Validation of reference genes for RT-qPCR studies in Stevia rebaudiana in response to elicitor agents

Reference genes for Eucalyptus spp. under Beauveria bassiana inoculation and subsequently infestation by the galling wasp Leptocybe invasa

Relative gene expression analysis through RT-qPCR is an important molecular technique that helps understanding different molecular mechanisms, such as the plant defense response to insect pests. However, the use of RT-qPCR for gene expression analysis can be affected by factors that directly affect the reliability of the results. Among these factors, the appropriate choice of reference genes is crucial and can strongly impact RT-qPCR relative gene expression analyses, highlighting the importance in correctly choosing the most suitable genes for the success of the analysis. Thus, this study aimed to select and validate reference genes for relative gene expression studies through RT-qPCR in hybrids of Eucalyptus tereticornis × Eucalyptus camaldulensis (drought tolerant and susceptible to Leptocybe invasa) under conditions of inoculation by the Beauveria bassiana fungus and subsequent infestation by L. invasa. The expression level and stability of eleven candidate genes were evaluated. Stability was analyzed using the RefFinder tool, which integrates the geNorm, NormFinder, BestKeeper, and Delta-Ct algorithms. The selected reference genes were validated through the expression analysis of the transcriptional factor EcDREB2 (dehydration-responsive element-binding protein 2). For all treatments evaluated, EcPTB, EcPP2A-1, and EcEUC12 were the best reference genes. The triplets EcPTB/EcEUC12/EcUBP6, EcPP2A-1/EcEUC12/EcPTB, EcIDH/EcSAND/Ecα-TUB, EcPP2A-1/Ecα-TUB/EcPTB, and EcPP2A-1/EcUPL7/EcSAND were the best reference genes for the control plants, mother plants, plants inoculated with B. bassiana, plants infested with L. invasa, and plants inoculated with B. bassiana and subsequently infested with L. invasa, respectively. The best determined reference genes were used to normalize the RT-qPCR expression data for each experimental condition evaluated. The results emphasize the importance of this type of study to ensure the reliability of relative gene expression analyses. Furthermore, the findings of this study can be used as a basis for future research, comprising gene expression analysis of different eucalyptus metabolic pathways.

Systematic Identification and Validation of Suitable Reference Genes for the Normalization of Gene Expression in Prunella vulgaris under Different Organs and Spike Development Stages

The quantitative real-time PCR (qRT-PCR) is an efficient and sensitive method for determining gene expression levels, but the accuracy of the results substantially depends on the stability of the reference gene (RG). Therefore, choosing an appropriate reference gene is a critical step in normalizing qRT-PCR data. Prunella vulgaris L. is a traditional Chinese medicine herb widely used in China. Its main medicinal part is the fruiting spike which is termed Spica Prunellae. However, thus far, few studies have been conducted on the mechanism of Spica Prunellae development. Meanwhile, no reliable RGs have been reported in P. vulgaris. The expression levels of 14 candidate RGs were analyzed in this study in various organs and at different stages of Spica Prunellae development. Four statistical algorithms (Delta Ct, BestKeeper, NormFinder, and geNorm) were utilized to identify the RGs' stability, and an integrated stability rating was generated via the RefFinder website online. The final ranking results revealed that eIF-2 was the most stable RG, whereas VAB2 was the least suitable as an RG. Furthermore, eIF-2 + Histon3.3 was identified as the best RG combination in different periods and the total samples. Finally, the expressions of the PvTAT and Pv4CL2 genes related to the regulation of rosmarinic acid synthesis in different organs were used to verify the stable and unstable RGs. The stable RGs in P. vulgaris were originally identified and verified in this work. This achievement provides strong support for obtaining a reliable qPCR analysis and lays the foundation for in-depth research on the developmental mechanism of Spica Prunellae.

Effect of light intensity on steviol glycosides production in leaves of Stevia rebaudiana plants

Stevia rebaudiana leaf extracts contain stevioside and rebaudioside A, two steviol glycosides (SGs) used as natural sweeteners because of their non-toxic, thermally stable and non-caloric properties. Indeed, leaf extracts can be up to 300 times sweeter than sucrose. Stevioside and rebaudioside A have organoleptic differences, the first one having an undesirable bitterness and the second one a higher sweetener capacity. Selection of the S. rebaudiana varieties and the best environmental conditions that elicit higher SGs content and the appropriate composition is an important goal. In this study we quantified and compared the amount of stevioside and rebaudioside A in two of the most used S. rebaudiana cultivars, Morita II and Criolla. Our results show a strong differential ratio of stevioside and rebaudioside A accumulated in the leaf between these cultivars. The Criolla cultivar showed about 3 times more stevioside per mg of dry weight than Morita II, whereas the Morita II accumulated almost 10 times more rebaudioside A than that produced in Criolla. We observed an enhanced expression in Morita II of three genes (SrKA13H, SrUGT74G1 and SrUGT76G1) known to encode three enzymes that participate in SGs biosynthesis, likely contributing to the differences in the stevioside and rebaudioside A accumulation. Not only genetic variation can affect SGs composition, but also environmental factors and crop management. Numerous studies have shown that the light regime in which S. rebaudiana cultivars grow can affect SGs accumulation. However, the optimal light regime to increase total SGs content is currently controversial. By applying various light intensities, we detected an increase of expression of these three biosynthetic genes at higher light intensity, accompanied by higher levels of stevioside and rebaudioside A, demonstrating that light intensity influences the synthesis of SGs.

Methyl jasmonate-induced resistance to Delia platura (Diptera: Anthomyiidae) in Lupinus mutabilis

BACKGROUND

Andean lupin (Lupinus mutabilis Sweet) is an important leguminous crop from South America with a high protein content. In Ecuador, lupin yields are severely affected by the infestation of Delia platura larvae on germinating seeds. The application of elicitor molecules with activity against herbivorous insects to control D. platura infestation constitutes an unexplored and promising alternative for chemical insecticides. In this study, methyl jasmonate (MeJA), hexanoic acid, menadione sodium bisulfite, and DL-β-aminobutyric acid were evaluated for their ability to induce resistance against D. platura in three commercial lupin cultivars.

RESULTS

Only seeds pretreated with MeJA significantly impaired insect performance during choice and no-choice assays. Additionally, fitness indicators such as seed germination and growth were not affected by MeJA treatment. To investigate the molecular mechanisms behind the MeJA-mediated resistance, RT-qPCR assays were performed. First, RT-qPCR reference genes were validated, showing that LmUBC was the most stable reference gene. Next, expression analysis over time revealed that MeJA application up-regulated the activity of the jasmonic acid biosynthetic genes LmLOX2 and LmAOS, together with other jasmonate-related defense genes, such as LmTPS1, LmTPS4, LmPI2, LmMBL, LmL/ODC, LmCSD1, and LmPOD.

CONCLUSION

This study indicates that MeJA can be used as an environmentally friendly elicitor molecule to protect Andean lupin from D. platura attack without fitness cost. MeJA application induces plant defense responses to insects in Andean lupin that may be modulated by the onset of terpenoid biosynthesis, proteinase inhibitors, lectins, polyamines, and antioxidative enzymes. © 2021 Society of Chemical Industry.

Selection and Validation of Candidate Reference Genes for Gene Expression Analysis by RT-qPCR in Rubus

Due to the lack of effective and stable reference genes, studies on functional genes in Rubus, a genus of economically important small berry crops, have been greatly limited. To select the best internal reference genes of different types, we selected four representative cultivars of blackberry and raspberry (red raspberry, yellow raspberry, and black raspberry) as the research material and used RT-qPCR technology combined with three internal stability analysis software programs (geNorm, NormFinder, and BestKeeper) to analyze 12 candidate reference genes for the stability of their expression. The number of most suitable internal reference genes for different cultivars, tissues, and fruit developmental stages of Rubus was calculated by geNorm software to be two. Based on the results obtained with the three software programs, the most stable genes in the different cultivars were RuEEF1A and Ru18S. Finally, to validate the reliability of selected reference genes, the expression pattern of the RuCYP73A gene was analyzed, and the results highlighted the importance of appropriate reference gene selection. RuEEF1A and Ru18S were screened as reference genes for their relatively stable expression, providing a reference for the further study of key functional genes in blackberry and raspberry and an effective tool for the analysis of differential gene expression.

Comparative transcriptome analysis provides insights into steviol glycoside synthesis in stevia (Stevia rebaudiana Bertoni) leaves under nitrogen deficiency

Transcriptome analysis revealed the potential mechanism of nitrogen regulating steviol glycosides synthesis via shifting of leaf carbon metabolic flux or inducing certain transcription factors. Nitrogen (N) plays key regulatory roles in both stevia (Stevia rebaudiana) growth and the synthesis of its functional metabolite steviol glycosides (SGs), but the mechanism by which this nutrient regulates SGs synthesis remains to be elucidated. To address this question, a pot experiment was performed in a greenhouse where stevia plants fertilized with N (the control as CK plants) and compared with plants without the supply of N. Physiological and biochemical analyses were conducted to test the growth and metabolic responses of plants to N regimes. Our results showed that N deficiency significantly inhibited plant growth and leaf photosynthesis, while increased leaf SGs contents in stevia (49.97, 46.64 and 84.80% respectively for rebaudioside A, stevioside, and rebaudioside C), which may be partly due to "concentration effect". Then, transcriptome analysis was conducted to understand the underlying mechanisms. A total of 535 differentially expressed genes were identified, and carbon metabolism-related events were highlighted by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Many of these genes were significantly upregulated by N-deficiency, including those involved in "phenylpropanoid biosynthesis", "flavonoid biosynthesis" and "starch and sucrose metabolism". Our study also analyzed the expression patterns of SGs synthesis-related genes under two N regimes and the potential transcription factors linking N nutrition and SG metabolism. N-deficiency may promote SGs synthesis by changing the carbon metabolism flux or inducing certain transcription factors. Our results provide deeper insight into the relationship between N nutrition and SGs synthesis in stevia plants.

The effect of the elicitors on the steviol glycosides biosynthesis pathway in Stevia rebaudiana

Stevia rebaudiana Bertoni has been promoted for having sweet leaves as well as pharmaceutical and industrial properties. The sweet taste of Stevia leaves is due to the presence of steviol glycosides (a group of diterpene glycosides) found in a small number of plants. In the biosynthetic pathway of steviol glycosides (SGs), 15 enzymes that express the genes are associated with these enzymes under the influence of the elicitors. Due to the individuality of the stevia and few studies on the biosynthesis pathway of SGs, this paper attempted to investigate the effects of some of the elicitors, including methyl jasmonate (MeJA), salicylic acid (SA), auxins (Aux), cytokinins (CKs), gibberellins (GAs) and its inhibitors including paclobutrazol (BPZ) and chloroquate (CCC)), on the responsible genes for the biosynthesis of SGs. Some of these elicitors, including MeJA, SA and GA have great potential in increasing secondary metabolites. Moreover, the biosynthetic pathway of GAs and SGs are shared till ent-kaurenoic acid (ent-KA) biosynthesis, which raises the question of whether this hormone and its inhibitors are effective in the SGs biosynthesis.

Selection of Suitable Reference Genes in Pinus massoniana Lamb. Under Different Abiotic Stresses for qPCR Normalization

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.

Accumulation of amino acids and flavonoids in hairy root cultures of common buckwheat (Fagopyrum esculentum)

Transformed hairy root culture in common buckwheat (Fagopyrum esculentum Moench Rubra cultivar) was investigated for accumulation of amino acids and specific flavonoids. Leaves and stems of F. esculentum were used a starting material for induction of hairy roots via the Agrobacterium rhizogenes A4 strain. The transformed lines were confirmed by PCR detection of rol B gene, and their capability to continuously form hairy roots. Three lines from each explant types depending upon growth kinetics were observed. The hairy root lines were used to measure the contents of 17 amino acids and 3 flavonoids. Overall, the hairy root lines exhibited elevated accumulation of semi-essential amino acids such as lysine, isoleucine, valine, histidine and phenylalanine. Content of proline was increased 3-5 times, likely due to the biotic stress reaction induced with A. rhizogenes. Determination of flavonoids by high-performance liquid chromatography, hesperidine and kaempferol-3-rutinoside, were accumulated in hairy root cultures and didn't detected in non-transformed root. The increase in flavonoids positively correlated with the antioxidant capacity of the hairy root cultures.