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Zhu P, Li H, Lu T, Liang R, Wan B. Combined analysis of mRNA and miRNA transcriptomes reveals the regulatory mechanism of Xanthomonas arboricola pv pruni resistance in Prunus persica. BMC Genomics 2024; 25:214. [PMID: 38413907 PMCID: PMC10898114 DOI: 10.1186/s12864-024-10113-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/11/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Peach bacterial shot hole, caused by Xanthomonas arboricola pv pruni (Xap), is a global bacterial disease that poses a threat to the yield and quality of cultivated peach trees (Prunus persica). RESULTS This study compared the mRNA and miRNA profiles of two peach varieties, 'Yanbao' (resistant) and 'Yingzui' (susceptible), after inoculation with Xap to identify miRNAs and target genes associated with peach tree resistance. mRNA sequencing results revealed that in the S0-vs-S3 comparison group, 1574 genes were upregulated and 3975 genes were downregulated. In the R0-vs-R3 comparison group, 1575 genes were upregulated and 3726 genes were downregulated. Through miRNA sequencing, a total of 112 known miRNAs belonging to 70 miRNA families and 111 new miRNAs were identified. Notably, some miRNAs were exclusively expressed in either resistant or susceptible varieties. Additionally, 59 miRNAs were downregulated and 69 miRNAs were upregulated in the R0-vs-R3 comparison group, while 46 miRNAs were downregulated and 52 miRNAs were upregulated in the S0-vs-S3 comparison group. Joint analysis of mRNA and miRNA identified 79 relationship pairs in the S0-vs-S3 comparison group, consisting of 48 miRNAs and 51 target genes. In the R0-vs-R3 comparison group, there were 58 relationship pairs, comprising 28 miRNAs and 20 target genes. Several target genes related to resistance, such as SPL6, TIFY6B, and Prupe.4G041800_v2.0.a1 (PPO), were identified through literature reports and GO/KEGG enrichment analysis. CONCLUSION In conclusion, this study discovered several candidate genes involved in peach tree resistance by analyzing differential expression of mRNA and miRNA. These findings provide valuable insights into the mechanisms underlying resistance to Xap in peach trees.
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Affiliation(s)
- Pengxiang Zhu
- Guangxi Academy of Specialty Crops, Guilin, 541004, China
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China
| | - Haiyan Li
- Guangxi Academy of Specialty Crops, Guilin, 541004, China
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China
| | - Tailiang Lu
- Guangxi Academy of Specialty Crops, Guilin, 541004, China
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China
| | - Ruizheng Liang
- Guangxi Academy of Specialty Crops, Guilin, 541004, China.
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China.
| | - Baoxiong Wan
- Guangxi Academy of Specialty Crops, Guilin, 541004, China.
- Guangxi Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guilin, 541004, China.
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Hao K, Yang M, Cui Y, Jiao Z, Gao X, Du Z, Wang Z, An M, Xia Z, Wu Y. Transcriptomic and Functional Analyses Reveal the Different Roles of Vitamins C, E, and K in Regulating Viral Infections in Maize. Int J Mol Sci 2023; 24:ijms24098012. [PMID: 37175719 PMCID: PMC10178231 DOI: 10.3390/ijms24098012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Maize lethal necrosis (MLN), one of the most important maize viral diseases, is caused by maize chlorotic mottle virus (MCMV) infection in combination with a potyvirid, such as sugarcane mosaic virus (SCMV). However, the resistance mechanism of maize to MLN remains largely unknown. In this study, we obtained isoform expression profiles of maize after SCMV and MCMV single and synergistic infection (S + M) via comparative analysis of SMRT- and Illumina-based RNA sequencing. A total of 15,508, 7567, and 2378 differentially expressed isoforms (DEIs) were identified in S + M, MCMV, and SCMV libraries, which were primarily involved in photosynthesis, reactive oxygen species (ROS) scavenging, and some pathways related to disease resistance. The results of virus-induced gene silencing (VIGS) assays revealed that silencing of a vitamin C biosynthesis-related gene, ZmGalDH or ZmAPX1, promoted viral infections, while silencing ZmTAT or ZmNQO1, the gene involved in vitamin E or K biosynthesis, inhibited MCMV and S + M infections, likely by regulating the expressions of pathogenesis-related (PR) genes. Moreover, the relationship between viral infections and expression of the above four genes in ten maize inbred lines was determined. We further demonstrated that the exogenous application of vitamin C could effectively suppress viral infections, while vitamins E and K promoted MCMV infection. These findings provide novel insights into the gene regulatory networks of maize in response to MLN, and the roles of vitamins C, E, and K in conditioning viral infections in maize.
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Affiliation(s)
- Kaiqiang Hao
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Miaoren Yang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yakun Cui
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhiyuan Jiao
- State Kay Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Xinran Gao
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhichao Du
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhiping Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Mengnan An
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Zihao Xia
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
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Biswal AK, Alakonya AE, Mottaleb KA, Hearne SJ, Sonder K, Molnar TL, Jones AM, Pixley KV, Prasanna BM. Maize Lethal Necrosis disease: review of molecular and genetic resistance mechanisms, socio-economic impacts, and mitigation strategies in sub-Saharan Africa. BMC PLANT BIOLOGY 2022; 22:542. [PMID: 36418954 PMCID: PMC9686106 DOI: 10.1186/s12870-022-03932-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Maize lethal necrosis (MLN) disease is a significant constraint for maize producers in sub-Saharan Africa (SSA). The disease decimates the maize crop, in some cases, causing total crop failure with far-reaching impacts on regional food security. RESULTS In this review, we analyze the impacts of MLN in Africa, finding that resource-poor farmers and consumers are the most vulnerable populations. We examine the molecular mechanism of MLN virus transmission, role of vectors and host plant resistance identifying a range of potential opportunities for genetic and phytosanitary interventions to control MLN. We discuss the likely exacerbating effects of climate change on the MLN menace and describe a sobering example of negative genetic association between tolerance to heat/drought and susceptibility to viral infection. We also review role of microRNAs in host plant response to MLN causing viruses as well as heat/drought stress that can be carefully engineered to develop resistant varieties using novel molecular techniques. CONCLUSIONS With the dual drivers of increased crop loss due to MLN and increased demand of maize for food, the development and deployment of simple and safe technologies, like resistant cultivars developed through accelerated breeding or emerging gene editing technologies, will have substantial positive impact on livelihoods in the region. We have summarized the available genetic resources and identified a few large-effect QTLs that can be further exploited to accelerate conversion of existing farmer-preferred varieties into resistant cultivars.
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Affiliation(s)
- Akshaya Kumar Biswal
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico-Veracruz, El Batan, Texcoco, C.P. 56237, Mexico.
| | - Amos Emitati Alakonya
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico-Veracruz, El Batan, Texcoco, C.P. 56237, Mexico
| | - Khondokar Abdul Mottaleb
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico-Veracruz, El Batan, Texcoco, C.P. 56237, Mexico
| | - Sarah J Hearne
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico-Veracruz, El Batan, Texcoco, C.P. 56237, Mexico
| | - Kai Sonder
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico-Veracruz, El Batan, Texcoco, C.P. 56237, Mexico
| | | | - Alan M Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kevin Vail Pixley
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico-Veracruz, El Batan, Texcoco, C.P. 56237, Mexico
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Jiang J, Zhu H, Li N, Batley J, Wang Y. The miR393-Target Module Regulates Plant Development and Responses to Biotic and Abiotic Stresses. Int J Mol Sci 2022; 23:ijms23169477. [PMID: 36012740 PMCID: PMC9409142 DOI: 10.3390/ijms23169477] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs (miRNAs), a class of endogenous small RNAs, are broadly involved in plant development, morphogenesis and responses to various environmental stresses, through manipulating the cleavage, translational expression, or DNA methylation of target mRNAs. miR393 is a conserved miRNA family present in many plants, which mainly targets genes encoding the transport inhibitor response1 (TIR1)/auxin signaling F-box (AFB) auxin receptors, and thus greatly affects the auxin signal perception, Aux/IAA degradation, and related gene expression. This review introduces the advances made on the miR393/target module regulating plant development and the plant’s responses to biotic and abiotic stresses. This module is valuable for genetic manipulation of optimized conditions for crop growth and development and would also be helpful in improving crop yield through molecular breeding.
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Affiliation(s)
- Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Haotian Zhu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Na Li
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
- Correspondence: (J.B.); (Y.W.)
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (J.B.); (Y.W.)
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5
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Liu X, Liu S, Chen X, Prasanna BM, Ni Z, Li X, He Y, Fan Z, Zhou T. Maize miR167-ARF3/30-polyamine oxidase 1 module-regulated H2O2 production confers resistance to maize chlorotic mottle virus. PLANT PHYSIOLOGY 2022; 189:1065-1082. [PMID: 35298645 PMCID: PMC9157100 DOI: 10.1093/plphys/kiac099] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/10/2022] [Indexed: 05/27/2023]
Abstract
Maize chlorotic mottle virus (MCMV) is the key pathogen causing maize lethal necrosis (MLN). Due to the sharply increased incidence of MLN in many countries, there is an urgent need to identify resistant lines and uncover the underlying resistance mechanism. Here, we showed that the abundance of maize (Zea mays) microR167 (Zma-miR167) positively modulates the degree of resistance to MCMV. Zma-miR167 directly targets Auxin Response Factor3 (ZmARF3) and ZmARF30, both of which negatively regulate resistance to MCMV. RNA-sequencing coupled with gene expression assays revealed that both ZmARF3 and ZmARF30 directly bind the promoter of Polyamine Oxidase 1 (ZmPAO1) and activate its expression. Knockdown or inhibition of enzymatic activity of ZmPAO1 suppressed MCMV infection. Nevertheless, MCMV-encoded p31 protein directly targets ZmPAO1 and enhances the enzyme activity to counteract Zma-miR167-mediated defense to some degree. We uncovered a role of the Zma-miR167-ZmARF3/30 module for restricting MCMV infection by regulating ZmPAO1 expression, while MCMV employs p31 to counteract this defense.
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Affiliation(s)
- Xuedong Liu
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Sijia Liu
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Xi Chen
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, Gigiri, Nairobi, Kenya
| | - Zhongfu Ni
- College of Agronomy, China Agricultural University, Beijing 100193, China
| | - Xiangdong Li
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Yueqiu He
- College of Agronomy, Yunnan Agricultural University, Kunming 650201, China
| | - Zaifeng Fan
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Tao Zhou
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing 100193, China
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6
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Ghorbani A, Izadpanah K, Tahmasebi A, Afsharifar A, Moghadam A, Dietzgen RG. Characterization of maize miRNAs responsive to maize Iranian mosaic virus infection. 3 Biotech 2022; 12:69. [PMID: 35223355 PMCID: PMC8837769 DOI: 10.1007/s13205-022-03134-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 01/28/2022] [Indexed: 11/26/2022] Open
Abstract
MicroRNAs (miRNAs) play key regulatory roles in the plant's response to biotic and abiotic stresses and have fundamental functions in plant-virus interactions. The study of changes in miRNAs in response to virus infection can provide molecular details for a better understanding of virus-host interactions. Maize Iranian mosaic virus (MIMV) infects maize and certain other poaceous plants but miRNA changes in response to MIMV infection are unknown. In the present study, we compared the miRNA profiles of MIMV-infected and uninfected maize and characterized their predicted roles in response to the virus. Small RNA sequencing of maize identified 257 conserved miRNAs of 26 conserved families in uninfected and MIMV-infected maize libraries. Among them, miR395, miR166 and miR156 family members were highly represented. Small RNA data were confirmed using RT-qPCR. In addition, 33 potential novel miRNAs were predicted. The data show that 13 miRNAs were up-regulated and 113 were down-regulated in response to MIMV infection. Several of those miRNAs are known to be important in the response to plant pathogens. To determine the potential roles of individual miRNAs in response to MIMV, miRNA targets, predicted interactions with circular RNAs and comparative transcriptome data were analyzed. The expression profiles of different miRNAs in response to MIMV provide novel insights into the roles of miRNAs in the interaction between MIMV and maize plants. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-022-03134-1.
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Affiliation(s)
- Abozar Ghorbani
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD Australia
| | | | - Ahmad Tahmasebi
- Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Alireza Afsharifar
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Moghadam
- Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD Australia
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7
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Wu R, Wu G, Wang L, Wang X, Liu Z, Li M, Tan W, Qing L. Tobacco curly shoot virus Down-Regulated the Expression of nbe-miR167b-3p to Facilitate Its Infection in Nicotiana benthamiana. Front Microbiol 2021; 12:791561. [PMID: 34975814 PMCID: PMC8716884 DOI: 10.3389/fmicb.2021.791561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/09/2021] [Indexed: 11/30/2022] Open
Abstract
Tobacco curly shoot virus (TbCSV) belongs to the genus Begomovirus of the family Geminiviridae, and causes leaf curling and curly shoot symptoms in tobacco and tomato crops. MicroRNAs (miRNAs) are pivotal modulators of plant development and host-virus interactions. However, the relationship between TbCSV infection and miRNAs accumulation has not been well investigated. The present study was conducted to analyze different expressions of miRNAs in Nicotiana benthamiana in response to the infection of TbCSV via small RNAs sequencing. The results showed that 15 up-regulated miRNAs and 12 down-regulated miRNAs were differentially expressed in TbCSV infected N. benthamiana, and nbe-miR167b-3p was down-regulated. To decipher the relationship between nbe-miR167b-3p expression and the accumulations of TbCSV DNA, pCVA mediation of miRNA overexpression and PVX based short tandem target mimic (STTM) were used in this study. It was found that overexpression of nbe-miR167b-3p attenuated leaf curling symptom of TbCSV and decreased viral DNA accumulation, but suppression of nbe-miR167b-3p expression enhanced the symptoms and accumulation of TbCSV. PRCP, the target gene of nbe-miR167b-3p, was silenced in plants using VIGS and this weakened the viral symptoms and DNA accumulation of TbCSV in the plants. Overall, this study clarified the effect of nbe-miR167b-3p on plant defense during TbCSV infection, and provided a framework to reveal the molecular mechanisms of miRNAs between plants and viruses.
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Affiliation(s)
- Rui Wu
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Gentu Wu
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Lyuxin Wang
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Xu Wang
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Zhuoying Liu
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Mingjun Li
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Wanzhong Tan
- College of Tropical Crops Sciences, Yunnan Agricultural University, Kunming, China
| | - Ling Qing
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
- *Correspondence: Ling Qing,
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8
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Wang Q, Liu J, Zeng J, Yang Z, Ran F, Wu L, Yang G, Mei Q, Wang X, Chen Q. Determination of miRNA derived from exosomes of prostate cancer via toehold-aided cyclic amplification combined with HRP enzyme catalysis and magnetic nanoparticles. Anal Biochem 2021; 630:114336. [PMID: 34400146 DOI: 10.1016/j.ab.2021.114336] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 01/08/2023]
Abstract
MicroRNAs (miRNAs) play a significant role in tumorigenesis and tumor development. Exosomal microRNA-141 (miRNA-141, miR-141) has been reported to be overexpressed in prostate cancer (PCa) and has become a potential biomarker for the diagnosis of PCa. Herein, a novel fluorescent biosensor based on toehold-aided cyclic amplification combined with horseradish peroxidase (HRP) enzyme catalysis and magnetic nanoparticles (MNPs) was designed for determination of the exosomes-derived microRNA-141 (miRNA-141, miR-141). The synergy of HRP enzyme catalysis and toehold mediated strand display reaction (TSDR) increase the sensitivity of the method, and the good separation ability of MNPs ensures the specificity of the method. Therefore, under the optimized experimental conditions, the highly sensitive and specific detection of miRNA-141 can be realized, and the detection limit is as low as 10 fM. More importantly, the biosensor successfully determinates the exosomal miR-141 in the plasma of patients with PCa.
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Affiliation(s)
- Qinjun Wang
- Department of Urology, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, China
| | - Jingjian Liu
- Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan, 442008, China
| | - Jiantao Zeng
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, 518101, China
| | - Zhiming Yang
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China
| | - Fengying Ran
- Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan, 442008, China
| | - Lun Wu
- Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan, 442008, China
| | - Guangyi Yang
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China
| | - Quanxi Mei
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China
| | - Xisheng Wang
- Department of Urology, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, China.
| | - Qinhua Chen
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China.
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Li Z, Zhang X, Zhao K, Zhao K, Qu C, Gao G, Gong F, Ma X, Yin D. Comprehensive Transcriptome Analyses Reveal Candidate Genes for Variation in Seed Size/Weight During Peanut ( Arachis hypogaea L.) Domestication. FRONTIERS IN PLANT SCIENCE 2021; 12:666483. [PMID: 34093624 PMCID: PMC8170302 DOI: 10.3389/fpls.2021.666483] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/22/2021] [Indexed: 05/05/2023]
Abstract
Seed size/weight, a key domestication trait, is also an important selection target during peanut breeding. However, the mechanisms that regulate peanut seed development are unknown. We re-sequenced 12 RNA samples from developing seeds of two cultivated peanut accessions (Lines 8106 and 8107) and wild Arachis monticola at 15, 30, 45, and 60 days past flowering (DPF). Transcriptome analyses showed that ∼36,000 gene loci were expressed in each of the 12 RNA samples, with nearly half exhibiting moderate (2 ≤ FPKM < 10) expression levels. Of these genes, 12.2% (4,523) were specifically expressed during seed development, mainly at 15 DPF. Also, ∼12,000 genes showed significant differential expression at 30, 45, and/or 60 DPF within each of the three peanut accessions, accounting for 31.8-34.1% of the total expressed genes. Using a method that combined comprehensive transcriptome analysis and previously mapped QTLs, we identified several candidate genes that encode transcription factor TGA7, topless-related protein 2, IAA-amino acid hydrolase ILR1-like 5, and putative pentatricopeptide repeat-containing (PPR) protein. Based on sequence variations identified in these genes, SNP markers were developed and used to genotype both 30 peanut landraces and a genetic segregated population, implying that EVM0025654 encoding a PPR protein may be associated with the increased seed size/weight of the cultivated accessions in comparison with the allotetraploid wild peanut. Our results provide additional knowledge for the identification and functional research into candidate genes responsible for the seed size/weight phenotype in peanut.
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