Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling

Selection and validation of reference genes for quantitative real-time PCR analysis across tissues at different developmental stages in Taraxacum kok-saghyz

Quantitative real-time polymerase chain reaction (qRT-PCR) is a highly sensitive and widely used method for analyzing gene expression profiles. Accurate qRT-PCR normalization requires the identification of stable reference genes under specific experimental conditions. Although seven reference genes have been used in Taraxacum kok-saghyz (TKS), an alternative natural rubber-producing crop, a systematic identification of reliable internal references for gene expression analysis across tissues at distinct developmental stages of TKS has not been conducted. In this study, we screened 12 candidate reference genes (CRGs) based on RNA-seq data from 26 TKS samples, representing five tissue types and nine developmental stages. The expression levels of the 12 CRGs, along with 7 previously reported reference genes (RRGs), were quantified by qRT-PCR across various tissues and developmental stages. The expression stability of the 19 genes was further evaluated by four commonly used algorithms (geNorm, NormFinder, comparative delta Ct, and BestKeeper), and their results were integrated by RefFinder to generate a comprehensive stability ranking. The final results revealed that TkADF1 and TkRPT6A were the most suitable internal control genes for the all-tissue group and leaf samples. TkUPL and TkSIZ1 were found to be optimal for root samples, while TkADF1 and TkSRPRA were preferred choices for latex samples. Moreover, validation using two rubber biosynthesis-related genes (TkFPS1 and TkSRPP2) confirmed the reliability of these recommended genes, showing a strong positive correlation with the RNA-seq data. This study provides reliable reference genes for qRT-PCR normalization in TKS, facilitating future research on developmental regulation and natural rubber biosynthesis.

Rice Reference Genes: redefining reference genes in rice by mining RNA-seq datasets

Reverse transcription quantitative real-time PCR (RT-qPCR) is esteemed for its precision and reliability, positioning it as the standard for evaluating gene expression. Selecting suitable reference genes is crucial for acquiring accurate data on target gene expression. However, identifying appropriate reference genes for specific rice tissues or growth conditions has been a challenge. To overcome this, we introduce the Rice Reference Genes (RRG) tool ( https://www.rrgenes.com/ ), which assists researchers in selecting reference genes for diverse experimental conditions in rice. This tool utilizes 4404 rice-derived RNA-seq datasets, categorized by five tissue types-leaf, root, seedling, panicle, and seed-and seven stress conditions (cold, disease, drought, heat, hormone, metal, and salt), along with corresponding control groups (mock). In this research, we employed the RRG web-based tool to identify candidate reference genes in rice leaves, roots, and seedlings exposed to salt and drought stress. These candidates were rigorously tested against conventionally established reference genes, confirming their accuracy and reliability. The RRG tool is designed to be user-friendly, allowing even those with limited experience to efficiently select optimal reference genes in rice with ease.

Selection and Validation of Reference Genes for Gene Expression Studies in Euonymus japonicus Based on RNA Sequencing

Euonymus japonicus is one of the most low-temperature-tolerant evergreen broad-leaved tree species in the world and is widely used in urban greening. However, there are very few molecular biology studies on its low-temperature tolerance mechanism. So far, no researcher has selected and reported on its reference genes. In this study, 21 candidate reference genes (12 traditional housekeeping genes and 9 other genes) were initially selected based on gene expression and coefficient of variation (CV) through RNA-Seq (unpublished data), and qRT-PCR was used to detect the expression levels of candidate reference genes in three different groups of samples (leaves under different temperature stresses, leaves of plants at different growth stages, and different organs). After further evaluating the expression stability of these genes using geNorm, NormFinder, Bestkeeper, and RefFind, the results show that the traditional housekeeping gene eIF5A and the new reference gene RTNLB1 have good stability in the three different groups of samples, so they are reference genes with universality. In addition, we used eIF5A and RTNLB1 as reference genes to calibrate the expression pattern of the target gene EjMAH1, which confirmed this view. This article is the first to select and report on the reference gene of E. japonicus, laying the foundation for its low-temperature tolerance mechanism and other molecular biology research.

Advancements in Reference Gene Selection for Fruit Trees: A Comprehensive Review

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.

Selection and validation of novel stable reference genes for qPCR analysis in EMT and MET

Quantitative real-time polymerase chain reaction is a powerful tool for quantifying gene expression. The relative quantification relies on normalizing the data to reference genes or internal controls not modulated by the experimental conditions. The most widely used internal controls occasionally show changed expression patterns in different experimental settings, such as the mesenchymal to epithelial transition. Thus, identifying appropriate internal controls is of utmost importance. We analyzed multiple RNA-Seq datasets using a combination of statistical approaches such as percent relative range and coefficient of variance to define a list of candidate internal control genes, which was then validated experimentally and by using in silico analyses as well. We identified a group of genes as strong internal control candidates with high stability compared to the classical ones. We also presented evidence for the superiority of the percent relative range method for calculating expression stability in data sets with larger sample sizes. We used multiple methods to analyze data collected from several RNA-Seq datasets; we identified Rbm17 and Katna1 as the most stable reference genes in EMT/MET studies. The percent relative range approach surpasses other methods when analyzing datasets of larger sample sizes.

Physiological, transcriptomic, and metabolic analyses reveal that mild salinity improves the growth, nutrition, and flavor properties of hydroponic Chinese chive (Allium tuberosum Rottler ex Spr)

Environmental stressors such as salinity have pronounced impacts on the growth, productivity, nutrition, and flavor of horticultural crops, though yield loss sometimes is inevitable. In this study, the salinity influences were evaluated using hydroponic Chinese chive (Allium tuberosum) treated with different concentrations of sodium chloride. The results demonstrated that lower salinity could stimulate plant growth and yield. Accordingly, the contents of soluble sugar, ascorbic acid, and soluble protein in leaf tissues increased, following the decrease of the nitrate content, under mild salinity (6.25 or 12.5 mM NaCl). However, a higher level of salinity (25 or 50 mM NaCl) resulted in growth inhibition, yield reduction, and leaf quality deterioration of hydroponic chive plants. Intriguingly, the chive flavor was boosted by the salinity, as evidenced by pungency analysis of salinity-treated leaf tissues. UPLC-MS/MS analysis reveals that mild salinity promoted the accumulation of glutamic acid, serine, glycine, and proline in leaf tissues, and thereby enhanced the umami and sweet flavors of Chinese chive upon salinity stress. Considering the balance between yield and flavor, mild salinity could conduce to hydroponic Chinese chive cultivation. Transcriptome analysis revealed that enhanced pungency could be ascribed to a salt stress-inducible gene, AtuFMO1, associated with the biosynthesis of S-alk(en)yl cysteine sulphoxides (CSOs). Furthermore, correlation analysis suggested that two transcription factors, AtubHLH and AtuB3, were potential regulators of AtuFMO1 expressions under salinity. Thus, these results revealed the molecular mechanism underlying mild salinity-induced CSO biosynthesis, as well as a practical possibility for producing high-quality Chinese chive hydroponically.

Selection and Validation of Reference Genes for RT-qPCR Analysis in Tibetan Medicinal Plant Saussurea Laniceps Callus under Abiotic Stresses and Hormone Treatments

Real-time quantitative PCR (RT-qPCR) is an important technique for studying gene expression analysis, but accurate and reliable results depend on the use of a stable reference gene. This study proposes to test the expression stability of candidate reference genes in the callus of Saussurea laniceps, a unique Tibetan medicinal plant. Based on the S. laniceps callus transcriptome, eleven candidate reference genes, including TUA2, TUB3, TUB8, TIF3B1, TIF3H1, ELF5A, PP2AA2, UEV1D, UBL5, UBC36, and SKIP1), were validated for RT-qPCR normalization in the callus under abiotic stress (salt, cold, and UV) and hormone treatments (abscisic acid, MeJA, and salicylic acid). The stability of the candidate genes was evaluated in all the samples of S. laniceps. Comprehensive analysis of all samples showed that the best reference genes were UBC36 and UBL5. ELF5A and TIF3B1 were ranked as the most stable genes in the sample sets under abiotic stress. For hormone stimulation, UBC36 and TIF3H1 genes had the best stability. This study provides useful guidelines and a starting point for reference gene selection for expression analysis using RT-qPCR techniques in S. laniceps.