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Bottino-Rojas V, James AA. Mosquito Transposon-Mediated Transgenesis. Cold Spring Harb Protoc 2024; 2024:pdb.top107687. [PMID: 37816607 PMCID: PMC11025883 DOI: 10.1101/pdb.top107687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Transposon-mediated transgenesis of mosquito vectors of disease pathogens followed the early success of transgenesis in the vinegar fly, Drosophila melanogaster The P transposable element used in Drosophila does not function canonically in mosquitoes, and repeatable, routine transgenesis in mosquitoes was not accomplished until new transposable elements were discovered and validated. A number of distinct transposons were subsequently identified that mediate the introduction of exogenous DNA in a stable and heritable manner in mosquito species, including members of the genera Aedes, Anopheles, and Culex The most versatile element, piggyBac, is functional in all of these mosquito genera, as well as in many other insects in diverse orders, and has been used extensively outside the class. Transposon-mediated transgenesis of recessive and dominant marker genes and reporter systems has been used to define functional fragments of gene control sequences, introduce exogenous DNA encoding products beneficial to medical interests, and act as "enhancer traps" to identify endogenous genes with specific expression characteristics.
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Affiliation(s)
- Vanessa Bottino-Rojas
- Department of Microbiology and Molecular Genetics, University of California, Irvine, California 92697-4500, USA
| | - Anthony A James
- Department of Microbiology and Molecular Genetics, University of California, Irvine, California 92697-4500, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA
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de Souza MR, Araújo IP, da Costa Arruda W, Lima AA, Ságio SA, Chalfun-Junior A, Barreto HG. RGeasy: a reference gene analysis tool for gene expression studies via RT-qPCR. BMC Genomics 2024; 25:907. [PMID: 39350049 PMCID: PMC11441100 DOI: 10.1186/s12864-024-10808-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 09/17/2024] [Indexed: 10/04/2024] Open
Abstract
Gene expression through RT-qPCR can be performed by the relative quantification method, which requires the expression normalization through reference genes. Therefore, it is essential to validate, experimentally, the candidate reference genes. Thus, although there are several studies that are performed to identify the most stable reference genes, most them validate genes for very specific conditions, not exploring the whole potential of the research since not all possible combinations of treatments and/or conditions of the study are explored. For this reason, new experiments must be conducted by researchers that have interest in analyzing gene expression of treatments and/or conditions present, but not explored, in these studies. Here, we present the RGeasy tool, which aims to facilitate the selection of reference genes, allowing the user to choose genes for a greater number of combinations of treatments/conditions, compared to the ones present in the original articles, through just a few clicks. RGeasy was validated with RT-qPCR data from gene expression studies performed in two coffee species, Coffea arabica and Coffea canephora, and it can be used for any animal, plant or microorganism species. In addition to displaying a rank of the most stable reference genes for each condition or treatment, the user also has access to the primer pairs for the selected reference genes.
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Affiliation(s)
- Micaele Rodrigues de Souza
- Laboratory of Molecular Analysis (LAM), Department of Life Sciences, Federal University of Tocantins, UFT, University Campus of Palmas, Palmas, TO, 402-970, Brazil
| | - Ivo Pontes Araújo
- Computer Science Course, Federal University of Tocantins, University Campus of Palmas, Palmas, TO, Brazil
| | - Wosley da Costa Arruda
- Computer Science Course, Federal University of Tocantins, University Campus of Palmas, Palmas, TO, Brazil
| | - André Almeida Lima
- Laboratory of Plant Molecular Physiology, Department of Biology, Federal University of Lavras, Lavras, MG, Brazil
| | - Solange Aparecida Ságio
- Laboratory of Molecular Analysis (LAM), Department of Life Sciences, Federal University of Tocantins, UFT, University Campus of Palmas, Palmas, TO, 402-970, Brazil
| | - Antonio Chalfun-Junior
- Laboratory of Plant Molecular Physiology, Department of Biology, Federal University of Lavras, Lavras, MG, Brazil
| | - Horllys Gomes Barreto
- Laboratory of Molecular Analysis (LAM), Department of Life Sciences, Federal University of Tocantins, UFT, University Campus of Palmas, Palmas, TO, 402-970, Brazil.
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Liu Y, Shi W, Zhang D. Development and evaluation of suitable reference genes for qRT-PCR normalization of hybrids derived from Lycium barbarum and Lycium ruthenicum. Mol Biol Rep 2024; 51:922. [PMID: 39162931 DOI: 10.1007/s11033-024-09848-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/30/2024] [Indexed: 08/21/2024]
Abstract
BACKGROUND A correct and stably expressing reference gene is prerequisite for successful quantitative real-time PCR (qRT-PCR). Investigating gene expression profiling during flower development could enhance our understanding of the molecular mechanisms of flower formation and fertility in Lycium. METHODS AND RESULTS In this study, 11 candidate reference genes in Lycium flower development were selected from transcriptome sequence data and evaluated with five traditional housekeeping genes from previous studies based on qRT-PCR amplification. Comparing the expression stability result of 16 candidate genes using GeNorm, NormFinder, BestKeeper, and Delta Ct algorithms, Lba04g01649 and Lba12g02820 were validated as the optimal reference genes for the flower development of Lycium. CONCLUSIONS The reference genes identified in this study would improve the accuracy of qRT-PCR quantification of target gene expression in Lycium flower development and facilitate future functional genomics studies on flower development. This research could lay the foundation for the study of the reproduction and development of the Lycium flower.
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Affiliation(s)
- Yu Liu
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, China
| | - Wenjun Shi
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, China
- Laboratory for Research and Utilization of Germplasm Resources on the Qinghai-Tibet Plateau, Xining, 810016, China
- Key Laboratory of Tree Genetics and Breeding of Qinghai Plateau, National Forestry and Grassland Administration, Xining, 810016, China
| | - Defang Zhang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, China.
- Laboratory for Research and Utilization of Germplasm Resources on the Qinghai-Tibet Plateau, Xining, 810016, China.
- Key Laboratory of Tree Genetics and Breeding of Qinghai Plateau, National Forestry and Grassland Administration, Xining, 810016, China.
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Rashid Z, Nabi A, Nabi N, Lateef I, Nisa Q, Fayaz T, Gulzar G, Bashir A, Shah MD, Zargar SM, Khan I, Nahvi AI, Itoo H, Shah RA, Padder BA. Selection of stable reference genes for qPCR expression of Colletotrichum lindemuthianum, the bean anthracnose pathogen. Fungal Biol 2024; 128:1771-1779. [PMID: 38796261 DOI: 10.1016/j.funbio.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/10/2024] [Accepted: 03/19/2024] [Indexed: 05/28/2024]
Abstract
Phaseolus vulgaris L., commonly known as the common bean, is a highly nutritious crop often called the "poor man's meat". However, it is susceptible to various diseases throughout the cropping season, with anthracnose caused by Colletotrichum lindemuthianum being a significant threat that leads to substantial losses. There is still a lack of understanding about the molecular basis of C. lindemuthianum pathogenicity. The first step in understanding this is to identify pathogenicity genes that express more during infection of common beans. A reverse transcription quantitative real-time PCR (qPCR) method can be used for virulence gene expression. However, this approach requires selecting appropriate reference genes to normalize relative gene expression data. Currently, there is no reference gene available for C. lindemuthianum. In this study, we selected eight candidate reference genes from the available genome of C. lindemuthianum to bridge the gap. These genes were ACT (Actin), β-tub (β-tubulin), EF (Elongation Factor), Cyt C (Cytochrome C), His H3 (Histone H3), CHS1 (Chitin synthetase), GAPDH (Glyceraldehyde-3-phosphate dehydrogenase) and abfA (Alpha-l-Arabinofuranosidase A). The primers for these candidate reference genes were able to amplify cDNA only from the pathogen, demonstrating their specificity. The qPCR efficiency of the primers ranged from 80% to 103%. We analyzed the stability of gene expression in C. lindemuthianum by exposing the mycelium to nine different stress conditions. We employed algorithms, such as GeNorm, NormFinder, BestKeeper, and RefFinder tools, to identify the most stable gene. The analysis using these tools revealed that EF, GAPDH, and β-tub most stable genes, while ACT and CHS1 showed relatively low expression stability. A large number of potential effector genes have been identified through bioinformatics analysis in C. lindemuthianum. The stable genes for qPCR (EF and GAPDH) discovered in this study will aid the scientific community in determining the relative expression of C. lindemuthianum effector genes.
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Affiliation(s)
- Zainab Rashid
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Aasiya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Naziya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Irtifa Lateef
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Qadrul Nisa
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Tabia Fayaz
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Gazala Gulzar
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Adfar Bashir
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - M D Shah
- Research Center for Residue and Quality Control Analysis, SKUAST-Kashmir, 190025, India
| | - Sajad M Zargar
- Division of Plant Biotechnology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Imran Khan
- Division of Agricultural Statistics, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Afsah Iqbal Nahvi
- Extension Training Centre, Malangpora, Pulwama, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - H Itoo
- Ambri Apple Research Centre, Pahnoo, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Rafiq A Shah
- Ambri Apple Research Centre, Pahnoo, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India.
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Ebrahimi A, Gharanjik S, Azadvari E, Rashidi-Monfared S. Characterizing reference genes for high-fidelity gene expression analysis under different abiotic stresses and elicitor treatments in fenugreek leaves. PLANT METHODS 2024; 20:40. [PMID: 38491388 PMCID: PMC10943880 DOI: 10.1186/s13007-024-01167-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND Quantifying gene expression is a critical aspect of applied genomics research across all organisms, and real-time PCR has emerged as a powerful tool for this purpose. However, selecting appropriate internal control genes for data normalization presents specific challenges. This study aimed to identify suitable reference genes for gene expression analysis under various conditions, encompassing salinity, low and high-temperature stresses, and different elicitor treatments. These treatments included titanium dioxide, cold plasma, 24-epibrassinolide, and melatonin, resulting in a total of 13 unique treatments and 148 treatment combinations applied to fenugreek plants. RESULTS As per the analysis performed with the BestKeeper tool, EEF-1α, and GAPDH were recognized as the most stable reference genes under the majority of conditions. Furthermore, the GeNorm and NormFinder tools identified β-tubulin and EEF-1α as the most stable reference genes. The findings of this research demonstrated that, although the stability of three reference genes expression was acceptable in almost all evaluated treatments, fluctuations in their expression were observed under the treatments of cold stress with TiO2 NPs application, cold plasma application with salinity stress, and cold plasma application with high-temperature stress compared to others. Simultaneously, the GeNorm analysis results demonstrated that in the mentioned treatments, relying on only one reference gene is inadequate. To corroborate the results, we examined the expression profile of the SSR gene, a pivotal gene in diosgenin biosynthesis, under all investigated treatments and treatment combinations. The outcomes suggested that employing stable reference genes yielded highly consistent results. CONCLUSIONS The varying expression patterns of the target genes emphasize the crucial need for precise optimization of experimental conditions and selecting stable reference genes to achieve accurate results in gene expression studies utilizing real-time PCR. These findings offer valuable insights into the selection of appropriate reference genes for gene expression analysis under diverse conditions using real-time PCR.
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Affiliation(s)
- Amin Ebrahimi
- Agronomy and Plant Breeding Department, Faculty of Agriculture, Shahrood University of Technology, Semnan, Iran.
| | - Shahrokh Gharanjik
- Department of Plant Breeding and Biotechnology, Faculty of Agricultural Engineering, Shahrood University of Technology, Shahrood, Iran.
| | - Elham Azadvari
- Horticultural Sciences Department, Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran
| | - Sajad Rashidi-Monfared
- Plant Breeding and Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
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Hu Z, Zhang N, Qin Z, Li J, Yang N, Chen Y, Kong J, Luo W, Xiong A, Zhuang J. Differential Response of MYB Transcription Factor Gene Transcripts to Circadian Rhythm in Tea Plants ( Camellia sinensis). Int J Mol Sci 2024; 25:657. [PMID: 38203827 PMCID: PMC10780195 DOI: 10.3390/ijms25010657] [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: 09/23/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
The circadian clock refers to the formation of a certain rule in the long-term evolution of an organism, which is an invisible 'clock' in the body of an organism. As one of the largest TF families in higher plants, the MYB transcription factor is involved in plant growth and development. MYB is also inextricably correlated with the circadian rhythm. In this study, the transcriptome data of the tea plant 'Baiyeyihao' were measured at a photoperiod interval of 4 h (24 h). A total of 25,306 unigenes were obtained, including 14,615 unigenes that were annotated across 20 functional categories within the GO classification. Additionally, 10,443 single-gene clusters were annotated to 11 sublevels of metabolic pathways using KEGG. Based on the results of gene annotation and differential gene transcript analysis, 22 genes encoding MYB transcription factors were identified. The G10 group in the phylogenetic tree had 13 members, of which 5 were related to the circadian rhythm, accounting for 39%. The G1, G2, G8, G9, G15, G16, G18, G19, G20, G21 and G23 groups had no members associated with the circadian rhythm. Among the 22 differentially expressed MYB transcription factors, 3 members of LHY, RVE1 and RVE8 were core circadian rhythm genes belonging to the G10, G12 and G10 groups, respectively. Real-time fluorescence quantitative PCR was used to detect and validate the expression of the gene transcripts encoding MYB transcription factors associated with the circadian rhythm.
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Affiliation(s)
- Zhihang Hu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China;
| | - Nan Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China;
| | - Zhiyuan Qin
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Jinwen Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Ni Yang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Yi Chen
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Jieyu Kong
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Wei Luo
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Aisheng Xiong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China;
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
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Bhattacharjee B, Ali A, Tuteja N, Gill S, Pattanayak A. Identification and expression pattern of aluminium-responsive genes in roots of rice genotype with reference to Al-sensitivity. Sci Rep 2023; 13:12184. [PMID: 37500702 PMCID: PMC10374657 DOI: 10.1038/s41598-023-39238-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/21/2023] [Indexed: 07/29/2023] Open
Abstract
Aluminium (Al) is the third most abundant element in the Earth's crust. Globally, acidic soil occupies 30-40% of ice-free land areas; Al toxicity is a major threat to crops. The first symptom of Al toxicity is the inhibition of root growth followed by poor root hair development, swollen root apices, necrosis of leaves and reduced yield. Although Rice (Oryza sativa) is an Al toxicity tolerant crop, it shows considerable variations among rice genotypes to Al exposure. Therefore, it is pertinent to understand Al toxicity and underlying mechanisms for Al tolerance in Rice. In the present study, 63 rice genotypes screened under Al stress showed significant variations of root growth. Expression stability of endogenous control genes (ECGs) revealed sulphite reductase (SR) as the most stable ECG that can be used as a reference gene for quantitative real-time PCR (qRT-PCR). Expression patterns of Al-responsive genes suggest genes associated with cytoskeletal dynamics, metabolism, and ion transporter could play significant roles in Al adaptation and tolerance in rice. The results showed Motodhan, Vietnam-1, Yimyu and N-861 as Al-toxicity tolerant, while Lespah, RCPL-13, VL-31329, and UPR2919-141-1 as most Al-sensitive genotypes among the studied rice lines cultivated in North-East India.
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Affiliation(s)
- Bijoya Bhattacharjee
- Division of Crop Science, ICAR Research Complex for NEH Region, Barapani, Meghalaya, India.
| | - Akib Ali
- Division of Crop Science, ICAR Research Complex for NEH Region, Barapani, Meghalaya, India
| | - Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Sarvajeet Gill
- Centre for Biotechnology, Maharishi Dayanand University, Rohtak, Haryana, India
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Ma D, Zhang Q, Zhou J, Lu Y, Duan X, He C, Yu J. Identification of Reliable Reference Genes under Different Stresses and in Different Tissues of Toxicodendron succedaneum. Genes (Basel) 2022; 13:genes13122396. [PMID: 36553662 PMCID: PMC9778191 DOI: 10.3390/genes13122396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Toxicodendron succedaneum (L.) Kuntze (T. succedaneum) is an economic tree species that produces urushiol and urushi wax, and it is of great value in industry and medicine. However, the stability of reference genes (RGs) has not been systematically reported in T. succedaneum to date. In this study, the expression of 10 candidate RGs was analyzed by RT-qPCR in different tissues (roots, stems, leaves), stress treatments (high/low temperature, drought), and hormone stimulation (jasmonic acid, JA). Then, the stability ranking of 10 candidate genes was evaluated by ∆Ct analysis and three software programs: geNorm, NormFinder, and BestKeeper. Finally, RefFinder was used to comprehensively analyze the expression stability of 10 candidate genes. The comprehensive analysis showed that TsRG05/06, TsRG01/06, and TsRG03/ACT were stable under high/low-temperature stress, drought stress, and JA treatment, respectively. TsRG03 and ACT had stable expression in different tissues. While the TsRG03 and ACT were recommended as the suitable RGs for T. succedaneum in all samples. Meanwhile, UBQ was the least suitable as a reference gene for T. succedaneum. In addition, the results of geNorm showed that the combination of two stable RGs could make the results of gene expression more accurate. These results provide alternative RGs for the study of gene function, correction, and normalization of target gene expression and directed molecular breeding in T. succedaneum.
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Affiliation(s)
- Dongxiao Ma
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Qin Zhang
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Jintao Zhou
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Yu Lu
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Xiaomeng Duan
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, China
| | - Chengzhong He
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, China
| | - Jinde Yu
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China
- Correspondence:
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Ariyoshi C, Sant’ana GC, Felicio MS, Sera GH, Nogueira LM, Rodrigues LMR, Ferreira RV, da Silva BSR, de Resende MLV, Destéfano SAL, Domingues DS, Pereira LFP. Genome-wide association study for resistance to Pseudomonas syringae pv. garcae in Coffea arabica. FRONTIERS IN PLANT SCIENCE 2022; 13:989847. [PMID: 36330243 PMCID: PMC9624508 DOI: 10.3389/fpls.2022.989847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Bacteria halo blight (BHB), a coffee plant disease caused by Pseudomonas syringae pv. garcae, has been gaining importance in producing mountain regions and mild temperatures areas as well as in coffee nurseries. Most Coffea arabica cultivars are susceptible to this disease. In contrast, a great source of genetic diversity and resistance to BHB are found in C. arabica Ethiopian accessions. Aiming to identify quantitative trait nucleotides (QTNs) associated with resistance to BHB and the influence of these genomic regions during the domestication of C. arabica, we conducted an analysis of population structure and a Genome-Wide Association Study (GWAS). For this, we used genotyping by sequencing (GBS) and phenotyping for resistance to BHB of a panel with 120 C. arabica Ethiopian accessions from a historical FAO collection, 11 C. arabica cultivars, and the BA-10 genotype. Population structure analysis based on single-nucleotide polymorphisms (SNPs) markers showed that the 132 accessions are divided into 3 clusters: most wild Ethiopian accessions, domesticated Ethiopian accessions, and cultivars. GWAS, using the single-locus model MLM and the multi-locus models mrMLM, FASTmrMLM, FASTmrEMMA, and ISIS EM-BLASSO, identified 11 QTNs associated with resistance to BHB. Among these QTNs, the four with the highest values of association for resistance to BHB are linked to g000 (Chr_0_434_435) and g010741 genes, which are predicted to encode a serine/threonine-kinase protein and a nucleotide binding site leucine-rich repeat (NBS-LRR), respectively. These genes displayed a similar transcriptional downregulation profile in a C. arabica susceptible cultivar and in a C. arabica cultivar with quantitative resistance, when infected with P. syringae pv. garcae. However, peaks of upregulation were observed in a C. arabica cultivar with qualitative resistance, for both genes. Our results provide SNPs that have potential for application in Marker Assisted Selection (MAS) and expand our understanding about the complex genetic control of the resistance to BHB in C. arabica. In addition, the findings contribute to increasing understanding of the C. arabica domestication history.
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Affiliation(s)
- Caroline Ariyoshi
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | | | - Mariane Silva Felicio
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
- Programa de pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista “Júlio de Mesquita Filho“ (UNESP), Instituto de Biociências, Campus de Botucatu, Botucatu, Brazil
| | - Gustavo Hiroshi Sera
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | - Livia Maria Nogueira
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | | | - Rafaelle Vecchia Ferreira
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | - Bruna Silvestre Rodrigues da Silva
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | | | | | - Douglas Silva Domingues
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (USP), Piracicaba, Brazil
| | - Luiz Filipe Protasio Pereira
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
- Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA-Café), Brasília, Brazil
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10
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Zhong Y, Gai Y, Gao J, Nie W, Bao Z, Wang W, Xu X, Wu J, He Y. Selection and validation of reference genes for quantitative real-time PCR normalization in Psoralea corylifolia (Babchi) under various abiotic stress. JOURNAL OF PLANT PHYSIOLOGY 2022; 274:153722. [PMID: 35605384 DOI: 10.1016/j.jplph.2022.153722] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Psoralea corylifolia L. is a popular herb and has long been used in traditional Ayurvedic and Chinese medicine owing to its extensive pharmacological activities, especially in the treatment of various shin diseases. To date, the systematic evaluation and selection of the optimum reference genes for gene expression analysis of P. corylifolia were not reported. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is a method for gene expression quantification. Selecting appropriate reference genes is the prerequisite for accurate normalization of RT-qPCR results. This study assessed the expression stability of 10 candidate reference genes under different abiotic stresses. First, amplification primers for RT-qPCR were designed and received testing and optimization. Then, expression data from each candidate gene were evaluated based on three statistical algorithms, and their results were further integrated into a comprehensive ranking based on the geometric mean. Additionally, one target gene, i.e., 1-aminocyclopropane-1-carboxylate oxidase (ACO), was used to validate the effectiveness of the selected reference. Our analysis suggested that thioredoxin-like protein YLS8 (YLS8), TIP41-like family protein (TIP41), and cyclophilin 2 (CYP2) genes provided superior expression normalization under different abiotic stresses. Overall, this work constitutes the first effort to select optimal endogenous controls for RT-qPCR studies of gene expression in P. corylifolia. It also provides a reasonable normalization standard and basis for further analysis of the gene expression of bioactive components in P. corylifolia.
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Affiliation(s)
- Yuan Zhong
- School of Pharmacy, Jiangsu Health Vocational College, Nanjing, 211800, China.
| | - Yanan Gai
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
| | - Jiajia Gao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China.
| | - Weifen Nie
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China.
| | - Zhenzhen Bao
- School of Pharmacy, Jiangsu Health Vocational College, Nanjing, 211800, China.
| | - Weiqi Wang
- School of Pharmacy, Jiangsu Health Vocational College, Nanjing, 211800, China.
| | - Xiaoqing Xu
- School of Pharmacy, Jiangsu Health Vocational College, Nanjing, 211800, China.
| | - Jie Wu
- School of Pharmacy, Jiangsu Health Vocational College, Nanjing, 211800, China.
| | - Yuedong He
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China.
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11
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Identification and testing of reference genes for qRT-PCR analysis during pear fruit development. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01087-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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12
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Simonova VV, Guzeev MA, Ekimova IV, Pastukhov YF. Chaperone Hsp70 (HSPA1) Is Involved in the Molecular Mechanisms of Sleep Cycle Integration. Int J Mol Sci 2022; 23:4464. [PMID: 35457282 PMCID: PMC9031996 DOI: 10.3390/ijms23084464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 11/17/2022] Open
Abstract
The molecular mechanisms of sleep cycle integration at the beginning and the end of the inactive period are not clear. Sleep cycles with a predominance of deep slow-wave sleep (SWS) seem to be associated with accelerated protein synthesis in the brain. The inducible Hsp70 chaperone corrects protein conformational changes and has protective properties. This research explores (1) whether the Hspa1 gene encoding Hsp70 protein activates during the daily rapid-eye-movement sleep (REMS) maximum, and (2) whether a lower daily deep SWS maximum affects the Hspa1 expression level during the subsequent REMS. Combining polysomnography in male Wistar rats, RT-qPCR, and Western blotting, we reveal a three-fold Hspa1 upregulation in the nucleus reticularis pontis oralis, which regulates REMS. Hspa1 expression increases during the daily REMS maximum, 5-7 h after the natural peak of deep SWS. Using short-term selective REMS deprivation, we demonstrate that REMS rebound after deprivation exceeds the natural daily maximum, but it is not accompanied by Hspa1 upregulation. The results suggest that a high proportion of deep SWS, usually observed after sleep onset, is a necessary condition for Hspa1 upregulation during subsequent REMS. The data obtained can inform the understanding of the molecular mechanisms integrating SWS and REMS and key biological function(s) of sleep.
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Affiliation(s)
- Valentina V. Simonova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 44 Thorez pr., 194223 St. Petersburg, Russia; (M.A.G.); (Y.F.P.)
| | | | - Irina V. Ekimova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 44 Thorez pr., 194223 St. Petersburg, Russia; (M.A.G.); (Y.F.P.)
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13
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Abstract
The gastrointestinal tract is continuously exposed to trillions of commensal microbes, collectively termed the microbiota, which are environmental stimuli that can direct health and disease within the host. In addition to well-established bacterial sensing pathways, microbial signals are also integrated through epigenetic modifications that calibrate the transcriptional program of host cells without altering the underlying genetic code. Microbiota-sensitive epigenetic changes include modifications to the DNA or histones, as well as regulation of non-coding RNAs. While microbiota-sensitive epigenetic mechanisms have been described in both local intestinal cells and as well in peripheral tissues, further research is required to fully decipher the complex relationship between the host and microbiota. This Review highlights current understandings of epigenetic regulation by gut microbiota and important implications of these findings in guiding therapeutic approaches to prevent or combat diseases driven by impaired microbiota-host interactions.
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Affiliation(s)
- Vivienne Woo
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Theresa Alenghat
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA,CONTACT Theresa Alenghat Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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14
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Santos MDL, de Resende MLV, dos Santos Ciscon BA, Freitas NC, Pereira MHDB, Reichel T, Mathioni SM. LysM receptors in Coffea arabica: Identification, characterization, and gene expression in response to Hemileia vastatrix. PLoS One 2022; 17:e0258838. [PMID: 35143519 PMCID: PMC8830669 DOI: 10.1371/journal.pone.0258838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/28/2022] [Indexed: 11/24/2022] Open
Abstract
Pathogen‐associated molecular patterns (PAMPs) are recognized by pattern recognition receptors (PRRs) localized on the host plasma membrane. These receptors activate a broad-spectrum and durable defense, which are desired characteristics for disease resistance in plant breeding programs. In this study, candidate sequences for PRRs with lysin motifs (LysM) were investigated in the Coffea arabica genome. For this, approaches based on the principle of sequence similarity, conservation of motifs and domains, phylogenetic analysis, and modulation of gene expression in response to Hemileia vastatrix were used. The candidate sequences for PRRs in C. arabica (Ca1-LYP, Ca2-LYP, Ca1-CERK1, Ca2-CERK1, Ca-LYK4, Ca1-LYK5 and Ca2-LYK5) showed high similarity with the reference PRRs used: Os-CEBiP, At-CERK1, At-LYK4 and At-LYK5. Moreover, the ectodomains of these sequences showed high identity or similarity with the reference sequences, indicating structural and functional conservation. The studied sequences are also phylogenetically related to the reference PRRs described in Arabidopsis, rice, and other plant species. All candidates for receptors had their expression induced after the inoculation with H. vastatrix, since the first time of sampling at 6 hours post‐inoculation (hpi). At 24 hpi, there was a significant increase in expression, for most of the receptors evaluated, and at 48 hpi, a suppression. The results showed that the candidate sequences for PRRs in the C. arabica genome display high homology with fungal PRRs already described in the literature. Besides, they respond to pathogen inoculation and seem to be involved in the perception or signaling of fungal chitin, acting as receptors or co-receptors of this molecule. These findings represent an advance in the understanding of the basal immunity of this species.
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Affiliation(s)
- Mariana de Lima Santos
- Programa de Pós-graduação em Biotecnologia Vegetal, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
- * E-mail: (MLS); (MLVR)
| | | | | | - Natália Chagas Freitas
- Departamento de Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | | | - Tharyn Reichel
- Departamento de Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Sandra Marisa Mathioni
- Departamento de Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
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15
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Reardon AJF, Rowan-Carroll A, Ferguson SS, Leingartner K, Gagne R, Kuo B, Williams A, Lorusso L, Bourdon-Lacombe JA, Carrier R, Moffat I, Yauk CL, Atlas E. Potency Ranking of Per- and Polyfluoroalkyl Substances Using High-Throughput Transcriptomic Analysis of Human Liver Spheroids. Toxicol Sci 2021; 184:154-169. [PMID: 34453843 DOI: 10.1101/2020.10.20.347328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Per- and polyfluoroalkyl substances (PFAS) are some of the most prominent organic contaminants in human blood. Although the toxicological implications of human exposure to perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) are well established, data on lesser-understood PFAS are limited. New approach methodologies (NAMs) that apply bioinformatic tools to high-throughput data are being increasingly considered to inform risk assessment for data-poor chemicals. The aim of this study was to compare the potencies (ie, benchmark concentrations: BMCs) of PFAS in primary human liver microtissues (3D spheroids) using high-throughput transcriptional profiling. Gene expression changes were measured using TempO-seq, a templated, multiplexed RNA-sequencing platform. Spheroids were exposed for 1 or 10 days to increasing concentrations of 23 PFAS in 3 subgroups: carboxylates (PFCAs), sulfonates (PFSAs), and fluorotelomers and sulfonamides. PFCAs and PFSAs exhibited trends toward increased transcriptional potency with carbon chain-length. Specifically, longer-chain compounds (7-10 carbons) were more likely to induce changes in gene expression and have lower transcriptional BMCs. The combined high-throughput transcriptomic and bioinformatic analyses support the capability of NAMs to efficiently assess the effects of PFAS in liver microtissues. The data enable potency ranking of PFAS for human liver cell spheroid cytotoxicity and transcriptional changes, and assessment of in vitro transcriptomic points of departure. These data improve our understanding of the possible health effects of PFAS and will be used to inform read-across for human health risk assessment.
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Affiliation(s)
- Anthony J F Reardon
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andrea Rowan-Carroll
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Stephen S Ferguson
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Karen Leingartner
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Remi Gagne
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Byron Kuo
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Luigi Lorusso
- Chemicals and Environmental Health Management Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Julie A Bourdon-Lacombe
- Water and Air Quality Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Richard Carrier
- Water and Air Quality Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Ivy Moffat
- Water and Air Quality Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ella Atlas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
- Department of Biochemistry, University of Ottawa, Ottawa, Ontario, Canada
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16
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Constitutive Defense Strategy of Coffee Under Field Conditions: A Comparative Assessment of Resistant and Susceptible Cultivars to Rust. Mol Biotechnol 2021; 64:263-277. [PMID: 34595725 DOI: 10.1007/s12033-021-00405-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Coffea arabica is the most economically important coffee species worldwide. However, its production is severely limited by diseases such as rust. The mechanisms underlying constitutive defense responses in coffee are still poorly understood, compared with induced defense mechanisms. We aimed to characterize constitutive defense responses of thirteen cultivars of C. arabica. Cultivars were classified under field conditions according to the level of resistance to rust: resistant (R), moderately resistant (MR), and susceptible (S). Based on this classification, the stability of eight reference genes (RGs) was evaluated. The most stable RGs were EF1α, APT1, and 24S. We also evaluated the expression of CaWRKY1, CaPAL1, CaCAD1, and CaPOX1, and activities of PAL, CAD, and POX, which are involved in lignin biosynthesis, and leaf content of total phenolic compounds and lignin. Gene expression and enzymatic activity were not correlated with defense metabolites in the R cultivar group but showed a negative correlation with phenolic compounds in MR cultivars. Cultivar S showed positive correlations of gene expression and enzyme activity with phenolic compounds. These results may assist coffee breeding programs regarding selection of genotypes and in optimization of rust resistance.
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17
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de Oliveira Santos M, Coelho LS, Carvalho GR, Botelho CE, Torres LF, Vilela DJM, Andrade AC, Silva VA. Photochemical efficiency correlated with candidate gene expression promote coffee drought tolerance. Sci Rep 2021; 11:7436. [PMID: 33795742 PMCID: PMC8016967 DOI: 10.1038/s41598-021-86689-y] [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: 11/04/2020] [Accepted: 03/15/2021] [Indexed: 02/01/2023] Open
Abstract
The aim of this study was to identify the correlation between photochemical efficiency and candidate genes expression to elucidate the drought tolerance mechanisms in coffee progenies (Icatu Vermelho IAC 3851-2 × Catimor UFV 1602-215) previously identified as tolerant in field conditions. Four progenies (2, 5, 12 and 15) were evaluated under water-deficit conditions (water deficit imposed 8 months after transplanting seedlings to the pots) and under irrigated system. Evaluations of physiological parameters and expression of candidate genes for drought tolerance were performed. Progeny 5 showed capacity to maintain water potential, which contributed to lower qP variation between irrigated and deficit conditions. However, the increases of qN and NPQ in response to stress indicate that this progeny is photochemically responsive to small variations of Ψam protecting the photosystem and maintaining qP. Data obtained for progeny 12 indicated a lower water status maintenance capacity, but with increased qN and NPQ providing maintenance of the ɸPSII and ETR parameters. A PCA analysis revealed that the genes coding regulatory proteins, ABA-synthesis, cellular protectors, isoforms of ascorbate peroxidase clearly displayed a major response to drought stress and discriminated the progenies 5 and 12 which showed a better photochemical response. The genes CaMYB1, CaERF017, CaEDR2, CaNCED, CaAPX1, CaAPX5, CaGolS3, CaDHN1 and CaPYL8a were up-regulated in the arabica coffee progenies with greater photochemical efficiency under deficit and therefore contributing to efficiency of the photosynthesis in drought tolerant progenies.
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Affiliation(s)
| | - Larissa Sousa Coelho
- Universidade Federal de Lavras, Campus Universitário, Lavras, Minas Gerais, Brazil
| | - Gladyston Rodrigues Carvalho
- Empresa de Pesquisa Agropecuária de Minas Gerais, Epamig Sul, Campus da Universidade Federal Lavras - UFLA, Rodovia Lavras/Ijaci Km 02, Cx. P. 176, Lavras, Minas Gerais, Brazil
| | - Cesar Elias Botelho
- Empresa de Pesquisa Agropecuária de Minas Gerais, Epamig Sul, Campus da Universidade Federal Lavras - UFLA, Rodovia Lavras/Ijaci Km 02, Cx. P. 176, Lavras, Minas Gerais, Brazil
| | | | | | - Alan Carvalho Andrade
- Embrapa Café, Inova Café, Campus Universitário da Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Vânia Aparecida Silva
- Empresa de Pesquisa Agropecuária de Minas Gerais, Epamig Sul, Campus da Universidade Federal Lavras - UFLA, Rodovia Lavras/Ijaci Km 02, Cx. P. 176, Lavras, Minas Gerais, Brazil.
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18
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Hul LM, Ibelli AMG, Peixoto JDO, Souza MR, Savoldi IR, Marcelino DEP, Tremea M, Ledur MC. Reference genes for proximal femoral epiphysiolysis expression studies in broilers cartilage. PLoS One 2020; 15:e0238189. [PMID: 32841273 PMCID: PMC7447007 DOI: 10.1371/journal.pone.0238189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 08/11/2020] [Indexed: 12/18/2022] Open
Abstract
The use of reference genes is required for relative quantification in gene expression analysis and the stability of these genes can be variable depending on the experimental design. Therefore, it is indispensable to test the reliability of endogenous genes previously to their use. This study evaluated nine candidate reference genes to select the most stable genes to be used as reference in gene expression studies with the femoral cartilage of normal and epiphysiolysis-affected broilers. The femur articular cartilage of 29 male broilers with 35 days of age was collected, frozen and further submitted to RNA extraction and quantitative PCR (qPCR) analysis. The candidate reference genes evaluated were GAPDH, HMBS, HPRT1, MRPS27, MRPS30, RPL30, RPL4, RPL5, and RPLP1. For the gene stability evaluation, three software were used: GeNorm, BestKeeper and NormFinder, and a global ranking was generated using the function RankAggreg. In this study, the RPLP1 and RPL5 were the most reliable endogenous genes being recommended for expression studies with femur cartilage in broilers with epiphysiolysis and possible other femur anomalies.
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Affiliation(s)
- Ludmila Mudri Hul
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, Paraná, Brazil
| | - Adriana Mércia Guaratini Ibelli
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, Paraná, Brazil
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | - Jane de Oliveira Peixoto
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, Paraná, Brazil
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | - Mayla Regina Souza
- Programa de Pós-Graduação em Zootecnia, UDESC-Oeste, Chapecó, Santa Catarina, Brazil
| | - Igor Ricardo Savoldi
- Programa de Pós-Graduação em Zootecnia, UDESC-Oeste, Chapecó, Santa Catarina, Brazil
| | | | - Mateus Tremea
- Universidade Federal de Santa Maria, campus Palmeira das Missões, Rio Grande do Sul, Brazil
| | - Mônica Corrêa Ledur
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
- Programa de Pós-Graduação em Zootecnia, UDESC-Oeste, Chapecó, Santa Catarina, Brazil
- * E-mail:
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19
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Baba VY, Braghini MT, Dos Santos TB, de Carvalho K, Soares JDM, Ivamoto-Suzuki ST, Maluf MP, Padilha L, Paccola-Meirelles LD, Pereira LF, Domingues DS. Transcriptional patterns of Coffea arabica L. nitrate reductase, glutamine and asparagine synthetase genes are modulated under nitrogen suppression and coffee leaf rust. PeerJ 2020; 8:e8320. [PMID: 31915587 PMCID: PMC6944126 DOI: 10.7717/peerj.8320] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 11/30/2019] [Indexed: 11/24/2022] Open
Abstract
This study evaluated the transcriptional profile of genes related to nitrogen (N) assimilation in coffee plants susceptible and resistant to rust fungi under N sufficiency and N suppression. For this purpose, we inoculated young coffee leaves with Hemileia vastatrix uredospores and collected them at 0, 12, 24 and 48 hours post-inoculation (HPI) to evaluate the relative expressions of genes encoding cytosolic glutamine synthetase (CaGS1), plastid glutamine synthetase (CaGS2), nitrate reductase (CaNR), and asparagine synthetase (CaAS). The genes exhibited distinct patterns of transcriptional modulation for the different genotypes and N nutritional regimes. The resistant genotype (I59) presented high levels of transcription in response to pathogen inoculation for CaNR and CaGS1 genes, evaluated under N sufficiency in the initial moments of infection (12 HPI). The gene CaGS1 also showed a peak at 48 HPI. The susceptible genotype (CV99) showed increased transcript rates of CaNR at 12 and 24 HPI in response to rust inoculation. The transcriptional patterns observed for CV99, under N suppression, were high levels for CaAS and CaGS2 at all post-inoculation times in response to coffee leaf rust disease. In addition, CaGS1 was up-regulated at 48 HPI for CV99. Cultivar I59 showed high transcript levels at 12 HPI for CaAS and peaks at 24 and 48 HPI for CaGS2 in inoculated samples. Consequently, total chlorophyl concentration was influenced by N suppression and by rust infection. Regarding enzyme activities in vitro for glutamine synthetase and CaNR, there was an increase in infected coffee leaves (I59) and under N sufficiency. Moreover, CV99 was modulated in both N nutritional regimes for GS activity in response to rust. Our results indicate that N transport genes trigger a differential modulation between genotypes through the action of rust disease.
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Affiliation(s)
- Viviane Yumi Baba
- Department of Agronomy, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.,Plant Biotechnology Laboratory, Instituto Agronômico do Paraná, Londrina, Paraná, Brazil
| | - Masako Toma Braghini
- Centro de Análise e Pesquisa Tecnológica do Agronegócio do Café "Alcides Carvalho," Instituto Agronômico de Campinas, Campinas, São Paulo, Brazil
| | - Tiago Benedito Dos Santos
- Plant Biotechnology Laboratory, Instituto Agronômico do Paraná, Londrina, Paraná, Brazil.,Programa de Pós-Graduação em Agronomia, Universidade do Oeste Paulista, Presidente Prudente, São Paulo, Brazil
| | - Kenia de Carvalho
- Plant Biotechnology Laboratory, Instituto Agronômico do Paraná, Londrina, Paraná, Brazil.,Plant Biotechnology Laboratory, Embrapa Soja, Londrina, Paraná, Brazil
| | | | - Suzana Tiemi Ivamoto-Suzuki
- Plant Biotechnology Laboratory, Instituto Agronômico do Paraná, Londrina, Paraná, Brazil.,Department of Botany, Instituto de Biociências, São Paulo State University, UNESP, Rio Claro, São Paulo, Brazil
| | - Mirian P Maluf
- Centro de Análise e Pesquisa Tecnológica do Agronegócio do Café "Alcides Carvalho," Instituto Agronômico de Campinas, Campinas, São Paulo, Brazil.,Plant Breeding, Embrapa Café, Brasília-DF, Brazil
| | - Lilian Padilha
- Centro de Análise e Pesquisa Tecnológica do Agronegócio do Café "Alcides Carvalho," Instituto Agronômico de Campinas, Campinas, São Paulo, Brazil.,Plant Breeding, Embrapa Café, Brasília-DF, Brazil
| | - Luzia D Paccola-Meirelles
- Department of Agronomy, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.,Department of Agronomy, Universidade Paranaense, Umuarama, Paraná, Brazil
| | - Luiz Filipe Pereira
- Plant Biotechnology Laboratory, Instituto Agronômico do Paraná, Londrina, Paraná, Brazil.,Plant Breeding, Embrapa Café, Brasília-DF, Brazil
| | - Douglas S Domingues
- Plant Biotechnology Laboratory, Instituto Agronômico do Paraná, Londrina, Paraná, Brazil.,Department of Botany, Instituto de Biociências, São Paulo State University, UNESP, Rio Claro, São Paulo, Brazil
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20
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Identification of Appropriate Reference Genes for Normalizing miRNA Expression in Citrus Infected by Xanthomonas citri subsp. citri. Genes (Basel) 2019; 11:genes11010017. [PMID: 31877985 PMCID: PMC7017248 DOI: 10.3390/genes11010017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 01/01/2023] Open
Abstract
MicroRNAs (miRNAs) are short noncoding RNA molecules that regulate gene expression at the posttranscriptional level. Reverse transcription-quantitative PCR (RT-qPCR) is one of the most common methods used for quantification of miRNA expression, and the levels of expression are normalized by comparing with reference genes. Thus, the selection of reference genes is critically important for accurate quantification. The present study was intended to identify appropriate miRNA reference genes for normalizing the level of miRNA expression in Citrus sinensis L. Osbeck and Citrus reticulata Blanco infected by Xanthomonas citri subsp. citri, which caused citrus canker disease. Five algorithms (Delta Ct, geNorm, NormFinder, BestKeeper and RefFinder) were used for screening reference genes, and two quantification approaches, poly(A) extension RT-qPCR and stem-loop RT-qPCR, were used to determine the most appropriate method for detecting expression patterns of miRNA. An overall comprehensive ranking output derived from the multi-algorithms showed that poly(A)-tailed miR162-3p/miR472 were the best reference gene combination for miRNA RT-qPCR normalization in citrus canker research. Candidate reference gene expression profiles determined by poly(A) RT-qPCR were more consistent in the two citrus species. To the best of our knowledge, this is the first systematic comparison of two miRNA quantification methods for evaluating reference genes. These results highlight the importance of rigorously assessing candidate reference genes and clarify some contradictory results in miRNA research on citrus.
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Wang T, Ping X, Cao Y, Jian H, Gao Y, Wang J, Tan Y, Xu X, Lu K, Li J, Liu L. Genome-wide exploration and characterization of miR172/euAP2 genes in Brassica napus L. for likely role in flower organ development. BMC PLANT BIOLOGY 2019; 19:336. [PMID: 31370790 PMCID: PMC6676641 DOI: 10.1186/s12870-019-1936-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 07/11/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND APETALA2-like genes encode plant-specific transcription factors, some of which possess one microRNA172 (miR172) binding site. The miR172 and its target euAP2 genes are involved in the process of phase transformation and flower organ development in many plants. However, the roles of miR172 and its target AP2 genes remain largely unknown in Brassica napus (B. napus). RESULTS In this study, 19 euAP2 and four miR172 genes were identified in the B. napus genome. A sequence analysis suggested that 17 euAP2 genes were targeted by Bna-miR172 in the 3' coding region. EuAP2s were classified into five major groups in B.napus. This classification was consistent with the exon-intron structure and motif organization. An analysis of the nonsynonymous and synonymous substitution rates revealed that the euAP2 genes had gone through purifying selection. Whole genome duplication (WGD) or segmental duplication events played a major role in the expansion of the euAP2 gene family. A cis-regulatory element (CRE) analysis suggested that the euAP2s were involved in the response to light, hormones, stress, and developmental processes including circadian control, endosperm and meristem expression. Expression analysis of the miR172-targeted euAP2s in nine different tissues showed diverse spatiotemporal expression patterns. Most euAP2 genes were highly expressed in the floral organs, suggesting their specific functions in flower development. BnaAP2-1, BnaAP2-5 and BnaTOE1-2 had higher expression levels in late-flowering material than early-flowering material based on RNA-seq and qRT-PCR, indicating that they may act as floral suppressors. CONCLUSIONS Overall, analyses of the evolution, structure, tissue specificity and expression of the euAP2 genes were peformed in B.napus. Based on the RNA-seq and experimental data, euAP2 may be involved in flower development. Three euAP2 genes (BnaAP2-1, BnaAP2-5 and BnaTOE1-2) might be regarded as floral suppressors. The results of this study provide insights for further functional characterization of the miR172 /euAP2 module in B.napus.
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Affiliation(s)
- Tengyue Wang
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing, China
| | - Xiaoke Ping
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing, China
| | - Yanru Cao
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing, China
| | - Hongju Jian
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing, China
| | - Yumin Gao
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing, China
| | - Jia Wang
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing, China
| | - Yingchao Tan
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing, China
| | - Xinfu Xu
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing, China
| | - Kun Lu
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing, China
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Selection of Suitable Reference Genes in Pinus massoniana Lamb. Under Different Abiotic Stresses for qPCR Normalization. FORESTS 2019. [DOI: 10.3390/f10080632] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The normalization of data by choosing suitable reference genes is fundamental for obtaining accurate and reliable results in quantitative real-time polymerase chain reaction (qPCR) analyses. In this study, the expression stability of 12 candidate reference genes of Pinus massoniana under different abiotic stresses was evaluated using four statistical algorithms: geNorm, NormFinder, BestKeeper, and RefFinder. The results indicate that the following genes could be used as reference genes under different treatments: Actin 2 (ACT2) and F-box family gene (F-box) for salinity treatment, cyclophilin (CYP) and alpha-tubulin (TUA) for ABA treatment, actin 7 (ACT7) and CYP for drought treatment, actin 1 (ACT1) and ACT7 for cold treatment, ACT1 and CYP for heat treatment, and TUA and ACT2 for the “Total” group. To validate the suitability of the selected reference genes in this study, the Short-Root protein (SHR), Alpha-pinene synthase (APS), and Pyrabactin resistance-like protein (PYL) gene expression patterns were analyzed. The expression patterns had significant biases when the most unstable reference genes were used for normalization, compared with when the optimum reference gene or gene combinations were used for normalization. These results will be beneficial for further studies on gene transcription in early-stage, unlignified seedlings of P. massoniana.
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Gijbels M, Lenaerts C, Vanden Broeck J, Marchal E. Juvenile Hormone receptor Met is essential for ovarian maturation in the Desert Locust, Schistocerca gregaria. Sci Rep 2019; 9:10797. [PMID: 31346226 PMCID: PMC6658565 DOI: 10.1038/s41598-019-47253-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/12/2019] [Indexed: 01/23/2023] Open
Abstract
Juvenile hormones (JH) are key endocrine regulators produced by the corpora allata (CA) of insects. Together with ecdysteroids, as well as nutritional cues, JH coordinates different aspects of insect postembryonic development and reproduction. The function of the recently characterized JH receptor, Methoprene-tolerant (Met), appears to be conserved in different processes regulated by JH. However, its functional interactions with other hormonal signalling pathways seem highly dependent on the feeding habits and on the developmental and reproductive strategies employed by the insect species investigated. Here we report on the effects of RNA interference (RNAi) mediated SgMet knockdown during the first gonadotrophic cycle in female desert locusts (Schistocerca gregaria). This voracious, phytophagous pest species can form migrating swarms that devastate field crops and harvests in several of the world’s poorest countries. A better knowledge of the JH signalling pathway may contribute to the development of novel, more target-specific insecticides to combat this very harmful swarming pest. Using RNAi, we show that the JH receptor Met is essential for ovarian maturation, vitellogenesis and associated ecdysteroid biosynthesis in adult female S. gregaria. Interestingly, knockdown of SgMet also resulted in a significant decrease of insulin-related peptide (SgIRP) and increase of neuroparsin (SgNP) 3 and 4 transcript levels in the fat body, illustrating the existence of an intricate regulatory interplay between different hormonal factors. In addition, SgMet knockdown in females resulted in delayed display of copulation behaviour with virgin males, when compared with dsGFP injected control animals. Moreover, we observed an incapacity of adult dsSgMet injected female locusts to oviposit during the time of the experimental setup. As such, SgMet is an essential gene playing crucial roles in the endocrine communication necessary for successful reproduction of the desert locust.
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Affiliation(s)
- Marijke Gijbels
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000, Leuven, Belgium
| | - Cynthia Lenaerts
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000, Leuven, Belgium
| | - Jozef Vanden Broeck
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000, Leuven, Belgium.
| | - Elisabeth Marchal
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000, Leuven, Belgium. .,Imec, Kapeldreef 75, B- 3001, Leuven, Belgium.
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Samarth, Jameson PE. Selection of reference genes for flowering pathway analysis in the masting plants, Celmisia lyallii and Chionochloa pallens, under variable environmental conditions. Sci Rep 2019; 9:9767. [PMID: 31278277 PMCID: PMC6611903 DOI: 10.1038/s41598-019-45780-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/13/2019] [Indexed: 12/20/2022] Open
Abstract
Mast flowering is characterised by mass synchronised flowering at irregular intervals over a wide geographical area. An understanding of the molecular drivers of mast flowering requires expression analysis of key developmentally regulated gene(s). Reverse transcription-quantitative PCR is the gold standard technique used to assess expression of target gene(s) and to validate high-throughput sequencing data. Selection and validation of appropriate reference gene(s), used as normalisation factors in transcript abundance analysis, is an essential step to avoid ambiguous expression results. Eight candidate reference genes were assessed to select the best internal normalisation factors in naturally growing masting plants Chionochloa pallens and Celmisia lyallii. Statistical packages geNorm, Normfinder, BestKeeper, ΔCt and RefFinder were used to determine the expression stability in plants translocated to different altitudes and sampled across the season. GAPDH and PP2a in Celmisia and ExP and THP in Chionochloa were found to be the best pairs of reference genes for normalisation of the gene expression data. Our study revealed environmentally-induced changes in reference gene expression, information that will be utilised as we investigate flowering phenology of masting plants under global climatic change.
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Affiliation(s)
- Samarth
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Paula E Jameson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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Selection and validation of reference genes for quantitative real-time PCR in Rosmarinus officinalis L. in various tissues and under elicitation. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Homeologous regulation of Frigida-like genes provides insights on reproductive development and somatic embryogenesis in the allotetraploid Coffea arabica. Sci Rep 2019; 9:8446. [PMID: 31186437 PMCID: PMC6560031 DOI: 10.1038/s41598-019-44666-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 05/22/2019] [Indexed: 01/10/2023] Open
Abstract
Coffea arabica is an allotetraploid of high economic importance. C. arabica transcriptome is a combination of the transcripts of two parental genomes (C. eugenioides and C. canephora) that gave rise to the homeologous genes of the species. Previous studies have reported the transcriptional dynamics of C. arabica. In these reports, the ancestry of homeologous genes was identified and the overall regulation of homeologous differential expression (HDE) was explored. One of these genes is part of the FRIGIDA-like family (FRL), which includes the Arabidopsis thaliana flowering-time regulation protein, FRIGIDA (FRI). As nonfunctional FRI proteins give rise to rapid-cycling summer annual ecotypes instead of vernalization-responsive winter-annuals, allelic variation in FRI can modulate flowering time in A. thaliana. Using bioinformatics, genomic analysis, and the evaluation of gene expression of homeologs, we characterized the FRL gene family in C. arabica. Our findings indicate that C. arabica expresses 10 FRL homeologs, and that, throughout flower and fruit development, these genes are differentially transcribed. Strikingly, in addition to confirming the expression of FRL genes during zygotic embryogenesis, we detected FRL expression during direct somatic embryogenesis, a novel finding regarding the FRL gene family. The HDE profile of FRL genes suggests an intertwined homeologous gene regulation. Furthermore, we observed that FLC gene of C. arabica has an expression profile similar to that of CaFRL genes.
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Prajapati GK, Pandey B, Mishra AK, Baek KH, Pandey DM. Identification of GCC-box and TCC-box motifs in the promoters of differentially expressed genes in rice (Oryza sativa L.): Experimental and computational approaches. PLoS One 2019; 14:e0214964. [PMID: 31026257 PMCID: PMC6485614 DOI: 10.1371/journal.pone.0214964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/23/2019] [Indexed: 01/22/2023] Open
Abstract
The transcription factor selectively binds with the cis-regulatory elements of the promoter and regulates the differential expression of genes. In this study, we aimed to identify and validate the presence of GCC-box and TCC-box motifs in the promoters of upregulated differentially expressed genes (UR-DEGs) and downregulated differentially expressed genes (DR-DEGs) under anoxia using molecular beacon probe (MBP) based real-time PCR. The GCC-box motif was detected in UR-DEGs (DnaJ and 60S ribosomal protein L7 genes), whereas, the TCC-box was detected in DR-DEGs (DnaK and CPuORF11 genes). In addition, the mechanism of interaction of AP2/EREBP family transcription factor (LOC_Os03g22170) with GCC-box promoter motif present in DnaJ gene (LOC_Os06g09560) and 60S ribosomal protein L7 gene (LOC_Os08g42920); and TCC-box promoter motif of DnaK gene (LOC_Os02g48110) and CPuORF11 gene (LOC_Os02g01240) were explored using molecular dynamics (MD) simulations analysis including binding free energy calculations, principal component analyses, and free energy landscapes. The binding free energy analysis revealed that AP2/EREBP model residues such as Arg68, Arg72, Arg83, Lys87, and Arg90 were commonly involved in the formation of hydrogen bonds with GCC and TCC-box promoter motifs, suggesting that these residues are critical for strong interaction. The movement of the entire protein bound to DNA was restricted, confirming the stability of the complex. This study provides comprehensive binding information and a more detailed view of the dynamic interaction between proteins and DNA.
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Affiliation(s)
- Gopal Kumar Prajapati
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Bharati Pandey
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Awdhesh Kumar Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
- * E-mail: (DP); (KB)
| | - Dev Mani Pandey
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
- * E-mail: (DP); (KB)
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Wu X, Shi T, Iqbal S, Zhang Y, Liu L, Gao Z. Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume. BMC PLANT BIOLOGY 2019; 19:64. [PMID: 30744565 PMCID: PMC6371585 DOI: 10.1186/s12870-019-1672-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 02/01/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are transcripts more than 200 bp in length do not encode proteins. Up to the present, it has been reported that lncRNAs play an essential role in developmental processes through their regulatory functions. However, their characteristics, expression inheritance patterns, and functions in Prunus mume are quite unidentified. RESULTS In this present study, we exposed the specific characters of pistil development process between single pistil cv 'Qingjia No.2' (QJN2) and multiple pistils cv 'Da Yu' (DY). We found that early October is the key stage for pistil differentiation. The similarity epidermis was observed between two types of pistil. We also further investigated a complete pistil development lncRNA profiles through RNA-seq in Prunus mume. 2572 unique lncRNAs and 24,648 genes mapped to Prunus mume genome, furthermore, 591 novel lncRNAs were predicted. Both unique lncRNAs and novel lncRNAs are shorter in length than the mRNAs, and the overall expression level of lncRNAs was lower than mRNAs in Prunus mume. 186 known lncRNAs, 1638 genes and 89 novel lncRNAs were identified as significant differential expressed in QJN2 compared with DY. We predicted 421 target genes of differentially expressed known lncRNAs (DEKLs) and 254 target genes of differentially expressed novel lncRNAs (DENLs). 153 miRNAs were predicted interacted with 100 DEKLs while 112 miRNAs were predicted interacted with 55 DENLs. Further analysis of the DEKLs showed that the lncRNA of XR_514690.2 down-regulated its target ppe-miR172d, and up-regulated AP2, respectively. Meanwhile, the other lncRNA of TCONS_00032517 induced cytokinin negative regulator gene A-ARR expression via repressing its target miRNA ppe-miR160a/b in DY. At the same time we found that the AP2 expression was significantly up-regulated by zeatin (ZT) treatment in flower buds. Our experiments suggest that the two lncRNAs of XR_514690.2 and TCONS_00032517 might contribute the formation of multiple pistils in Prunus mume. CONCLUSION This study shows the first characterization of lncRNAs involved in pistil development and provides new indications to elucidate how lncRNAs and their targets play role in pistil differentiation and flower development in Prunus mume.
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Affiliation(s)
- Xinxin Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210095 China
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shahid Iqbal
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yong Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
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29
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Zhou ZW, Deng HL, Wu QY, Liu BB, Yue C, Deng TT, Lai ZX, Sun Y. Validation of reference genes for gene expression studies in post-harvest leaves of tea plant ( Camellia sinensis). PeerJ 2019; 7:e6385. [PMID: 30723635 PMCID: PMC6360078 DOI: 10.7717/peerj.6385] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 12/28/2018] [Indexed: 01/14/2023] Open
Abstract
Tea is one of three major non-alcoholic beverages that are popular all around the world. The economic value of tea product largely depends on the post-harvest physiology of tea leaves. The utilization of quantitative reverse transcription polymerase chain reaction is a widely accepted and precise approach to determine the target gene expression of tea plants, and the reliability of results hinges on the selection of suitable reference genes. A few reliable reference genes have been documented using various treatments and different tissues of tea plants, but none has been done on post-harvest leaves during the tea manufacturing process. The present study selected and analyzed 15 candidate reference genes: Cs18SrRNA, CsGADPH, CsACT, CsEF-1α, CsUbi, CsTUA, Cs26SrRNA, CsRuBP, CsCYP, CselF-4α, CsMON1, CsPCS1, CsSAND, CsPPA2, CsTBP. This study made an assessment on the expression stability under two kinds of post-harvest treatment, turn over and withering, using three algorithms-GeNorm, Normfinder, and Bestkeeper. The results indicated that the three commonly used reference genes, CsTUA, Cs18SrRNA, CsRuBP, together with Cs26SrRNA, were the most unstable genes in both the turn over and withering treatments. CsACT, CsEF-1α, CsPPA2, and CsTBP were the top four reference genes in the turn over treatment, while CsTBP, CsPCS1, CsPPA2, CselF-4α, and CsACT were the five best reference genes in the withering group. The expression level of lipoxygenase genes, which were involved in a number of diverse aspects of plant physiology, including wounding, was evaluated to validate the findings. To conclude, we found a basis for the selection of reference genes for accurate transcription normalization in post-harvest leaves of tea plants.
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Affiliation(s)
- Zi-Wei Zhou
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture Fujian Agriculture and Forestry University, Fuzhou, P. R. China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Hui-Li Deng
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture Fujian Agriculture and Forestry University, Fuzhou, P. R. China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Qing-Yang Wu
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture Fujian Agriculture and Forestry University, Fuzhou, P. R. China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Bin-Bin Liu
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture Fujian Agriculture and Forestry University, Fuzhou, P. R. China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Chuan Yue
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Ting-Ting Deng
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Zhong-Xiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Yun Sun
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture Fujian Agriculture and Forestry University, Fuzhou, P. R. China
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Abdin M, Ahmad J, Nasrullah N, Quadri N, Nissar U, Kumar S. Selection of suitable reference genes for reverse transcription-quantitative polymerase chain reaction normalization in Artemisia annua L. plants at different stages of growth and development. Pharmacogn Mag 2019. [DOI: 10.4103/pm.pm_600_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Ashrafi M, Azimi Moqadam MR, Moradi P, Mohsenifard E, Shekari F. Evaluation and validation of housekeeping genes in two contrast species of thyme plant to drought stress using real-time PCR. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:54-60. [PMID: 30172853 DOI: 10.1016/j.plaphy.2018.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/06/2018] [Accepted: 08/06/2018] [Indexed: 06/08/2023]
Abstract
To decrease errors and increase accuracy and reliability of quantitative real-time PCR (qRT-PCR) results, the use of a reference gene is inevitable. Despite the industrial importance of genus Thymus, not any validated reference gene has not been reported for T. kotschyanus and T. vulgaris which could limit such investigations. In this study, the expression stability of seven housekeeping genes including Actin, Cyclophilin-18, elongation factor-1A, glyceraldehyde-3-phosphate dehydrogenase, 18S ribosomal RNA, Cullin, and Polypyrimidine tract-binding protein were evaluated in T. kotschyanus and T. vulgaris which grown at four levels of drought stress using geNorm, NormFinder, and BestKeeper algorithms. Histone deacetylase-6 (HDA-6) gene was also used for validation of evaluated reference genes. In T. vulgaris, all of the algorithms similarly ranked elongation factor-1A and glyceraldehyde-3-phosphate dehydrogenase as the two most stably expressed genes. In T. kotschyanus, only NormFinder and BestKeeper had a similar ranking and identified Actin and glyceraldehyde-3-phosphate dehydrogenase as the two most stably expressed genes, but geNorm algorithm ranked elongation factor-1A and glyceraldehyde-3-phosphate dehydrogenase as the best two reference genes. On the other hand, all algorithms ranked 18S rRNA and Cyclophilin-18 as the least stable genes in T. kotschyanus and T. vulgaris, respectively. Validation results indicated that there was a significant change (0.53-3.19 fold change) in relative expression of HDA-6 normalized by the best stable gene compare to the least ranked gene. Our study presented the first systematic validation of reference gene(s) selection in T. kotschyanus and T. vulgaris and provided useful information to obtain more accurate qRT-PCR results in these species.
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Affiliation(s)
- Mohsen Ashrafi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | | | - Parviz Moradi
- Research Division of Natural Resources, Zanjan Agricultural and Natural Resources Research and Education Centre, AREEO, Zanjan, Iran
| | - Ehsan Mohsenifard
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | - Farid Shekari
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
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Sreedharan SP, Kumar A, Giridhar P. Primer design and amplification efficiencies are crucial for reliability of quantitative PCR studies of caffeine biosynthetic N-methyltransferases in coffee. 3 Biotech 2018; 8:467. [PMID: 30402369 PMCID: PMC6212373 DOI: 10.1007/s13205-018-1487-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/19/2018] [Indexed: 11/02/2022] Open
Abstract
Primers having suboptimal amplification efficiencies were shown to falsely represent fold change expression of the N-methyltransferases gene family involved in caffeine biosynthesis in Coffea canephora. To study this phenomenon, the role of stability of the internal reference gene, as well as the amplification efficiency correction of the primers was investigated. GAPDH and Ubiquitin exhibited a good stability for studying the ontogeny of endosperm tissue, as well as the leaf transcriptome during stress from salicylic acid, methyl jasmonate, PEG-mediated drought and sudden exposure to light. Ubiquitin manifested low variation in Cq under all these stress regimes and in endosperm ontogeny with 30.1-30.9 in the best dataset and 28.8-30.9 in the most deviating dataset. It was observed that problems arising due to improper amplification efficiency of the target or reference genes or both could lead to misinterpretation of gene expression levels. Quantitative RT-PCR performed at a sub-optimal efficiency of GAPDH reference gene at 1.68 led to the faulty interpretation of 2.007 folds upregulation by the 2-ΔΔCt method and 1.705 folds upregulation by Efficiency method for the first NMT (Xanthosine methyltransferase), which actually is repressed during dark acclimatization of coffee plants. Efficiency correction improved the reliability of the expression data and also indicated a downregulation of this gene by 0.485 folds and 0.474 folds using 2-ΔΔCt and E method, respectively, in concordance to earlier reports. Hence, efficiency correction of the primers having suboptimal efficiencies is an absolute prerequisite for the accurate calculation of fold change using quantitative RT-PCR.
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Selection of suitable reference genes for qRT-PCR normalisation under different experimental conditions in Eucommia ulmoides Oliv. Sci Rep 2018; 8:15043. [PMID: 30301911 PMCID: PMC6177395 DOI: 10.1038/s41598-018-33342-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/26/2018] [Indexed: 01/09/2023] Open
Abstract
Normalisation of data, by choosing the appropriate reference genes, is fundamental for obtaining reliable results in quantitative real-time PCR (qPCR). This study evaluated the expression stability of 11 candidate reference genes with different varieties, developmental periods, tissues, and abiotic stresses by using four statistical algorithms: geNorm, NormFinder, BestKeeper, and RefFinder. The results indicated that ubiquitin-conjugating enzyme S (UBC) and ubiquitin-conjugating enzyme E2 (UBC E2) could be used as reference genes for different E. ulmoides varieties and tissues, UBC and histone H4 (HIS4) for different developmental periods, beta-tubulin (TUB) and UBC for cold treatment, ubiquitin extension protein (UBA80) and HIS4 for drought treatment, and ubiquitin-60S ribosomal protein L40 (UBA52) and UBC E2 for salinity treatment. UBC and UBC E2 for the group “Natural growth” and “Total”, UBA80 and UBC for the group “Abiotic stresses”. To validate the suitability of the selected reference genes in this study, mevalonate kinase (MK), phenylalanine ammonia-lyase (PAL), and 4-coumarate-CoA ligase (4CL) gene expression patterns were analysed. When the most unstable reference genes were used for normalisation, the expression patterns had significant biases compared with the optimum reference gene combinations. These results will be beneficial for more accurate quantification of gene expression levels in E. ulmoides.
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Quintero FOC, Pinto LG, Barsalobres-Cavallari CF, Arcuri MDLC, Pino LE, Peres LEP, Maluf MP, Maia IG. Identification of a seed maturation protein gene from Coffea arabica (CaSMP) and analysis of its promoter activity in tomato. PLANT CELL REPORTS 2018; 37:1257-1268. [PMID: 29947954 DOI: 10.1007/s00299-018-2310-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
A seed maturation protein gene (CaSMP) from Coffea arabica is expressed in the endosperm of yellow/green fruits. The CaSMP promoter drives reporter expression in the seeds of immature tomato fruits. In this report, an expressed sequence tag-based approach was used to identify a seed-specific candidate gene for promoter isolation in Coffea arabica. The tissue-specific expression of the cognate gene (CaSMP), which encodes a yet uncharacterized coffee seed maturation protein, was validated by RT-qPCR. Additional expression analysis during coffee fruit development revealed higher levels of CaSMP transcript accumulation in the yellow/green phenological stage. Moreover, CaSMP was preferentially expressed in the endosperm and was down-regulated during water imbibition of the seeds. The presence of regulatory cis-elements known to be involved in seed- and endosperm-specific expression was observed in the CaSMP 5'-upstream region amplified by genome walking (GW). Additional histochemical analysis of transgenic tomato (cv. Micro-Tom) lines harboring the GW-amplified fragment (~ 1.4 kb) fused to uidA reporter gene confirmed promoter activity in the ovule of immature tomato fruits, while no activity was observed in the seeds of ripening fruits and in the other organs/tissues examined. These results indicate that the CaSMP promoter can be used to drive transgene expression in coffee beans and tomato seeds, thus representing a promising biotechnological tool.
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Affiliation(s)
- Fabíola OCampo Quintero
- Department of Genetics, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-689, Brazil
| | - Layra G Pinto
- Department of Genetics, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-689, Brazil
| | - Carla F Barsalobres-Cavallari
- Department of Genetics, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-689, Brazil
| | - Mariana de Lara Campos Arcuri
- Department of Genetics, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-689, Brazil
| | - Lilian Ellen Pino
- Department of Biological Sciences (LCB), Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), University of Sao Paulo (USP), Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Lázaro Eustáquio Pereira Peres
- Department of Biological Sciences (LCB), Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), University of Sao Paulo (USP), Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Mirian P Maluf
- Embrapa Coffee and Coffee Center Alcides Carvalho, Agronomic Institute of Campinas, Campinas, Sao Paulo, 13012-970, Brazil
| | - Ivan G Maia
- Department of Genetics, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-689, Brazil.
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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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Qian J, Gao Y, Wáng Y, Wu Y, Wāng Y, Zhao Y, Chen H, Bao D, Xu J, Bian X. Selection and Evaluation of Appropriate Reference Genes for RT-qPCR Normalization of Volvariella volvacea Gene Expression under Different Conditions. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6125706. [PMID: 30079349 PMCID: PMC6069580 DOI: 10.1155/2018/6125706] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/10/2018] [Indexed: 11/18/2022]
Abstract
Volvariella volvacea (V. volvacea), commonly referred to as Chinese (paddy straw) mushroom, is a basidiomycete with a protein-rich volva and pileus. Selecting appropriate reference genes is a crucial step in the normalization of quantitative real-time PCR data. Therefore, 12 candidate reference genes were selected from the V. volvacea transcriptome based on previous studies and then BestKeeper, geNorm, and NormFinder were used to identify reference genes stably expressed during different developmental stages and conditions. Of the 12 candidate reference genes, SPRY domain protein (SPRYp), alpha-tubulin (TUBα), cyclophilin (CYP), L-asparaginase (L-asp), and MSF1-domain-containing protein (MSF1) were the most stably expressed under different experimental conditions, while 18S ribosomal RNA (18S), 28S ribosomal RNA (28S), and beta-actin (ACTB) were the least stably expressed. This investigation not only revealed potential factors influencing the suitability of reference genes, but also identified optimal reference genes from a pool of candidate genes under a wide range of conditions.
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Affiliation(s)
- Jiang Qian
- School of Life Science and Technology, China Pharmaceutical University, No. 24, Tongjiaxiang, Gulou District, Nanjing 210009, China
| | - Yingnv Gao
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Ying Wáng
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Yingying Wu
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Ying Wāng
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Yucheng Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Hongyu Chen
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Dapeng Bao
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Jiyang Xu
- School of Life Science and Technology, China Pharmaceutical University, No. 24, Tongjiaxiang, Gulou District, Nanjing 210009, China
| | - Xiaohong Bian
- School of Life Science and Technology, China Pharmaceutical University, No. 24, Tongjiaxiang, Gulou District, Nanjing 210009, China
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Zhang Y, Peng X, Liu Y, Li Y, Luo Y, Wang X, Tang H. Evaluation of suitable reference genes for qRT-PCR normalization in strawberry (Fragaria × ananassa) under different experimental conditions. BMC Mol Biol 2018; 19:8. [PMID: 29933763 PMCID: PMC6013875 DOI: 10.1186/s12867-018-0109-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/13/2018] [Indexed: 12/20/2022] Open
Abstract
Background Strawberry has received much attention due to its nutritional value, unique flavor, and attractive appearance. The availability of the whole genome sequence and multiple transcriptome databases allows the great possibility to explore gene functions, comprehensively. Gene expression profiles of a target gene can provide clues towards the understanding of its biological function. Quantitative real-time PCR (qRT-PCR) is a preferred method for rapid quantification of gene expression. The accuracy of the results obtained by this method requires the reference genes with consistently stable expression to normalize its data. Results In present study, the expression stability of seven candidate reference genes in diverse sample subsets of different tissues and fruit developmental stages, and plant subjected to light quality and low temperature treatments was evaluated using three statistical algorithms, geNorm, NormFinder, and BestKeeper. Our data indicated that the expression stability of reference genes varied under different experimental conditions. Overall, DBP, HISTH4, ACTIN1 and GAPDH expressed much more stably. PIRUV, ACTIN2 and 18S were not recommended for normalization in given experimental conditions due to low stability. In addition, the relative expression pattern of HY5 (ELONGATED HYPOCOTYL5) was conducted to further confirm the reliability of the reference genes, which demonstrated the correct adoption of reference genes was of great importance in qRT-PCR analysis. Conclusions Expression stability of reference genes from strawberry varied across selected experimental conditions. Systematic validation of reference genes prior to calculation of target gene expression level should be done to improve the accuracy and consistency of qRT-PCR analysis. Electronic supplementary material The online version of this article (10.1186/s12867-018-0109-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaorui Peng
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yi Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yali Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.,Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.
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Identification and characterization of some putative genes involved in arabinoxylan biosynthesis in Plantago ovata. 3 Biotech 2018; 8:266. [PMID: 29868304 DOI: 10.1007/s13205-018-1289-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 05/14/2018] [Indexed: 01/18/2023] Open
Abstract
Plantago ovata is an important source of Psyllium (Isabgol), which swells upon contact with water forming mucilaginous mass, largely composed of arabinoxylans. In this study, we analyzed the expression pattern of arabinoxylan biosynthetic pathway genes at different stages of seed development in P. ovata. Besides, arabinoxylans were quantified at different stages of seed development in water extractable and water unextractable fractions. The expression analysis revealed 5-8 fold increase in the levels of expression of some genes involved in arabinoxylan biosynthetic pathway such as UDP-arabinopyranose mutase, UDP-xylosyltransferase 2 and xylan glucuronosyltransferase at 15 days after pollination stage in seed. The xylose and arabinose units were analyzed at different stages of seed development and also in water-soluble (cold water and hot water), alkali and ethanolic fractions. The concentration of xylose and arabinose units increased steadily after pollination. Overall, alkali extract had high concentration of xylose (0.70 ± 0.022 mg/g) and arabinose units (0.10 ± 0.01 mg/g) at 15 days after pollination stage.
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Selection and validation of reference genes for quantitative real-time PCR in Artemisia sphaerocephala based on transcriptome sequence data. Gene 2018; 657:39-49. [PMID: 29505835 DOI: 10.1016/j.gene.2018.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 02/28/2018] [Accepted: 03/02/2018] [Indexed: 11/24/2022]
Abstract
Artemisia sphaerocephala, a dicotyledonous perennial semi-shrub belonging to the Artemisia genus of the Compositae family, is widely distributed in northwestern China. This shrub is one of the most important pioneer plants which is capable of protecting rangelands from wind erosion. It therefore plays a vital role in maintaining desert ecosystem stability. In addition, to its use as a forage grass, it has excellent prospective applications as a source of plant oil and as a plant-based fuel. The use of internal genes is the basis for accurately assessing Real time quantitative PCR. In this study, based on transcriptome data of A. sphaerocephala, we analyzed 21 candidate internal genes to determine the optimal internal genes in this shrub. The stabilities of candidate genes were evaluated in 16 samples of A. sphaerocephala. Finally, UBC9 and TIP41-like were determined as the optimal reference genes in A. sphaerocephala by Delta Ct and three various programs. There were GeNorm, NormFinder and BestKeeper.
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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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41
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Validation of house-keeping genes for normalization of gene expression data during diurnal/circadian studies in rice by RT-qPCR. Sci Rep 2018; 8:3203. [PMID: 29453432 PMCID: PMC5816630 DOI: 10.1038/s41598-018-21374-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 02/01/2018] [Indexed: 11/25/2022] Open
Abstract
The circadian clock in plants is the intrinsic rhythmic expression of thousands of genes in a 24 h period, which is set by the day-night cycles in the environment. The study of the circadian clock often requires expression profiling of genes over a large number of samples for which RT-qPCR is invariably used. Reliability of the results depends largely on the house-keeping genes, which serve as control and thus should be chosen carefully to prevent erroneous results. In this study, ten house-keeping genes were chosen from rice for stability analysis with 48 tissue samples harvested from plants subjected to diurnal/circadian cycles. Although, all the genes were found to be stable, however, six of them showed cyclic expression patterns and caused major changes in the expression profiles of the target genes when used to normalize their expression data, thereby making them poor candidates for diurnal/circadian studies. In conclusion, reference genes need to be selected for diurnal/circadian studies with extra caution as more than 80% of transcriptome in plants undergoes cycling, which remains undetected by the gene stability assessment software and can severely affect the RT-qPCR based gene expression profiling. The geometric mean of two or more most stable reference genes is hence recommended for diurnal/circadian studies in plants.
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Zhao X, Fu J, Jiang L, Zhang W, Shao Y, Jin C, Xiong J, Li C. Transcriptome-based identification of the optimal reference genes as internal controls for quantitative RT-PCR in razor clam (Sinonovacula constricta). Genes Genomics 2018; 40:603-613. [PMID: 29892942 DOI: 10.1007/s13258-018-0661-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/18/2018] [Indexed: 12/28/2022]
Abstract
Quantitative real-time PCR (qRT-PCR) is a standard method to measure gene expression in function exploring. Accurate and reproducible data of qRT-PCR requires appropriate reference genes, which are stably expressed under different experimental conditions. However, no housekeeping genes were validated as internal controls for qRT-PCR in Sinonovacula constricta. In this study, we classified the transcriptome data of two tissues for Vibrio infection and Cd2+ stress into ten clusters based on the gene expression patterns. Among them, cluster 5 had the most stable gene expression patterns regardless of tissues and treatments as the database for candidate reference genes. A total of 55 orthologs of classical housekeeping genes in the clam transcriptome were annotated. Combined the expression profiles and housekeeping genes in S. constricta, we chose eight candidate reference genes and validated their expression in Vibrio-infected samples and different tissues by qRT-PCR. Their expression stability was analyzed by three different algorithms geNorm, NormFinder and BestKeeper. Although the rank of the eight candidate reference genes is different in different treatments using different software, RS9 could be the best reference genes for normalization of qRT-PCR expression data in S. constricta under various treatments considering the above analysis. Meanwhile, the ranking of genes based on the CV values of transcriptomic data was similar to the validation results. This study provides for the first time a list of suitable reference genes for S. constricta and a valuable resource for further studies of clam immune defense systems.
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Affiliation(s)
- Xuelin Zhao
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People's Republic of China
| | - Jianping Fu
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People's Republic of China
| | - Liting Jiang
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People's Republic of China
| | - Weiwei Zhang
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People's Republic of China
| | - Yina Shao
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People's Republic of China
| | - Chunhua Jin
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People's Republic of China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People's Republic of China
| | - Chenghua Li
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People's Republic of China.
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Kim JS, Chae S, Jun KM, Pahk YM, Lee TH, Chung PJ, Kim YK, Nahm BH. Genome-wide identification of grain filling genes regulated by the OsSMF1 transcription factor in rice. RICE (NEW YORK, N.Y.) 2017; 10:16. [PMID: 28444616 PMCID: PMC5405039 DOI: 10.1186/s12284-017-0155-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 04/13/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND Spatial- and temporal-specific expression patterns are primarily regulated at the transcriptional level by gene promoters. Therefore, it is important to identify the binding motifs of transcription factors to better understand the networks associated with embryogenesis. RESULTS Here, we used a protein-binding microarray (PBM) to identify the binding motifs of OsSMF1, which is a basic leucine zipper transcription factor involved in the regulation of rice seed maturation. OsSMF1 (previously called RISBZ1 or OsbZIP58) is known to interact with GCN4 motifs (TGA(G/C)TCA) to regulate seed storage protein synthesis, and it functions as a key regulator of starch synthesis. Quadruple 9-mer-based PBM analysis and electrophoretic mobility shift assay revealed that OsSMF1 bound to the GCN4 (TGA(G/C)TCA), ACGT (CCACGT(C/G)), and ATGA (GGATGAC) motifs with three different affinities. We predicted 44 putative OsSMF1 target genes using data obtained from both the PBM and RiceArrayNet. Among these putative target genes, 18, 21, and 13 genes contained GCN4, ACGT, and ATGA motifs within their 1-kb promoter regions, respectively. Among them, six genes encoding major grain filling proteins and transcription factors were chosen to confirm the activation of their expression in vivo. OsSMF1 was shown to bind directly to the promoters of Os03g0168500 (GCN4 motif), patatin-like gene (GCN4 motif), α-globulin (ACGT motif), rice prolamin box-binding factor (RPBF) (ATGA motif), and ONAC024 (GCN4 and ACGT motifs) and to regulate their expression. CONCLUSIONS The results of this study suggest that OsSMF1 is one of the key transcription factors that functions in a wide range of seed developmental processes with different specific binding affinities for the three DNA-binding motifs.
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Affiliation(s)
- Joung Sug Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, Republic of Korea
| | - Songhwa Chae
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, Republic of Korea
| | - Kyong Mi Jun
- Genomics Genetics Institute, GreenGene BioTech Inc., Yongin, Kyonggido, 449-728, Republic of Korea
| | - Yoon-Mok Pahk
- Genomics Genetics Institute, GreenGene BioTech Inc., Yongin, Kyonggido, 449-728, Republic of Korea
| | - Tae-Ho Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, 370 Nongsaengmyeong-ro, Wansan-gu, Jeonju, North Jeolla Province, 54874, Republic of Korea
| | - Pil Joong Chung
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Yeon-Ki Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, Republic of Korea
| | - Baek Hie Nahm
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, Republic of Korea.
- Genomics Genetics Institute, GreenGene BioTech Inc., Yongin, Kyonggido, 449-728, Republic of Korea.
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Dinh SN, Kang H. An endoplasmic reticulum-localized Coffea arabica BURP domain-containing protein affects the response of transgenic Arabidopsis plants to diverse abiotic stresses. PLANT CELL REPORTS 2017; 36:1829-1839. [PMID: 28803325 DOI: 10.1007/s00299-017-2197-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/05/2017] [Indexed: 06/07/2023]
Abstract
The Coffea arabica BURP domain-containing gene plays an important role in the response of transgenic Arabidopsis plants to abiotic stresses via regulating the level of diverse proteins. Although the functions of plant-specific BURP domain-containing proteins (BDP) have been determined for a few plants, their roles in the growth, development, and stress responses of most plant species, including coffee plant (Coffea arabica), are largely unknown. In this study, the function of a C. arabica BDP, designated CaBDP1, was investigated in transgenic Arabidopsis plants. The expression of CaBDP1 was highly modulated in coffee plants subjected to drought, cold, salt, or ABA. Confocal analysis of CaBDP1-GFP fusion proteins revealed that CaBDP1 is localized in the endoplasmic reticulum. The ectopic expression of CaBDP1 in Arabidopsis resulted in delayed germination of the transgenic plants under abiotic stress and in the presence of ABA. Cotyledon greening and seedling growth of the transgenic plants were inhibited in the presence of ABA due to the upregulation of ABA signaling-related genes like ABI3, ABI4, and ABI5. Proteome analysis revealed that the levels of several proteins are modulated in CaBDP1-expressing transgenic plants. The results of this study underscore the importance of BURP domain proteins in plant responses to diverse abiotic stresses.
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Affiliation(s)
- Sy Nguyen Dinh
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, Korea
- Institute of Environment and Biotechnology, Taynguyen University, 567 Le Duan Street, Buon Ma Thuot, Daklak Province, Vietnam
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, Korea.
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Barbierato V, Sala T, Rinaldi P, Bassolino L, Barchi L, Rotino GL, Toppino L. A spiking strategy facilitates housekeeping selection for RT-qPCR analysis under different biotic stresses in eggplant. PROTOPLASMA 2017; 254:2215-2223. [PMID: 28429149 DOI: 10.1007/s00709-017-1111-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/04/2017] [Indexed: 05/27/2023]
Abstract
Endogenous housekeeping genes are traditionally employed to normalize the expression of target genes in RT-qPCR studies. Assuming that a perfect housekeeping suitable for every condition does not exist, expression stability of the chosen reference gene should be evaluated at every new experiment. The housekeeping selection process reveals furthermore complicated and time-consuming when different conditions have to be compared in the same experimental dataset. As an alternative strategy, we spiked an external reference transcript (ERT) into all RNA samples of our dataset (eggplant roots subjected to different biotic stresses), and used it to normalize the expression levels of native candidate housekeeping. ERT expression resulted highly stable across all samples and enabled to indicate glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as the most stable endogenous housekeeping. This result was confirmed by the use of GeNorm, Normfinder, and BestKeeper algorithms. This method might be generally applied to expedite the selection process of the best reference gene.
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Affiliation(s)
- Valeria Barbierato
- CREA- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Unità di Ricerca per l'Orticoltura, Via Paullese, 28 Montanaso Lombardo, 26836, Lodi, Italy
| | - Tea Sala
- CREA- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Unità di Ricerca per l'Orticoltura, Via Paullese, 28 Montanaso Lombardo, 26836, Lodi, Italy
| | - Paola Rinaldi
- CREA- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Unità di Ricerca per l'Orticoltura, Via Paullese, 28 Montanaso Lombardo, 26836, Lodi, Italy
| | - Laura Bassolino
- CREA- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Unità di Ricerca per l'Orticoltura, Via Paullese, 28 Montanaso Lombardo, 26836, Lodi, Italy
| | - Lorenzo Barchi
- DISAFA Plant Genetics and Breeding, University of Torino, Grugliasco, 10095, Torino, Italy
| | - Giuseppe Leonardo Rotino
- CREA- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Unità di Ricerca per l'Orticoltura, Via Paullese, 28 Montanaso Lombardo, 26836, Lodi, Italy
| | - Laura Toppino
- CREA- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Unità di Ricerca per l'Orticoltura, Via Paullese, 28 Montanaso Lombardo, 26836, Lodi, Italy.
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Carmona R, Arroyo M, Jiménez-Quesada MJ, Seoane P, Zafra A, Larrosa R, Alché JDD, Claros MG. Automated identification of reference genes based on RNA-seq data. Biomed Eng Online 2017; 16:65. [PMID: 28830520 PMCID: PMC5568602 DOI: 10.1186/s12938-017-0356-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Background Gene expression analyses demand appropriate reference genes (RGs) for normalization, in order to obtain reliable assessments. Ideally, RG expression levels should remain constant in all cells, tissues or experimental conditions under study. Housekeeping genes traditionally fulfilled this requirement, but they have been reported to be less invariant than expected; therefore, RGs should be tested and validated for every particular situation. Microarray data have been used to propose new RGs, but only a limited set of model species and conditions are available; on the contrary, RNA-seq experiments are more and more frequent and constitute a new source of candidate RGs. Results An automated workflow based on mapped NGS reads has been constructed to obtain highly and invariantly expressed RGs based on a normalized expression in reads per mapped million and the coefficient of variation. This workflow has been tested with Roche/454 reads from reproductive tissues of olive tree (Olea europaea L.), as well as with Illumina paired-end reads from two different accessions of Arabidopsis thaliana and three different human cancers (prostate, small-cell cancer lung and lung adenocarcinoma). Candidate RGs have been proposed for each species and many of them have been previously reported as RGs in literature. Experimental validation of significant RGs in olive tree is provided to support the algorithm. Conclusion Regardless sequencing technology, number of replicates, and library sizes, when RNA-seq experiments are designed and performed, the same datasets can be analyzed with our workflow to extract suitable RGs for subsequent PCR validation. Moreover, different subset of experimental conditions can provide different suitable RGs. Electronic supplementary material The online version of this article (doi:10.1186/s12938-017-0356-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rosario Carmona
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Macarena Arroyo
- Servicio de Neumología, Hospital Regional Universitario de Málaga, Avda Carlos Haya s/n, Malaga, Spain
| | - María José Jiménez-Quesada
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Pedro Seoane
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Malaga, Spain
| | - Adoración Zafra
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Rafael Larrosa
- Departamento de Arquitectura de Computadores, Universidad de Málaga, Malaga, Spain
| | - Juan de Dios Alché
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - M Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Malaga, Spain.
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Evaluation of reference genes for reverse transcription quantitative real-time PCR (RT-qPCR) studies in Silene vulgaris considering the method of cDNA preparation. PLoS One 2017; 12:e0183470. [PMID: 28817728 PMCID: PMC5560574 DOI: 10.1371/journal.pone.0183470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 08/04/2017] [Indexed: 01/05/2023] Open
Abstract
Accurate gene expression measurements are essential in studies of both crop and wild plants. Reverse transcription quantitative real-time PCR (RT-qPCR) has become a preferred tool for gene expression estimation. A selection of suitable reference genes for the normalization of transcript levels is an essential prerequisite of accurate RT-qPCR results. We evaluated the expression stability of eight candidate reference genes across roots, leaves, flower buds and pollen of Silene vulgaris (bladder campion), a model plant for the study of gynodioecy. As random priming of cDNA is recommended for the study of organellar transcripts and poly(A) selection is indicated for nuclear transcripts, we estimated gene expression with both random-primed and oligo(dT)-primed cDNA. Accordingly, we determined reference genes that perform well with oligo(dT)- and random-primed cDNA, making it possible to estimate levels of nucleus-derived transcripts in the same cDNA samples as used for organellar transcripts, a key benefit in studies of cyto-nuclear interactions. Gene expression variance was estimated by RefFinder, which integrates four different analytical tools. The SvACT and SvGAPDH genes were the most stable candidates across various organs of S. vulgaris, regardless of whether pollen was included or not.
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Cao LY, Li XX, Wang D, Sun HF, Gao JP. Validation of Reliable Reference Genes for Accurate Normalization in RT-qPCR Analysis of Codonopsis pilosula. CHINESE HERBAL MEDICINES 2017. [DOI: 10.1016/s1674-6384(17)60099-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Song H, Dang X, He YQ, Zhang T, Wang HY. Selection of housekeeping genes as internal controls for quantitative RT-PCR analysis of the veined rapa whelk ( Rapana venosa). PeerJ 2017; 5:e3398. [PMID: 28584723 PMCID: PMC5455708 DOI: 10.7717/peerj.3398] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/09/2017] [Indexed: 12/13/2022] Open
Abstract
Background The veined rapa whelk Rapana venosa is an important commercial shellfish in China and quantitative real-time PCR (qRT-PCR) has become the standard method to study gene expression in R. venosa. For accurate and reliable gene expression results, qRT-PCR assays require housekeeping genes as internal controls, which display highly uniform expression in different tissues or stages of development. However, to date no studies have validated housekeeping genes in R. venosa for use as internal controls for qRT-PCR. Methods In this study, we selected the following 13 candidate genes for suitability as internal controls: elongation factor-1α (EF-1α), α-actin (ACT), cytochrome c oxidase subunit 1 (COX1), nicotinamide adenine dinucleotide dehydrogenase (ubiquinone) 1α subcomplex subunit 7 (NDUFA7), 60S ribosomal protein L5 (RL5), 60S ribosomal protein L28 (RL28), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), β-tubulin (TUBB), 40S ribosomal protein S25 (RS25), 40S ribosomal protein S8 (RS8), ubiquitin-conjugating enzyme E2 (UBE2), histone H3 (HH3), and peptidyl-prolyl cis-trans isomerase A (PPIA). We measured the expression levels of these 13 candidate internal controls in eight different tissues and twelve larvae developmental stages by qRT-PCR. Further analysis of the expression stability of the tested genes was performed using GeNorm and RefFinder algorithms. Results Of the 13 candidate genes tested, we found that EF-1α was the most stable internal control gene in almost all adult tissue samples investigated with RL5 and RL28 as secondary choices. For the normalization of a single specific tissue, we suggested that EF-1α and NDUFA7 are the best combination in gonad, as well as COX1 and RL28 for intestine, EF-1α and RL5 for kidney, EF-1α and COX1 for gill, EF-1α and RL28 for Leiblein and mantle, EF-1α, RL5, and NDUFA7 for liver, GAPDH, PPIA, and RL28 for hemocyte. From a developmental perspective, we found that RL28 was the most stable gene in all developmental stages measured, and COX1 and RL5 were appropriate secondary choices. For the specific developmental stage, we recommended the following combination for normalization, PPIA, RS25, and RL28 for stage 1, RL5 and RL28 for stage 2 and 5, RL28 and NDUFA7 for stage 3, and PPIA and TUBB for stage 4. Discussion Our results are instrumental for the selection of appropriately validated housekeeping genes for use as internal controls for gene expression studies in adult tissues or larval development of R. venosa in the future.
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Affiliation(s)
- Hao Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xin Dang
- College of Fisheries, Ocean University of China, Qingdao, China
| | - Yuan-Qiu He
- College of Fisheries, Ocean University of China, Qingdao, China
| | - Tao Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hai-Yan Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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