1
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Ivanova Z, Petrova V, Grigorova N, Vachkova E. Identification of the Reference Genes for Relative qRT-PCR Assay in Two Experimental Models of Rabbit and Horse Subcutaneous ASCs. Int J Mol Sci 2024; 25:2292. [PMID: 38396967 PMCID: PMC10889259 DOI: 10.3390/ijms25042292] [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: 01/22/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Obtaining accurate and reliable gene expression results in real-time RT-PCR (qRT-PCR) data analysis requires appropriate normalization by carefully selected reference genes, either a single or a combination of multiple housekeeping genes (HKGs). The optimal reference gene/s for normalization should demonstrate stable expression across varying conditions to diminish potential influences on the results. Despite the extensive database available, research data are lacking regarding the most appropriate HKGs for qRT-PCR data analysis in rabbit and horse adipose-derived stem cells (ASCs). Therefore, in our study, we comprehensively assessed and compared the suitability of some widely used HKGs, employing RefFinder and NormFinder, two extensively acknowledged algorithms for robust data interpretation. The rabbit and horse ASCs were obtained from subcutaneous stromal vascular fraction. ASCs were induced into tri-lineage differentiation, followed by the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) treatment of the adipose-differentiated rabbit ASCs, while horse experimental groups were formed based on adipogenic, osteogenic, and chondrogenic differentiation. At the end of the experiment, the total mRNA was obtained and used for the gene expression evaluation of the observed factors. According to our findings, glyceraldehyde 3-phosphate dehydrogenase was identified as the most appropriate endogenous control gene for rabbit ASCs, while hypoxanthine phosphoribosyltransferase was deemed most suitable for horse ASCs. The obtained results underscore that these housekeeping genes exhibit robust stability across diverse experimental conditions, remaining unaltered by the treatments. In conclusion, the current research can serve as a valuable baseline reference for experiments evaluating gene expression in rabbit and horse ASCs. It highlights the critical consideration of housekeeping gene abundance and stability in qPCR experiments, emphasizing the need for an individualized approach tailored to the specific requirements of the study.
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Affiliation(s)
- Zhenya Ivanova
- Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, 6000 Stara Zagora, Bulgaria; (V.P.); (N.G.); (E.V.)
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2
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Wang F, Li P, Liu Q, Nie G, Zhu Y, Zhang X. Selection and Validation of Reference Genes in Sudan Grass ( Sorghum sudanense (Piper) Stapf) under Various Abiotic Stresses by qRT-PCR. Genes (Basel) 2024; 15:210. [PMID: 38397200 PMCID: PMC10887928 DOI: 10.3390/genes15020210] [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: 01/08/2024] [Revised: 01/28/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Quantitative reverse transcription PCR (qRT-PCR) can screen applicable reference genes of species, and reference genes can be used to reduce experimental errors. Sudan grass (Sorghum sudanense (Piper) Stapf) is a high-yield, abiotic-tolerant annual high-quality forage with a wide range of uses. However, no studies have reported reference genes suitable for Sudan grass. Therefore, we found eight candidate reference genes, including UBQ10, HIS3, UBQ9, Isoform0012931, PP2A, ACP2, eIF4α, and Actin, under salt stress (NaCl), drought stress (DR), acid aluminum stress (AlCl3), and methyl jasmonate treatment (MeJA). By using geNorm, NormFinder, BestKeeper, and RefFinder, we ranked eight reference genes on the basis of their expression stabilities. The results indicated that the best reference gene was PP2A under all treatments. eIF4α can be used in CK, MeJA, NaCl, and DR. HIS3 can serve as the best reference gene in AlCl3. Two target genes (Isoform0007606 and Isoform0002387) belong to drought-stress-response genes, and they are highly expressed in Sudan grass according to transcriptome data. They were used to verify eight candidate reference genes under drought stress. The expression trends of the two most stable reference genes were similar, but the trend in expression for Actin showed a significant difference. The reference genes we screened provided valuable guidance for future research on Sudan grass.
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Affiliation(s)
- Fangyan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (F.W.); (P.L.); (G.N.)
| | - Peng Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (F.W.); (P.L.); (G.N.)
| | - Qiuxu Liu
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China;
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (F.W.); (P.L.); (G.N.)
| | - Yongqun Zhu
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China;
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (F.W.); (P.L.); (G.N.)
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Peng S, Ali Sabir I, Hu X, Chen J, Qin Y. Advancements in Reference Gene Selection for Fruit Trees: A Comprehensive Review. Int J Mol Sci 2024; 25:1142. [PMID: 38256212 PMCID: PMC10816256 DOI: 10.3390/ijms25021142] [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: 11/26/2023] [Revised: 12/30/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Real-time quantitative polymerase chain reaction (qRT-PCR) has been widely used in gene expression analyses due to its advantages of sensitivity, accuracy and high throughput. The stability of internal reference genes has progressively emerged as a major factor affecting the precision of qRT-PCR results. However, the stability of the expression of the reference genes needs to be determined further in different cells or organs, physiological and experimental conditions. Methods for evaluating these candidate internal reference genes have also evolved from simple single software evaluation to more reliable and accurate internal reference gene evaluation by combining different software tools in a comprehensive analysis. This study intends to provide a definitive reference for upcoming research that will be conducted on fruit trees. The primary focus of this review is to summarize the research progress in recent years regarding the selection and stability analysis of candidate reference genes for different fruit trees.
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Affiliation(s)
- Shujun Peng
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.P.); (X.H.); (J.C.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
| | - Irfan Ali Sabir
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
| | - Xinglong Hu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.P.); (X.H.); (J.C.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
| | - Jiayi Chen
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.P.); (X.H.); (J.C.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
| | - Yonghua Qin
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.P.); (X.H.); (J.C.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
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Vodiasova E, Meger Y, Uppe V, Tsiupka V, Chelebieva E, Smykov A. Class III Peroxidases in the Peach ( Prunus persica): Genome-Wide Identification and Functional Analysis. PLANTS (BASEL, SWITZERLAND) 2024; 13:127. [PMID: 38202438 PMCID: PMC10780707 DOI: 10.3390/plants13010127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/18/2023] [Accepted: 12/31/2023] [Indexed: 01/12/2024]
Abstract
Class III peroxidases are plant-specific and play a key role in the response to biotic and abiotic stresses, as well as in plant growth and development. In this study, we investigated 60 POD genes from Prunus persica based on genomic and transcriptomic data available in NCBI and analysed the expression of individual genes with qPCR. Peroxidase genes were clustered into five subgroups using the phylogenetic analysis. Their exon-intron structure and conserved motifs were analysed. Analysis of the transcriptomic data showed that the expression of PpPOD genes varied significantly in different tissues, at different developmental stages and under different stress treatments. All genes were divided into low- and high-expressed genes, and the most highly expressed genes were identified for individual tissues (PpPOD12 and PpPOD42 in flower buds and PpPOD73, PpPOD12, PpPOD42, and PpPOD31 in fruits). The relationship between cold tolerance and the level of peroxidase expression was revealed. These studies were carried out for the first time in the peach and confirmed that chilling tolerance may be related to the specificity of antioxidant complex gene expression.
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Affiliation(s)
- Ekaterina Vodiasova
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (Y.M.); (V.U.); (V.T.); (E.C.); (A.S.)
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, 299011 Sevastopol, Russia
| | - Yakov Meger
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (Y.M.); (V.U.); (V.T.); (E.C.); (A.S.)
| | - Victoria Uppe
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (Y.M.); (V.U.); (V.T.); (E.C.); (A.S.)
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, 299011 Sevastopol, Russia
| | - Valentina Tsiupka
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (Y.M.); (V.U.); (V.T.); (E.C.); (A.S.)
| | - Elina Chelebieva
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (Y.M.); (V.U.); (V.T.); (E.C.); (A.S.)
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, 299011 Sevastopol, Russia
| | - Anatoly Smykov
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (Y.M.); (V.U.); (V.T.); (E.C.); (A.S.)
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Johnson N, Rodriguez Diaz D, Ganapathy S, Bass JS, Kutchan TM, Khan AL, Flavier AB. Evaluation of reference genes for qRT-PCR studies in the colchicine producing Gloriosa superba L. PLANT BIOTECHNOLOGY REPORTS 2023; 17:1-11. [PMID: 37359494 PMCID: PMC10195008 DOI: 10.1007/s11816-023-00840-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/28/2023] [Accepted: 05/09/2023] [Indexed: 06/28/2023]
Abstract
The flame lily, Gloriosa superba L., is one of the two primary sources of the anti-inflammatory drug, colchicine. Previous studies have shown that a higher level of colchicine production occurs in the rhizomes than in leaves and roots. Earlier precursor feeding and transcriptome analysis of G. superba have provided a putative pathway and candidate genes involved in colchicine biosynthesis. Comparative analysis of expression levels of candidate pathway genes in different tissues of G. superba using quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) can reveal highly expressed genes in the rhizome compared to other tissues which could suggest roles of the gene products in colchicine biosynthesis. Normalization is an important step in effectively analyzing differential gene expression by qRT-PCR with broader applications. The current study selected candidate reference genes from the transcriptome datasets and analyzed them to determine the most stable genes for normalization of colchicine biosynthesis-related genes. Using RefFinder, one stable reference gene, UBC22, was selected to normalize gene expression levels of candidate methyltransferase (MT) genes in the leaves, roots, and rhizomes of G. superba. With UBC22 as reference gene, the methyltransferases, GsOMT1, GsOMT3, and GsOMT4 showed significantly higher expression levels in the rhizome of G. superba, while MT31794 was more highly expressed in the roots. In conclusion, the current results showed a viable reference gene expression analysis system that could help elucidate colchicine biosynthesis and its exploitation for increased production of the drug in G. superba. Supplementary Information The online version contains supplementary material available at 10.1007/s11816-023-00840-x.
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Affiliation(s)
- Nekha Johnson
- Department of Engineering Technology, Technology Division, Cullen College of Engineering, University of Houston, Houston, TX 77204 USA
- Present Address: Lonza Biologics, Inc., 14905 Kirby Dr, Houston, TX 77047 USA
| | - Diana Rodriguez Diaz
- Department of Engineering Technology, Technology Division, Cullen College of Engineering, University of Houston, Houston, TX 77204 USA
- Present Address: Lonza Biologics, Inc., 14905 Kirby Dr, Houston, TX 77047 USA
| | - Sivakumar Ganapathy
- Department of Engineering Technology, Technology Division, Cullen College of Engineering, University of Houston, Houston, TX 77204 USA
| | - John S. Bass
- Department of Engineering Technology, Technology Division, Cullen College of Engineering, University of Houston, Houston, TX 77204 USA
- Present Address: Solugen, Inc., 14549 Minetta St, Houston, TX 77035 USA
| | - Toni M. Kutchan
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132 USA
| | - Abdul L. Khan
- Department of Engineering Technology, Technology Division, Cullen College of Engineering, University of Houston, Houston, TX 77204 USA
| | - Albert B. Flavier
- Department of Engineering Technology, Technology Division, Cullen College of Engineering, University of Houston, Houston, TX 77204 USA
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6
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Yu J, Wang R, Ma W, Lei S, Zhu M, Yang G. Pectate Lyase Gene VvPL1 Plays a Role in Fruit Cracking of Table Grapes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:1643-1654. [PMID: 36638364 DOI: 10.1021/acs.jafc.2c05996] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Fruit cracking seriously affects the commercial value of table grapes. To explore whether cell wall disassembly influences grape berry cracking, first, the differences in the cell wall metabolism were compared between cracking-resistant "Shennongjinhuanghou" (SN) and cracking-susceptible "Xiangfei" (XF) varieties. Our results showed that cell wall disassembly events were extremely different between "SN" and "XF." The cracking-resistant "SN" had a higher pectinmethylesterase activity in the early stage and lower polygalacturonase, β-galactosidase, pectate lyase, and cellulase activities from veraison, cooperatively yielding higher ionically bound pectin, covalently bound pectin, hemicellulose, and lower water-soluble pectin, leading to a stronger skin break force and elasticity and conferring "SN" with higher cracking resistance. Furthermore, the function of the VvPL1 gene in fruit cracking was verified by heterologously transforming tomatoes. The transgenic experiment showed that overexpressed fruits had a higher activity of pectate lyase from the breaking stage and a lower level of covalently bound pectin, ionically bound pectin, cellulose, and hemicellulose and a higher level of water-soluble pectin at the red ripe stage, which resulted in a significantly reduced skin break force and flesh firmness and increased fruit cracking incidences. In conclusion, our results demonstrated that the cracking susceptibility of the grape berry is closely related to cell wall disassembly events and VvPL1 plays an important role in fruit cracking.
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Affiliation(s)
- Jun Yu
- College of Horticulture, Hunan Agricultural University, Nongda Road No. 1, Furong District, Changsha410128, Hunan, China
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi417000, Hunan, China
| | - Rong Wang
- College of Horticulture, Hunan Agricultural University, Nongda Road No. 1, Furong District, Changsha410128, Hunan, China
| | - Wentao Ma
- College of Horticulture, Hunan Agricultural University, Nongda Road No. 1, Furong District, Changsha410128, Hunan, China
| | - Shumin Lei
- College of Horticulture, Hunan Agricultural University, Nongda Road No. 1, Furong District, Changsha410128, Hunan, China
| | - Mingtao Zhu
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi417000, Hunan, China
| | - Guoshun Yang
- College of Horticulture, Hunan Agricultural University, Nongda Road No. 1, Furong District, Changsha410128, Hunan, China
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7
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Yao J, Zhu G, Liang D, He B, Wang Y, Cai Y, Zhang Q. Reference Gene Selection for qPCR Analysis in Schima superba under Abiotic Stress. Genes (Basel) 2022; 13:genes13101887. [PMID: 36292772 PMCID: PMC9601953 DOI: 10.3390/genes13101887] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
Quantitative real-time PCR (qPCR) is an indispensable technique for gene expression analysis in modern molecular biology. The selection and evaluation of suitable reference genes is a prerequisite for accurate gene expression analysis. Schimasuperba is a valuable tree species that is environmentally adaptable and highly fire-resistant. In this study, 12 candidate reference genes were selected to check their stability of gene expression in different tissues under abiotic stresses: cold stress, salt stress, and drought stress by ΔCt, geNorm, NormFinder, BestKeeper, and RefFinder. The results indicated that AP-2 was the most stably expressed overall and for the cold stress and drought stress. eIF-5α gene expression was the most stable under the salt stress treatment, while UBQ expression was the most stable across mature leaves, shoots, stems, and roots. In contrast, UBC20, GAPDH, and TUB were the least stably expressed genes tested. This study delivers valid reference genes in S. superba under the different experimental conditions, providing an important resource for the subsequent elucidation of the abiotic stress adaptation mechanisms and genes with biological importance.
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Affiliation(s)
- Jun Yao
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Gang Zhu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Dongcheng Liang
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Boxiang He
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Yingli Wang
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Yanling Cai
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Qian Zhang
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
- Correspondence: ; Tel.: +86-020-87033420
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He F, Gui L, Zhang Y, Zhu B, Zhang X, Shen M, Wan F, Yang L, Xiao J. Validation of reference genes for gene expression analysis in fruit development of Vaccinium bracteatum Thunb. using quantitative real-time PCR. Sci Rep 2022; 12:16946. [PMID: 36210363 PMCID: PMC9548497 DOI: 10.1038/s41598-022-20864-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/20/2022] [Indexed: 12/29/2022] Open
Abstract
Vaccinium bracteatum Thunb. (VBT) is widely distributed in the mountainous areas in eastern and southern China. VBT leaves have great medical value and can be used to stain rice to produce "Wumifan". Its fruits also contain rich nutrients. However, there has been limited attention to exploring the molecular content of VBT. Previously, we performed RNA-seq on three typical VBT fruits that were at various stages of ripening, although a reliable reference gene was lost in validation.In this study, we selected ten candidate reference genes based on previous studies and transcriptomics analyses. Subsequently, these genes were evaluated using a combination of methods, including geNorm, NormFinder, and Bestkeeper, with a comprehensive ranking assessment. As a result, we found that the actin2, NADH, and ADK genes have high reliability for analysing the expression levels of genes involved in fruit development. Furthermore, the transcript levels of 15 DEGs from transcriptomic analysis were assessed using NADH as a reference gene, and RT-qPCR data were highly consistent with the transcriptomic data. These results provide reliable reference genes for further studying gene expression, which will be beneficial for comprehensively exploring VBT.
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Affiliation(s)
- Feng He
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Liangxian Gui
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Yan Zhang
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Bo Zhu
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Xiaoping Zhang
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Min Shen
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Fengying Wan
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Lu Yang
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Jiaxin Xiao
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
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9
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Fan H, He Q, Dong Y, Xu W, Lou Y, Hua X, Xu T. Selection of suitable candidate genes for mRNA expression normalization in bulbil development of Pinellia ternata. Sci Rep 2022; 12:8849. [PMID: 35614175 PMCID: PMC9133075 DOI: 10.1038/s41598-022-12782-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/03/2022] [Indexed: 11/09/2022] Open
Abstract
Pinellia ternata (Thunb.) Breit. (Abbreviated as P. ternata). It is a commonly prescribed Chinese traditional medicinal herb for the treatment of phlegm, cough, and morning sick. Bulbil reproduction is one of the main reproductive methods of P. ternata. The accurate quantification of gene expression patterns associated with bulbil development might be helpful to explore the molecular mechanism involved in P. ternata reproduction. Quantitative real-time PCR was the most preferred method for expression profile and function analysis of mRNA. However, the reference genes in different tissues of P. ternata in different periods of bulbil development have not been studied in detail. In present study, the expression stability of eight candidate reference genes were determined with programs: geNorm, NormFinder, BestKeeper, and refFinder. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was identified as the top- rated reference gene in all samples of P. ternata, while different combinations of reference gene proved to be the most stable depending on development stage and tissue type. Furthermore, the reliability of GAPDH expression was verified by six P. ternata related genes in hormone and nutrient biosynthesis pathways, and the expression profiles of these genes were agreed with the results of RNA-seq digital gene expression analysis. These results can contribute to studies of gene expression patterns and functional analysis of P. ternata involved in bulbil development.
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Affiliation(s)
- Haoyu Fan
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Qiuling He
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China.
| | - Yiheng Dong
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Wenxin Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yanlin Lou
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xuejun Hua
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Tao Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China.
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Pan L, Lu Z, Yan L, Zeng W, Shen Z, Yu M, Bu L, Cui G, Niu L, Wang Z. NLR1 is a strong candidate for the Rm3 dominant green peach aphid (Myzus persicae) resistance trait in peach. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1357-1369. [PMID: 35022695 DOI: 10.1093/jxb/erab506] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
The green peach aphid (GPA), Myzus persicae, is a polyphagous, sap-sucking aphid and a vector of many plant viruses. In peach, Prunus persica, three individual dominant GPA resistance loci have been genetically defined (Rm1-3), but knowledge of the underlying genes is limited. In this study, we focused on the Rm3 locus. Bulk segregant analysis (BSA) mapping in segregating progeny populations delimited Rm3 to an interval spanning 160 kb containing 21 genes on chromosome 1. RNA-seq data provided no evidence of candidate genes, but chromosomal structural variations were predicted around a nucleotide-binding site-leucine-rich repeat (NLR) gene (ppa000596m) within the Rm3 fine-mapping interval. Following bacterial artificial chromosome (BAC) library construction for a GPA-resistant peach cultivar and the sequencing of three target BAC clones, a chromosomal structural variation encompassing two novel TIR-NLR-class disease resistance (R) protein-coding genes was identified, and the expressed NLR gene (NLR1) was identified as a candidate for M. persicae resistance. Consistent with its proposed role in controlling GPA resistance, NLR1 was only expressed in the leaves of resistant peach phenotypes. A molecular marker that was designed based on the NLR1 sequence co-segregated with the GPA-resistant phenotype in four segregating populations, 162 peach cultivars, and 14 wild relatives, demonstrating the dominant inheritance of the Rm3 locus. Our findings can be exploited to facilitate future breeding for GPA-resistance in peach.
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Affiliation(s)
- Lei Pan
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhenhua Lu
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Lele Yan
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Wenfang Zeng
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhijun Shen
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Mingliang Yu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lulu Bu
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Guochao Cui
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Liang Niu
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhiqiang Wang
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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Identification of Suitable Reference Genes for qRT-PCR Normalization in Kiwifruit. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020170] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Reference genes are used for the correction of qRT-PCR data, and it is necessary to investigate the optimum reference gene under certain conditions. The expression levels of seven traditional reference genes ACT1, ACT2, GAPDH, 18S rRNA, UBQ, TUB and CYP were analyzed using qRT-PCR in different varieties, tissues, developmental stages and hormone (or pollen polysaccharide) treatments in kiwifruit. Gene expression stability was assessed with the help of three common software (geNorm, NormFinder, BestKeeper), and the minimum number of reference genes necessary for normalization was also determined. GAPDH, ACT1 and ACT2 were selected as reference genes for different genotypes of kiwifruit. GAPDH and UBQ were the best combinations of reference genes for root, stem, leaf, flower and fruit. GAPDH and ACT1 could be the preferred reference genes for normalization of qRT-PCR data during fruit development. The pairing of ACT1 and UBQ constituted the optimal combination of reference genes in kiwifruit treated with different hormones (or pollen polysaccharide). This study provides a new and reliable option for the use of reference genes in the analysis of gene expression patterns of interest in kiwifruit.
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12
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Selection and Validation of Reliable Reference Genes for Gene Expression Studies in Different Genotypes and TRV-Infected Fruits of Peach (Prunus persica L. Batsch) during Ripening. Genes (Basel) 2022; 13:genes13010160. [PMID: 35052500 PMCID: PMC8775616 DOI: 10.3390/genes13010160] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
Real-time quantitative PCR (RT-qPCR) is a powerful tool to detect and quantify transcription abundance, and the stability of the reference gene determines its success. However, the most suitable reference gene for different genotypes and tobacco rattle virus (TRV) infected fruits was unclear in peach (Prunus persica L. Batsch). In this study, 10 reference genes were selected and gene expression was characterized by RT-qPCR across all samples, including different genotypes and TRV-infected fruits during ripening. Four statistical algorithms (geNorm, NormFinder, BestKeeper, and RefFinder) were used to calculate the stability of 10 reference genes. The geNorm analysis indicated that two suitable reference genes should be used for gene expression normalization. In general, the best combination of reference genes was CYP2 and Tua5 for TRV-infected fruits and CYP2 and Tub1 for different genotypes. In 18S, GADPH, and TEF2, there is an unacceptable variability of gene expression in all experimental conditions. Furthermore, to confirm the validity of the reference genes, the expression levels of PpACO1, PpEIN2, and PpPL were normalized at different fruit storage periods. In summary, our results provide guidelines for selecting reliable reference genes in different genotypes and TRV-infected fruits and lay the foundation for accurate evaluation of gene expression for RT-qPCR analysis in peach.
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