Reference gene selection for qRT-PCR analyses of luffa (Luffa cylindrica) plants under abiotic stress conditions

Chen, Mindong; Wang, Bin; Li, Yongping; Zeng, Mei-Juan; JianTing, Liu; Xinru, YE; Zhu, Haishan; Qingfang, Wen

doi:10.1038/s41598-021-81524-w

Cited by 22 publications

(15 citation statements)

References 51 publications

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“…Stem-loop qPCR analysis showed that the expression level of mature miR319 was rapidly upregulated after 6 h of LT treatment, but decreased to control (0 h) level after 24 h ( Figure 6 B). Some studies have shown the EF-1α was sufficient for accurate normalization in cold-treated samples, and the EF-1α gene was the frequently-used internal control in the genus chrysanthemum for normalizing transcription data [ 70 , 71 , 72 ]. When performing microRNA detection, because a better strategy is choosing a constitutively expressed small noncoding RNA as a reference, we often chose the U6 gene [ 73 , 74 , 75 ].…”

Section: Resultsmentioning

confidence: 99%

Characterization of the TCP Gene Family in Chrysanthemum nankingense and the Role of CnTCP4 in Cold Tolerance

Tian

Zhai

Zhu

et al. 2022

Plants

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Plant-specific TCP transcription factors play a key role in plant development and stress responses. Chrysanthemum nankingense shows higher cold tolerance than its ornamental polyploid counterpart. However, whether the TCP gene family plays a role in conferring cold tolerance upon C. nankingense remains unknown. Here, we identified 23 CnTCP genes in C. nankingense, systematically analyzed their phylogenetic relationships and synteny with TCPs from other species, and evaluated their expression profiles at low temperature. Phylogenetic analysis of the protein sequences suggested that CnTCP proteins fall into two classes and three clades, with a typical bHLH domain. However, differences between C. nankingense and Arabidopsis in predicted protein structure and binding sites suggested a unique function of CnTCPs in C. nankingense. Furthermore, expression profiles showed that expression of most CnTCPs were downregulated under cold conditions, suggesting their importance in plant responses to cold stress. Notably, expression of miR319 and of its predicted target genes, CnTCP2/4/14, led to fast responses to cold. Overexpression of Arabidopsis CnTCP4 led to hypersensitivity to cold, suggesting that CnTCP4 might play a negative role in C. nankingense responses to cold stress. Our results provide a foundation for future functional genomic studies on this gene family in chrysanthemum.

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Section: Resultsmentioning

confidence: 99%

Characterization of the TCP Gene Family in Chrysanthemum nankingense and the Role of CnTCP4 in Cold Tolerance

Tian

Zhai

Zhu

et al. 2022

Plants

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“…Similarly, a study aiming to screen out suitable reference genes in two thyme species (Lamiaceae family), recommended GAPDH and 18S rRNA as the best and the worst genes, respectively [ 24 ]. Much research has also demonstrated that the expression levels of reference genes might vary not only within tissues or development stages but also even get influenced by various biotic and abiotic stresses [ 7 , 26 ]. For example, a study with genome-wide identification and assessment of novel reference genes in wheat identified stable expression for ACT and UBQ , but not in tomato plants [ 27 , 28 ].…”

Section: Discussionmentioning

confidence: 99%

Selection and Validation of the Most Suitable Reference Genes for Quantitative Real-Time PCR Normalization in Salvia rosmarinus under In Vitro Conditions

Bharati

Sen

Kumar

et al. 2022

Plants

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Salvia rosmarinus L. (rosemary) is known to have a wide range of pharmacological effects including antidiabetic, anticarcinogenic, and antitumorigenic properties owing to its secondary metabolites. Studies aiming to elevate these metabolites have utilized various elicitors and stresses under in vitro conditions, although underlying molecular mechanisms remain unexplored. Gene expression studies using RT-qPCR might provide valuable information regarding how plant and plant cells interact and perceive various treatments and elicitors. However, despite being able to calculate accurate fold changes, the accuracy of the RT-qPCR data highly depends on the expression of reference genes. To the best of our knowledge, there is no information available on the stable reference genes in rosemary under in vitro conditions. Thus, in this paper, we assessed the stability of seven commonly used reference genes under different elicitor and stress conditions using RT-qPCR. Thereafter, the five most commonly used software and algorithms (comparative ΔCt, BestKeeper, NormFinder, geNorm, and RefFinder) were used to rank the candidates based on their expression stabilities. In conclusion, we recommend using a combination of F1-ATPase, ATP synthase and ACCase to normalize the gene expression experiments in rosemary under in vitro conditions. The selected reference genes were verified using 4-coumarate-CoA ligase, a pharmacologically important gene, whose expression might alter under nanoparticle treatment. Additionally, reference genes for several plant tissues, elicitors, and stresses are also proposed. The conclusions obtained from this current study will accelerate the future molecular work in S. rosmarinus and other related species.

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“…Elongation factor 1α ( EF-1α ) (MN548044) was used as a housekeeping gene (internal control), previously reported by Chen [ 53 ]. ABI PRISM 7900HT sequence detection system (Applied Biosystems Applera, Darmstadt, Germany) was used for gene amplification and real-time detection.…”

Section: Methodsmentioning

confidence: 99%

Immunomodulatory Molecular Mechanisms of Luffa cylindrica for Downy Mildews Resistance Induced by Growth-Promoting Endophytic Fungi

Rauf

Ur-Rahman

Arif

et al. 2022

JoF

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Downy mildew (DM), caused by P. cubensis, is harmful to cucurbits including luffa, with increased shortcomings associated with its control through cultural practices, chemical fungicides, and resistant cultivars; there is a prompt need for an effective, eco-friendly, economical, and safe biocontrol approach. Current research is therefore dealt with the biocontrol of luffa DM1 through the endophytic fungi (EF) consortium. Results revealed that T. harzianum (ThM9) and T. virens (TvA1) showed pathogen-dependent inducible metabolic production of squalene and gliotoxins by higher gene expression induction of SQS1/ERG9 (squalene synthase) and GliP (non-ribosomal peptide synthetase). Gene expression of lytic enzymes of EF was also induced with subsequently higher enzyme activities upon confrontation with P. cubensis. EF-inoculated luffa seeds showed efficient germination with enhanced growth potential and vigor of seedlings. EF-inoculated plants showed an increased level of growth-promoting hormone GA with higher gene expression of GA2OX8. EF-pre-inoculated seedlings were resistant to DM and showed an increased GSH content and antioxidant enzyme activities (SOD, CAT, POD). The level of MDA, H2O2, REL, and disease severity was reduced by EF. ACC, JA, ABA, and SA were overproduced along with higher gene expression of LOX, ERF, NCED2, and PAL. Expression of defense-marker genes (PPO, CAT2, SOD, APX, PER5, LOX, NBS-LRR, PSY, CAS, Ubi, MLP43) was also modulated in EF-inoculated infected plants. Current research supported the use of EF inoculation to effectively escalate the systemic immunity against DM corresponding to the significant promotion of induced systemic resistance (ISR) and systemic acquired resistance (SAR) responses through initiating the defense mechanism by SA, ABA, ET, and JA biosynthesis and signaling pathways in luffa.

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Reference gene selection for qRT-PCR analyses of luffa (Luffa cylindrica) plants under abiotic stress conditions

Cited by 22 publications

References 51 publications

Characterization of the TCP Gene Family in Chrysanthemum nankingense and the Role of CnTCP4 in Cold Tolerance

Characterization of the TCP Gene Family in Chrysanthemum nankingense and the Role of CnTCP4 in Cold Tolerance

Selection and Validation of the Most Suitable Reference Genes for Quantitative Real-Time PCR Normalization in Salvia rosmarinus under In Vitro Conditions

Immunomodulatory Molecular Mechanisms of Luffa cylindrica for Downy Mildews Resistance Induced by Growth-Promoting Endophytic Fungi

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