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Ferrante R, Campagni C, Vettori C, Checcucci A, Garosi C, Paffetti D. Meta-analysis of plant growth-promoting rhizobacteria interaction with host plants: implications for drought stress response gene expression. FRONTIERS IN PLANT SCIENCE 2024; 14:1282553. [PMID: 38288406 PMCID: PMC10823023 DOI: 10.3389/fpls.2023.1282553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/18/2023] [Indexed: 01/31/2024]
Abstract
Introduction The molecular and physiological mechanisms activated in plants during drought stress tolerance are regulated by several key genes with both metabolic and regulatory roles. Studies focusing on crop gene expression following plant growth-promoting rhizobacteria (PGPR) inoculation may help understand which bioinoculant is closely related to the induction of abiotic stress responses. Methods Here, we performed a meta-analysis following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to summarise information regarding plant-PGPR interactions, focusing on the regulation of nine genes involved in plant drought stress response. The literature research yielded 3,338 reports, of which only 41 were included in the meta-analysis based on the chosen inclusion criteria. The meta-analysis was performed on four genes (ACO, APX, ACS and DREB2); the other five genes (ERD15, MYB, MYC, acdS, WRKY) had an insufficient number of eligible articles. Results Forest plots obtained through each meta-analysis showed that the overexpression of ACO, APX, ACS and DREB2 genes was not statistically significant. Unlike the other genes, DREB2 showed statistically significant results in both the presence and absence of PGPR. Considering I2>75 %, the results showed a high heterogeneity among the studies included, and the cause for this was examined using subgroup analysis. Moreover, the funnel plot and Egger's test showed that the analyses were affected by strong publication bias. Discussion This study argues that the presence of PGPR may not significantly influence the expression of drought stress response-related crop genes. This finding may be due to high heterogeneity, lack of data on the genes examined, and significant publication bias.
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Affiliation(s)
- Roberta Ferrante
- National Biodiversity Future Center (NBFC), Palermo, Italy
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), Università degli Studi di Firenze, Florence, Italy
| | - Chiara Campagni
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), Università degli Studi di Firenze, Florence, Italy
| | - Cristina Vettori
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), Università degli Studi di Firenze, Florence, Italy
- Istituto di Bioscienze e Biorisorse (IBBR), Consiglio Nazionale delle Ricerche (CNR), Sesto Fiorentino, Italy
| | - Alice Checcucci
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), Università degli Studi di Firenze, Florence, Italy
| | - Cesare Garosi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), Università degli Studi di Firenze, Florence, Italy
| | - Donatella Paffetti
- National Biodiversity Future Center (NBFC), Palermo, Italy
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), Università degli Studi di Firenze, Florence, Italy
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Zhang W, Zhi W, Qiao H, Huang J, Li S, Lu Q, Wang N, Li Q, Zhou Q, Sun J, Bai Y, Zheng X, Bai M, Van Breusegem F, Xiang F. H2O2-dependent oxidation of the transcription factor GmNTL1 promotes salt tolerance in soybean. THE PLANT CELL 2023; 36:112-135. [PMID: 37770034 PMCID: PMC10734621 DOI: 10.1093/plcell/koad250] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023]
Abstract
Reactive oxygen species (ROS) play an essential role in plant growth and responses to environmental stresses. Plant cells sense and transduce ROS signaling directly via hydrogen peroxide (H2O2)-mediated posttranslational modifications (PTMs) on protein cysteine residues. Here, we show that the H2O2-mediated cysteine oxidation of NAC WITH TRANS-MEMBRANE MOTIF1-LIKE 1 (GmNTL1) in soybean (Glycine max) during salt stress promotes its release from the endoplasmic reticulum (ER) membrane and translocation to the nucleus. We further show that an oxidative posttranslational modification on GmNTL1 residue Cys-247 steers downstream amplification of ROS production by binding to and activating the promoters of RESPIRATORY BURST OXIDASE HOMOLOG B (GmRbohB) genes, thereby creating a feed-forward loop to fine-tune GmNTL1 activity. In addition, oxidation of GmNTL1 Cys-247 directly promotes the expression of CATION H+ EXCHANGER 1 (GmCHX1)/SALT TOLERANCE-ASSOCIATED GENE ON CHROMOSOME 3 (GmSALT3) and Na+/H+ Antiporter 1 (GmNHX1). Accordingly, transgenic overexpression of GmNTL1 in soybean increases the H2O2 levels and K+/Na+ ratio in the cell, promotes salt tolerance, and increases yield under salt stress, while an RNA interference-mediated knockdown of GmNTL1 elicits the opposite effects. Our results reveal that the salt-induced oxidation of GmNTL1 promotes its relocation and transcriptional activity through an H2O2-mediated posttranslational modification on cysteine that improves resilience of soybean against salt stress.
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Affiliation(s)
- Wenxiao Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Wenjiao Zhi
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Hong Qiao
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Shuo Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Qing Lu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Nan Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Qiang Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Qian Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Jiaqi Sun
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Yuting Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Xiaojian Zheng
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Mingyi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Fengning Xiang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
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Zhang W, Li J, Li H, Zhang D, Zhu B, Yuan H, Gao T. Transcriptomic analysis of humic acid in relieving the inhibitory effect of high nitrogen on soybean nodulation. FRONTIERS IN PLANT SCIENCE 2023; 14:1196939. [PMID: 37564385 PMCID: PMC10410467 DOI: 10.3389/fpls.2023.1196939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/06/2023] [Indexed: 08/12/2023]
Abstract
Introduction Nitrogen fertilizer intake promotes soybean growth before the formation of nodules, but excess nitrogen has an inhibitory effect on soybean nodulation. It is important to balance nitrogen levels to meet both growth and nodulation needs. Methods the nitrogen level suitable for soybean growth and nodulation was studied, the role of humic acid (HA) in alleviating the inhibition of high nitrogen on soybean nodulation was analyzed, and transcriptomic analysis was performed to understand its mechanism. Results The results showed that a lower level of nitrogen with 36.4 mg urea per pot could increase the number of nodules of soybean, and a higher level of nitrogen with 145.9 mg urea per pot (U4 group) had the best growth indicators but inhibited nodulation significantly. HA relieved the inhibitory effect at high nitrogen level, and the number of nodules increased by 122.1% when 1.29 g HA was added (H2 group) compared with the U4 group. The transcriptome analysis was subsequently performed on the H2 and U4 groups, showing that there were 2995 differentially expressed genes (DEGs) on the 25th day, accounting for 6.678% of the total annotated genes (44,848) under the test conditions. These DEGs were enriched in mitogen-activated protein kinase signaling pathway-plant, flavonoid biosynthesis, and plant hormone signal transduction based on the -log10 (P adjusted) value in the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG). Discussion HA balanced the nitrogen level through the above pathways in soybean planting to control the number of nodules.
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Affiliation(s)
- Wenhua Zhang
- Hebei Engineering Research Center for Resource Utilization of Agricultural Waste, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Jia Li
- Hebei Engineering Research Center for Resource Utilization of Agricultural Waste, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Hongya Li
- Hebei Engineering Research Center for Resource Utilization of Agricultural Waste, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Dongdong Zhang
- Hebei Engineering Research Center for Resource Utilization of Agricultural Waste, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Baocheng Zhu
- Hebei Engineering Research Center for Resource Utilization of Agricultural Waste, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Tongguo Gao
- Hebei Engineering Research Center for Resource Utilization of Agricultural Waste, College of Life Sciences, Hebei Agricultural University, Baoding, China
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Tian H, Watanabe Y, Nguyen KH, Tran CD, Abdelrahman M, Liang X, Xu K, Sepulveda C, Mostofa MG, Van Ha C, Nelson DC, Mochida K, Tian C, Tanaka M, Seki M, Miao Y, Tran LSP, Li W. KARRIKIN UPREGULATED F-BOX 1 negatively regulates drought tolerance in Arabidopsis. PLANT PHYSIOLOGY 2022; 190:2671-2687. [PMID: 35822606 PMCID: PMC9706471 DOI: 10.1093/plphys/kiac336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
The karrikin (KAR) receptor and several related signaling components have been identified by forward genetic screening, but only a few studies have reported on upstream and downstream KAR signaling components and their roles in drought tolerance. Here, we characterized the functions of KAR UPREGULATED F-BOX 1 (KUF1) in drought tolerance using a reverse genetics approach in Arabidopsis (Arabidopsis thaliana). We observed that kuf1 mutant plants were more tolerant to drought stress than wild-type (WT) plants. To clarify the mechanisms by which KUF1 negatively regulates drought tolerance, we performed physiological, transcriptome, and morphological analyses. We found that kuf1 plants limited leaf water loss by reducing stomatal aperture and cuticular permeability. In addition, kuf1 plants showed increased sensitivity of stomatal closure, seed germination, primary root growth, and leaf senescence to abscisic acid (ABA). Genome-wide transcriptome comparisons of kuf1 and WT rosette leaves before and after dehydration showed that the differences in various drought tolerance-related traits were accompanied by differences in the expression of genes associated with stomatal closure (e.g. OPEN STOMATA 1), lipid and fatty acid metabolism (e.g. WAX ESTER SYNTHASE), and ABA responsiveness (e.g. ABA-RESPONSIVE ELEMENT 3). The kuf1 mutant plants had higher root/shoot ratios and root hair densities than WT plants, suggesting that they could absorb more water than WT plants. Together, these results demonstrate that KUF1 negatively regulates drought tolerance by modulating various physiological traits, morphological adjustments, and ABA responses and that the genetic manipulation of KUF1 in crops is a potential means of enhancing their drought tolerance.
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Affiliation(s)
- Hongtao Tian
- Jilin Da’an Agro-ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
| | - Yasuko Watanabe
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kien Huu Nguyen
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Vietnam Academy of Agricultural Science, Pham-Van-Dong Str., Hanoi, 100000, Vietnam
| | - Cuong Duy Tran
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Vietnam Academy of Agricultural Science, Pham-Van-Dong Str., Hanoi, 100000, Vietnam
| | - Mostafa Abdelrahman
- Botany Department, Faculty of Science, Aswan University, Aswan 81528, Egypt
- Molecular Biotechnology Program, Faculty of Science, Galala University, Suze, New Galala 43511, Egypt
| | - Xiaohan Liang
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
| | - Kun Xu
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
| | - Claudia Sepulveda
- Department of Botany & Plant Sciences, University of California, Riverside, California 92521, USA
| | - Mohammad Golam Mostofa
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas 79409, USA
| | - Chien Van Ha
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas 79409, USA
| | - David C Nelson
- Department of Botany & Plant Sciences, University of California, Riverside, California 92521, USA
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
- School of Information and Data Sciences, Nagasaki University, Nagasaki, Japan
| | - Chunjie Tian
- Jilin Da’an Agro-ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Yuchen Miao
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
| | | | - Weiqiang Li
- Author for correspondence: or (W.L.), (L.-S.P.T.)
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Kim JM, Lyu JI, Kim DG, Hung NN, Seo JS, Ahn JW, Lim YJ, Eom SH, Ha BK, Kwon SJ. Genome wide association study to detect genetic regions related to isoflavone content in a mutant soybean population derived from radiation breeding. FRONTIERS IN PLANT SCIENCE 2022; 13:968466. [PMID: 36061785 PMCID: PMC9433930 DOI: 10.3389/fpls.2022.968466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Isoflavones are major secondary metabolites that are exclusively produced by legumes, including soybean. Soy isoflavones play important roles in human health as well as in the plant defense system. The isoflavone content is influenced by minor-effect quantitative trait loci, which interact with polygenetic and environmental factors. It has been difficult to clarify the regulation of isoflavone biosynthesis because of its complex heritability and the influence of external factors. Here, using a genotype-by-sequencing-based genome-wide association mapping study, 189 mutant soybean genotypes (the mutant diversity pool, MDP) were genotyped on the basis of 25,646 high-quality single nucleotide polymorphisms (SNPs) with minor allele frequency of >0.01 except for missing data. All the accessions were phenotyped by determining the contents of 12 isoflavones in the soybean seeds in two consecutive years (2020 and 2021). Then, quantitative trait nucleotides (QTNs) related to isoflavone contents were identified and validated using multi-locus GWAS models. A total of 112 and 46 QTNs related to isoflavone contents were detected by multiple MLM-based models in 2020 and 2021, respectively. Of these, 12 and 5 QTNs were related to more than two types of isoflavones in 2020 and 2021, respectively. Forty-four QTNs were detected within the 441-Kb physical interval surrounding Gm05:38940662. Of them, four QTNs (Gm05:38936166, Gm05:38936167, Gm05:38940662, and Gm05:38940717) were located at Glyma.05g206900 and Glyma.05g207000, which encode glutathione S-transferase THETA 1 (GmGSTT1), as determined from previous quantitative trait loci annotations and the literature. We detected substantial differences in the transcript levels of GmGSTT1 and two other core genes (IFS1 and IFS2) in the isoflavone biosynthetic pathway between the original cultivar and its mutant. The results of this study provide new information about the factors affecting isoflavone contents in soybean seeds and will be useful for breeding soybean lines with high and stable concentrations of isoflavones.
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Affiliation(s)
- Jung Min Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
- Division of Plant Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Jae Il Lyu
- Department of Horticulture, College of Industrial Sciences, Kongju National University, Yesan, South Korea
| | - Dong-Gun Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Nguyen Ngoc Hung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
- Division of Plant Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Ji Su Seo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
- Division of Plant Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - You Jin Lim
- Department of Horticultural Biotechnology, Institute of Life Sciences & Resources, Kyung Hee University, Yongin, South Korea
| | - Seok Hyun Eom
- Department of Horticultural Biotechnology, Institute of Life Sciences & Resources, Kyung Hee University, Yongin, South Korea
| | - Bo-Keun Ha
- Division of Plant Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
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Silva LCC, Mayrink DB, Bueno RD, Piovesan ND, Ribeiro C, Dal-Bianco M. Reference Genes and Expression Analysis of Seed Desaturases Genes in Soybean Mutant Accessions. Biochem Genet 2022; 60:937-952. [PMID: 34554351 DOI: 10.1007/s10528-021-10135-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 09/15/2021] [Indexed: 10/20/2022]
Abstract
Soybean oil is the second most-produced vegetable oil worldwide. To enhance the nutritional quality and oxidative stability of soybean oil, many soybean breeding programs are trying to increase oleic acid content and reduce linoleic and linolenic acid contents. The fatty acid profile of soybean oil is controlled by many genes, including those which code for omega-3 and omega-6 desaturases. Mutations in GmFAD2-1 and GmFAD3 genes are widely studied and their combinations can produce soybean oil with high oleic and low linoleic and linolenic content. However, few studies evaluate the effect of these mutations on gene expression. Therefore, the present study sought to identify reference genes, evaluate the expression of GmFAD2-1 and GmFAD3 seed desaturase genes in thirteen wild-type and mutated soybean accessions, and associate the expression patterns with fatty acid composition and with the GmFAD2-1 and GmFAD3 genotypes. GmCONS7 and GmUKN2 were identified as the best reference genes for combined use to normalize data. The GmFAD2-1A mutation of PI603452 accession was associated with a decrease in gene expression of GmFAD2-1A; however, downregulation may not be due to the truncated enzyme structure alone. These results suggested that there are factors other than GmFAD2-1A and GmFAD2-1B that have a considerable effect on oleic content, at least in soybeans with mutations in these two genes.
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Affiliation(s)
- Luiz Cláudio Costa Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, BA, 44036-900, Brazil.
| | | | - Rafael Delmond Bueno
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Newton Deniz Piovesan
- Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Cleberson Ribeiro
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Maximiller Dal-Bianco
- Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
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Li J, Sun M, Liu Y, Sun X, Yin K. Genome-Wide Identification of Wild Soybean Mitochondrial Calcium Uniporter Family Genes and Their Responses to Cold and Carbonate Alkaline Stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:867503. [PMID: 35592573 PMCID: PMC9111538 DOI: 10.3389/fpls.2022.867503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
The mitochondrial calcium uniporter (MCU), as an important component of the Ca2+ channel uniporter complex, plays a regulatory role in intracellular Ca2+ signal transduction. However, only a few studies to date have investigated plant MCU genes. In this study, we identified the MCU family genes in wild soybean and investigated their expression under cold and carbonate alkaline stresses. Eleven Glycine soja MCU genes (GsMCUs) were identified and clustered into two subgroups (subgroups I and II), and subgroup II could be further divided into two branches (MCU5 and MCU6). A total of 21 pairs of GsMCUs were characterized as duplicated genes, and displayed a similar exon-intron architecture. All GsMCU proteins contained one conserved MCU domain, within which two transmembrane domains were found. An analysis of the conserved motifs further supported that the GsMCUs showed high conservation in protein sequence and structure. Moreover, we found that all GsMCUs were expressed ubiquitously in different tissues and organs, and GsMCUs from the same subgroup displayed varied tissue expression profiles. In addition, based on RNA-seq and qRT-PCR assays, six and nine GsMCUs were differentially expressed under cold and carbonate alkaline stress, respectively. Promoter analysis also uncovered the existence of two canonical cold-related cis-acting elements, LTR and DRE/CRT, as well as stress-related phytohormone-responsive elements. Our results provide valuable information about the MCU family in soybean responses to cold and carbonate alkaline stress, which will be helpful in further characterizing their biological roles in response to abiotic stress.
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Affiliation(s)
- Jianwei Li
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Mingzhe Sun
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, China
| | - Yu Liu
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xiaoli Sun
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Kuide Yin
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
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Xu HR, Liu Y, Yu TF, Hou ZH, Zheng JC, Chen J, Zhou YB, Chen M, Fu JD, Ma YZ, Wei WL, Xu ZS. Comprehensive Profiling of Tubby-Like Proteins in Soybean and Roles of the GmTLP8 Gene in Abiotic Stress Responses. FRONTIERS IN PLANT SCIENCE 2022; 13:844545. [PMID: 35548296 PMCID: PMC9083326 DOI: 10.3389/fpls.2022.844545] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/15/2022] [Indexed: 05/24/2023]
Abstract
Tubby-like proteins (TLPs) are transcription factors that are widely present in eukaryotes and generally participate in growth and developmental processes. Using genome databases, a total of 22 putative TLP genes were identified in the soybean genome, and unevenly distributed across 13 chromosomes. Phylogenetic analysis demonstrated that the predicted GmTLP proteins were divided into five groups (I-V). Gene structure, protein motifs, and conserved domains were analyzed to identify differences and common features among the GmTLPs. A three-dimensional protein model was built to show the typical structure of TLPs. Analysis of publicly available gene expression data showed that GmTLP genes were differentially expressed in response to abiotic stresses. Based on those data, GmTLP8 was selected to further explore the role of TLPs in soybean drought and salt stress responses. GmTLP8 overexpressors had improved tolerance to drought and salt stresses, whereas the opposite was true of GmTLP8-RNAi lines. 3,3-diaminobenzidine and nitro blue tetrazolium staining and physiological indexes also showed that overexpression of GmTLP8 enhanced the tolerance of soybean to drought and salt stresses; in addition, downstream stress-responsive genes were upregulated in response to drought and salt stresses. This study provides new insights into the function of GmTLPs in response to abiotic stresses.
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Affiliation(s)
- Hong-Ru Xu
- College of Agriculture, Yangtze University/Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ying Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Tai-Fei Yu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ze-Hao Hou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Jia-Cheng Zheng
- College of Agronomy, Anhui Science and Technology University, Fengyang, China
| | - Jun Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Yong-Bin Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ming Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Jin-Dong Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - You-Zhi Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Wen-Liang Wei
- College of Agriculture, Yangtze University/Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou, China
| | - Zhao-Shi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
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9
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Alves da Silva A, Oliveira Silva C, do Rosario Rosa V, Silva Santos MF, Naomi Kuki K, Dal-Bianco M, Delmond Bueno R, Alves de Oliveira J, Santos Brito D, Costa AC, Ribeiro C. Metabolic adjustment and regulation of gene expression are essential for increased resistance to severe water deficit and resilience post-stress in soybean. PeerJ 2022; 10:e13118. [PMID: 35321407 PMCID: PMC8935993 DOI: 10.7717/peerj.13118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/23/2022] [Indexed: 01/12/2023] Open
Abstract
Background Soybean is the main oilseed crop grown in the world; however, drought stress affects its growth and physiology, reducing its yield. The objective of this study was to characterize the physiological, metabolic, and genetic aspects that determine differential resistance to water deficit in soybean genotypes. Methods Three soybean genotypes were used in this study, two lineages (L11644 and L13241), and one cultivar (EMBRAPA 48-C48). Plants were grown in pots containing 8 kg of a mixture of soil and sand (2:1) in a greenhouse under sunlight. Soil moisture in the pots was maintained at field capacity until the plants reached the stage of development V4 (third fully expanded leaf). At this time, plants were subjected to three water treatments: Well-Watered (WW) (plants kept under daily irrigation); Water Deficit (WD) (withholding irrigation until plants reached the leaf water potential at predawn of -1.5 ± 0.2 MPa); Rewatered (RW) (plants rehydrated for three days after reached the water deficit). The WW and WD water treatments were evaluated on the eighth day for genotypes L11644 and C48, and on the tenth day for L13241, after interruption of irrigation. For the three genotypes, the treatment RW was evaluated after three days of resumption of irrigation. Physiological, metabolic and gene expression analyses were performed. Results Water deficit inhibited growth and gas exchange in all genotypes. The accumulation of osmolytes and the concentrations of chlorophylls and abscisic acid (ABA) were higher in L13241 under stress. The metabolic adjustment of lineages in response to WD occurred in order to accumulate amino acids, carbohydrates, and polyamines in leaves. The expression of genes involved in drought resistance responses was more strongly induced in L13241. In general, rehydration provided recovery of plants to similar conditions of control treatment. Although the C48 and L11644 genotypes have shown some tolerance and resilience responses to severe water deficit, greater efficiency was observed in the L13241 genotype through adjustments in morphological, physiological, genetic and metabolic characteristics that are combined in the same plant. This study contributes to the advancement in the knowledge about the resistance to drought in cultivated plants and provides bases for the genetic improvement of the soybean culture.
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Affiliation(s)
- Adinan Alves da Silva
- Ecophysiology and Plant Productivity Laboratory, Instituto Federal Goiano-Campus Rio Verde, Rio Verde, Goiás, Brazil
| | - Cíntia Oliveira Silva
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | | | - Kacilda Naomi Kuki
- Department of Agronomy, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Maximiller Dal-Bianco
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Rafael Delmond Bueno
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Danielle Santos Brito
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Alan Carlos Costa
- Ecophysiology and Plant Productivity Laboratory, Instituto Federal Goiano-Campus Rio Verde, Rio Verde, Goiás, Brazil
| | - Cleberson Ribeiro
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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10
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Xu Y, Yan F, Zong Y, Li J, Gao H, Liu Y, Wang Y, Zhu Y, Wang Q. Proteomic and lipidomics analyses of high fatty acid AhDGAT3 transgenic soybean reveals the key lipase gene associated with the lipid internal mechanism. Genome 2022; 65:153-164. [PMID: 34995159 DOI: 10.1139/gen-2021-0043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Vegetable oil is one of the most important components of human nutrition. Soybean (Glycine max) is an important oil crop worldwide and contains rich unsaturated fatty acids. Diacylglycerol acyltransferase (DGAT) is a key rate-limiting enzyme in the Kennedy pathway from diacylglycerol (DAG) to triacylglycerol (TAG). In this study, we conducted further research using T3 AhDGAT3 transgenic soybean. A high-performance gas chromatography flame ionization detector showed that oleic acid (18:1) content and total fatty acid content of transgenic soybean were significantly higher than those of the wild type (WT). However, linoleic acid (18:2) was much lower than that in the WT. For further mechanistic studies, 20 differentially expressed proteins (DEPs) and 119 differentially expressed metabolites (DEMs) were identified between WT (JACK) and AhDGAT3 transgenic soybean mature seeds using proteomic and lipidomics analyses. Combined proteomic and lipidomics analyses showed that the upregulation of the key DEP (lipase GDSL domain-containing protein) in lipid transport and metabolic process induced an increase in the total fatty acid and 18:1 composition, but a decrease in the 18:2 composition of fatty acids. Our study provides new insights into the deep study of molecular mechanism underlying the enhancement of fatty acids in transgenic soybeans, especially oleic acid and total fatty acid, which are enhanced by over-expression of AhDGAT3.
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Affiliation(s)
- Yang Xu
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Fan Yan
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Yu Zong
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Jingwen Li
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Han Gao
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Yajing Liu
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Ying Wang
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Youcheng Zhu
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Qingyu Wang
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
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11
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Selection and Validation of Reference Genes for Quantitative Real-Time PCR Analysis of Development and Tissue-Dependent Flower Color Formation in Cymbidium lowianum. Int J Mol Sci 2022; 23:ijms23020738. [PMID: 35054922 PMCID: PMC8776083 DOI: 10.3390/ijms23020738] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/31/2021] [Accepted: 01/07/2022] [Indexed: 02/07/2023] Open
Abstract
The development and tissue-dependent color formation of the horticultural plant results in various color pattern flowers. Anthocyanins and carotenoids contribute to the red and yellow colors, respectively. In this study, quantitative real-time polymerase chain reaction (qRT-PCR) is used to analyze the expression profiles of anthocyanin and carotenoids biosynthesis genes in Cymbidium lowianum (Rchb.f.) Rchb.f. Appropriate reference gene selection and validation are required before normalization of gene expression in qRT-PCR analysis. Thus, we firstly selected 12 candidate reference genes from transcriptome data, and used geNorm and Normfinder to evaluate their expression stability in lip (divided into abaxial and adaxial), petal, and sepal of the bud and flower of C. lowianum. Our results show that the two most stable reference genes in different tissues of C. lowianum bud and flower are EF1δ and 60S, the most unstable reference gene is 26S. The expression profiles of the CHS and BCH genes were similar to FPKM value profiles after normalization to the two most stable reference genes, EF1δ and 60S, with the upregulated CHS and BCH expression in flower stage, indicating that the ABP and CBP were activated across the stages of flower development. However, when the most unstable reference gene, 26S, was used to normalize the qRT-PCR data, the expression profiles of CHS and BCH differed from FPKM value profiles, indicating the necessity of selecting stable reference genes. Moreover, CHS and BCH expression was highest in the abaxial lip and adaxial lip, respectively, indicating that the ABP and CBP were activated in abaxial and adaxial lip, respectively, resulting in a presence of red or yellow segments in abaxial and adaxial lip. This study is the first to provide reference genes in C. lowianum, and also provide useful information for studies that aim to understand the molecular mechanisms of flower color formation in C. lowianum.
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12
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Sinha R, Bala M, Prabha P, Ranjan A, Chahota RK, Sharma TR, Singh AK. Identification and validation of reference genes for qRT-PCR based studies in horse gram ( Macrotyloma uniflorum). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2859-2873. [PMID: 35035141 PMCID: PMC8720121 DOI: 10.1007/s12298-021-01104-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED The quantitative real-time polymerase chain reaction (qRT-PCR) is the most sensitive and commonly used technique for gene expression studies in biological systems. However, the reliability of qRT-PCR results depends on the selection of reference gene(s) for data normalization. Horse gram (Macrotyloma uniflorum) is an important legume crop on which several molecular studies have been reported. However, the stability of reference genes has not been evaluated. In the present study, nine candidate reference genes were identified from horse gram RNA-seq data and evaluated in two horse gram genotypes, HPK4 and HPKM317 under six abiotic stresses viz. cold, drought, salinity, heat, abscisic acid and methyl viologen-induced oxidative stress. The results were evaluated using geNorm, Bestkeeper, Normfinder and delta-delta Ct methods and comprehensive ranking was assigned using RefFinder and RankAggreg software. The overall result showed that TCTP was one of the most stable genes in all samples and in genotype HPK4, while in HPKM317 profilin was most stably expressed. However, PSMA5 was identified as least stable in all the experimental conditions. Expression of target genes dehydrin and early response to dehydration 6 under drought stress was also validated using TCTP and profilin for data normalization, either alone or in combination, which confirmed their suitability for qRT-PCR data normalization. Thus, TCTP and profilin genes may be used for qRT-PCR data normalization for molecular and genomic studies in horse gram. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01104-0.
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Affiliation(s)
- Ragini Sinha
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Meenu Bala
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Pragya Prabha
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Alok Ranjan
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Rakesh K. Chahota
- Department of Agricultural Biotechnology, Choudhary Sarwan Kumar Himachal Pradesh Agricultural University, Palampur, 176061 India
| | - Tilak Raj Sharma
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Anil Kumar Singh
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
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13
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Xu Y, Yan F, Liu Y, Wang Y, Gao H, Zhao S, Zhu Y, Wang Q, Li J. Quantitative proteomic and lipidomics analyses of high oil content GmDGAT1-2 transgenic soybean illustrate the regulatory mechanism of lipoxygenase and oleosin. PLANT CELL REPORTS 2021; 40:2303-2323. [PMID: 34427748 DOI: 10.1007/s00299-021-02768-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Proteomic and lipidomics analyses of WT and GmDGAT1-2 transgenic soybeans showed that GmDGAT1-2 over-expression induced lipoxygenase down-regulatation and oleoin up-regulatation, which significantly changed the compositions and total fatty acid. The main goal of soybean breeding is to increase the oil content. Diacylglycerol acyltransferase (DGAT) is a key rate-limiting enzyme in fatty acid metabolism and may regulate oil content. Herein, 10 GmDGAT genes were isolated from soybean and transferred into wild-type (WT) Arabidopsis. The total fatty acid was 1.2 times higher in T3 GmDGAT1-2 transgenic Arabidopsis seeds than in WT. Therefore, GmDGAT1-2 was transferred into WT soybean (JACK), and four T3 transgenic soybean lines were obtained. The results of high-performance gas chromatography and Soxhlet extractor showed that, compared with those of JACK, oleic acid (18:1), and total fatty acid levels in transgenic soybean plants were much higher, but linoleic acid (18:2) was lower than WT. Palmitic acid (16:0), stearic acid (18:0), and linolenic acid (18:3) were not significantly different. For mechanistic studies, 436 differentially expressed proteins (DEPs) and 180 differentially expressed metabolites (DEMs) were identified between WT (JACK) and transgenic soybean pods using proteomic and lipidomics analyses. Four lipoxygenase proteins were down-regulated in linoleic acid metabolism while four oleosin proteins were up-regulated in the final oil formation. The results showed an increase in the total fatty acid and 18:1 composition, and a decrease in the 18:2 composition of fatty acid. Our study brings new insights into soybean genetic transformation and the deep study of molecular mechanism that changes the total fatty acid, 18:1, and 18:2 compositions in GmDGAT1-2 transgenic soybean.
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Affiliation(s)
- Yang Xu
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Fan Yan
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Yajing Liu
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Ying Wang
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Han Gao
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Shihui Zhao
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Youcheng Zhu
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Qingyu Wang
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China.
| | - Jingwen Li
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China.
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14
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Zhu X, Wang B, Wang X, Wei X. Screening of stable internal reference gene of Quinoa under hormone treatment and abiotic stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2459-2470. [PMID: 34924704 PMCID: PMC8639980 DOI: 10.1007/s12298-021-01094-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED Real-time quantitative polymerase chain reaction is the most commonly used method to accurately detect gene expression patterns. The method requires stable internal reference genes to standardize the data. However, studies have shown that there is no stable expression of internal reference genes in different tissues and under different treatments. Therefore, in order to study the optimal reference genes of quinoa under different hormones and abiotic stress, leaves and stems from quinoa seedlings treated with low temperature (4 °C), salt (200 mmol/L) and abscisic acid (200 mmol/L) were used as experimental materials. Using ACT-1, eIF, EF1α, GAPDH, TUA, TUB-9, TUB-1, H2A and L8-1 as candidate reference genes, the expression stability of these 9 quinoa candidate reference genes under different hormone treatment and abiotic stress was evaluated by using geNorm, NormFinder and BestKeeper software. The results showed that TUB-1 gene under salt stress, L8-1 gene under low temperature stress, EF-1α gene induced by ABA. PLIM2c WLIM1and WLIM2b were selected to verify the candidate internal reference genes, and finally the expression of GAPDH was most unstable under the three treatments, which was not suitable to be the internal reference gene of quinoa under specific conditions, while EF1α showed good stability under the three different treatments and was suitable to be used as the internal reference gene. In conclusion, the results of this study could provide an important reference for quantifying the expression level of reference genes in quinoa. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01094-z.
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Affiliation(s)
- Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
| | - Baoqiang Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xian Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xiaohong Wei
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
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15
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Hoang XLT, Chuong NN, Hoa TTK, Doan H, Van PHP, Trang LDM, Huyen PNT, Le DT, Tran LSP, Thao NP. The Drought-Mediated Soybean GmNAC085 Functions as a Positive Regulator of Plant Response to Salinity. Int J Mol Sci 2021; 22:8986. [PMID: 34445699 PMCID: PMC8396556 DOI: 10.3390/ijms22168986] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 01/01/2023] Open
Abstract
Abiotic stress factors, such as drought and salinity, are known to negatively affect plant growth and development. To cope with these adverse conditions, plants have utilized certain defense mechanisms involved in various aspects, including morphological, biochemical and molecular alterations. Particularly, a great deal of evidence for the biological importance of the plant-specific NAM, ATAF1/2, CUC2 (NAC) transcription factors (TFs) in plant adaptation to abiotic stress conditions has been reported. A previous in planta study conducted by our research group demonstrated that soybean (Glycine max) GmNAC085 mediated drought resistance in transgenic Arabidopsis plants. In this study, further characterization of GmNAC085 function in association with salt stress was performed. The findings revealed that under this condition, transgenic soybean plants overexpressing GmNAC085 displayed better germination rates than wild-type plants. In addition, biochemical and transcriptional analyses showed that the transgenic plants acquired a better defense system against salinity-induced oxidative stress, with higher activities of antioxidant enzymes responsible for scavenging hydrogen peroxide or superoxide radicals. Higher transcript levels of several key stress-responsive genes involved in the proline biosynthetic pathway, sodium ion transporter and accumulation of dehydrins were also observed, indicating better osmoprotection and more efficient ion regulation capacity in the transgenic lines. Taken together, these findings and our previous report indicate that GmNAC085 may play a role as a positive regulator in plant adaptation to drought and salinity conditions.
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Affiliation(s)
- Xuan Lan Thi Hoang
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc City, Ho Chi Minh City 700000, Vietnam; (X.L.T.H.); (N.N.C.); (T.T.K.H.); (H.D.); (P.H.P.V.); (L.D.M.T.); (P.N.T.H.)
- Vietnam National University, Thu Duc City, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Nguyen Chuong
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc City, Ho Chi Minh City 700000, Vietnam; (X.L.T.H.); (N.N.C.); (T.T.K.H.); (H.D.); (P.H.P.V.); (L.D.M.T.); (P.N.T.H.)
- Vietnam National University, Thu Duc City, Ho Chi Minh City 700000, Vietnam
| | - Tran Thi Khanh Hoa
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc City, Ho Chi Minh City 700000, Vietnam; (X.L.T.H.); (N.N.C.); (T.T.K.H.); (H.D.); (P.H.P.V.); (L.D.M.T.); (P.N.T.H.)
- Vietnam National University, Thu Duc City, Ho Chi Minh City 700000, Vietnam
| | - Hieu Doan
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc City, Ho Chi Minh City 700000, Vietnam; (X.L.T.H.); (N.N.C.); (T.T.K.H.); (H.D.); (P.H.P.V.); (L.D.M.T.); (P.N.T.H.)
- Vietnam National University, Thu Duc City, Ho Chi Minh City 700000, Vietnam
| | - Pham Hoang Phuong Van
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc City, Ho Chi Minh City 700000, Vietnam; (X.L.T.H.); (N.N.C.); (T.T.K.H.); (H.D.); (P.H.P.V.); (L.D.M.T.); (P.N.T.H.)
- Vietnam National University, Thu Duc City, Ho Chi Minh City 700000, Vietnam
| | - Le Dang Minh Trang
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc City, Ho Chi Minh City 700000, Vietnam; (X.L.T.H.); (N.N.C.); (T.T.K.H.); (H.D.); (P.H.P.V.); (L.D.M.T.); (P.N.T.H.)
- Vietnam National University, Thu Duc City, Ho Chi Minh City 700000, Vietnam
| | - Pham Ngoc Thai Huyen
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc City, Ho Chi Minh City 700000, Vietnam; (X.L.T.H.); (N.N.C.); (T.T.K.H.); (H.D.); (P.H.P.V.); (L.D.M.T.); (P.N.T.H.)
- Vietnam National University, Thu Duc City, Ho Chi Minh City 700000, Vietnam
| | - Dung Tien Le
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Pham Van Dong Str., Hanoi 100000, Vietnam;
| | - Lam-Son Phan Tran
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA
| | - Nguyen Phuong Thao
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc City, Ho Chi Minh City 700000, Vietnam; (X.L.T.H.); (N.N.C.); (T.T.K.H.); (H.D.); (P.H.P.V.); (L.D.M.T.); (P.N.T.H.)
- Vietnam National University, Thu Duc City, Ho Chi Minh City 700000, Vietnam
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16
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Soni P, Shivhare R, Kaur A, Bansal S, Sonah H, Deshmukh R, Giri J, Lata C, Ram H. Reference gene identification for gene expression analysis in rice under different metal stress. J Biotechnol 2021; 332:83-93. [PMID: 33794279 DOI: 10.1016/j.jbiotec.2021.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/27/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Real-time quantitative polymerase chain reaction (RT-qPCR) is the most common approach to quantify changes in gene expression. Appropriate internal reference genes are essential for normalization of data of RT-qPCR. In the present study, we identified suitable reference genes for analysis of gene expression in rice seedlings subjected to different heavy metal stresses such as deficiencies of iron and zinc and toxicities of cobalt, cadmium and nickel. First, from publically available RNA-Seq data we identified 10 candidate genes having stable expression. We also included commonly used house-keeping gene OsUBQ5 (Ubiquitin 5) in our analysis. Expression stability of all the 11 genes was determined by two independent tools, NormFinder and geNorm. Our results show that selected candidate reference genes have higher stability in their expression compared to that of OsUBQ5. Genes with locus ID LOC_Os03g16690, encoding an oxysterol-binding protein (OsOBP) and LOC_Os01g56580, encoding Casein Kinase_1a.3 (OsCK1a.3) were identified to be the most stably expressed reference genes under most of the conditions tested. Finally, the study reveals that it is better to use a specific reference gene for a specific heavy metal stress condition rather than using a common reference gene for multiple heavy metal stress conditions. The reference genes identified here would be very useful for gene expression studies under heavy metal stresses in rice.
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Affiliation(s)
- Praveen Soni
- Department of Botany, University of Rajasthan, Jaipur, 302004, India
| | - Radha Shivhare
- CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Amandeep Kaur
- National Agri-Food Biotechnology Institute, Mohali, 140308, India
| | - Sakshi Bansal
- National Agri-Food Biotechnology Institute, Mohali, 140308, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute, Mohali, 140308, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute, Mohali, 140308, India
| | - Jitender Giri
- National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Charu Lata
- CSIR-National Institute of Science Communication and Information Resources, New Delhi, 110067, India.
| | - Hasthi Ram
- National Agri-Food Biotechnology Institute, Mohali, 140308, India; National Institute of Plant Genome Research, New Delhi, 110067, India.
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17
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Identification and validation of new reference genes for accurate quantitative reverse transcriptase-PCR normalization in the Antarctic plant Colobanthus quitensis under abiotic stress conditions. Polar Biol 2021. [DOI: 10.1007/s00300-021-02801-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
AbstractThe Antarctic ecotype of Colobanthus quitensis is a vascular plant highly adapted to the harsh environmental conditions of Maritime Antarctica which is now facing with the rapid local warming experienced in the Antarctic Peninsula during the last decades. Thus, the identification of the molecular mechanisms leading to the adaptation to this warming trend is a new target for modern cell physiology. The selection of suitable reference genes for quantification of key stress-responsive genes through quantitative Reverse Transcriptase-Polymerase Chain Reaction (qRT-PCR) is important to ensure accurate and reliable results. In this study, we evaluated the expression stability of eleven candidate genes in C. quitensis under different abiotic stress conditions using geNorm and RefFinder tools. The statistical analysis showed that the appropriate reference genes varied depending on the experimental conditions, even if EF1α and PP2Acs ranked as the most stable reference genes when all stress conditions were considered. To further validate the stability of the selected reference genes, the expression patterns of C. quitensis catalase gene (CqCAT) was analyzed. The reference genes validated in this study will be useful for improving the accuracy of qRT-PCR analysis for gene expression studies of the Antarctic ecotype of C. quitensis and could be extended to other ecotypes adapted to low temperatures.
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18
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Nasr Esfahani M, Inoue K, Nguyen KH, Chu HD, Watanabe Y, Kanatani A, Burritt DJ, Mochida K, Tran LSP. Phosphate or nitrate imbalance induces stronger molecular responses than combined nutrient deprivation in roots and leaves of chickpea plants. PLANT, CELL & ENVIRONMENT 2021; 44:574-597. [PMID: 33145807 DOI: 10.1111/pce.13935] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 05/25/2023]
Abstract
The negative effects of phosphate (Pi) and/or nitrate (NO3- ) fertilizers on the environment have raised an urgent need to develop crop varieties with higher Pi and/or nitrogen use efficiencies for cultivation in low-fertility soils. Achieving this goal depends upon research that focuses on the identification of genes involved in plant responses to Pi and/or NO3- starvation. Although plant responses to individual deficiency in either Pi (-Pi/+NO3- ) or NO3- (+Pi/-NO3- ) have been separately studied, our understanding of plant responses to combined Pi and NO3- deficiency (-Pi/-NO3- ) is still very limited. Using RNA-sequencing approach, transcriptome changes in the roots and leaves of chickpea cultivated under -Pi/+NO3- , +Pi/-NO3- or -Pi/-NO3- conditions were investigated in a comparative manner. -Pi/-NO3- treatment displayed lesser effect on expression changes of genes related to Pi or NO3- transport, signalling networks, lipid remodelling, nitrogen and Pi scavenging/remobilization/recycling, carbon metabolism and hormone metabolism than -Pi/+NO3- or +Pi/-NO3- treatments. Therefore, the plant response to -Pi/-NO3- is not simply an additive result of plant responses to -Pi/+NO3- and +Pi/-NO3- treatments. Our results indicate that nutrient imbalance is a stronger stimulus for molecular reprogramming than an overall deficiency.
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Affiliation(s)
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Kien Huu Nguyen
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Ha Duc Chu
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Yasuko Watanabe
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Asaka Kanatani
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - David J Burritt
- Department of Botany, University of Otago, Dunedin, New Zealand
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Microalgae Production Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, Japan
| | - Lam-Son Phan Tran
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, USA
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19
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Echeverria A, Larrainzar E, Li W, Watanabe Y, Sato M, Tran CD, Moler JA, Hirai MY, Sawada Y, Tran LSP, Gonzalez EM. Medicago sativa and Medicago truncatula Show Contrasting Root Metabolic Responses to Drought. FRONTIERS IN PLANT SCIENCE 2021; 12:652143. [PMID: 33968107 PMCID: PMC8097159 DOI: 10.3389/fpls.2021.652143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/19/2021] [Indexed: 05/16/2023]
Abstract
Drought is an environmental stressor that affects crop yield worldwide. Understanding plant physiological responses to stress conditions is needed to secure food in future climate conditions. In this study, we applied a combination of plant physiology and metabolomic techniques to understand plant responses to progressive water deficit focusing on the root system. We chose two legume plants with contrasting tolerance to drought, the widely cultivated alfalfa Medicago sativa (Ms) and the model legume Medicago truncatula (Mt) for comparative analysis. Ms taproot (tapR) and Mt fibrous root (fibR) biomass increased during drought, while a progressive decline in water content was observed in both species. Metabolomic analysis allowed the identification of key metabolites in the different tissues tested. Under drought, carbohydrates, abscisic acid, and proline predominantly accumulated in leaves and tapRs, whereas flavonoids increased in fibRs in both species. Raffinose-family related metabolites accumulated during drought. Along with an accumulation of root sucrose in plants subjected to drought, both species showed a decrease in sucrose synthase (SUS) activity related to a reduction in the transcript level of SUS1, the main SUS gene. This study highlights the relevance of root carbon metabolism during drought conditions and provides evidence on the specific accumulation of metabolites throughout the root system.
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Affiliation(s)
- Andres Echeverria
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra, Pamplona, Spain
| | - Estíbaliz Larrainzar
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra, Pamplona, Spain
| | - Weiqiang Li
- State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, Kaifeng, China
- Henan Joint International Laboratory for Crop Multi-Omics Research, Henan University, Kaifeng, China
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yasuko Watanabe
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Muneo Sato
- Metabolic System Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Cuong Duy Tran
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Jose A. Moler
- Department of Statistics, Computing and Mathematics, Public University of Navarra, Pamplona, Spain
| | - Masami Yokota Hirai
- Metabolic System Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yuji Sawada
- Metabolic System Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Lam-Son Phan Tran
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
- Lam-Son Phan Tran,
| | - Esther M. Gonzalez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra, Pamplona, Spain
- *Correspondence: Esther M. Gonzalez,
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20
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Yin X, Fan H, Chen Y, Li LZ, Song W, Fan Y, Zhou W, Ma G, Alolga RN, Li W, Zhang B, Li P, Tran LSP, Lu X, Qi LW. Integrative omic and transgenic analyses reveal the positive effect of ultraviolet-B irradiation on salvianolic acid biosynthesis through upregulation of SmNAC1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:781-799. [PMID: 32772407 DOI: 10.1111/tpj.14952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 07/21/2020] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
Salvianolic acids (SalAs), a group of secondary metabolites in Salvia miltiorrhiza, are widely used for treating cerebrovascular diseases. Their biosynthesis is modulated by a variety of abiotic factors, including ultraviolet-B (UV-B) irradiation; however, the underlying mechanisms remain largely unknown. Here, an integrated metabolomic, proteomic, and transcriptomic approach coupled with transgenic analyses was employed to dissect the mechanisms underlying UV-B irradiation-induced SalA biosynthesis. Results of metabolomics showed that 28 metabolites, including 12 SalAs, were elevated in leaves of UV-B-treated S. miltiorrhiza. Meanwhile, the contents of several phytohormones, including jasmonic acid and salicylic acid, which positively modulate the biosynthesis of SalAs, also increased in UV-B-treated S. miltiorrhiza. Consistently, 20 core biosynthetic enzymes and numerous transcription factors that are involved in SalA biosynthesis were elevated in treated samples as indicated by a comprehensive proteomic analysis. Correlation and gene expression analyses demonstrated that the NAC1 gene, encoding a NAC transcriptional factor, was positively involved in UV-B-induced SalA biosynthesis. Accordingly, overexpression and RNA interference of NAC1 increased and decreased SalA contents, respectively, through regulation of key biosynthetic enzymes. Furthermore, ChIP-qPCR and Dual-LUC assays showed that NAC1 could directly bind to the CATGTG and CATGTC motifs present in the promoters of the SalA biosynthesis-related genes PAL3 and TAT3, respectively, and activate their expression. Our results collectively demonstrate that NAC1 plays a crucial role in UV-B irradiation-induced SalA biosynthesis. Taken together, our findings provide mechanistic insights into the UV-B-induced SalA biosynthesis in S. miltiorrhiza, and shed light on a great potential for the development of SalA-abundant varieties through genetic engineering.
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Affiliation(s)
- Xiaojian Yin
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, Institute of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Hui Fan
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, Institute of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
| | - Yan Chen
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Lan-Zhu Li
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Wei Song
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, Institute of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
| | - Yuanming Fan
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Wei Zhou
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Gaoxiang Ma
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Raphael N Alolga
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Weiqiang Li
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Baolong Zhang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China
| | - Ping Li
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Lam-Son P Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Vietnam
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, 230-0045, Japan
| | - Xu Lu
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Lian-Wen Qi
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
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21
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Screening and verification of reference genes for analysis of gene expression in winter rapeseed (Brassica rapa L.) under abiotic stress. PLoS One 2020; 15:e0236577. [PMID: 32941459 PMCID: PMC7498103 DOI: 10.1371/journal.pone.0236577] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 07/08/2020] [Indexed: 02/04/2023] Open
Abstract
Winter rapeseed (Brassica rapa L.) is the main oilseed crop in northern China and can safely overwinter at 35 (i.e., Tianshui, China) to 48 degrees north latitude (i.e., Altai, Heilongjiang, Raohe, and Xinjiang, China). In order to identify stable reference genes to understand the molecular mechanisms of stress tolerance in winter rapeseed, internal reference genes of winter rapeseed under four abiotic stresses were analyzed using GeNorm, NormFinder, BestKeeper, and RefFinder software. The most stable combinations of internal reference genes were β-actin and SAND in cold-stressed leaves, β-actin and EF1a in cold-stressed roots, F-box and SAND in high temperature-stressed leaves, and PP2A and RPL in high temperature-stressed roots, SAND and PP2A in NaCl-stressed leaves, RPL and UBC in NaCl-stressed roots, RPL and PP2A in PEG-stressed leaves, and PP2A and RPL in PEG-stressed roots. Expression profiles of PXG3 were used to verify these results. The stable reference genes identified in this study are useful tools for identifying stress-responsive genes to understand the molecular mechanisms of stress tolerance in winter rapeseed.
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22
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Ku YS, Ni M, Muñoz NB, Xiao Z, Lo AWY, Chen P, Li MW, Cheung MY, Xie M, Lam HM. ABAS1 from soybean is a 1R-subtype MYB transcriptional repressor that enhances ABA sensitivity. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2970-2981. [PMID: 32061092 PMCID: PMC7260724 DOI: 10.1093/jxb/eraa081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/11/2020] [Indexed: 05/06/2023]
Abstract
Transcription factors (TFs) help plants respond to environmental stresses by regulating gene expression. Up till now, studies on the MYB family of TFs have mainly focused on the highly abundant R2R3-subtype. While the less well-known 1R-subtype has been generally shown to enhance abscisic acid (ABA) sensitivity by acting as transcriptional activators, the mechanisms of their functions are unclear. Here we identified an ABA sensitivity-associated gene from soybean, ABA-Sensitive 1 (GmABAS1), of the 1R-subtype of MYB. Using the GFP-GmABAS1 fusion protein, we demonstrated that GmABAS1 is localized in the nucleus, and with yeast reporter systems, we showed that it is a transcriptional repressor. We then identified the target gene of GmABAS1 to be Glyma.01G060300, an annotated ABI five-binding protein 3 and showed that GmABAS1 binds to the promoter of Glyma.01G060300 both in vitro and in vivo. Furthermore, Glyma.01G060300 and GmABAS1 exhibited reciprocal expression patterns under osmotic stress, inferring that GmABAS1 is a transcriptional repressor of Glyma.01G060300. As a further confirmation, AtAFP2, an orthologue of Glyma.01G060300, was down-regulated in GmABAS1-transgenic Arabidopsis thaliana, enhancing the plant's sensitivity to ABA. This is the first time a 1R-subtype of MYB from soybean has been reported to enhance ABA sensitivity by acting as a transcriptional repressor.
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Affiliation(s)
- Yee-Shan Ku
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Meng Ni
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Nacira B Muñoz
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias–INTA, Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Zhixia Xiao
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Annie Wing-Yi Lo
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Pei Chen
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Man-Wah Li
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ming-Yan Cheung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Min Xie
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
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Rodrigues NF, Nogueira FCS, Domont GB, Margis R. Identification of soybean trans-factors associated with plastid RNA editing sites. Genet Mol Biol 2020; 43:e20190067. [PMID: 32459826 PMCID: PMC7231544 DOI: 10.1590/1678-4685-gmb-2019-0067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/09/2019] [Indexed: 12/05/2022] Open
Abstract
RNA editing is a posttranscriptional process that changes nucleotide sequences, among which cytosine-to-uracil by a deamination reaction can revert non-neutral codon mutations. Pentatricopeptide repeat (PPR) proteins comprise a family of RNA-binding proteins, with members acting as editing trans-factors that recognize specific RNA cis-elements and perform the deamination reaction. PPR proteins are classified into P and PLS subfamilies. In this work, we have designed RNA biotinylated probes based in soybean plastid RNA editing sites to perform trans-factor specific protein isolation. Soybean cis-elements from these three different RNA probes show differences in respect to other species. Pulldown samples were submitted to mass spectrometry for protein identification. Among detected proteins, five corresponded to PPR proteins. More than one PPR protein, with distinct functional domains, was pulled down with each one of the RNA probes. Comparison of the soybean PPR proteins to Arabidopsis allowed identification of the closest homologous. Differential gene expression analysis demonstrated that the PPR locus Glyma.02G174500 doubled its expression under salt stress, which correlates with the increase of its potential rps14 editing. The present study represents the first identification of RNA editing trans-factors in soybean. Data also indicated that potential multiple trans-factors should interact with RNA cis-elements to perform the RNA editing.
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Affiliation(s)
- Nureyev F. Rodrigues
- Universidade Federal do Rio Grande do Sul (UFRGS), Centro de Biotecnologia,
Programa de Pós-Graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre,
RS, Brazil
| | - Fábio C. S. Nogueira
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Departamento de Bioquímica, Programa de Pós-Graduação em Bioquímica (PPGBq), Unidade
Proteômica, Rio de Janeiro, RJ, Brazil
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Laboratório de Apoio ao Desenvolvimento Tecnológico (LADETEC), Rio de Janeiro, RJ,
Brazil
| | - Gilberto B. Domont
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Departamento de Bioquímica, Programa de Pós-Graduação em Bioquímica (PPGBq), Unidade
Proteômica, Rio de Janeiro, RJ, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul (UFRGS), Centro de Biotecnologia,
Programa de Pós-Graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre,
RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Departamento de
Biofísica, Porto Alegre, RS, Brazil
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Zhong M, Yang X, Hu Y, Huang L, Peng Y, Li Z, Liu Q, Wang X, Zhang X, Nie G. Identification of candidate reference genes for quantitative RT-PCR in Miscanthus sinensis subjected to various abiotic stresses. Mol Biol Rep 2020; 47:2913-2927. [PMID: 32222917 DOI: 10.1007/s11033-020-05392-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 03/24/2020] [Indexed: 12/22/2022]
Abstract
Quantitative real-time PCR (qRT-PCR) has been widely used for studying gene expression at the transcript level. Its accuracy usually relies on the reference genes that are utilized for data normalization. Miscanthus sinensis, a perennial C4 grass with high biomass and strong resistance to adversities, is often utilized as a high value energy crop. However, no reliable reference genes have been investigated for normalizing gene expression for this species. In this study, 12 candidate reference genes were selected to identify their stability under five different abiotic stress treatments (drought, salt, cadmium, chromium and arsenic) by using geNorm, NormFinder, BestKeeper and RefFinder softwares. The results showed that 18S rRNA and Unigene33312 were the best reference genes under drought treatments. Unigene33312 and Unigene33024 were found to be the most stably expressed genes under salt stress and Cd stress. Moreover, Unigene33024 and PP2A were the most suitable reference genes under Cr stress and Unigene33024 and Sb09g019750 were deemed more suitable reference genes under As stress. In total, considering all the samples, Unigene33024 and PP2A were the most stable genes while ACTIN and Unigene26576 were the least stable reference genes for internal control. The expression patterns of two target genes (Cu/Zn SOD and CAT) were used to further verify those selected reference genes under different conditions. The results showed that the most and the least stable reference genes had clearly different expression patterns. This work comprehensively estimated the stability of reference genes in M. sinensis which may give insight to the reference genes selection in other tissues as well as other related varieties. These suggested reference genes would assist in further putative gene expression validation in M. sinensis.
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Affiliation(s)
- Minyi Zhong
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xinying Yang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yiyue Hu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yan Peng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhou Li
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiuxu Liu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xia Wang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Gang Nie
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Yu Y, Zhang G, Chen Y, Bai Q, Gao C, Zeng L, Li Z, Cheng Y, Chen J, Sun X, Guo L, Xu J, Yan Z. Selection of Reference Genes for qPCR Analyses of Gene Expression in Ramie Leaves and Roots across Eleven Abiotic/Biotic Treatments. Sci Rep 2019; 9:20004. [PMID: 31882847 PMCID: PMC6934855 DOI: 10.1038/s41598-019-56640-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/16/2019] [Indexed: 12/25/2022] Open
Abstract
Quantitative real-time PCR (qPCR) is commonly used for deciphering gene functions. For effective qPCR analyses, suitable reference genes are needed for normalization. The objective of this study is to identify the appropriate reference gene(s) for qPCR analyses of the leaves and roots of ramie (Boehmeria nivea L.), an important natural fiber crop. To accomplish this goal, we investigated the expression patterns of eight common plant qPCR reference genes in ramie leaves and roots under five abiotic stresses, five hormonal treatments, and one biotic stress. The relative expression stabilities of the eight genes were evaluated using four common but different approaches: geNorm, NormFinder, BestKeeper, and RefFinder. Across the 11 tested conditions, ACT1 was the most stably expressed among the eight genes while GAPDH displayed the biggest variation. Overall, while variations in the suggested reference genes were found for different tissue x treatment combinations, our analyses revealed that together, genes ACT1, CYP2, and UBQ can provide robust references for gene expression studies of ramie leaves under most conditions, while genes EF-1α, TUB, and ACT1 can be used for similar studies of ramie roots. Our results should help future functional studies of the genes in ramie genome across tissues and environmental conditions.
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Affiliation(s)
- Yongting Yu
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Gang Zhang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, 712406, China
| | - Yikun Chen
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Qingqing Bai
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, 712406, China
| | - Chunsheng Gao
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Liangbin Zeng
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Zhimin Li
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Yi Cheng
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Jia Chen
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Xiangping Sun
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Litao Guo
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
| | - Jianping Xu
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China. .,Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
| | - Zhun Yan
- Department of Plant Protection, Institute of Bast Fiber Crops and Center for Southern Economic Crops, Chinese Academy of Agricultural Science, Changsha, 410205, China
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Li S, Wang N, Ji D, Zhang W, Wang Y, Yu Y, Zhao S, Lyu M, You J, Zhang Y, Wang L, Wang X, Liu Z, Tong J, Xiao L, Bai MY, Xiang F. A GmSIN1/GmNCED3s/GmRbohBs Feed-Forward Loop Acts as a Signal Amplifier That Regulates Root Growth in Soybean Exposed to Salt Stress. THE PLANT CELL 2019; 31:2107-2130. [PMID: 31227558 PMCID: PMC6751118 DOI: 10.1105/tpc.18.00662] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 05/07/2019] [Accepted: 06/17/2019] [Indexed: 05/18/2023]
Abstract
Abscisic acid (ABA) and reactive oxygen species (ROS) act as key signaling molecules in the plant response to salt stress; however, how these signals are transduced and amplified remains unclear. Here, a soybean (Glycine max) salinity-induced NAM/ATAF1/2/CUC2 (NAC) transcription factor encoded by SALT INDUCED NAC1 (GmSIN1) was shown to be a key component of this process. Overexpression of GmSIN1 in soybean promoted root growth and salt tolerance and increased yield under salt stress; RNA interference-mediated knockdown of GmSIN1 had the opposite effect. The rapid induction of GmSIN1 in response to salinity required ABA and ROS, and the effect of GmSIN1 on root elongation and salt tolerance was achieved by boosting cellular ABA and ROS contents. GmSIN1 upregulated 9-cis-epoxycarotenoid dioxygenase coding genes in soybean (GmNCED3s, associated with ABA synthesis) and Respiratory burst oxidase homolog B genes in soybean (GmRbohBs, associated with ROS generation) by binding to their promoters at a site that has not been described to date. Together, GmSIN1, GmNCED3s, and GmRbohBs constitute a positive feed-forward system that enables the rapid accumulation of ABA and ROS, effectively amplifying the initial salt stress signal. These findings suggest that the combined modulation of ABA and ROS contents enhances soybean salt tolerance.
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Affiliation(s)
- Shuo Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Nan Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Dandan Ji
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Wenxiao Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Ying Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Yanchong Yu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Shizhen Zhao
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Menghua Lyu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Juanjuan You
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Yangyang Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Luli Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Xiaofang Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Zhenhua Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Ming-Yi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Fengning Xiang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
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Selection of suitable reference genes for qRT-PCR analysis of Begonia semperflorens under stress conditions. Mol Biol Rep 2019; 46:6027-6037. [DOI: 10.1007/s11033-019-05038-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/20/2019] [Indexed: 02/06/2023]
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Hao Q, Zhang L, Yang Y, Shan Z, Zhou XA. Genome-Wide Analysis of the WOX Gene Family and Function Exploration of GmWOX18 in Soybean. PLANTS 2019; 8:plants8070215. [PMID: 31373320 PMCID: PMC6681341 DOI: 10.3390/plants8070215] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/04/2019] [Accepted: 07/09/2019] [Indexed: 11/16/2022]
Abstract
WUSCHEL-related homeobox (WOX) is a family of transcription factors that are unique to plants and is characterized by the presence of a homeodomain. The WOX transcription factor plays an important role in regulating plant growth and development and the response to abiotic stress. Soybean is one of the most important oil crops worldwide. In this study, based on the available genome data of soybean, the WOX gene family was identified by bioinformatics analysis. The chromosome distribution, gene and protein structures, phylogenetic relationship and gene expression patterns of this family were comprehensively compared. The results showed that a total of 33 putative WOX genes in the soybean genome were found and then designated as GmWOX1- GmWOX33, which were distributed across 19 chromosomes except chromosome 16. Multiple sequence analysis of the GmWOX gene family revealed a highly conserved homeodomain. Phylogenetic tree analysis showed that 33 WOX genes could be divided into three major clades (modern/WUS, intermediate and ancient) in soybean. Of these 33 WOX genes, some showed differential expression patterns in the tested tissues (leaves, pods, unopen and open flowers, nodules, seed, roots, root hairs, stems, shoot apical meristems and shoot tips). In addition, the expression profile and qRT-PCR analysis showed that most of the GmWOX genes responded to different abiotic stress treatments (cold and drought). According to the expression pattern of GmWOX genes in the high regeneration capacity soybean material P3, overexpression of GmWOX18 was selected for function analysis. The overexpression of GmWOX18 increased the regeneration ability of clustered buds. The results will provide valuable information for further studies on the roles of WOX genes in regulating soybean growth, development and responses to abiotic stress, as well as a basis for the functional identification and analysis of WOX genes in soybean.
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Affiliation(s)
- Qingnan Hao
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Ling Zhang
- Jilin Provincial Key laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, Jilin 130033, China.
| | - Yanyan Yang
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China
| | - Zhihui Shan
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China.
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
| | - Xin-An Zhou
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China.
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
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Selection of suitable reference genes for quantitive real-time PCR normalization in Miscanthus lutarioriparia. Mol Biol Rep 2019; 46:4545-4553. [PMID: 31228041 DOI: 10.1007/s11033-019-04910-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/07/2019] [Indexed: 12/18/2022]
Abstract
Miscanthus lutarioriparia, which is found widespread in China, has attracted great attention as a most potential bioenergy plant for years. The quantitative real time PCR (RT-qPCR) has appeared as a sensitive and powerful technique to measure gene expression in living organisms during different development stages. In this study, we evaluated ten candidate genes, including 25S ribosomal RNA gene (25S rRNA), actin1 gene (ACT1), carotenoid-binding protein 20 gene (CBP20), glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH), Ubiquitin gene (UBQ), eukaryotic elongation factor 1-αgene (eEF-1α), α-tubulin gene (α-TUB), β-tubulin gene (β-TUB), eukaryotic translation initiation factor 4α-1 gene (eIF-4α) and NAC domain protein gene(NAC) in a series of 30 M. lutarioriparia samples followed by statistical algorithms geNorm and Normfinder to analyze the gene expression stability. The results indicated that eIF-4αand UBQ were the most stable expressed genes while CBP20 showed as the least stable among all the samples. Based on above research, we recommend that at least two top-ranked reference genes should be employed for expression data normalization. The best genes selected in this study will provide a starting point to select reference genes in the future in other tissues and under other experimental conditions in this energy crop candidate.
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30
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Dumschott K, Dechorgnat J, Merchant A. Water Deficit Elicits a Transcriptional Response of Genes Governing d-pinitol Biosynthesis in Soybean ( Glycine max). Int J Mol Sci 2019; 20:E2411. [PMID: 31096655 PMCID: PMC6566849 DOI: 10.3390/ijms20102411] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/08/2019] [Indexed: 11/16/2022] Open
Abstract
d-pinitol is the most commonly accumulated sugar alcohol in the Leguminosae family and has been observed to increase significantly in response to abiotic stress. While previous studies have identified genes involved in d-pinitol synthesis, no study has investigated transcript expression in planta. The present study quantified the expression of several genes involved in d-pinitol synthesis in different plant tissues and investigated the accumulation of d-pinitol, myo-inositol and other metabolites in response to a progressive soil drought in soybean (Glycine max). Expression of myo-inositol 1-phosphate synthase (INPS), the gene responsible for the conversion of glucose-6-phosphate to myo-inositol-1-phosphate, was significantly up regulated in response to a water deficit for the first two sampling weeks. Expression of myo-inositol O-methyl transferase (IMT1), the gene responsible for the conversion of myo-inositol into d-ononitol was only up regulated in stems at sampling week 3. Assessment of metabolites showed significant changes in their concentration in leaves and stems. d-Pinitol concentration was significantly higher in all organs sampled from water deficit plants for all three sampling weeks. In contrast, myo-inositol, had significantly lower concentrations in leaf samples despite up regulation of INPS suggesting the transcriptionally regulated flux of carbon through the myo-inositol pool is important during water deficit.
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Affiliation(s)
- Kathryn Dumschott
- Rheinisch-Westfälische Technische Hochschule Aachen University, 52062 Aachen, NRW, Germany.
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31
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Sinha R, Sharma TR, Singh AK. Validation of reference genes for qRT-PCR data normalisation in lentil ( Lens culinaris) under leaf developmental stages and abiotic stresses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:123-134. [PMID: 30804635 PMCID: PMC6352542 DOI: 10.1007/s12298-018-0609-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/04/2018] [Accepted: 09/24/2018] [Indexed: 05/07/2023]
Abstract
Lentil (Lens culinaris) is one of the most important staple food crops of developing countries. Transcriptome based global gene expression profiling followed by validation of expression of important genes through quantitative real time-PCR (qRT-PCR) has achieved significance in recent years. However, there is a severe scarcity of information regarding stable reference genes in lentil, which is mandatory for qRT-PCR data normalisation. Hence, the present study was under-taken to identify the most stable reference gene(s) in lentil. Expression stability of eight candidate genes viz. ribulose 1,5-bisphosphate carboxylase large subunit (Rbcl), ribosomal protein L2 (RPL2), 18S rRNA, tubulin (Tub), elongation factor 1α (EF1α), glyceraldehydes-3-phosphate dehydrogenase (GAPDH), heat shock protein (HSP70), and Maturase (mat K) was evaluated in five varieties of lentil at three different stages of leaf development and abiotic stress conditions using qRT-PCR. The results were analysed using four types of statistical software viz., geNorm, BestKeeper, NormFinder and RefFinder; all softwares identified RPL2 as most stable under abiotic stress conditions and developmental stages followed by Tub and Rbcl; while, HSP70 was identified as least stable. Relative expression of the target genes, defensin and PR4, was evaluated under abiotic stress conditions and data normalisation was done using two stable reference genes, RPL2 and Tub, either alone or in combination and with two least stable genes, HSP70 and 18S. The present work provides a list of potential reference genes in lentil, which will help in selection of appropriate reference gene for qRT-PCR data normalization depending upon the experiment.
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Affiliation(s)
- Ragini Sinha
- ICAR-Indian Institute of Agricultural Biotechnology, Garhkhatanga, Ranchi, 834 010 India
| | - T. R. Sharma
- ICAR-Indian Institute of Agricultural Biotechnology, Garhkhatanga, Ranchi, 834 010 India
| | - Anil Kumar Singh
- ICAR-Indian Institute of Agricultural Biotechnology, Garhkhatanga, Ranchi, 834 010 India
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32
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Reference gene validation for normalization of RT-qPCR assay associated with germination and survival of rice under hypoxic condition. J Appl Genet 2018; 59:419-430. [DOI: 10.1007/s13353-018-0466-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/22/2018] [Accepted: 08/28/2018] [Indexed: 02/06/2023]
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33
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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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34
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Selection of reference genes for quantitative real-time PCR normalization in Narcissus pseudonarcissu in different cultivars and different organs. Heliyon 2018; 4:e00686. [PMID: 29998201 PMCID: PMC6039305 DOI: 10.1016/j.heliyon.2018.e00686] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/25/2018] [Accepted: 07/04/2018] [Indexed: 11/26/2022] Open
Abstract
Quantitative real-time PCR (qRT-PCR) has been a widely used accurate technique for gene expression analysis in various species. However, its results require data normalization by reliable reference genes. Despite the horticultural importance of Narcissus pseudonarcissus, and genome sequence has become available for the species, no gene expression study based on the stability of reference genes in qRT-PCR has been conducted. To boost the use of qRT-PCR in N. pseudonarcissus, we uncovered eight commonly used candidate reference genes for their stability. The expression levels of the eight genes were detected for the normalization in five different organs (bulbs, scapes, leaves, perianths and coronas) of three N. pseudonarcissus cultivars (‘Marieke’, ‘Pinza’ and ‘Slim Whitman’) by qRT-PCR. Subsequently, three commonly used computational programs were applied for evaluating the stability of the candidate reference gene's expressions. It turned out that for all the samples and most subgroups, ACT and GAPDH were the most suitable reference genes for normalization. However, the best reference genes were found not always the same one across diverse samples by different computational programs. Our study was the first reference gene evaluation in N. pseudonarcissus and will promote future studies on gene expression levels of N. pseudonarcissus.
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Wang B, Du H, Yao Z, Ren C, Ma L, Wang J, Zhang H, Ma H. Validation of reference genes for accurate normalization of gene expression with quantitative real-time PCR in Haloxylon ammodendron under different abiotic stresses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:455-463. [PMID: 29692553 PMCID: PMC5911265 DOI: 10.1007/s12298-018-0520-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/20/2017] [Accepted: 02/08/2018] [Indexed: 05/27/2023]
Abstract
Haloxylon ammodendron plays an important role in maintaining the structure and function of the entire ecosystem where it grows. No suitable reference genes have been reported in H. ammodendron plants to date. In this study, a total of 8 reference genes (18S, ACT1, ACT7, UBC18, TUA5, GAPDH, EF-1α and UBQ10) were selected from the available trancriptome database, and the expression stability of these 8 candidate genes was validated under different abiotic stress with three different statistical algorithms (geNorm, NormFinder and BestKeeper). The results produced from different models were in agreement with each other essentially: 18S and TUA5 were the most stable genes under drought stress, 18S, the most stable gene under heat stress and mechanical damage, ACT7 and UBC18, stable under salt stress while TUA5 and GAPDH expressed constantly under mechanical damage, and ACT1 expressed steadily under cold conditions. Expression profiles of several stress response genes, including FT-5, FT-9, DREB2A and DREB2C, were further confirmed with various candidate reference genes. None of the candidate genes showed a constant expression among all tested samples. Hence, it's essential to use more than one reference gene in order to guarantee the accuracy of quantitative real-time PCR. The results of this study will contribute to the accuracy and reliability in transcripts quantification, which is of significance to transcription-based studies and applications in this important shrub H. ammodendron.
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Affiliation(s)
- Bo Wang
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Huihui Du
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Zhengpei Yao
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Cai Ren
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Li Ma
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Jiao Wang
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Hua Zhang
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Hao Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
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Silva LCC, Bueno RD, da Matta LB, Pereira PHS, Mayrink DB, Piovesan ND, Sediyama CS, Fontes EPB, Cardinal AJ, Dal-Bianco M. Characterization of a new GmFAD3A allele in Brazilian CS303TNKCA soybean cultivar. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1099-1110. [PMID: 29397403 DOI: 10.1007/s00122-018-3061-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/19/2018] [Indexed: 06/07/2023]
Abstract
KEY MESSAGE We molecularly characterized a new mutation in the GmFAD3A gene associated with low linolenic content in the Brazilian soybean cultivar CS303TNKCA and developed a molecular marker to select this mutation. Soybean is one of the most important crops cultivated worldwide. Soybean oil has 13% palmitic acid, 4% stearic acid, 20% oleic acid, 55% linoleic acid and 8% linolenic acid. Breeding programs are developing varieties with high oleic and low polyunsaturated fatty acids (linoleic and linolenic) to improve the oil oxidative stability and make the varieties more attractive for the soy industry. The main goal of this study was to characterize the low linoleic acid trait in CS303TNKCA cultivar. We sequenced CS303TNKCA GmFAD3A, GmFAD3B and GmFAD3C genes and identified an adenine point deletion in the GmFAD3A exon 5 (delA). This alteration creates a premature stop codon, leading to a truncated protein with just 207 residues that result in a non-functional enzyme. Analysis of enzymatic activity by heterologous expression in yeast support delA as the cause of low linolenic acid content in CS303TNKCA. Thus, we developed a TaqMan genotyping assay to associate delA with low linolenic acid content in segregating populations. Lines homozygous for delA had a linolenic acid content of 3.3 to 4.4%, and the variation at this locus accounted for 50.83 to 73.70% of the phenotypic variation. This molecular marker is a new tool to introgress the low linolenic acid trait into elite soybean cultivars and can be used to combine with high oleic trait markers to produce soybean with enhanced economic value. The advantage of using CS303TNKCA compared to other lines available in the literature is that this cultivar has good agronomic characteristics and is adapted to Brazilian conditions.
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Affiliation(s)
- Luiz Claudio Costa Silva
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Rafael Delmond Bueno
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | | | | | - Danyelle Barbosa Mayrink
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Newton Deniz Piovesan
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | | | | | - Andrea J Cardinal
- Crop Science Department, North Carollina State University, Raleigh, NC, 27695, USA
- Syngenta Biotechnology, Inc, 3054 Cornwallis Rd., Research Triangle Park, NC, 27709, USA
| | - Maximiller Dal-Bianco
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO and Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil.
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Selection and validation of reference genes for quantitative gene expression analyses in black locust (Robinia pseudoacacia L.) using real-time quantitative PCR. PLoS One 2018. [PMID: 29529054 PMCID: PMC5846725 DOI: 10.1371/journal.pone.0193076] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Black locust (Robinia pseudoacacia L.) is an easy to raise, fast growing, medium-sized deciduous tree species highly tolerant to harsh eco-conditions, i.e., drought and harsh winters, and it is widely adaptable to sandy, loamy, and marshy soils. The basis for this adaptability remains to be investigated at the transcriptomic level using real-time quantitative PCR (qPCR). Selection of a reliable gene for the normalization of qPCR data is important for obtaining accurate results in gene expression. The goal of this study was to identify an appropriate reference gene from 12 candidate genes for gene expression analysis in black locust exposed to various stressors such as abscisic acid (ABA), NaCl, polyethylene glycol (PEG) and varying temperatures. In GeNorm and NormFinder analyses, ACT (actin) and GAPDH (glyceraldehyde-3-phosphate dehydrogenase) gene expression were the most stable in all conditions except heat stress, but in BestKeeper analysis, GAPDH and helicase gene expression were the most stable under NaCl and heat stress. In contrast, ACT and GAPDH were highest under abscisic acid (ABA), GAPDH and βTUB (beta tubulin) under cold stress, and helicase and EF1α (elongation factor 1 alpha) under PEG stress. We found that the most stable reference gene combination for all conditions was ACT and GAPDH. Additionally, the expression pattern of NAC2 (a transcription factor) and BGL2 in different tissues and under different stress conditions was analyzed relative to ACT and GAPDH and UBQ (ubiquitin) the least stably expressed gene. NAC2 and BGL2 both had highest expression in flowers and pods under ABA stress at 48h. This study provides useful reference genes for future gene expression studies in black locust.
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Joseph JT, Poolakkalody NJ, Shah JM. Plant reference genes for development and stress response studies. J Biosci 2018; 43:173-187. [PMID: 29485125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Many reference genes are used by different laboratories for gene expression analyses to indicate the relative amount of input RNA/DNA in the experiment. These reference genes are supposed to show least variation among the treatments and with the control sets in a given experiment. However, expression of reference genes varies significantly from one set of experiment to the other. Thus, selection of reference genes depends on the experimental conditions. Sometimes the average expression of two or three reference genes is taken as standard. This review consolidated the details of about 120 genes attempted for normalization during comparative expression analysis in 16 different plants. Plant species included in this review are Arabidopsis thaliana, cotton (Gossypium hirsutum), tobacco (Nicotiana benthamiana and N. tabacum), soybean (Glycine max), rice (Oryza sativa), blueberry (Vaccinium corymbosum), tomato (Solanum lycopersicum), wheat (Triticum aestivum), potato (Solanum tuberosum), sugar cane (Saccharum sp.), carrot (Daucus carota), coffee (Coffea arabica), cucumber (Cucumis sativus), kiwi (Actinidia deliciosa) and grape (Vitis vinifera). The list includes model and cultivated crop plants from both monocot and dicot classes. We have categorized plant-wise the reference genes that have been used for expression analyses in any or all of the four different conditions such as biotic stress, abiotic stress, developmental stages and various organs and tissues, reported till date. This review serves as a guide during the reference gene hunt for gene expression analysis studies.
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Affiliation(s)
- Joyous T Joseph
- Department of Plant Science, Central University of Kerala, Padannakkad, Kasaragod 671 314, India
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Wan Q, Chen S, Shan Z, Yang Z, Chen L, Zhang C, Yuan S, Hao Q, Zhang X, Qiu D, Chen H, Zhou X. Stability evaluation of reference genes for gene expression analysis by RT-qPCR in soybean under different conditions. PLoS One 2017; 12:e0189405. [PMID: 29236756 PMCID: PMC5728501 DOI: 10.1371/journal.pone.0189405] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 11/26/2017] [Indexed: 12/23/2022] Open
Abstract
Real-time quantitative reverse transcription PCR is a sensitive and widely used technique to quantify gene expression. To achieve a reliable result, appropriate reference genes are highly required for normalization of transcripts in different samples. In this study, 9 previously published reference genes (60S, Fbox, ELF1A, ELF1B, ACT11, TUA5, UBC4, G6PD, CYP2) of soybean [Glycine max (L.) Merr.] were selected. The expression stability of the 9 genes was evaluated under conditions of biotic stress caused by infection with soybean mosaic virus, nitrogen stress, across different cultivars and developmental stages. ΔCt and geNorm algorithms were used to evaluate and rank the expression stability of the 9 reference genes. Results obtained from two algorithms showed high consistency. Moreover, results of pairwise variation showed that two reference genes were sufficient to normalize the expression levels of target genes under each experimental setting. For virus infection, ELF1A and ELF1B were the most stable reference genes for accurate normalization. For different developmental stages, Fbox and G6PD had the highest expression stability between two soybean cultivars (Tanlong No. 1 and Tanlong No. 2). ELF1B and ACT11 were identified as the most stably expressed reference genes both under nitrogen stress and among different cultivars. The results showed that none of the candidate reference genes were uniformly expressed at different conditions, and selecting appropriate reference genes was pivotal for gene expression studies with particular condition and tissue. The most stable combination of genes identified in this study will help to achieve more accurate and reliable results in a wide variety of samples in soybean.
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Affiliation(s)
- Qiao Wan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Shuilian Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Zhihui Shan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Zhonglu Yang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Limiao Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Chanjuan Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Songli Yuan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Qinnan Hao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Xiaojuan Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Dezhen Qiu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Haifeng Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Xinan Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
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Nasr Esfahani M, Inoue K, Chu HD, Nguyen KH, Van Ha C, Watanabe Y, Burritt DJ, Herrera-Estrella L, Mochida K, Tran LSP. Comparative transcriptome analysis of nodules of two Mesorhizobium-chickpea associations with differential symbiotic efficiency under phosphate deficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017. [PMID: 28628240 DOI: 10.1111/tpj.13616] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Phosphate (Pi) deficiency is known to be a major limitation for symbiotic nitrogen fixation (SNF), and hence legume crop productivity globally. However, very little information is available on the adaptive mechanisms, particularly in the important legume crop chickpea (Cicer arietinum L.), which enable nodules to respond to low-Pi availability. Thus, to elucidate these mechanisms in chickpea nodules at molecular level, we used an RNA sequencing approach to investigate transcriptomes of the nodules in Mesorhizobium mediterraneum SWRI9-(MmSWRI9)-chickpea and M. ciceri CP-31-(McCP-31)-chickpea associations under Pi-sufficient and Pi-deficient conditions, of which the McCP-31-chickpea association has a better SNF capacity than the MmSWRI9-chickpea association during Pi starvation. Our investigation revealed that more genes showed altered expression patterns in MmSWRI9-induced nodules than in McCP-31-induced nodules (540 vs. 225) under Pi deficiency, suggesting that the Pi-starvation-more-sensitive MmSWRI9-induced nodules required expression change in a larger number of genes to cope with low-Pi stress than the Pi-starvation-less-sensitive McCP-31-induced nodules. The functional classification of differentially expressed genes (DEGs) was examined to gain an understanding of how chickpea nodules respond to Pi starvation, caused by soil Pi deficiency. As a result, more DEGs involved in nodulation, detoxification, nutrient/ion transport, transcriptional factors, key metabolic pathways, Pi remobilization and signalling were found in Pi-starved MmSWRI9-induced nodules than in Pi-starved McCP-31-induced nodules. Our findings have enabled the identification of molecular processes that play important roles in the acclimation of nodules to Pi deficiency, ultimately leading to the development of Pi-efficient chickpea symbiotic associations suitable for Pi-deficient soils.
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Affiliation(s)
| | - Komaki Inoue
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Ha Duc Chu
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Pham Van Dong, North Tu Liem, Hanoi, Vietnam
| | - Kien Huu Nguyen
- Plant Abiotic Stress Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, 70000, Vietnam
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Chien Van Ha
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Pham Van Dong, North Tu Liem, Hanoi, Vietnam
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - David J Burritt
- Department of Botany, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, 36500 Irapuato, Guanajuato, Mexico
| | - Keiichi Mochida
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama, 710-0046, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
| | - Lam-Son Phan Tran
- Plant Abiotic Stress Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, 70000, Vietnam
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
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Ram C, Koramutla MK, Bhattacharya R. Identification and comprehensive evaluation of reference genes for RT-qPCR analysis of host gene-expression in Brassica juncea-aphid interaction using microarray data. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 116:57-67. [PMID: 28527971 DOI: 10.1016/j.plaphy.2017.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 05/12/2023]
Abstract
Brassica juncea is a chief oil yielding crop in many parts of the world including India. With advancement of molecular techniques, RT-qPCR based study of gene-expression has become an integral part of experimentations in crop breeding. In RT-qPCR, use of appropriate reference gene(s) is pivotal. The virtue of the reference genes, being constant in expression throughout the experimental treatments, needs to be validated case by case. Appropriate reference gene(s) for normalization of gene-expression data in B. juncea during the biotic stress of aphid infestation is not known. In the present investigation, 11 reference genes identified from microarray database of Arabidopsis-aphid interaction at a cut off FDR ≤0.1, along with two known reference genes of B. juncea, were analyzed for their expression stability upon aphid infestation. These included 6 frequently used and 5 newly identified reference genes. Ranking orders of the reference genes in terms of expression stability were calculated using advanced statistical approaches such as geNorm, NormFinder, delta Ct and BestKeeper. The analysis suggested CAC, TUA and DUF179 as the most suitable reference genes. Further, normalization of the gene-expression data of STP4 and PR1 by the most and the least stable reference gene, respectively has demonstrated importance and applicability of the recommended reference genes in aphid infested samples of B. juncea.
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Affiliation(s)
- Chet Ram
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi 110012, India
| | - Murali Krishna Koramutla
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi 110012, India
| | - Ramcharan Bhattacharya
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi 110012, India.
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Li T, Diao H, Zhao L, Xing Y, Zhang J, Liu N, Yan Y, Tian X, Sun W, Liu B. Identification of suitable reference genes for real-time quantitative PCR analysis of hydrogen peroxide-treated human umbilical vein endothelial cells. BMC Mol Biol 2017; 18:10. [PMID: 28381210 PMCID: PMC5381023 DOI: 10.1186/s12867-017-0086-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 03/21/2017] [Indexed: 11/25/2022] Open
Abstract
Background Oxidative stress can induce cell injury in vascular endothelial cells, which is the initial event in the development of atherosclerosis. Although quantitative real-time polymerase chain reaction (qRT-PCR) has been widely used in gene expression studies in oxidative stress injuries, using carefully validated reference genes has not received sufficient attention in related studies. The objective of this study, therefore, was to select a set of stably expressed reference genes for use in qRT-PCR normalization in oxidative stress injuries in human umbilical vein endothelial cells (HUVECs) induced by hydrogen peroxide (H2O2). Results Using geNorm analysis, we found that five stably expressed reference genes were sufficient for normalization in qRT-PCR analysis in HUVECs treated with H2O2. Genes with the most stable expression according to geNorm were U6, TFRC, RPLP0, GAPDH, and ACTB, and according to NormFinder were ALAS1, TFRC, U6, GAPDH, and ACTB. Conclusion Taken together, our study demonstrated that the expression stability of reference genes may differ according to the statistical program used. U6, TFRC, RPLP0, GAPDH, and ACTB was the optimal set of reference genes for studies on gene expression performed by qRT-PCR assays in HUVECs under oxidative stress study.
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Affiliation(s)
- Tianyi Li
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Hongying Diao
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Lei Zhao
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Yue Xing
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Jichang Zhang
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Ning Liu
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Youyou Yan
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Xin Tian
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Wei Sun
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Bin Liu
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China.
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Zhang Y, Han X, Chen S, Zheng L, He X, Liu M, Qiao G, Wang Y, Zhuo R. Selection of suitable reference genes for quantitative real-time PCR gene expression analysis in Salix matsudana under different abiotic stresses. Sci Rep 2017; 7:40290. [PMID: 28120870 PMCID: PMC5264508 DOI: 10.1038/srep40290] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/05/2016] [Indexed: 12/22/2022] Open
Abstract
Salix matsudana is a deciduous, rapidly growing willow species commonly cultivated in China, which can tolerate drought, salt, and heavy metal stress conditions. Selection of suitable reference genes for quantitative real-time PCR is important for normalizing the expression of the key genes associated with various stresses. To validate suitable reference genes, we selected 11 candidate reference genes (five traditional housekeeping genes and six novel genes) and analyzed their expression stability in various samples, including different tissues and under different abiotic stress treatments. The expression of these genes was determined using five programs-geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder. The results showed that α-TUB2 (alpha-tubulin 2) and DnaJ (chaperone protein DnaJ 49) were the most stable reference genes across all the tested samples. We measured the expression profiles of the defense response gene SmCAT (catalase) using the two most stable and one least stable reference genes in all samples of S. matsudana. The relative quantification of SmCAT varied greatly according to the different reference genes. We propose that α-TUB2 and DnaJ should be the preferred reference genes for normalization and quantification of transcript levels in future gene expression studies in willow species under various abiotic stress conditions.
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Affiliation(s)
- Yunxing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- School of Architectural and Artistic Design, Henan Polytechnic University, Jiaozuo, Henan 454000, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Shuangshuang Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Liu Zheng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Xuelian He
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Mingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Guirong Qiao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yang Wang
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
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Gao M, Liu Y, Ma X, Shuai Q, Gai J, Li Y. Evaluation of Reference Genes for Normalization of Gene Expression Using Quantitative RT-PCR under Aluminum, Cadmium, and Heat Stresses in Soybean. PLoS One 2017; 12:e0168965. [PMID: 28046130 PMCID: PMC5207429 DOI: 10.1371/journal.pone.0168965] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/09/2016] [Indexed: 02/06/2023] Open
Abstract
Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used to analyze the relative gene expression level, however, the accuracy of qRT-PCR is greatly affected by the stability of reference genes, which is tissue- and environment- dependent. Therefore, choosing the most stable reference gene in a specific tissue and environment is critical to interpret gene expression patterns. Aluminum (Al), cadmium (Cd), and heat stresses are three important abiotic factors limiting soybean (Glycine max) production in southern China. To identify the suitable reference genes for normalizing the expression levels of target genes by qRT-PCR in soybean response to Al, Cd and heat stresses, we studied the expression stability of ten commonly used housekeeping genes in soybean roots and leaves under these three abiotic stresses, using five approaches, BestKeeper, Delta Ct, geNorm, NormFinder and RefFinder. We found TUA4 is the most stable reference gene in soybean root tips under Al stress. Under Cd stress, Fbox and UKN2 are the most stable reference genes in roots and leaves, respectively, while 60S is the most suitable reference gene when analyzing both roots and leaves together. For heat stress, TUA4 and UKN2 are the most stable housekeeping genes in roots and leaves, respectively, and UKN2 is the best reference gene for analysis of roots and leaves together. To validate the reference genes, we quantified the relative expression levels of six target genes that were involved in soybean response to Al, Cd or heat stresses, respectively. The expression patterns of these target genes differed between using the most and least stable reference genes, suggesting the selection of a suitable reference gene is critical for gene expression studies.
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Affiliation(s)
- Mengmeng Gao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yaping Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xiao Ma
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Qin Shuai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Niu K, Shi Y, Ma H. Selection of Candidate Reference Genes for Gene Expression Analysis in Kentucky Bluegrass ( Poa pratensis L.) under Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2017; 8:193. [PMID: 28261247 PMCID: PMC5306334 DOI: 10.3389/fpls.2017.00193] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/31/2017] [Indexed: 05/20/2023]
Abstract
Kentucky bluegrass (Poa pratensis L.) belong to Gramineae and is widely used in lawns, golf courses, landscapes, and sport fields as a prominent cool-season grass. Gene expression patterns during different stages of plant development can provide clues toward the understanding of its biological functions. The selection and validation of reference genes are the first steps in any real-time quantitative PCR gene expression study. Therefore, suitable reference genes are necessary for obtaining reliable results in real-time quantitative PCR analyses of Kentucky bluegrass. In the present study, 9 candidate reference genes were chosen, and their expression stability in the leaves and roots of Kentucky bluegrass under different stresses (drought, salt, heat, and cold) were evaluated using the GeNorm, NormFinder, BestKeeper, and RefFinder programs. The results showed that the expression stability of the candidate reference genes was dependent on the experimental conditions. The combination of SAM with GAPDH was the most stable in leaves under salt stress and cold stress, while TUB combined with ACT or GAPDH was stable in roots under salt or cold stress, respectively. ACT and SAM maintained stable expression in drought-treated leaves, and GAPDH combined with ACT was stable in drought-treated roots. SAM and TUB exhibited stable expression in heat-treated leaves. ACT and RPL were stable in heat-treated roots. In addition, the expression patterns of PpFEH in response to drought and cold stress were used to confirm the reliability of the selected reference genes, indicating that the use of an inappropriate reference gene as the internal control will cause erroneous results. This work is the first study on the expression stability of reference genes in Kentucky bluegrass and will be particularly useful in the selection of stress-tolerance genes and the identification of the molecular mechanisms conferring stress tolerance in this species.
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Jaramillo ML, Ammar D, Quispe RL, Guzman F, Margis R, Nazari EM, Müller YMR. Identification and evaluation of reference genes for expression studies by RT-qPCR during embryonic development of the emerging model organism, Macrobrachium olfersii. Gene 2016; 598:97-106. [PMID: 27825774 DOI: 10.1016/j.gene.2016.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/25/2016] [Accepted: 11/02/2016] [Indexed: 11/28/2022]
Abstract
RT-qPCR is a sensitive and highly efficient technique that is widely used in gene expression analysis and to provide insight into the molecular mechanisms underlying embryonic development. The freshwater prawn, Macrobrachium olfersii is an emerging model organism, but, the stable reference genes of this species need to be identified and validated for RT-qPCR analysis. Thus, the aim of this study was to evaluate the expression stability of six genes (β-act, GAPDH, EF-1α, RpL8, RpS6, AK) in embryos and in adult tissues (cerebral ganglia, muscle and hepatopancreas) of M. olfersii. The expression stabilities of these genes were evaluated using geNorm, NormFinder, BestKeeper, ΔCt method and integrated tool RefFinder. In the general ranking, RpL8 and RpS6 were the most stable genes in embryos, while RpS6 and RpL8 were the most stable in a combined adult tissue analysis. Analysis of the adult tissues revealed that β-act and AK were the most stable genes in cerebral ganglia, RpL8 and AK in muscle, and RpS6 and β-act in hepatopancreas. EF-1α and GAPDH were the least stable genes and as normalizer genes in RT-qPCR affected expression of the Distal-less gene during M. olfersii development. This study provides suitable reference genes for RT-qPCR analysis and allows future studies of the gene expression in M. olfersii for understanding the molecular mechanisms of their development. To our knowledge, this is the first published study that identifies and evaluates reference genes for RT-qPCR analysis in M. olfersii and could be useful as basis for evaluations of reference genes in other prawns.
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Affiliation(s)
- Michael L Jaramillo
- Universidade Federal de Santa Catarina, Departamento de Biologia Celular, Embriologia e Genética, 88040-900 Florianópolis, Santa Catarina, Brazil
| | - Dib Ammar
- Universidade Federal de Santa Catarina, Departamento de Biologia Celular, Embriologia e Genética, 88040-900 Florianópolis, Santa Catarina, Brazil; Centro Universitário - Católica de Santa Catarina, 89203-005 Joinville, SC, Brazil
| | - Ruth L Quispe
- Universidade Federal de Santa Catarina, Programa de Pós-Graduação em Neurociências, Campus Universitário, 88040-900 Florianópolis, SC, Brazil
| | - Frank Guzman
- Universidade Federal do Rio Grande do Sul, PPGBCM, Centro de Biotecnologia, 91501-970 Porto Alegre, RS, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul, Departamento de Biofisica, 91501-970 Porto Alegre, RS, Brazil
| | - Evelise M Nazari
- Universidade Federal de Santa Catarina, Departamento de Biologia Celular, Embriologia e Genética, 88040-900 Florianópolis, Santa Catarina, Brazil.
| | - Yara M R Müller
- Universidade Federal de Santa Catarina, Departamento de Biologia Celular, Embriologia e Genética, 88040-900 Florianópolis, Santa Catarina, Brazil
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Liu F, Guo DD, Tu YH, Xue YR, Gao Y, Guo ML. Identification of reference genes for gene expression normalization in safflower (Carthamus tinctorius). REVISTA BRASILEIRA DE FARMACOGNOSIA-BRAZILIAN JOURNAL OF PHARMACOGNOSY 2016. [DOI: 10.1016/j.bjp.2016.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cassol D, Cruz FP, Espindola K, Mangeon A, Müller C, Loureiro ME, Corrêa RL, Sachetto-Martins G. Identification of reference genes for quantitative RT-PCR analysis of microRNAs and mRNAs in castor bean (Ricinus communis L.) under drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 106:101-7. [PMID: 27156134 DOI: 10.1016/j.plaphy.2016.02.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 02/15/2016] [Accepted: 02/16/2016] [Indexed: 06/05/2023]
Abstract
Quantitative real-time PCR (RT-qPCR) is one of the most powerful and sensitive techniques to the study of gene expression. Several factors influence RT-qPCR performance though, including the stability of the reference genes used for data normalization. While the selection of appropriate reference genes is crucial for accurate and reliable gene expression analysis, no suitable reference genes have been previously identified in castor bean under drought stress. In this study, the expression stability of eleven mRNAs, thirteen microRNAs (miRNAs) and one small nuclear RNA were analyzed in roots and leaves across different levels of water deficit. Three different algorithms were employed to analyze the RT-qPCR data, and the resulting outputs were merged using a non-weighted unsupervised rank aggregation method. Our analysis indicated that the Elongation factor 1-beta (EF1B), Protein phosphatase 2A (PP2A) and ADP-ribosylation factor (ADP) ranked as the best candidates across diverse samples submitted to different levels of drought conditions. EF1B and Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and EF1B and SKP1/ASK-interacting protein 16 (SKIP16) were found as the most suitable reference genes for expression analysis in roots and leaves, respectively. In addition, miRNAs miR168, miR160 and miR397 were selected as optimal reference genes across all tissues and treatments. miR168 and miR156 were recommended as reference for roots, while miR168 and miR160 were recommended for leaves. Together, our results constitute the first attempt to identify and validate the most suitable reference genes for accurate normalization of gene expression in castor bean under drought stress.
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Affiliation(s)
- Daniela Cassol
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, 21944-970, Brazil.
| | - Fernanda P Cruz
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, 21944-970, Brazil.
| | - Kauê Espindola
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, 21944-970, Brazil; Department of Plant Biology, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil.
| | - Amanda Mangeon
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, 21944-970, Brazil.
| | - Caroline Müller
- Department of Plant Biology, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil.
| | - Marcelo Ehlers Loureiro
- Department of Plant Biology, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil.
| | - Régis L Corrêa
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, 21944-970, Brazil.
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Wang P, Xiong A, Gao Z, Yu X, Li M, Hou Y, Sun C, Qu S. Selection of Suitable Reference Genes for RT-qPCR Normalization under Abiotic Stresses and Hormone Stimulation in Persimmon (Diospyros kaki Thunb). PLoS One 2016; 11:e0160885. [PMID: 27513755 PMCID: PMC4981405 DOI: 10.1371/journal.pone.0160885] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/23/2016] [Indexed: 11/19/2022] Open
Abstract
The success of quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) to quantify gene expression depends on the stability of the reference genes used for data normalization. To date, systematic screening for reference genes in persimmon (Diospyros kaki Thunb) has never been reported. In this study, 13 candidate reference genes were cloned from 'Nantongxiaofangshi' using information available in the transcriptome database. Their expression stability was assessed by geNorm and NormFinder algorithms under abiotic stress and hormone stimulation. Our results showed that the most suitable reference genes across all samples were UBC and GAPDH, and not the commonly used persimmon reference gene ACT. In addition, UBC combined with RPII or TUA were found to be appropriate for the "abiotic stress" group and α-TUB combined with PP2A were found to be appropriate for the "hormone stimuli" group. For further validation, the transcript level of the DkDREB2C homologue under heat stress was studied with the selected genes (CYP, GAPDH, TUA, UBC, α-TUB, and EF1-α). The results suggested that it is necessary to choose appropriate reference genes according to the test materials or experimental conditions. Our study will be useful for future studies on gene expression in persimmon.
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Affiliation(s)
- Peihong Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Aisheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinyi Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Man Li
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yingjun Hou
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chao Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shenchun Qu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- * E-mail:
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