently, an annotated draft genome sequence for a distantly related ascidian, Halocynthia roretzi, has become available, but miRNAs in H. roretzi have not been previously studied. RESULTS We report the prediction of 319 candidate H. roretzi miRNAs, obtained through three complementary methods. Experimental validation suggests that more than half of these candidate miRNAs are expressed during embryogenesis. The majority of predicted H. roretzi miRNAs appear specific to ascidians or tunicates, and only 32 candidates, belonging to 25 families, are widely conserved across metazoans. CONCLUSION Our study presents a comprehensive identification of candidate H. roretzi miRNAs. This resource will facilitate the study of the mechanisms for miRNA-controlled gene regulatory networks during ascidian development. Further, our analysis suggests that the majority of Halocynthia miRNAs are specific to ascidian or tunicates, with only a small number of widely conserved miRNAs. This result is consistent with the general notion that animal miRNAs are less conserved between taxa than plant ones.
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Affiliation(s)
- Kai Wang
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan. .,Present address: Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Science, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, People's Republic of China.
| | - Christelle Dantec
- Centre de Recherches de Biologie cellulaire de Montpellier (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090, Montpellier, France
| | - Patrick Lemaire
- Centre de Recherches de Biologie cellulaire de Montpellier (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090, Montpellier, France
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
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Wan H, Chen L, Guo J, Li Q, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Genome-Wide Association Study Reveals the Genetic Architecture Underlying Salt Tolerance-Related Traits in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2017; 8:593. [PMID: 28491067 PMCID: PMC5405135 DOI: 10.3389/fpls.2017.00593] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/31/2017] [Indexed: 05/02/2023]
Abstract
Soil salinity is a serious threat to agriculture sustainability worldwide. Salt tolerance at the seedling stage is crucial for plant establishment and high yield in saline soils; however, little information is available on rapeseed (Brassica napus L.) salt tolerance. We evaluated salt tolerance in different rapeseed accessions and conducted a genome-wide association study (GWAS) to identify salt tolerance-related quantitative trait loci (QTL). A natural population comprising 368 B. napus cultivars and inbred lines was genotyped with a Brassica 60K Illumina Infinium SNP array. The results revealed that 75 single-nucleotide polymorphisms (SNPs) distributed across 14 chromosomes were associated with four salt tolerance-related traits. These SNPs integrated into 25 QTLs that explained 4.21-9.23% of the phenotypic variation in the cultivars. Additionally, 38 possible candidate genes were identified in genomic regions associated with salt tolerance indices. These genes fell into several functional groups that are associated with plant salt tolerance, including transcription factors, aquaporins, transporters, and enzymes. Thus, salt tolerance in rapeseed involves complex molecular mechanisms. Our results provide valuable information for studying the genetic control of salt tolerance in B. napus seedlings and may facilitate marker-based breeding for rapeseed salt tolerance.
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Identification and Target Prediction of MicroRNAs in Ulmus pumila L. Seedling Roots under Salt Stress by High-Throughput Sequencing. FORESTS 2016. [DOI: 10.3390/f7120318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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