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Zhao F, Maren NA, Kosentka PZ, Liao YY, Lu H, Duduit JR, Huang D, Ashrafi H, Zhao T, Huerta AI, Ranney TG, Liu W. An optimized protocol for stepwise optimization of real-time RT-PCR analysis. HORTICULTURE RESEARCH 2021; 8:179. [PMID: 34333545 PMCID: PMC8325682 DOI: 10.1038/s41438-021-00616-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/11/2021] [Accepted: 06/06/2021] [Indexed: 05/07/2023]
Abstract
Computational tool-assisted primer design for real-time reverse transcription (RT) PCR (qPCR) analysis largely ignores the sequence similarities between sequences of homologous genes in a plant genome. It can lead to false confidence in the quality of the designed primers, which sometimes results in skipping the optimization steps for qPCR. However, the optimization of qPCR parameters plays an essential role in the efficiency, specificity, and sensitivity of each gene's primers. Here, we proposed an optimized approach to sequentially optimizing primer sequences, annealing temperatures, primer concentrations, and cDNA concentration range for each reference (and target) gene. Our approach started with a sequence-specific primer design that should be based on the single-nucleotide polymorphisms (SNPs) present in all the homologous sequences for each of the reference (and target) genes under study. By combining the efficiency calibrated and standard curve methods with the 2-ΔΔCt method, the standard cDNA concentration curve with a logarithmic scale was obtained for each primer pair for each gene. As a result, an R2 ≥ 0.9999 and the efficiency (E) = 100 ± 5% should be achieved for the best primer pair of each gene, which serve as the prerequisite for using the 2-ΔΔCt method for data analysis. We applied our newly developed approach to identify the best reference genes in different tissues and at various inflorescence developmental stages of Tripidium ravennae, an ornamental and biomass grass, and validated their utility under varying abiotic stress conditions. We also applied this approach to test the expression stability of six reference genes in soybean under biotic stress treatment with Xanthomonas axonopodis pv. glycines (Xag). Thus, these case studies demonstrated the effectiveness of our optimized protocol for qPCR analysis.
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Affiliation(s)
- Fangzhou Zhao
- Soybean Research Institute, Nanjing Agricultural University, 210095, Nanjing, China
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27607, USA
| | - Nathan A Maren
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27607, USA
- Mountain Crop Improvement Lab, Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, NC, 28759, USA
| | - Pawel Z Kosentka
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27607, USA
| | - Ying-Yu Liao
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27607, USA
| | - Hongyan Lu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27607, USA
- College of Biosystems Engineering and Food Science, Zhejiang University, 310058, Hangzhou, China
| | - James R Duduit
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27607, USA
| | - Debao Huang
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27607, USA
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27607, USA
| | - Tuanjie Zhao
- Soybean Research Institute, Nanjing Agricultural University, 210095, Nanjing, China
| | - Alejandra I Huerta
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27607, USA
| | - Thomas G Ranney
- Mountain Crop Improvement Lab, Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, NC, 28759, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27607, USA.
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Zou X, Li L, Liao F, Chen W. iTRAQ-based quantitative proteomic analysis reveals NtGNL1-dependent regulatory network underlying endosome trafficking for pollen tube polar growth. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 161:200-209. [PMID: 33636685 DOI: 10.1016/j.plaphy.2021.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Endosome trafficking has been reported to play an essential role in pollen tube polar growth and NtGNL1 (Nicotiana tabacum GNOM-LIKE 1) regulates the polar growth through endosome trafficking. However, the regulation network and detailed molecular mechanisms underlying endosome trafficking remain unclear. Here, comparative proteomic analysis was carried out to survey the overall effect of NtGNL1 on pollen tube polar growth and NtGNL1-dependent endosome trafficking. With multiple comparative systems (RNAi, Wild type, and BFA or wortmannin treatments), 481 distinct proteins were identified including 43 common DEPs (differentially expressed proteins), of which 16 significant DEPs were common among RNAi, BFA, and wortmannin treated pollen tubes, indicating their close relation to the endosome trafficking. GO annotation indicates that the vesicle trafficking of gnl1HE pollen tubes differs from that of the BFA and wortmannin treated pollen tubes in the COPII-coated vesicle budding process. KEGG pathway analysis suggests that the Pentose phosphate pathway is critical for the NtGNL1-dependent endosome trafficking. Yeast two-hybrid further confirmed that the NtGNL1-Sec7 domain interacted strongly with VPS32.2, TCTP, PIS2, and PDIL2-1, suggesting that the core functional region of NtGNL1 is the Sec7 domain. Therefore, NtGNL1 likely functions via its Sec7 binding with these proteins to affect endosome trafficking. Our results provide a clear outline of proteins involving in NtGNL1-dependent endosome trafficking and valuable clues for understanding the regulatory mechanism of NtGNL1 guided pollen tube polar growth.
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Affiliation(s)
- Xinjian Zou
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Ling Li
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Fanglei Liao
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China; Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, 321004, China.
| | - Wenrong Chen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China; Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, 321004, China.
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Meng X, Yu Y, Zhao J, Cui N, Song T, Yang Y, Fan H. The Two Translationally Controlled Tumor Protein Genes, CsTCTP1 and CsTCTP2, Are Negative Modulators in the Cucumis sativus Defense Response to Sphaerotheca fuliginea. FRONTIERS IN PLANT SCIENCE 2018; 9:544. [PMID: 29922303 PMCID: PMC5996911 DOI: 10.3389/fpls.2018.00544] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/09/2018] [Indexed: 05/04/2023]
Abstract
Pathogen stress often significantly decreases cucumber production. However, knowledge regarding the molecular mechanism and signals of cucumber disease resistance is far from complete. Here, we report two translationally controlled tumor protein genes, CsTCTP1 and CsTCTP2, that are both negative modulators in the Cucumis sativus defense response to Sphaerotheca fuliginea. Subcellular localization analysis showed that CsTCTP1 and CsTCTP2 were both localized in the cytoplasm. Expression analysis indicated that the transcript levels of CsTCTP1 and CsTCTP2 were linked to the degree of cucumber resistance to S. fuliginea. Transient overexpression of either CsTCTP1 or CsTCTP2 in cucumber cotyledons impaired resistance to S. fuliginea, whereas silencing of either CsTCTP1 or CsTCTP2 enhanced cucumber resistance to S. fuliginea. The relationship of several defense-related genes and ABA and target of rapamycin (TOR) signaling pathway-related genes to the overexpressing and silencing of CsTCTP1/CsTCTP2 in non-infested cucumber plants was investigated. The results indicated that CsTCTP1 participates in the defense response to S. fuliginea by regulating the expression of certain defense-associated genes and/or ABA signaling pathway-associated genes, and CsTCTP2 participates through regulating the expression of TOR signaling pathway-associated genes. Our findings will guide enhancing the resistance of cucumber to powdery mildew.
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Affiliation(s)
- Xiangnan Meng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Yang Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Junyue Zhao
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Na Cui
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Tiefeng Song
- Vegetable Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yun Yang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Haiyan Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang Agricultural University, Shenyang, China
- *Correspondence: Haiyan Fan,
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