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Khan Q, Qin Y, Guo DJ, Huang YY, Yang LT, Liang Q, Song XP, Xing YX, Li YR. Comparative Analysis of Sucrose-Regulatory Genes in High- and Low-Sucrose Sister Clones of Sugarcane. PLANTS (BASEL, SWITZERLAND) 2024; 13:707. [PMID: 38475553 DOI: 10.3390/plants13050707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Sugarcane is a significant primitive source of sugar and energy worldwide. The progress in enhancing the sugar content in sugarcane cultivars remains limited due to an insufficient understanding of specific genes related to sucrose production. The present investigation examined the enzyme activities, levels of reducing and non-reducing sugars, and transcript expression using RT-qPCR to assess the gene expression associated with sucrose metabolism in a high-sucrose sugarcane clone (GXB9) in comparison to a low-sucrose sister clone (B9). Sucrose phosphate synthase (SPS), sucrose phosphate phosphatase (SPP), sucrose synthase (SuSy), cell wall invertase (CWI), soluble acid invertase (SAI), and neutral invertase (NI) are essential enzymes involved in sucrose metabolism in sugarcane. The activities of these enzymes were comparatively quantified and analyzed in immature and maturing internodes of the high- and low-sucrose clones. The results showed that the higher-sucrose-accumulating clone had greater sucrose concentrations than the low-sucrose-accumulating clone; however, maturing internodes had higher sucrose levels than immature internodes in both clones. Hexose concentrations were higher in immature internodes than in maturing internodes for both clones. The SPS and SPP enzymes activities were higher in the high-sucrose-storing clone than in the low-sucrose clone. SuSy activity was higher in the low-sucrose clone than in the high-sucrose clone; further, the degree of SuSy activity was higher in immature internodes than in maturing internodes for both clones. The SPS gene expression was considerably higher in mature internodes of the high-sucrose clones than the low-sucrose clone. Conversely, the SuSy gene exhibited up-regulated expression in the low-sucrose clone. The enhanced expression of SPS in the high-sucrose clone compared to the low-sucrose clone suggests that SPS plays a major role in the increased accumulation of sucrose. These findings provide the opportunity to improve sugarcane cultivars by regulating the activity of genes related to sucrose metabolism using transgenic techniques.
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Affiliation(s)
- Qaisar Khan
- Guangxi Key Laboratory of Sugarcane, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ying Qin
- Guangxi Key Laboratory of Sugarcane, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Dao-Jun Guo
- Guangxi Key Laboratory of Sugarcane, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yu-Yan Huang
- Guangxi Key Laboratory of Sugarcane, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Li-Tao Yang
- Guangxi Key Laboratory of Sugarcane, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Qiang Liang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Nanning 530003, China
| | - Xiu-Peng Song
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Nanning 530003, China
| | - Yong-Xiu Xing
- Guangxi Key Laboratory of Sugarcane, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yang-Rui Li
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Nanning 530003, China
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Jia X, Xiong Y, Xiong Y, Li D, Yu Q, Lei X, You M, Bai S, Zhang J, Ma X. Identification and Validation of Reference Genes for RT-qPCR Analysis in Reed Canary Grass during Abiotic Stress. Genes (Basel) 2023; 14:1790. [PMID: 37761930 PMCID: PMC10530813 DOI: 10.3390/genes14091790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Reed canary grass (Phalaris arundinacea L.) is known for its tolerance to drought, heavy metals, and waterlogging, making it a popular choice for forage production and wetland restoration in the Qinghai-Tibet Plateau (QTP). To accurately assess gene expression in reed canary grass under different abiotic stresses, suitable reference genes need to be identified and validated. Thirteen candidate reference gene sequences were selected and screened using RT-qPCR to detect their expression levels in reed canary grass leaves under drought, salt, cadmium, and waterlogging stresses. Four algorithms were used to assess the stability of the expression levels of the candidate reference genes. The most stably expressed genes were UBC and H3 under drought Cd, ETF and CYT under salt stress, and ETF and TUB under waterlogging stress. GAPDH was found to be less stable under abiotic stresses. PIP-1, PAL, NAC 90, and WRKY 72A were selected as response genes for quantitative expression assessment under drought, salt, Cd, and waterlogging stresses to confirm the accuracy of the selected stable reference genes. These results provide a theoretical reference for assessing gene expression in reed canary grass under abiotic stresses.
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Affiliation(s)
- Xuejie Jia
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
| | - Daxu Li
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Qinqin Yu
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Minghong You
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Shiqie Bai
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621002, China
| | - Jianbo Zhang
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
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Venail J, da Silva Santos PH, Manechini JR, Alves LC, Scarpari M, Falcão T, Romanel E, Brito M, Vicentini R, Pinto L, Jackson SD. Analysis of the PEBP gene family and identification of a novel FLOWERING LOCUS T orthologue in sugarcane. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2035-2049. [PMID: 34893811 PMCID: PMC8982381 DOI: 10.1093/jxb/erab539] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 12/09/2021] [Indexed: 05/21/2023]
Abstract
Sugarcane (Saccharum spp.) is an important economic crop for both sugar and biomass, the yields of which are negatively affected by flowering. The molecular mechanisms controlling flowering in sugarcane are nevertheless poorly understood. RNA-seq data analysis and database searches have enabled a comprehensive description of the PEBP gene family in sugarcane. It is shown to consist of at least 13 FLOWERING LOCUS T (FT)-like genes, two MOTHER OF FT AND TFL (MFT)-like genes, and four TERMINAL FLOWER (TFL)-like genes. As expected, these genes all show very high homology to their corresponding genes in Sorghum, and also to FT-like, MFT-like, and TFL-like genes in maize, rice, and Arabidopsis. Functional analysis in Arabidopsis showed that the sugarcane ScFT3 gene can rescue the late flowering phenotype of the Arabidopsis ft-10 mutant, whereas ScFT5 cannot. High expression levels of ScFT3 in leaves of short day-induced sugarcane plants coincided with initial stages of floral induction in the shoot apical meristem as shown by histological analysis of meristem dissections. This suggests that ScFT3 is likely to play a role in floral induction in sugarcane; however, other sugarcane FT-like genes may also be involved in the flowering process.
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Affiliation(s)
- Julien Venail
- School of Life Sciences, University of Warwick, Gibbet Hill, Coventry CV4 7AL, UK
| | | | - Joao Ricardo Manechini
- Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | | | - Maximiliano Scarpari
- Centro de Cana, Instituto Agronômico de Campinas (IAC), Ribeirão Preto, São Paulo, Brazil
| | - Thais Falcão
- Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), São Paulo, Brazil
| | - Elisson Romanel
- Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), São Paulo, Brazil
| | - Michael Brito
- Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo (UNIFESP), São José dos Campos, São Paulo, Brazil
| | - Renato Vicentini
- Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Lucia Pinto
- Centro de Cana, Instituto Agronômico de Campinas (IAC), Ribeirão Preto, São Paulo, Brazil
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Identification of Suitable Reference Genes for qRT-PCR Normalization in Kiwifruit. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020170] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Reference genes are used for the correction of qRT-PCR data, and it is necessary to investigate the optimum reference gene under certain conditions. The expression levels of seven traditional reference genes ACT1, ACT2, GAPDH, 18S rRNA, UBQ, TUB and CYP were analyzed using qRT-PCR in different varieties, tissues, developmental stages and hormone (or pollen polysaccharide) treatments in kiwifruit. Gene expression stability was assessed with the help of three common software (geNorm, NormFinder, BestKeeper), and the minimum number of reference genes necessary for normalization was also determined. GAPDH, ACT1 and ACT2 were selected as reference genes for different genotypes of kiwifruit. GAPDH and UBQ were the best combinations of reference genes for root, stem, leaf, flower and fruit. GAPDH and ACT1 could be the preferred reference genes for normalization of qRT-PCR data during fruit development. The pairing of ACT1 and UBQ constituted the optimal combination of reference genes in kiwifruit treated with different hormones (or pollen polysaccharide). This study provides a new and reliable option for the use of reference genes in the analysis of gene expression patterns of interest in kiwifruit.
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Yan M, Jin X, Liu Y, Chen H, Ye T, Hou Z, Su Z, Chen Y, Aslam M, Qin Y, Niu X. Identification and evaluation of the novel genes for transcript normalization during female gametophyte development in sugarcane. PeerJ 2021; 9:e12298. [PMID: 34721982 PMCID: PMC8532975 DOI: 10.7717/peerj.12298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/21/2021] [Indexed: 11/23/2022] Open
Abstract
Background Sugarcane (Saccharum spontaneum L.), the major sugar and biofuel feedstock crop, is cultivated mainly by vegetative propagation worldwide due to the infertility of female reproductive organs resulting in the reduction of quality and output of sugar. Deciphering the gene expression profile during ovule development will improve our understanding of the complications underlying sexual reproduction in sugarcane. Optimal reference genes are essential for elucidating the expression pattern of a given gene by quantitative real-time PCR (qRT-PCR). Method In this study, based on transcriptome data obtained from sugarcane ovule, eighteen candidate reference genes were identified, cloned, and their expression levels were evaluated across five developmental stages ovule (AC, MMC, Meiosis, Mitosis, and Mature). Results Our results indicated that FAB2 and MOR1 were the most stably expressed genes during sugarcane female gametophyte development. Moreover, two genes, cell cycle-related genes REC8 and CDK, were selected, and their feasibility was validated. This study provides important insights into the female gametophyte development of sugarcane and reports novel reference genes for gene expression research on sugarcane sexual reproduction.
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Affiliation(s)
- Maokai Yan
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Xingyue Jin
- Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuzhou, China
| | - Yanhui Liu
- Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuzhou, China
| | - Huihuang Chen
- Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuzhou, China
| | - Tao Ye
- Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuzhou, China
| | - Zhimin Hou
- Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuzhou, China
| | - Zhenxia Su
- Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuzhou, China
| | - Yingzhi Chen
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Mohammad Aslam
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yuan Qin
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China.,Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuzhou, China
| | - Xiaoping Niu
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
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Gabriel C, Fernhout J, Fichtner F, Feil R, Lunn JE, Kossmann J, Lloyd JR, van der Vyver C. Genetic manipulation of trehalose-6-phosphate synthase results in changes in the soluble sugar profile in transgenic sugarcane stems. PLANT DIRECT 2021; 5:e358. [PMID: 34765864 PMCID: PMC8573382 DOI: 10.1002/pld3.358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/05/2021] [Accepted: 10/15/2021] [Indexed: 05/11/2023]
Abstract
Trehalose is a non-reducing disaccharide widely distributed in nature. The trehalose biosynthetic intermediate, trehalose 6-phosphate (Tre6P) is an essential regulatory and signaling molecule involved in both regulation of carbon metabolism and photosynthesis. To investigate the effect of altered trehalose synthesis on sucrose accumulation in sugarcane (Saccharum spp. hybrid), we independently overexpressed the Escherichia coli otsA (trehalose-6-phosphate synthase; TPS) and otsB (trehalose-6-phosphate phosphatase; TPP) genes and additionally partially silenced native TPS expression. In mature cane, sucrose levels in the otsA transgenic plants were lowered, whereas sucrose levels in the otsB transgenic plants were increased. Partial silencing of TPS expression in sugarcane transformed with a TPS-targeted microRNA recombinant construct was confirmed in leaf and mature internode tissue of transgenic plants. Most of the silencing transgenic lines accumulated trehalose at lower levels than the wild-type (WT) plants. The immature stalk tissue of these transgenic lines had lower levels of glucose and fructose, whereas the mature internode tissue had lower sucrose and glucose levels, when compared with the WT. Furthermore, various minor metabolites and sugars were detected in the sugarcane plants, which mostly decreased as the stalk tissue of the cane matured. The results demonstrate that manipulation of Tre6P/trehalose metabolism has the potential to modify the profile of soluble sugars accumulated in sugarcane stems.
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Affiliation(s)
- Casey Gabriel
- Institute for Plant Biotechnology, Department of GeneticsUniversity of StellenboschStellenboschSouth Africa
| | - Jean‐Jacque Fernhout
- Institute for Plant Biotechnology, Department of GeneticsUniversity of StellenboschStellenboschSouth Africa
| | | | - Regina Feil
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - John E. Lunn
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Jens Kossmann
- Institute for Plant Biotechnology, Department of GeneticsUniversity of StellenboschStellenboschSouth Africa
| | - James R. Lloyd
- Institute for Plant Biotechnology, Department of GeneticsUniversity of StellenboschStellenboschSouth Africa
| | - Christell van der Vyver
- Institute for Plant Biotechnology, Department of GeneticsUniversity of StellenboschStellenboschSouth Africa
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Tofanello VR, Andrade LM, Flores-Borges DNA, Kiyota E, Mayer JLS, Creste S, Machado EC, Yin X, Struik PC, Ribeiro RV. Role of bundle sheath conductance in sustaining photosynthesis competence in sugarcane plants under nitrogen deficiency. PHOTOSYNTHESIS RESEARCH 2021; 149:275-287. [PMID: 34091828 DOI: 10.1007/s11120-021-00848-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
The role of bundle sheath conductance (gbs) in sustaining sugarcane photosynthesis under nitrogen deficiency was investigated. Sugarcane was grown under different levels of nitrogen supply and gbs was estimated using simultaneous measurements of leaf gas exchange and chlorophyll fluorescence at 21% or 2% [O2] and varying air [CO2] and light intensity. Maximum rates of PEPC carboxylation, Rubisco carboxylation, and ATP production increased with an increase in leaf nitrogen concentration (LNC) from 1 to 3 g m-2. Low nitrogen supply reduced Rubisco and PEPC abundancies, the quantum efficiency of CO2 assimilation and gbs. Because of reduced gbs, low photosynthetic rates were not associated with increased leakiness under nitrogen deficiency. In fact, low nitrogen supply increased bundle sheath cell wall thickness, probably accounting for low gbs and increased estimates of [CO2] at Rubisco sites. Effects of nitrogen on expression of ShPIP2;1 and ShPIP1;2 aquaporins did not explain changes in gbs. Our data revealed that reduced Rubisco carboxylation was the main factor causing low sugarcane photosynthesis at low nitrogen supply, in contrast to the previous report on the importance of an impaired CO2 concentration mechanism under N deficiency. Our findings suggest higher investment of nitrogen into Rubisco protein would favour photosynthesis and plant performance under low nitrogen availability.
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Affiliation(s)
- Vanessa R Tofanello
- Laboratory of Crop Physiology (LCroP), Dept. Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Larissa M Andrade
- Centro de Cana, Instituto Agronômico (IAC), Ribeirão Preto, SP, Brazil
| | - Denisele N A Flores-Borges
- Laboratory of Crop Physiology (LCroP), Dept. Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Eduardo Kiyota
- Laboratory of Crop Physiology (LCroP), Dept. Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Juliana L S Mayer
- Laboratory of Crop Physiology (LCroP), Dept. Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Silvana Creste
- Centro de Cana, Instituto Agronômico (IAC), Ribeirão Preto, SP, Brazil
| | - Eduardo C Machado
- Laboratory of Plant Physiology "Coaracy M. Franco", Center for Research and Development in Ecophysiology and Biophysics, IAC, Campinas, SP, Brazil
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Dept. Plant Sciences, Wageningen University & Research, Wageningen, The Netherlands
| | - Paul C Struik
- Centre for Crop Systems Analysis, Dept. Plant Sciences, Wageningen University & Research, Wageningen, The Netherlands
| | - Rafael V Ribeiro
- Laboratory of Crop Physiology (LCroP), Dept. Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.
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Mohan C, Shibao PYT, de Paula FFP, Toyama D, Vieira MAS, Figueira A, Scotton D, Soares-Costa A, Henrique-Silva F. hRNAi-mediated knock-down of Sphenophorus levis V-ATPase E in transgenic sugarcane (Saccharum spp interspecific hybrid) affects the insect growth and survival. PLANT CELL REPORTS 2021; 40:507-516. [PMID: 33389048 DOI: 10.1007/s00299-020-02646-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Transgenic sugarcane expressing V-ATPase subunit E dsRNA affects growth and survival of Sphenophorus levis. Plants being sessile organisms are constantly confronted with several biotic and abiotic stresses. Sugarcane (Saccharum spp) is a major tropical crop widely cultivated for its sugar and other by-products. In Brazil, sugarcane plantations account for significant production losses due to Sphenophorus levis (sugarcane weevil) infestations. With the existing control measures being less effective, there arises a necessity for advanced strategies. Our bioassay injection experiments with V-ATPase E dsRNA in S. levis larvae showed significant mortality and reduction in transcription levels. Furthermore, we down-regulated the V-ATPase E gene of S. levis in transgenic sugarcane using an RNAi approach. The resultant RNAi transgenic lines exhibited reduction in larval growth and survival, without compromising plant performance under controlled environment. Our results illustrate that RNAi-mediated down-regulation of key genes is a promising approach in imparting resistance to sugarcane weevil.
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Affiliation(s)
- Chakravarthi Mohan
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | | | | | - Danyelle Toyama
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | | | - Antonio Figueira
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Danielle Scotton
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Andrea Soares-Costa
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Flavio Henrique-Silva
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil.
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Selection and validation of reference genes by RT-qPCR under photoperiodic induction of flowering in sugarcane (Saccharum spp.). Sci Rep 2021; 11:4589. [PMID: 33633157 PMCID: PMC7907395 DOI: 10.1038/s41598-021-83918-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 02/03/2021] [Indexed: 11/09/2022] Open
Abstract
Although reference genes have previously been used in the expression analysis of genes involved in sugarcane flowering they had not been experimentally validated for stability and consistency of expression between different samples over a wide range of experimental conditions. Here we report the analysis of candidate reference genes in different tissue types, at different temporal time-points, in both short and long day photoperiodic treatments. The stability of the candidate reference genes in all conditions was evaluated with NormFinder, BestKeeper, and RefFinder algorithms that complement each other for a more robust analysis. As the Normfinder algorithm was more appropriate for our experimental conditions, greater emphasis was placed on Normfinder when choosing the most stable genes. UBQ1 and TUB were shown to be the most stable reference genes to use for normalizing RT-qPCR gene expression data during floral induction, whilst 25SrRNA1 and GAPDH were the least stable. Their use as a reference gene pair was validated by analyzing the expression of two differentially expressed target genes (PIL5 and LHP1). The UBQ1/TUB reference genes combination was able to reveal small significant differences in gene expression of the two target genes that were not detectable when using the least stable reference gene combination. These results can be used to inform the choice of reference genes to use in the study of the sugarcane floral induction pathway. Our work also demonstrates that both PIL5 and LHP1 are significantly up-regulated in the initial stages of photoperiodic induction of flowering in sugarcane.
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10
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Nandakumar M, Viswanathan R, Malathi P, Ramesh Sundar A. Selection of reference genes for normalization of microRNA expression in sugarcane stalks during its interaction with Colletotrichum falcatum. 3 Biotech 2021; 11:72. [PMID: 33489689 DOI: 10.1007/s13205-020-02632-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/28/2020] [Indexed: 02/05/2023] Open
Abstract
The microRNAs role in various cellular and metabolic functions is gaining more limelight in line with second-generation NGS technology. For the validation of candidate miRNA genes, the quantitative real-time PCR is the widely trusted and efficient method to follow. Sugarcane miRNAs are less explored in sugarcane defense response during their interaction with Colletotrichum falcatum inciting red rot. Further, for RT-qPCR experiments involving sugarcane miRNA expression studies, a stable internal reference gene is required. Hence, we have taken a study involving 20 candidate genes to identify stable expressing reference genes using NormFinder, geNorm, BestKeeper, and deltaCt statistical algorithms. The candidate reference genes included miRNAs and protein-coding genes. The results indicated that there is a variation in ranking among the algorithms. We found miR1862c as the stably expressed miRNA reference gene among the candidates and miR444b.2 along miR1862c formed the best reference gene pair combination, which can be used in the experiments aiming to explore sugarcane miRNAs in the defense mechanism against C. falcatum. The stable miRNA reference gene was further validated with other lesser stable reference gene candidates to assess the effect of stable reference genes during normalization. The present study evaluating the sugarcane miRNAs as reference genes for normalizing RT-qPCR expression data involving miRNAs during sugarcane × C. falcatum interaction is the first of its kind. Further, this systematic approach can be followed to assess the reference gene in various experimental conditions involving sugarcane miRNAs.
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Affiliation(s)
- M Nandakumar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - R Viswanathan
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - P Malathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - A Ramesh Sundar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
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11
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Expression profiling of MADS-box gene family revealed its role in vegetative development and stem ripening in S. spontaneum. Sci Rep 2020; 10:20536. [PMID: 33239664 PMCID: PMC7688973 DOI: 10.1038/s41598-020-77375-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/22/2020] [Indexed: 01/10/2023] Open
Abstract
Sugarcane is the most important sugar and biofuel crop. MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in plants. Systematic analyses of MADS-box genes have been reported in many plant species, but its identification and characterization were not possible until a reference genome of autotetraploid wild type sugarcane specie, Saccharum spontaneum is available recently. We identified 182 MADS-box sequences in the S. spontaneum genome, which were annotated into 63 genes, including 6 (9.5%) genes with four alleles, 21 (33.3%) with three, 29 (46%) with two, 7 (11.1%) with one allele. Paralogs (tandem duplication and disperse duplicated) were also identified and characterized. These MADS-box genes were divided into two groups; Type-I (21 Mα, 4 Mβ, 4 Mγ) and Type-II (32 MIKCc, 2 MIKC*) through phylogenetic analysis with orthologs in Arabidopsis and sorghum. Structural diversity and distribution of motifs were studied in detail. Chromosomal localizations revealed that S. spontaneum MADS-box genes were randomly distributed across eight homologous chromosome groups. The expression profiles of these MADS-box genes were analyzed in leaves, roots, stem sections and after hormones treatment. Important alleles based on promoter analysis and expression variations were dissected. qRT-PCR analysis was performed to verify the expression pattern of pivotal S. spontaneum MADS-box genes and suggested that flower timing genes (SOC1 and SVP) may regulate vegetative development.
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Liu X, Liu S, Zhang J, Wu Y, Wu W, Zhang Y, Liu B, Tang R, He L, Li R, Jia X. Optimization of reference genes for qRT-PCR analysis of microRNA expression under abiotic stress conditions in sweetpotato. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:379-386. [PMID: 32623093 DOI: 10.1016/j.plaphy.2020.06.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Sweetpotato (Ipomoea batatas. L) is an important food crop, harvested for its nutrient-rich tuberous roots. Drought and salt stresses are two major factors limiting the sweetpotato production. Since microRNAs (miRNAs) are well known to play crucial roles in regulation of plant stress responses, quantitative profiling of miRNA expression under stress conditions will facilitate identification and genetic manipulation of novel miRNAs to improve stress tolerance. Real-time quantitative reverse transcription PCR (qRT-PCR) is a commonly used tool for this purpose, but not without challenges. Although stem-loop and poly(A)-tail modified qRT-PCR methods were developed for characterizing miRNA expression, accurate profiling of miRNAs is still difficult in many plant species because of a lack of reliable reference genes for normalizing miRNA transcripts. To identify reference genes that are suitable for normalizing miRNA expression in sweetpotato, the expression stability of eight candidate miRNAs and two commonly used reference genes were tested in 96 samples involving four tissues and two cultivars under drought and salt stress treatments. Data analysis using the geNorm, NormFinder and Bestkeeper algorithms demonstrated that miRn60, miR482, and their combination were reliable references. We further validated the reference genes by expression analysis of the well-characterized miR319 and miR156 that regulate drought and salt stress responses, respectively. The reference genes identified in this study will facilitate future miRNA analysis under abiotic stress conditions in sweetpotato.
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Affiliation(s)
- Xiayu Liu
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Shifang Liu
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Jie Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yuhao Wu
- Institute of Cotton Research, Shanxi Academy of Agricultural Sciences, Yuncheng, 044000, Shanxi, China
| | - Wanyi Wu
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yi Zhang
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Baoling Liu
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Ruimin Tang
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Liheng He
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Runzhi Li
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Xiaoyun Jia
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
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13
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Nawae W, Shearman JR, Tangphatsornruang S, Punpee P, Yoocha T, Sangsrakru D, Naktang C, Sonthirod C, Wirojsirasak W, Ukoskit K, Sriroth K, Klomsa-Ard P, Pootakham W. Differential expression between drought-tolerant and drought-sensitive sugarcane under mild and moderate water stress as revealed by a comparative analysis of leaf transcriptome. PeerJ 2020; 8:e9608. [PMID: 33240580 PMCID: PMC7676377 DOI: 10.7717/peerj.9608] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/05/2020] [Indexed: 01/17/2023] Open
Abstract
Sugarcane contributes 80% of global sugar production and to bioethanol generation for the bioenergy industry. Its productivity is threatened by drought that can cause up to 60% yield loss. This study used RNA-Seq to gain a better understanding of the underlying mechanism by which drought-tolerant sugarcane copes with water stress. We compared gene expression in KPS01-12 (drought-tolerant genotype) and UT12 (drought-sensitive genotype) that have significantly different yield loss rates under drought conditions. We treated KPS01-12 and UT12 with mild and moderate water stress and found differentially expressed genes in various biological processes. KPS01-12 had higher expression of genes that were involved in water retention, antioxidant secondary metabolite biosynthesis, and oxidative and osmotic stress response than UT12. In contrast, the sensitive genotype had more down-regulated genes that were involved in photosynthesis, carbon fixation and Calvin cycle than the tolerant genotype. Our obtained expression profiles suggest that the tolerant sugarcane has a more effective genetic response than the sensitive genotype at the initiation of drought stress. The knowledge gained from this study may be applied in breeding programs to improve sugarcane production in drought conditions.
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Affiliation(s)
- Wanapinun Nawae
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Jeremy R Shearman
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Prapat Punpee
- Mitr Phol Sugarcane Research Center Co., Ltd., Phu Khiao, Chaiyaphum, Thailand
| | - Thippawan Yoocha
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Warodom Wirojsirasak
- Mitr Phol Sugarcane Research Center Co., Ltd., Phu Khiao, Chaiyaphum, Thailand.,Department of Biotechnology, Faculty of Science and Technology, Thammasat University (Rangsit Campus), Pathum Thani, Thailand
| | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University (Rangsit Campus), Pathum Thani, Thailand
| | - Klanarong Sriroth
- Mitr Phol Sugarcane Research Center Co., Ltd., Phu Khiao, Chaiyaphum, Thailand
| | - Peeraya Klomsa-Ard
- Mitr Phol Sugarcane Research Center Co., Ltd., Phu Khiao, Chaiyaphum, Thailand
| | - Wirulda Pootakham
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
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14
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Jose S, Abbey J, Jaakola L, Percival D. Selection and validation of reliable reference genes for gene expression studies from Monilinia vaccinii-corymbosi infected wild blueberry phenotypes. Sci Rep 2020; 10:11688. [PMID: 32678232 PMCID: PMC7366731 DOI: 10.1038/s41598-020-68597-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/19/2020] [Indexed: 01/24/2023] Open
Abstract
Monilinia blight disease caused by Monilinia vaccinii-corymbosi (Reade) Honey (M.vc) causes severe damage and economic losses in wild blueberry growing regions. Molecular mechanisms regulating defence responses of wild blueberry phenotypes towards this causal fungus are not yet fully known. A reliable quantification of gene expression using quantitative real time PCR (qPCR) is fundamental for measuring changes in target gene expression. A crucial aspect of accurate normalisation is the choice of appropriate reference genes. This study evaluated the expression stability of seven candidate reference genes (GAPDH, UBC9, UBC28, TIP41, CaCSa, PPR and RH8) in floral tissues of diploid and tetraploid wild blueberry phenotypes challenged with M.vc. The expression stability was calculated using five algorithms: geNorm, NormFinder, BestKeeper, deltaCt and RefFinder. The results indicated that UBC9 and GAPDH were the most stable reference genes, while RH8 and PPR were the least stable ones. To further validate the suitability of the analyzed reference genes, the expression level of a pathogenesis related protein gene (i.e., PR3) was analysed for both phenotypes at four time points of infection. Our results may be beneficial for future studies involving the quantification of relative gene expression levels in wild blueberry species.
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Affiliation(s)
- Sherin Jose
- Wild Blueberry Research Program, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada.
| | - Joel Abbey
- Wild Blueberry Research Program, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Laura Jaakola
- Climate Laboratory Holt, Department of Arctic and Marine Biology, The Arctic University of Norway, 9037, Tromsø, Norway.,NIBIO, Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431, Ås, Norway
| | - David Percival
- Wild Blueberry Research Program, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
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15
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Zhao J, Zhou M, Meng Y. Identification and Validation of Reference Genes for RT-qPCR Analysis in Switchgrass under Heavy Metal Stresses. Genes (Basel) 2020; 11:E502. [PMID: 32375288 PMCID: PMC7291066 DOI: 10.3390/genes11050502] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 11/22/2022] Open
Abstract
Switchgrass (Panicum Virgatum L.) has been recognized as the new energy plant, which makes it ideal for the development of phytoremediation on heavy metal contamination in soils with great potential. This study aimed to screen the best internal reference genes for the real-time quantitative PCR (RT-qPCR) in leaves and roots of switchgrass for investigating its response to various heavy metals, such as cadmium (Cd), lead (Pb), mercury (Hg), chromium (Cr), and arsenic (As). The stability of fourteen candidate reference genes was evaluated by BestKeeper, GeNorm, NormFinder, and RefFinder software. Our results identified U2AF as the best reference gene in Cd, Hg, Cr, and As treated leaves as well as in Hg, Pb, As, and Cr stressed root tissues. In Pb treated leaf tissues, 18S rRNA was demonstrated to be the best reference gene. CYP5 was determined to be the optimal reference gene in Cd treated root tissues. The least stable reference gene was identified to be CYP2 in all tested samples except for root tissues stressed by Pb. To further validate the initial screening results, we used the different sets of combinatory internal reference genes to analyze the expression of two metal transport associated genes (PvZIP4 and PvPDB8) in young leaves and roots of switchgrass. Our results demonstrated that the relative expression of the target genes consistently changed during the treatment when CYP5/UBQ1, U2AF/ACT12, eEF1a/U2AF, or 18S rRNA/ACT12 were combined as the internal reference genes. However, the time-dependent change pattern of the target genes was significantly altered when CYP2 was used as the internal reference gene. Therefore, the selection of the internal reference genes appropriate for specific experimental conditions is critical to ensure the accuracy and reliability of RT-qPCR. Our findings established a solid foundation to further study the gene regulatory network of switchgrass in response to heavy metal stress.
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Affiliation(s)
- Junming Zhao
- Department of Grassland Science, Sichuan Agricultural University, Chengdu 611130, China;
| | - Man Zhou
- Zonation Fringe Technology Co., Metro Vancouver, BC V5C 2A0, Canada;
| | - Yu Meng
- College of Science and Technology, Wenzhou-Kean University, Wenzhou 325060, China
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16
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Selection of the Reference Gene for Expression Normalization in Papaver s omniferum L. under Abiotic Stress and Hormone Treatment. Genes (Basel) 2020; 11:genes11020124. [PMID: 31979407 PMCID: PMC7074096 DOI: 10.3390/genes11020124] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 01/21/2023] Open
Abstract
Papaver somniferum L. is an important medical plant that produces analgesic drugs used for the pain caused by cancers and surgeries. Recent studies have focused on the expression genes involved in analgesic drugs biosynthesis, and the real-time quantitative polymerase chain reaction (RT-qPCR) technique is the main strategy. However, no reference genes have been reported for gene expression normalization in P. somniferum. Herein, nine reference genes (actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), cyclophilin 2 (CYP2), elongation factor 1-alpha (EF-1α), glyceraldehyde-3-phosphate dehydrogenase 2, cytosolic (GAPC2), nuclear cap-binding protein subunit 2 (NCBP2), protein phosphatase 2A (PP2A), TIP41-like protein (TIP41), and tubulin beta chain (TUB)) of P. somniferum were selected and analyzed under five different treatments (cold, drought, salt, heavy metal, and hormone stress). Then, BestKeeper, NormFinder, geNorm, and RefFinder were employed to analyze their gene expression stability. The results reveal that NCBP2 is the most stable reference gene under various experimental conditions. The work described here is the first report regarding on reference gene selection in P. somniferum, which could be used for the accurate normalization of the gene expression involved in analgesic drug biosynthesis.
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17
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Li M, Xie F, He Q, Li J, Liu J, Sun B, Luo Y, Zhang Y, Chen Q, Zhang F, Gong R, Wang Y, Wang X, Tang H. Expression Analysis of XTH in Stem Swelling of Stem Mustard and Selection of Reference Genes. Genes (Basel) 2020; 11:genes11010113. [PMID: 31968559 PMCID: PMC7016721 DOI: 10.3390/genes11010113] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/08/2020] [Accepted: 01/15/2020] [Indexed: 02/05/2023] Open
Abstract
Accurate analysis of gene expression requires selection of appropriate reference genes. In this study, we report analysis of eight candidate reference genes (ACTIN, UBQ, EF-1α, UBC, IF-4α, TUB, PP2A, and HIS), which were screened from the genome and transcriptome data in Brassica juncea. Four statistical analysis softwares geNorm, NormFinder, BestKeeper, and RefFinder were used to test the reliability and stability of gene expression of the reference genes. To further validate the stability of reference genes, the expression levels of two CYCD3 genes (BjuB045330 and BjuA003219) were studied. In addition, all genes in the xyloglucan endotransglucosylase/hydrolase (XTH) family were identified in B. juncea and their patterns at different periods of stem enlargement were analyzed. Results indicated that UBC and TUB genes showed stable levels of expression and are recommended for future research. In addition, XTH genes were involved in regulation of stem enlargement expression. These results provide new insights for future research aiming at exploring important functional genes, their expression patterns and regulatory mechanisms for mustard development.
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Affiliation(s)
- Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Fangjie Xie
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Qi He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Jie Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Jiali Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Fen Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Ronggao Gong
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (M.L.); (F.X.); (J.L.); (B.S.); (Y.L.); (Y.Z.); (Q.C.); (F.Z.); (Y.W.); (X.W.)
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: ; Tel.: +86-288-629-1949
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18
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Rego ECS, Pinheiro TDM, Antonino JD, Alves GSC, Cotta MG, Fonseca FCDA, Miller RNG. Stable reference genes for RT-qPCR analysis of gene expression in the Musa acuminata-Pseudocercospora musae interaction. Sci Rep 2019; 9:14592. [PMID: 31601872 PMCID: PMC6787041 DOI: 10.1038/s41598-019-51040-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 09/20/2019] [Indexed: 11/30/2022] Open
Abstract
Leaf pathogens are limiting factors in banana (Musa spp.) production, with Pseudocercospora spp. responsible for the important Sigatoka disease complex. In order to investigate cellular processes and genes involved in host defence responses, quantitative real-time PCR (RT-qPCR) is an analytical technique for gene expression quantification. Reliable RT-qPCR data, however, requires that reference genes for normalization of mRNA levels in samples are validated under the conditions employed for expression analysis of target genes. We evaluated the stability of potential reference genes ACT1, α-TUB, UBQ1, UBQ2, GAPDH, EF1α, APT and RAN. Total RNA was extracted from leaf tissues of Musa acuminata genotypes Calcutta 4 (resistant) and Cavendish Grande Naine (susceptible), both subjected to P. musae infection. Expression stability was determined with NormFinder, BestKeeper, geNorm and RefFinder algorithms. UBQ2 and RAN were the most stable across all M. acuminata samples, whereas when considering inoculated and non-inoculated leaf samples, APT and UBQ2 were appropriate for normalization in Calcutta 4, with RAN and α-TUB most stable in Cavendish Grande Naine. This first study of reference genes for relative quantification of target gene expression in the M. acuminata-P. musae interaction will enable reliable analysis of gene expression in this pathosystem, benefiting elucidation of disease resistance mechanisms.
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Affiliation(s)
- Erica Cristina Silva Rego
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Brasília, DF, Brazil
| | - Tatiana David Miranda Pinheiro
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Brasília, DF, Brazil
| | - Jose Dijair Antonino
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Brasília, DF, Brazil.,Departamento de Agronomia-Entomologia, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros s/n, Dois Irmãos, 52171-900, Recife, PE, Brazil
| | - Gabriel Sergio Costa Alves
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Brasília, DF, Brazil
| | - Michelle Guitton Cotta
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Brasília, DF, Brazil
| | - Fernando Campos De Assis Fonseca
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Brasília, DF, Brazil
| | - Robert Neil Gerard Miller
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Brasília, DF, Brazil.
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Parvaiz A, Mustafa G, Khan HMWA, Joyia FA, Niazi AK, Anwar S, Khan MS. Field evaluation ratified by transcript and computational analyses unveils myco-protective role of SUGARWIN proteins in sugarcane. 3 Biotech 2019; 9:377. [PMID: 31588401 DOI: 10.1007/s13205-019-1896-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/16/2019] [Indexed: 10/25/2022] Open
Abstract
Nine elite sugarcane genotypes (SPF-234, CPF-246, CPF-247, CPF-248, HSF-240, CP-77-400, S-2006-US-658, S-2003-US-127 and S-2006-US-633) were assessed for field level tolerance against Colletotrichum falcatum followed by quantitative expression and computational analyses of mycoprotective proteins. Plug inoculation method was used to assess level of tolerance of aforementioned genotypes while growing in the field. Genotype S-2006-US-658 was categorized as resistant whereas genotypes CPF-246, CPF-248, HSF-240, S-2003-US-127, S-2006-US-633 and CP-77-400 were categorized as moderately resistant and genotypes SPF-234, CPF-247 as moderately susceptible. Quantitative transcript analyses also revealed that the expression of mycoprotective genes (SUGARWIN1 and SUGARWIN2) was maximum in genotype CPF-246 whereas lowest in genotype SPF-234. Hence these mycoprotective proteins play some critical role in fungal pathogen protection as genotypes with higher expression are more tolerant compared to the genotypes with lower expression of mycoprotective proteins. In-silico interaction of these mycoprotective proteins with chitin, glucan, chitosan and mannan (the core constituents of fungal cell wall) also validated their role in disease susceptibility or resistance. These studies will prove a step forward in understanding mycoprotective proteins and can be employed to develop molecular markers for the selection and screening of red rot resistant sugarcane varieties resulting in enhanced productivity of this valuable cash crop.
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Coêlho MRV, Rivas R, Ferreira-Neto JRC, Pandolfi V, Bezerra-Neto JP, Benko-Iseppon AM, Santos MG. Reference genes selection for Calotropis procera under different salt stress conditions. PLoS One 2019; 14:e0215729. [PMID: 30998798 PMCID: PMC6472812 DOI: 10.1371/journal.pone.0215729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 04/08/2019] [Indexed: 02/04/2023] Open
Abstract
Calotropis procera is a perennial Asian shrub with significant adaptation to adverse climate conditions and poor soils. Given its increased salt and drought stress tolerance, C. procera stands out as a powerful candidate to provide alternative genetic resources for biotechnological approaches. The qPCR (real-time quantitative polymerase chain reaction), widely recognized among the most accurate methods for quantifying gene expression, demands suitable reference genes (RGs) to avoid over- or underestimations of the relative expression and incorrect interpretation. This study aimed at evaluating the stability of ten RGs for normalization of gene expression of root and leaf of C. procera under different salt stress conditions and different collection times. The selected RGs were used on expression analysis of three target genes. Three independent experiments were carried out in greenhouse with young plants: i) Leaf100 = leaf samples collected 30 min, 2 h, 8 h and 45 days after NaCl-stress (100 mM NaCl); ii) Root50 and iii) Root200 = root samples collected 30 min, 2 h, 8 h and 1day after NaCl-stress (50 and 200 mM NaCl, respectively). Stability rank among the three algorithms used showed high agreement for the four most stable RGs. The four most stable RGs showed high congruence among all combination of collection time, for each software studied, with minor disagreements. CYP23 was the best RG (rank of top four) for all experimental conditions (Leaf100, Root50, and Root200). Using appropriated RGs, we validated the relative expression level of three differentially expressed target genes (NAC78, CNBL4, and ND1) in Leaf100 and Root200 samples. This study provides the first selection of stable reference genes for C. procera under salinity. Our results emphasize the need for caution when evaluating the stability RGs under different amplitude of variable factors.
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Affiliation(s)
- Maria R. V. Coêlho
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Fisiologia Vegetal, Recife, PE, Brazil
| | - Rebeca Rivas
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Fisiologia Vegetal, Recife, PE, Brazil
| | - José Ribamar C. Ferreira-Neto
- Universidade Federal de Pernambuco, Departamento de Genética, Laboratório Genética e Biotecnologia Vegetal, Recife, PE, Brazil
| | - Valesca Pandolfi
- Universidade Federal de Pernambuco, Departamento de Genética, Laboratório Genética e Biotecnologia Vegetal, Recife, PE, Brazil
| | - João P. Bezerra-Neto
- Universidade Federal de Pernambuco, Departamento de Genética, Laboratório Genética e Biotecnologia Vegetal, Recife, PE, Brazil
| | - Ana Maria Benko-Iseppon
- Universidade Federal de Pernambuco, Departamento de Genética, Laboratório Genética e Biotecnologia Vegetal, Recife, PE, Brazil
| | - Mauro G. Santos
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Fisiologia Vegetal, Recife, PE, Brazil
- * E-mail:
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Sun H, Jiang X, Sun M, Cong H, Qiao F. Evaluation of reference genes for normalizing RT-qPCR in leaves and suspension cells of Cephalotaxus hainanensis under various stimuli. PLANT METHODS 2019; 15:31. [PMID: 30962812 PMCID: PMC6434779 DOI: 10.1186/s13007-019-0415-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Reverse transcription quantitative real-time PCR (RT-qPCR) is a widely used approach for investigating gene expression levels in plants because of its high reproducibility, sensitivity, accuracy and rapidness. Evaluation of reference genes for normalizing RT-qPCR data is a necessary step, especially in new plant varieties. Cephalotaxus hainanensis is a precious medicinal plant belonging to the family of Cephalotaxaceae and no RT-qPCR studies have been reported on it. RESULTS In this study, 9 candidate reference genes were selected from the transcriptome data of C. hainanensis; 3 statistical algorithms (geNorm, NormFinder, BestKeeper) were applied to evaluate their expression stabilities through 180 samples under 6 stimuli treatments in leaves and leaf-derived suspension cultured cells; a comprehensive stabilities ranking was also performed by RefFinder. The results showed that suitable reference genes in C. hainanensis should be selected for normalization relative to different experimental sets. 18S showed a higher stability than other candidate reference genes which ranked at the top two suitable genes under all experimental setups in this study. CONCLUSION This study is the first to evaluate the stability of reference genes in C. hainanensis and supply an important foundation to use the RT-qPCR for an accurate and far-reaching gene expression analysis in C. hainanensis.
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Affiliation(s)
- Huapeng Sun
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture/Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan People’s Republic of China
| | - Xuefei Jiang
- Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources/Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan People’s Republic of China
| | - Mengli Sun
- Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources/Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan People’s Republic of China
| | - Hanqing Cong
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture/Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan People’s Republic of China
| | - Fei Qiao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture/Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan People’s Republic of China
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da Silva MF, Gonçalves MC, Dos Santos Brito M, Nóbile PM, de Andrade LM, Medeiros CN, Creste S, Pinto LR. Reference genes for gene expression studies targeting sugarcane infected with Sugarcane mosaic virus (SCMV). BMC Res Notes 2019; 12:149. [PMID: 30885257 PMCID: PMC6423880 DOI: 10.1186/s13104-019-4168-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/06/2019] [Indexed: 12/22/2022] Open
Abstract
Objective The selection of reference genes in sugarcane under Sugarcane mosaic virus (SCMV) infection has not been reported and is indispensable to get reliable reverse transcription quantitative PCR (RT-qPCR) results for validation of transcriptome analysis. In this regard, seven potential reference genes were tested by RT-qPCR and ranked according to their stability using BestKeeper, NormFinder and GeNorm algorithms, and RefFinder WEB-based software in an experiment performed with samples from two sugarcane cultivars contrasting for SCMV resistance, when mechanically inoculated with a severe SCMV strain and using mock inoculated plant controls. Results The genes Uridylate kinase (UK) and Ubiquitin-conjugating enzyme 18 (UBC18) were the most stable according to GeNorm algorithm and the Pearson correlation coefficients with the BestKeeper index. On the other hand, ribosomal protein L35-4 (RPL1), Actin (ACT) and Ubiquitin1 (UBQ1) were the least stable genes for all algorithms tested. Electronic supplementary material The online version of this article (10.1186/s13104-019-4168-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Michael Dos Santos Brito
- Instituto de Ciência e Tecnologia da Universidade Federal de São Paulo, São José dos Campos, SP, Brazil
| | - Paula Macedo Nóbile
- Instituto Agronômico, Centro de Cana, CP 206, Ribeirão Preto, SP, CEP 14001-970, Brazil
| | | | | | - Silvana Creste
- Instituto Agronômico, Centro de Cana, CP 206, Ribeirão Preto, SP, CEP 14001-970, Brazil
| | - Luciana Rossini Pinto
- Instituto Agronômico, Centro de Cana, CP 206, Ribeirão Preto, SP, CEP 14001-970, Brazil.
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Shukla P, Reddy RA, Ponnuvel KM, Rohela GK, Shabnam AA, Ghosh MK, Mishra RK. Selection of suitable reference genes for quantitative real-time PCR gene expression analysis in Mulberry (Morus alba L.) under different abiotic stresses. Mol Biol Rep 2019; 46:1809-1817. [PMID: 30694457 DOI: 10.1007/s11033-019-04631-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/19/2019] [Indexed: 01/02/2023]
Abstract
Mulberry (Morus alba L.) is the sole food source for the mulberry silkworm, Bombyx mori and therefore important for sericulture industry. Different abiotic stress conditions like drought, salt, heat and cold stress adversely affect the productivity and quality of mulberry leaves. Quantitative real time PCR (qPCR) is a reliable and widely used method to identify abiotic stress responsive genes and molecular mechanism in different plant species. Selection of suitable reference genes is important requirement for normalizing the expression of genes through qRT-PCR study. In the present study, we have selected eight candidate reference genes in mulberry for analyzing their expression stability in different abiotic stress treatments including drought, salt, heat and cold stresses. The expression stability of these reference genes was determined using geNorm, NormFinder and RefFinder statistical algorithms. The results showed that Ubiquitin and protein phosphatase 2A regulatory subunit A (PP2A) were the most stable genes across all the treatment samples. However, analysis of individual stresses revealed different expression profiles and stability of reference genes. Actin3 and PP2A were most stable in drought and salt conditions respectively. RPL3 most preferred in heat stress and Ubiquitin was most stable in cold stress. We propose the ubiquitin and PP2A are the preferred reference genes for normalization of gene expression data from abiotic stresses. In addition, Actin3 are preferred for drought stress, PP2A for salt stress, RPL3 for heat stress and Ubiquitin for cold stress studies.
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Affiliation(s)
- Pawan Shukla
- Central Sericultural Research and Training Institute, Central Silk Board, NH-1A, Gallandar, Pampore -192 121, Jammu and Kashmir, Srinagar, India.
| | - Ramesha A Reddy
- Seri-biotech Research Laboratory (SBRL), Carmelram Post, Kodathi, Bangalore, 560035, India
| | - Kangayam M Ponnuvel
- Seri-biotech Research Laboratory (SBRL), Carmelram Post, Kodathi, Bangalore, 560035, India
| | - Gulab Khan Rohela
- Central Sericultural Research and Training Institute, Central Silk Board, NH-1A, Gallandar, Pampore -192 121, Jammu and Kashmir, Srinagar, India
| | - Aftab A Shabnam
- Central Sericultural Research and Training Institute, Central Silk Board, NH-1A, Gallandar, Pampore -192 121, Jammu and Kashmir, Srinagar, India
| | - M K Ghosh
- Central Sericultural Research and Training Institute, Central Silk Board, NH-1A, Gallandar, Pampore -192 121, Jammu and Kashmir, Srinagar, India
| | - Rakesh Kumar Mishra
- Seri-biotech Research Laboratory (SBRL), Carmelram Post, Kodathi, Bangalore, 560035, India
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Andrade LM, Peixoto-Junior RF, Ribeiro RV, Nóbile PM, Brito MS, Marchiori PER, Carlin SD, Martins APB, Goldman MHS, Llerena JPP, Fregonesi C, Perecin D, Nebó JFCDO, Figueira A, Benatti TR, da Silva J, Mazzafera P, Creste S. Biomass Accumulation and Cell Wall Structure of Rice Plants Overexpressing a Dirigent-Jacalin of Sugarcane ( ShDJ) Under Varying Conditions of Water Availability. FRONTIERS IN PLANT SCIENCE 2019; 10:65. [PMID: 30815002 PMCID: PMC6381051 DOI: 10.3389/fpls.2019.00065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/16/2019] [Indexed: 05/03/2023]
Abstract
A sugarcane gene encoding a dirigent-jacalin, ShDJ, was induced under drought stress. To elucidate its biological function, we integrated a ShDJ-overexpression construction into the rice Nipponbare genome via Agrobacterium-mediated transformation. Two transgenic lines with a single copy gene in T0 were selected and evaluated in both the T1 and T4 generations. Transgenic lines had drastically improved survival rate under water deficit conditions, at rates close to 100%, while WT did not survive. Besides, transgenic lines had improved biomass production and higher tillering under water deficit conditions compared with WT plants. Reduced pectin and hemicellulose contents were observed in transgenic lines compared with wild-type plants under both well-watered and water deficit conditions, whereas cellulose content was unchanged in line #17 and reduced in line #29 under conditions of low water availability. Changes in lignin content under water deficit were only observed in line #17. However, improvements in saccharification were found in both transgenic lines along with changes in the expression of OsNTS1/2 and OsMYB58/63 secondary cell wall biosynthesis genes. ShDJ-overexpression up-regulated the expression of the OsbZIP23, OsGRAS23, OsP5CS, and OsLea3 genes in rice stems under well-watered conditions. Taken together, our data suggest that ShDJ has the potential for improving drought tolerance, plant biomass accumulation, and saccharification efficiency.
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Affiliation(s)
- Larissa Mara Andrade
- Instituto Agronômico (IAC), Centro de Cana, Ribeirão Preto, Brazil
- PPG - Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Rafael Fávero Peixoto-Junior
- Instituto Agronômico (IAC), Centro de Cana, Ribeirão Preto, Brazil
- PPG - Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | | | | | - Michael Santos Brito
- Instituto Agronômico (IAC), Centro de Cana, Ribeirão Preto, Brazil
- Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo, São José dos Campos, Brazil
| | - Paulo Eduardo Ribeiro Marchiori
- Instituto Agronômico (IAC), Centro de Ecofisiologia e Biofísica, Campinas, Brazil
- Departamento de Biologia, Universidade Federal de Lavras, Lavras, Brazil
| | | | - Alexandre Palma Boer Martins
- Instituto Agronômico (IAC), Centro de Cana, Ribeirão Preto, Brazil
- PPG - Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Maria Helena S. Goldman
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | | | | | - Dilermando Perecin
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
| | | | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura (CENA), University of São Paulo, Piracicaba, Brazil
| | | | - Jorge da Silva
- Texas A&M Agrilife Research & Extension Center, Weslaco, TX, United States
| | - Paulo Mazzafera
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Silvana Creste
- Instituto Agronômico (IAC), Centro de Cana, Ribeirão Preto, Brazil
- *Correspondence: Silvana Creste,
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Comparison of Reliable Reference Genes Following Different Hormone Treatments by Various Algorithms for qRT-PCR Analysis of Metasequoia. Int J Mol Sci 2018; 20:ijms20010034. [PMID: 30577651 PMCID: PMC6337471 DOI: 10.3390/ijms20010034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 12/23/2022] Open
Abstract
Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is the most sensitive technique for evaluating gene expression levels. Choosing appropriate reference genes for normalizing target gene expression is important for verifying expression changes. Metasequoia is a high-quality and economically important wood species. However, few systematic studies have examined reference genes in Metasequoia. Here, the expression stability of 14 candidate reference genes in different tissues and following different hormone treatments were analyzed using six algorithms. Candidate reference genes were used to normalize the expression pattern of FLOWERING LOCUS T and pyrabactin resistance-like 8. Analysis using the GrayNorm algorithm showed that ACT2 (Actin 2), HIS (histone superfamily protein H3) and TATA (TATA binding protein) were stably expressed in different tissues. ACT2, EF1α (elongation factor-1 alpha) and HIS were optimal for leaves treated with the flowering induction hormone solution, while Cpn60β (60-kDa chaperonin β-subunit), GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and HIS were the best reference genes for treated buds. EF1α, HIS and TATA were useful reference genes for accurate normalization in abscisic acid-response signaling. Our results emphasize the importance of validating reference genes for qRT-PCR analysis in Metasequoia. To avoid errors, suitable reference genes should be used for different tissues and hormone treatments to increase normalization accuracy. Our study provides a foundation for reference gene normalization when analyzing gene expression in Metasequoia.
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Jatav PK, Sharma A, Dahiya DK, Khan A, Agarwal A, Kothari SL, Kachhwaha S. Identification of suitable internal control genes for transcriptional studies in Eleusine coracana under different abiotic stress conditions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:793-807. [PMID: 30150855 PMCID: PMC6103957 DOI: 10.1007/s12298-018-0544-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/14/2018] [Accepted: 05/02/2018] [Indexed: 06/08/2023]
Abstract
Finger millet [Eleusine coracana (L.) Gaertn] is an excellent food and forage crop of arid and semiarid areas in Africa and Asia. It is well adapted to drought, heat, high salinity, poor soil fertility and low pH with an efficient C4 carbon fixation mechanism for high yield potential. To normalize the target gene expression data, the identification of suitable reference genes is essential. Ten candidate reference genes were selected and their expression stability was analyzed in various samples treated with different abiotic stress conditions. Five different statistical algorithms: geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder were used to determine the stability of these genes. Our results revealed GAPDH, EEF1a, ACT and CYC as highly stable reference genes and PP2A and eIF4A as least stable reference genes across all the samples and suggesting that these genes could be used for accurate transcript normalization under abiotic stress. To the best of our knowledge, this is the first report on identification of suitable reference genes for accurate transcript normalization using qRT-PCR in finger millet under abiotic stress.
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Affiliation(s)
- Pradeep K. Jatav
- Department of Botany, University of Rajasthan, Jaipur, 302004 India
| | - Ankita Sharma
- National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - Dinesh K. Dahiya
- Post Graduate Institute of Veterinary Education and Research, Jaipur, 302020 India
| | - Arif Khan
- Post Graduate Institute of Veterinary Education and Research, Jaipur, 302020 India
| | - Atika Agarwal
- Department of Botany, University of Rajasthan, Jaipur, 302004 India
| | - S. L. Kothari
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 302006 India
| | - Sumita Kachhwaha
- Department of Botany, University of Rajasthan, Jaipur, 302004 India
- Bioinformatics Infrastructure Facility, University of Rajasthan, Jaipur, 302004 India
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Nikalje GC, Srivastava AK, Sablok G, Pandey GK, Nikam TD, Suprasanna P. Identification and validation of reference genes for quantitative real-time PCR under salt stress in a halophyte, Sesuvium portulacastrum. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.plgene.2017.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Evaluation of reference genes for reverse transcription quantitative real-time PCR (RT-qPCR) studies in Silene vulgaris considering the method of cDNA preparation. PLoS One 2017; 12:e0183470. [PMID: 28817728 PMCID: PMC5560574 DOI: 10.1371/journal.pone.0183470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 08/04/2017] [Indexed: 01/05/2023] Open
Abstract
Accurate gene expression measurements are essential in studies of both crop and wild plants. Reverse transcription quantitative real-time PCR (RT-qPCR) has become a preferred tool for gene expression estimation. A selection of suitable reference genes for the normalization of transcript levels is an essential prerequisite of accurate RT-qPCR results. We evaluated the expression stability of eight candidate reference genes across roots, leaves, flower buds and pollen of Silene vulgaris (bladder campion), a model plant for the study of gynodioecy. As random priming of cDNA is recommended for the study of organellar transcripts and poly(A) selection is indicated for nuclear transcripts, we estimated gene expression with both random-primed and oligo(dT)-primed cDNA. Accordingly, we determined reference genes that perform well with oligo(dT)- and random-primed cDNA, making it possible to estimate levels of nucleus-derived transcripts in the same cDNA samples as used for organellar transcripts, a key benefit in studies of cyto-nuclear interactions. Gene expression variance was estimated by RefFinder, which integrates four different analytical tools. The SvACT and SvGAPDH genes were the most stable candidates across various organs of S. vulgaris, regardless of whether pollen was included or not.
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