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Mao T, Wang X, Gao H, Gong Z, Liu R, Jiang N, Zhang Y, Zhang H, Guo X, Yu C. Ectopic Expression of MADS-Box Transcription Factor VvAGL12 from Grape Promotes Early Flowering, Plant Growth, and Production by Regulating Cell-Wall Architecture in Arabidopsis. Genes (Basel) 2023; 14:2078. [PMID: 38003021 PMCID: PMC10671436 DOI: 10.3390/genes14112078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
The MADS-box family, a substantial group of plant transcription factors, crucially regulates plant growth and development. Although the functions of AGL12-like subgroups have been elucidated in Arabidopsis, rice, and walnut, their roles in grapes remain unexplored. In this study, we isolated VvAGL12, a member of the grape MADS-box group, and investigated its impact on plant growth and biomass production. VvAGL12 was found to localize in the nucleus and exhibit expression in both vegetative and reproductive organs. We introduced VvAGL12 into Arabidopsis thaliana ecotype Columbia-0 and an agl12 mutant. The resulting phenotypes in the agl12 mutant, complementary line, and overexpressed line underscored VvAGL12's ability to promote early flowering, augment plant growth, and enhance production. This was evident from the improved fresh weight, root length, plant height, and seed production, as well as the reduced flowering time. Subsequent transcriptome analysis revealed significant alterations in the expression of genes associated with cell-wall modification and flowering in the transgenic plants. In summary, the findings highlight VvAGL12's pivotal role in the regulation of flowering timing, overall plant growth, and development. This study offers valuable insights, serving as a reference for understanding the influence of the VvAGL12 gene in other plant species and addressing yield-related challenges.
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Affiliation(s)
- Tingting Mao
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Xueting Wang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Hongsheng Gao
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Zijian Gong
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Ruichao Liu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Ning Jiang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Yaru Zhang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Hongxia Zhang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, 21 Zhichubei Road, Yantai 264001, China
| | - Xiaotong Guo
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Chunyan Yu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
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Wang W, Zhang X, Xu X, Xu X, Fu L, Chen H. Systematic identification of reference genes for qRT-PCR of Ardisia kteniophylla A. DC under different experimental conditions and for anthocyanin-related genes studies. FRONTIERS IN PLANT SCIENCE 2023; 14:1284007. [PMID: 38023897 PMCID: PMC10656778 DOI: 10.3389/fpls.2023.1284007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
Ardisia kteniophylla A. DC, widely known as folk medicinal herb and ornamental plant, has been extensively investigated due to its unique leaf color, anti-cancer and other pharmacological activities. The quantitative real-time PCR (qRT-PCR) was an excellent tool for the analysis of gene expression with its high sensitivity and quantitative properties. Normalizing gene expression with stable reference genes was essential for qRT-PCR accuracy. In addition, no studies have yet been performed on the selection, verification and stability of internal reference genes suitable for A. kteniophylla, which has greatly hindered the biomolecular researches of this species. In this study, 29 candidate genes were successfully screened according to stable expression patterns of large-scale RNA seq data that from a variety of tissues and the roots of different growth stages in A. kteniophylla. The candidates were then further determined via qRT-PCR in various experimental samples, including MeJA, ABA, SA, NaCl, CuSO4, AgNO3, MnSO4, CoCl2, drought, low temperature, heat, waterlogging, wounding and oxidative stress. To assess the stability of the candidates, five commonly used strategies were employed: delta-CT, geNorm, BestKeeper, NormFinder, and the comprehensive tool RefFinder. In summary, UBC2 and UBA1 were found to be effective in accurately normalizing target gene expression in A. kteniophella regardless of experimental conditions, while PP2A-2 had the lowest stability. Additionally, to verify the reliability of the recommended reference genes under different colored leaf samples, we examined the expression patterns of six genes associated with anthocyanin synthesis and regulation. Our findings suggested that PAP1 and ANS3 may be involved in leaf color change in A. kteniphella. This study successfully identified the ideal reference gene for qRT-PCR analysis in A. kteniphella, providing a foundation for future research on gene function, particularly in the biosynthesis of anthocyanins.
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Affiliation(s)
- Wentao Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Modern Agricultural Sciences, University of Chinese Acadamy of Science, Beijing, China
| | - Xiaohang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Modern Agricultural Sciences, University of Chinese Acadamy of Science, Beijing, China
| | - Xiaoxia Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Modern Agricultural Sciences, University of Chinese Acadamy of Science, Beijing, China
| | - Xingchou Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Life Science, Gannan Normal University, Ganzhou, China
| | - Lin Fu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hongfeng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Chen J, Wang Y, Yang Z, Liu D, Jin Y, Li X, Deng Y, Wang B, Zhang Z, Ma Y. Identification and validation of the reference genes in the echiuran worm Urechis unicinctus based on transcriptome data. BMC Genomics 2023; 24:248. [PMID: 37165306 PMCID: PMC10170059 DOI: 10.1186/s12864-023-09358-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Real-time quantitative PCR (RT-qPCR) is a crucial and widely used method for gene expression analysis. Selecting suitable reference genes is extremely important for the accuracy of RT-qPCR results. Commonly used reference genes are not always stable in various organisms or under different environmental conditions. With the increasing application of high-throughput sequencing, transcriptome analysis has become an effective method for identifying novel stable reference genes. RESULTS In this study, we identified candidate reference genes based on transcriptome data covering embryos and larvae of early development, normal adult tissues, and the hindgut under sulfide stress using the coefficient of variation (CV) method in the echiuran Urechis unicinctus, resulting in 6834 (15.82%), 7110 (16.85%) and 13880 (35.87%) candidate reference genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the candidate reference genes were significantly enriched in cellular metabolic process, protein metabolic process and ribosome in early development and normal adult tissues as well as in cellular localization and endocytosis in the hindgut under sulfide stress. Subsequently, ten genes including five new candidate reference genes and five commonly used reference genes, were validated by RT-qPCR. The expression stability of the ten genes was analyzed using four methods (geNorm, NormFinder, BestKeeper, and ∆Ct). The comprehensive results indicated that the new candidate reference genes were more stable than most commonly used reference genes. The commonly used ACTB was the most unstable gene. The candidate reference genes STX12, EHMT1, and LYAG were the most stable genes in early development, normal adult tissues, and hindgut under sulfide stress, respectively. The log2(TPM) of the transcriptome data was significantly negatively correlated with the Ct values of RT-qPCR (Ct = - 0.5405 log2(TPM) + 34.51), which made it possible to estimate the Ct value before RT-qPCR using transcriptome data. CONCLUSION Our study is the first to select reference genes for RT-qPCR from transcriptome data in Echiura and provides important information for future gene expression studies in U. unicinctus.
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Affiliation(s)
- Jiao Chen
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunjian Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhi Yang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Danwen Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yao Jin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xixi Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuhang Deng
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Boya Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
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Hämälä T, Ning W, Kuittinen H, Aryamanesh N, Savolainen O. Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata. eLife 2022; 11:83115. [PMID: 36306157 PMCID: PMC9616567 DOI: 10.7554/elife.83115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding what factors influence plastic and genetic variation is valuable for predicting how organisms respond to changes in the selective environment. Here, using gene expression and DNA methylation as molecular phenotypes, we study environmentally induced variation among Arabidopsis lyrata plants grown at lowland and alpine field sites. Our results show that gene expression is highly plastic, as many more genes are differentially expressed between the field sites than between populations. These environmentally responsive genes evolve under strong selective constraint – the strength of purifying selection on the coding sequence is high, while the rate of adaptive evolution is low. We find, however, that positive selection on cis-regulatory variants has likely contributed to the maintenance of genetically variable environmental responses, but such variants segregate only between distantly related populations. In contrast to gene expression, DNA methylation at genic regions is largely insensitive to the environment, and plastic methylation changes are not associated with differential gene expression. Besides genes, we detect environmental effects at transposable elements (TEs): TEs at the high-altitude field site have higher expression and methylation levels, suggestive of a broad-scale TE activation. Compared to the lowland population, plants native to the alpine environment harbor an excess of recent TE insertions, and we observe that specific TE families are enriched within environmentally responsive genes. Our findings provide insight into selective forces shaping plastic and genetic variation. We also highlight how plastic responses at TEs can rapidly create novel heritable variation in stressful conditions.
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Affiliation(s)
- Tuomas Hämälä
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Weixuan Ning
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Helmi Kuittinen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Nader Aryamanesh
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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Cheng SS, Ku YS, Cheung MY, Lam HM. Identification of stably expressed reference genes for expression studies in Arabidopsis thaliana using mass spectrometry-based label-free quantification. FRONTIERS IN PLANT SCIENCE 2022; 13:1001920. [PMID: 36247637 PMCID: PMC9557097 DOI: 10.3389/fpls.2022.1001920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Arabidopsis thaliana has been used regularly as a model plant in gene expression studies on transcriptional reprogramming upon pathogen infection, such as that by Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), or when subjected to stress hormone treatments including jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA). Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) has been extensively employed to quantitate these gene expression changes. However, the accuracy of the quantitation is largely dependent on the stability of the expressions of reference genes used for normalization. Recently, RNA sequencing (RNA-seq) has been widely used to mine stably expressed genes for use as references in RT-qPCR. However, the amplification step in RNA-seq creates an intrinsic bias against those genes with relatively low expression levels, and therefore does not provide an accurate quantification of all expressed genes. In this study, we employed mass spectrometry-based label-free quantification (LFQ) in proteomic analyses to identify those proteins with abundances unaffected by Pst DC3000 infection. We verified, using RT-qPCR, that the levels of their corresponding mRNAs were also unaffected by Pst DC3000 infection. Compared to commonly used reference genes for expression studies in A. thaliana upon Pst DC3000 infection, the candidate reference genes reported in this study generally have a higher expression stability. In addition, using RT-qPCR, we verified that the mRNAs of the candidate reference genes were stably expressed upon stress hormone treatments including JA, SA, and ABA. Results indicated that the candidate genes identified here had stable expressions upon these stresses and are suitable to be used as reference genes for RT-qPCR. Among the 18 candidate reference genes reported in this study, many of them had greater expression stability than the commonly used reference genes, such as ACT7, in previous studies. Here, besides proposing more appropriate reference genes for Arabidopsis expression studies, we also demonstrated the capacity of mass spectrometry-based LFQ to quantify protein abundance and the possibility to extend protein expression studies to the transcript level.
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Calvo‐Baltanás V, De Jaeger‐Braet J, Cher WY, Schönbeck N, Chae E, Schnittger A, Wijnker E. Knock-down of gene expression throughout meiosis and pollen formation by virus-induced gene silencing in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:19-37. [PMID: 35340073 PMCID: PMC9543169 DOI: 10.1111/tpj.15733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Through the inactivation of genes that act during meiosis it is possible to direct the genetic make-up of plants in subsequent generations and optimize breeding schemes. Offspring may show higher recombination of parental alleles resulting from elevated crossover (CO) incidence, or by omission of meiotic divisions, offspring may become polyploid. However, stable mutations in genes essential for recombination, or for either one of the two meiotic divisions, can have pleiotropic effects on plant morphology and line stability, for instance by causing lower fertility. Therefore, it is often favorable to temporarily change gene expression during meiosis rather than relying on stable null mutants. It was previously shown that virus-induced gene silencing (VIGS) can be used to transiently reduce CO frequencies. We asked if VIGS could also be used to modify other processes throughout meiosis and during pollen formation in Arabidopsis thaliana. Here, we show that VIGS-mediated knock-down of FIGL1, RECQ4A/B, OSD1 and QRT2 can induce (i) an increase in chiasma numbers, (ii) unreduced gametes and (iii) pollen tetrads. We further show that VIGS can target both sexes and different genetic backgrounds and can simultaneously silence different gene copies. The successful knock-down of these genes in A. thaliana suggests that VIGS can be exploited to manipulate any process during or shortly after meiosis. Hence, the transient induction of changes in inheritance patterns can be used as a powerful tool for applied research and biotechnological applications.
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Affiliation(s)
- Vanesa Calvo‐Baltanás
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6700 AAthe Netherlands
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Joke De Jaeger‐Braet
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Wei Yuan Cher
- A*STAR, Institute of Molecular and Cell Biology (IMCB)61 Biopolis DriveProteos138673Singapore
| | - Nils Schönbeck
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
- UKEMartinistrasse 5220251HamburgGermany
| | - Eunyoung Chae
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Arp Schnittger
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Erik Wijnker
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6700 AAthe Netherlands
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Fan H, He Q, Dong Y, Xu W, Lou Y, Hua X, Xu T. Selection of suitable candidate genes for mRNA expression normalization in bulbil development of Pinellia ternata. Sci Rep 2022; 12:8849. [PMID: 35614175 PMCID: PMC9133075 DOI: 10.1038/s41598-022-12782-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/03/2022] [Indexed: 11/09/2022] Open
Abstract
Pinellia ternata (Thunb.) Breit. (Abbreviated as P. ternata). It is a commonly prescribed Chinese traditional medicinal herb for the treatment of phlegm, cough, and morning sick. Bulbil reproduction is one of the main reproductive methods of P. ternata. The accurate quantification of gene expression patterns associated with bulbil development might be helpful to explore the molecular mechanism involved in P. ternata reproduction. Quantitative real-time PCR was the most preferred method for expression profile and function analysis of mRNA. However, the reference genes in different tissues of P. ternata in different periods of bulbil development have not been studied in detail. In present study, the expression stability of eight candidate reference genes were determined with programs: geNorm, NormFinder, BestKeeper, and refFinder. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was identified as the top- rated reference gene in all samples of P. ternata, while different combinations of reference gene proved to be the most stable depending on development stage and tissue type. Furthermore, the reliability of GAPDH expression was verified by six P. ternata related genes in hormone and nutrient biosynthesis pathways, and the expression profiles of these genes were agreed with the results of RNA-seq digital gene expression analysis. These results can contribute to studies of gene expression patterns and functional analysis of P. ternata involved in bulbil development.
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Affiliation(s)
- Haoyu Fan
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Qiuling He
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China.
| | - Yiheng Dong
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Wenxin Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yanlin Lou
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xuejun Hua
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Tao Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China.
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Municio C, Antosz W, Grasser KD, Kornobis E, Van Bel M, Eguinoa I, Coppens F, Bräutigam A, Lermontova I, Bruckmann A, Zelkowska K, Houben A, Schubert V. The Arabidopsis condensin CAP-D subunits arrange interphase chromatin. THE NEW PHYTOLOGIST 2021; 230:972-987. [PMID: 33475158 DOI: 10.1111/nph.17221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Condensins are best known for their role in shaping chromosomes. Other functions such as organizing interphase chromatin and transcriptional control have been reported in yeasts and animals, but little is known about their function in plants. To elucidate the specific composition of condensin complexes and the expression of CAP-D2 (condensin I) and CAP-D3 (condensin II), we performed biochemical analyses in Arabidopsis. The role of CAP-D3 in interphase chromatin organization and function was evaluated using cytogenetic and transcriptome analysis in cap-d3 T-DNA insertion mutants. CAP-D2 and CAP-D3 are highly expressed in mitotically active tissues. In silico and pull-down experiments indicate that both CAP-D proteins interact with the other condensin I and II subunits. In cap-d3 mutants, an association of heterochromatic sequences occurs, but the nuclear size and the general histone and DNA methylation patterns remain unchanged. Also, CAP-D3 influences the expression of genes affecting the response to water, chemicals, and stress. The expression and composition of the condensin complexes in Arabidopsis are similar to those in other higher eukaryotes. We propose a model for the CAP-D3 function during interphase in which CAP-D3 localizes in euchromatin loops to stiffen them and consequently separates centromeric regions and 45S rDNA repeats.
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Affiliation(s)
- Celia Municio
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Wojciech Antosz
- Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Klaus D Grasser
- Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Etienne Kornobis
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, 75015, Paris, France
- Hub de Bioinformatique et Biostatistique -Département Biologie Computationnelle, Institut Pasteur, 75015, Paris, France
| | - Michiel Van Bel
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, 9052, Gent, Belgium
| | - Ignacio Eguinoa
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, 9052, Gent, Belgium
| | - Frederik Coppens
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, 9052, Gent, Belgium
| | - Andrea Bräutigam
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, CZ-62500, Czech Republic
| | - Astrid Bruckmann
- Department for Biochemistry I, Biochemistry Center, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Katarzyna Zelkowska
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
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Wang W, Hu S, Cao Y, Chen R, Wang Z, Cao X. Selection and evaluation of reference genes for qRT-PCR of Scutellaria baicalensis Georgi under different experimental conditions. Mol Biol Rep 2021; 48:1115-1126. [PMID: 33511512 PMCID: PMC7842394 DOI: 10.1007/s11033-021-06153-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/12/2021] [Indexed: 10/28/2022]
Abstract
Scutellaria baicalensis Georgi is a famous medicinal plant with its dried roots having been used as a traditional Chinese medicinal for more than 2000 years. Although its genome sequence has previously been published and molecular biology methods have been used to study this species, no suitable internal reference genes have been investigated for standardization of gene expression via quantitative real-time polymerase chain reaction (qRT-PCR). Here, the stabilities of 10 candidate reference genes, ACT11, ACT7, α-TUB, β-TUB, GAPDH, UBC, RPL, SAM, HSP70, and PP2A, were analyzed by four different procedures of GeNorm, NormFinder, BestKeeper, and RefFinder. Their expression stabilities were evaluated under various conditions, including different tissue types (root, stem, leaf, and flower), hormone stimuli treatments (methyl jasmonate, salicylic acid, and abscisic acid), and abiotic stresses (heavy metal, salt, drought, cold, and wounding). The results indicated that β-TUB was the most stable gene for all tested samples, while ACT11 was the most unstable. The most stable reference gene was not consistent under different conditions. β-TUB exhibited the highest stability for different tissue types and abiotic stresses, while for hormone stimuli treatments, ACT7 showed the highest stability. To confirm the applicability of suitable reference genes, we selected to SbF6H and SbF8H as target genes to analyze their expression levels in different tissues. This study helps to the accurate quantification of the relative expression levels of interest genes in S. baicalensis via qRT-PCR analysis.
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Affiliation(s)
- Wentao Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China
| | - Suying Hu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China
| | - Yao Cao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China
| | - Rui Chen
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China
| | - Zhezhi Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China.
| | - Xiaoyan Cao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China.
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10
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Calvo‐Baltanás V, Wijnen CL, Yang C, Lukhovitskaya N, de Snoo CB, Hohenwarter L, Keurentjes JJB, de Jong H, Schnittger A, Wijnker E. Meiotic crossover reduction by virus-induced gene silencing enables the efficient generation of chromosome substitution lines and reverse breeding in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1437-1452. [PMID: 32955759 PMCID: PMC7756339 DOI: 10.1111/tpj.14990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 08/11/2020] [Accepted: 08/19/2020] [Indexed: 05/16/2023]
Abstract
Plant breeding applications exploiting meiotic mutant phenotypes (like the increase or decrease of crossover (CO) recombination) have been proposed over the last years. As recessive meiotic mutations in breeding lines may affect fertility or have other pleiotropic effects, transient silencing techniques may be preferred. Reverse breeding is a breeding technique that would benefit from the transient downregulation of CO formation. The technique is essentially the opposite of plant hybridization: a method to extract parental lines from a hybrid. The method can also be used to efficiently generate chromosome substitution lines (CSLs). For successful reverse breeding, the two homologous chromosome sets of a heterozygous plant must be divided over two haploid complements, which can be achieved by the suppression of meiotic CO recombination and the subsequent production of doubled haploid plants. Here we show the feasibility of transiently reducing CO formation using virus-induced gene silencing (VIGS) by targeting the meiotic gene MSH5 in a wild-type heterozygote of Arabidopsis thaliana. The application of VIGS (rather than using lengthy stable transformation) generates transgene-free offspring with the desired genetic composition: we obtained parental lines from a wild-type heterozygous F1 in two generations. In addition, we obtained 20 (of the 32 possible) CSLs in one experiment. Our results demonstrate that meiosis can be modulated at will in A. thaliana to generate CSLs and parental lines rapidly for hybrid breeding. Furthermore, we illustrate how the modification of meiosis using VIGS can open routes to develop efficient plant breeding strategies.
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Affiliation(s)
- Vanesa Calvo‐Baltanás
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
- Present address:
Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Cris L. Wijnen
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Chao Yang
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
- Department of Developmental BiologyInstitut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Nina Lukhovitskaya
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
- Centre National de la Recherche ScientifiqueInstitut de Biologie Moléculaire des PlantesUniversité de Strasbourg12, rue du général ZimmerStrasbourg67084France
- Present address:
Division of VirologyDepartment of PathologyUniversity of CambridgeTennis Court RdCambridgeCB2 1QPUK
| | - C. Bastiaan de Snoo
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
- Rijk Zwaan R&D FijnaartEerste Kruisweg 9Fijnaart4793 RSthe Netherlands
| | - Linus Hohenwarter
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
- Department of Developmental BiologyInstitut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Joost J. B. Keurentjes
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Hans de Jong
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Arp Schnittger
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
- Department of Developmental BiologyInstitut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Erik Wijnker
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
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11
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Yang J, Yang X, Kuang Z, Li B, Lu X, Cao X, Kang J. Selection of suitable reference genes for qRT-PCR expression analysis of Codonopsis pilosula under different experimental conditions. Mol Biol Rep 2020; 47:4169-4181. [PMID: 32410139 DOI: 10.1007/s11033-020-05501-8] [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: 10/05/2019] [Accepted: 05/06/2020] [Indexed: 11/28/2022]
Abstract
Codonopsis pilosula is a well-known medicinal plant. Although its transcriptome sequence has been published, suitable reference genes have not been systematically identified for conducting expression analyses via quantitative real-time polymerase chain reaction (qRT-PCR). To screen appropriate genes for use with this species, we applied four different methods-GeNorm, NormFinder, BestKeeper, and RefFinder-to evaluate the stability of 13 candidates: CpiEF1Bb, CpiCACS, CpiF-Box, Cpiβ-Tubulin, CpiGAPDH, CpiActin2, CpiAPT1, CpiActin7, CpiActin8, CpiRPL6, CpiHAF1, CpiTubulin6, and CpiUBQ12. Expression was examined by qRT-PCR for various tissue types, chemical treatments, and developmental stages. For all tested samples, CpiGAPDH proved to be the most stable. Comprehensive analysis indicated that the most stable internal reference genes were CpiF-Box and CpiCACS in different tissues and at different developmental stages, respectively. Under NaCl stress, CpiAPT1 was the best internal reference gene. For methyl jasmonate and abscisic acid treatments, CpiGAPDH and CpiF-Box, respectively, presented the highest degree of expression stability. Based on these findings, we chose CpiSPL9 as the target gene for validating the suitability of these selected reference genes. All of these results provide a foundation for accurate quantification of expression levels by genes of interest in C. pilosula.
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Affiliation(s)
- Jing Yang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an, 710062, China.,Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiaozeng Yang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Zheng Kuang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Bin Li
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an, 710062, China
| | - Xiayang Lu
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an, 710062, China.,Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiaoyan Cao
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an, 710062, China.
| | - Jiefang Kang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an, 710062, China.
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12
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Long X, Lu J, Kav NNV, Qin Y, Fang Y. Identification and evaluation of suitable reference genes for gene expression analysis in rubber tree leaf. Mol Biol Rep 2020; 47:1921-1933. [PMID: 32020426 DOI: 10.1007/s11033-020-05288-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/28/2020] [Indexed: 10/25/2022]
Abstract
Gene expression profiles are increasingly applied to investigate molecular mechanism for which, normalization with suitable reference genes is critical. Previously we have reported several suitable reference genes for laticifer samples from rubber tree, however, little is known in leaf. The main objective of this current study was to identify some stable expression reference genes at various developmental stages of leaf, as well as during abiotic (high and low temperature extremes) and biotic stresses (pathogen stress). Gene expression profilings identified the ubiquitin-proteasome system as excellent potential as reference genes for rubber tree leaf. Among a total of 30 tested genes investigated, 24 new candidate (including 11 genes involved in the ubiquitin-proteasome system), 4 previously identified and 2 specific genes, were further evaluated using quantitative real-time PCR. Our results indicated that the new candidate genes had better expression stability comparing with others. For instance, an ubiquitin conjugating enzyme (RG0099) and three ubiquitin-protein ligases (RG0928, RG2190 and RG0118) expressed stably in all samples, and were confirmed to be suitable reference genes for rubber tree leaf under four different conditions. Finally, we suggest that using more than one reference gene may be appropriate in gene expression studies when employing different software to normalize gene expression data. Our findings have significant implications for the reliability of data obtained from genomics studies in rubber tree and perhaps in other species.
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Affiliation(s)
- Xiangyu Long
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
| | - Jilai Lu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.,College of Forestry, Hainan University, Haikou, 570228, Hainan, China
| | - Nat N V Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G 2P5, Canada
| | - Yunxia Qin
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Yongjun Fang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
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13
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Du W, Hu F, Yuan S, Liu C. Selection of reference genes for quantitative real-time PCR analysis of photosynthesis-related genes expression in Lilium regale. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:1497-1506. [PMID: 31736551 PMCID: PMC6825105 DOI: 10.1007/s12298-019-00707-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/08/2019] [Accepted: 08/20/2019] [Indexed: 05/05/2023]
Abstract
Photosynthesis is closely related to the growth of plants. A stable reference gene is fundamental for studies of the molecular mechanism of photosynthesis in Lilium regale. Therefore, it is very important to select a suitable reference gene for qRT-PCR analysis on genes of photosynthetic system, chlorophyll biosynthetic pathway and chloroplast development in Lilium regale. Three kinds of tissues, leaves and bulbs (abnormal leaves) of tissue culture plantlets and cotyledons of seedlings of the wild-type and mutant Lilium regale were selected as materials for qRT-PCR. Six housekeeping genes were selected as candidate genes from transcriptome sequencing data of the wild-type and yellow seedling lethal mutant of Lilium regale. Finally, the expression stability of six candidate reference genes was analyzed using geNorm, NormFinder, and BestKeeper software, the comparative ∆Ct method, and the RefFinder program. The results showed that LrActin2 was the best reference gene for qRT-PCR analysis of photosynthesis-related genes expression in leaves of tissue culture plantlets and seedlings of Lilium regale. This study provided useful data for further research on molecular mechanism of photosynthesis in the Lilium.
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Affiliation(s)
- Wenkai Du
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037 China
| | - Fengrong Hu
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037 China
| | - Suxia Yuan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Chun Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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14
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Nguyen KL, Grondin A, Courtois B, Gantet P. Next-Generation Sequencing Accelerates Crop Gene Discovery. TRENDS IN PLANT SCIENCE 2019; 24:263-274. [PMID: 30573308 DOI: 10.1016/j.tplants.2018.11.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 05/22/2023]
Abstract
The identification and isolation of genes underlying quantitative trait loci (QTLs) associated with agronomic traits in crops have been recently accelerated thanks to next-generation sequencing (NGS)-based technologies combined with plant genetics. With NGS, various revisited genetic approaches, which benefited from higher marker density, have been elaborated. These approaches improved resolution in QTL position and assisted in determining functional causative variations in genes. Examples of QTLs/genes associated with agronomic traits in crops and identified using different strategies based on whole-genome sequencing (WGS)/whole-genome resequencing (WGR) or RNA-seq are presented and discussed in this review. More specifically, we summarize and illustrate how NGS boosted bulk-segregant analysis (BSA), expression profiling, and the construction of polymorphism databases to facilitate the detection of QTLs and causative genes.
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Affiliation(s)
- Khanh Le Nguyen
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France; LMI RICE 2, AGI, Km2 Pham Van Dong, Tu Liem, Hanoi, Vietnam
| | - Alexandre Grondin
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France
| | - Brigitte Courtois
- CIRAD, UMR AGAP, F-34398 Montpellier, France; Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Pascal Gantet
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France; Centre of the Region Haná for Biotechnological and Agricultural Research, Dept. of Molecular Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic.
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15
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Zhang C, Zheng H, Wu X, Xu H, Han K, Peng J, Lu Y, Lin L, Xu P, Wu X, Li G, Chen J, Yan F. Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria. PeerJ 2018; 6:e5642. [PMID: 30345167 PMCID: PMC6188008 DOI: 10.7717/peerj.5642] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/27/2018] [Indexed: 01/07/2023] Open
Abstract
Lagenaria siceraria is an economically important cucurbitaceous crop, but suitable reference genes (RGs) to use when the plants are infected by cucumber green mottle mosaic virus (CGMMV) have not been determined. Sixteen candidate RGs of both leaf and fruit and 18 candidate RGs mostly from separate RNA-Seq datasets of bottle gourd leaf or fruit were screened and assessed by RT-qPCR. The expression stability of these genes was determined and ranked using geNorm, NormFinder, BestKeeper and RefFinder. Comprehensive analysis resulted in the selection of LsCYP, LsH3, and LsTBP as the optimal RGs for bottle gourd leaves, and LsP4H, LsADP, and LsTBP for fruits. LsWD, LsGAPDH, and LsH3 were optimal for use in both leaves and fruits under the infection of CGMMV. Isopentenyl transferase (IPT) and DNA-directed RNA polymerase (DdRP) were used to validate the applicability of the most stable identified RGs from bottle gourd in response to CGMMV. All the candidate RGs performed in RT-qPCR consistently with the data from the transcriptome database. The results demonstrated that LsWD, LsGAPDH and LsH3 were the most suitable internal RGs for the leaf, and LsH3, LsGAPDH, LsP4H and LsCYP for the fruit.
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Affiliation(s)
- Chenhua Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongying Zheng
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyang Wu
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Heng Xu
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Kelei Han
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiejun Peng
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuwen Lu
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lin Lin
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Pei Xu
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaohua Wu
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guojing Li
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jianping Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fei Yan
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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16
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Pfab A, Breindl M, Grasser KD. The Arabidopsis histone chaperone FACT is required for stress-induced expression of anthocyanin biosynthetic genes. PLANT MOLECULAR BIOLOGY 2018; 96:367-374. [PMID: 29332189 DOI: 10.1007/s11103-018-0701-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/10/2018] [Indexed: 05/06/2023]
Abstract
The histone chaperone FACT is involved in the expression of genes encoding anthocyanin biosynthetic enzymes also upon induction by moderate high-light and therefore contributes to the stress-induced plant pigmentation. The histone chaperone FACT consists of the SSRP1 and SPT16 proteins and associates with transcribing RNAPII (RNAPII) along the transcribed region of genes. FACT can promote transcriptional elongation by destabilising nucleosomes in the path of RNA polymerase II, thereby facilitating efficient transcription of chromatin templates. Transcript profiling of Arabidopsis plants depleted in SSRP1 or SPT16 demonstrates that only a small subset of genes is differentially expressed relative to wild type. The majority of these genes is either up- or down-regulated in both the ssrp1 and spt16 plants. Among the down-regulated genes, those encoding enzymes of the biosynthetic pathway of the plant secondary metabolites termed anthocyanins (but not regulators of the pathway) are overrepresented. Upon exposure to moderate high-light stress several of these genes are up-regulated to a lesser extent in ssrp1/spt16 compared to wild type plants, and accordingly the mutant plants accumulate lower amounts of anthocyanin pigments. Moreover, the expression of SSRP1 and SPT16 is induced under these conditions. Therefore, our findings indicate that FACT is a novel factor required for the accumulation of anthocyanins in response to light-induction.
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Affiliation(s)
- Alexander Pfab
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Matthias Breindl
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany.
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17
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Reference gene identification and validation for quantitative real-time PCR studies in developing Xenopus laevis. Sci Rep 2018; 8:496. [PMID: 29323148 PMCID: PMC5764961 DOI: 10.1038/s41598-017-18684-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/11/2017] [Indexed: 01/25/2023] Open
Abstract
Reference genes are essential for gene expression analysis when using real-time quantitative PCR (RT-qPCR). Xenopus laevis is a popular amphibian model for studying vertebrate embryogenesis and development. Further, X. laevis is ideal for studying thyroid signaling due to its thyroid dependent metamorphosis, a stage comparable to birth in humans. When using PCR based studies, a primary concern is the choice of reference genes. Commonly used references are eef1a1, odc1, rpl8, and actnB, although there is a lack of ad hoc reference genes for X. laevis. Here, we used previously published RNA-seq data on different X. laevis stages and identified the top 14 candidate genes with respect to their expression levels as a function of developmental stage and degree of variation. We further evaluated the stability of these and other candidate genes using RT-qPCR on various stages including the unfertilised eggs, whole embryos during early development and brains during late development. We used four different statistical software packages: deltaCT, geNorm, NormFinder and BestKeeper. We report optimized reference gene pair combinations for studying development (early whole embryos), brains at later stages (metamorphosis and adult), and thyroid signalling. These reference gene pairs are suitable for studying different aspects of X. laevis development and organogenesis.
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18
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Nakamura Y, Kudo T, Terashima S, Saito M, Nambara E, Yano K. CATchUP: A Web Database for Spatiotemporally Regulated Genes. PLANT & CELL PHYSIOLOGY 2017; 58:e3. [PMID: 28013273 DOI: 10.1093/pcp/pcw199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 11/06/2016] [Indexed: 06/06/2023]
Abstract
For proper control of biological activity, some key genes are highly expressed in a particular spatiotemporal domain. Mining of such spatiotemporally expressed genes using large-scale gene expression data derived from a broad range of experimental sources facilitates our understanding of genome-scale functional gene networks. However, comprehensive information on spatiotemporally expressed genes is lacking in plants. To collect such information, we devised a new index, Δdmax, which is the maximum difference in relative gene expression levels between sample runs which are neighboring when sorted by the levels. Employing this index, we comprehensively evaluated transcripts using large-scale RNA sequencing (RNA-Seq) data stored in the Sequence Read Archive for eight plant species: Arabidopsis thaliana (Arabidopsis), Solanum lycopersicum (tomato), Solanum tuberosum (potato), Oryza sativa (rice), Sorghum bicolor (sorghum), Vitis vinifera (grape), Medicago truncatula (Medicago), and Glycine max (soybean). Based on the frequency distribution of the Δdmax values, approximately 70,000 transcripts showing 0.3 or larger Δdmax values were extracted for the eight species. Information on these genes including the Δdmax values, functional annotations, conservation among species, and experimental conditions where the genes show high expression levels is provided in a new database, CATchUP (http://plantomics.mind.meiji.ac.jp/CATchUP). The CATchUP database assists in identifying genes specifically expressed under particular conditions with powerful search functions and an intuitive graphical user interface.
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Affiliation(s)
- Yukino Nakamura
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Toru Kudo
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Shin Terashima
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Misa Saito
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Eiji Nambara
- Department of Cell & Systems Biology, University of Toronto, Willcocks Street, Toronto, Ontario, Canada
| | - Kentaro Yano
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
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