Identification and evaluation of reference genes for reliable normalization of real-time quantitative PCR data in acerola fruit, leaf, and flower

Screening and Validation of Appropriate Reference Genes for Real-Time Quantitative PCR under PEG, NaCl and ZnSO4 Treatments in Broussonetia papyrifera

Real-time quantitative PCR (RT-qPCR) has a high sensitivity and strong specificity, and is widely used in the analysis of gene expression. Selecting appropriate internal reference genes is the key to accurately analyzing the expression changes of target genes by RT-qPCR. To find out the most suitable internal reference genes for studying the gene expression in Broussonetia papyrifera under abiotic stresses (including drought, salt, and ZnSO4 treatments), seven different tissues of B. papyrifera, as well as the roots, stems, and leaves of B. papyrifera under the abiotic stresses were used as test materials, and 15 candidate internal reference genes were screened based on the transcriptome data via RT-qPCR. Then, the expression stability of the candidate genes was comprehensively evaluated through the software geNorm (v3.5), NormFinder (v0.953), BestKeeper (v1.0), and RefFinder. The best internal reference genes and their combinations were screened out according to the analysis results. rRNA and Actin were the best reference genes under drought stress. Under salt stress, DOUB, HSP, NADH, and rRNA were the most stable reference genes. Under heavy metal stress, HSP and NADH were the most suitable reference genes. EIF3 and Actin were the most suitable internal reference genes in the different tissues of B. papyrifera. In addition, HSP, rRNA, NADH, and UBC were the most suitable internal reference genes for the abiotic stresses and the different tissues of B. papyrifera. The expression patterns of DREB and POD were analyzed by using the selected stable and unstable reference genes. This further verified the reliability of the screened internal reference genes. This study lays the foundation for the functional analysis and regulatory mechanism research of genes in B. papyrifera.

Evaluation and validation of reference genes in Cymbidium faberi for real-time quantitative PCR

For all organs at all Cymbidium faberi stages, ACT, UBQ3 and GAPDH can be selected as reference genes. For organs of the vegetative stage, UBQ2 and UBQ3 can be chosen for analysis of normalized gene expression. For the bud stage, ACT and UBQ3 can be used for analysis of gene expression. For the full blossom stage, ACT, UBQ3 and UBQ2 can be introduced into relative gene expression analysis. For vegetative organs, UBQ2 and ACT can be used as reference genes. For reproductive organs, ACT, UBQ3 and UBQ2 can be used as a reference for data processing. CfAG1 gene expression is more consistent when UBQ3, GAPDH and ACT are used as reference genes.

Identification of Reference Genes for RT-qPCR Analysis in Gleditsia microphylla under Abiotic Stress and Hormone Treatment

Gleditsia microphylla is an important galactomannan gums source plant with characteristics of drought resistance, barren tolerance, and good adaptability. However, the underlying molecular mechanisms of the biological process are not yet fully understood. Real-time quantitative PCR (RT-qPCR) is an accurate and convenient method to quantify the gene expression level and transcription abundance of suitable reference genes. This study aimed to screen the best internal reference genes in G. microphylla under abiotic stresses, hormone treatments, and different tissues. Based on the transcriptome data, twelve candidate reference genes were selected, and ultimately, nine of them were further evaluated by the geNorm, NormFinder, BestKeeper, and RefFinder algorithms. These results show that TATA-binding protein 1 (TBP1)and Eukaryotic translation initiation factor 4A1 (EIF4A1)were the two most stable reference genes, and glyceraldehyde-3-phosphate dehydrogenase A subunit, chloroplastic (GAPA)and glyceraldehyde-3-phosphate dehydrogenase B subunit, chloroplastic (GAPB)were the two most unstable reference genes across all samples under the given experimental conditions. Meanwhile, the most stable reference genes varied among the different groups and tissues. Therefore, this study suggests that it is better to use a specific reference gene for a particular case rather than using a common reference gene.

The selection and identification of compound housekeeping genes for quantitative real-time polymerase chain reaction analysis in rat fetal kidney

During quantitative real-time polymerase chain reaction (RT-qPCR) data analysis, the selection of optimal housekeeping gene is necessary to ensure the accuracy of results. It is noteworthy that housekeeping genes commonly used in adult studies may not be applicable for fetus. However, the stability analysis of housekeeping gene in fetal kidney has not been reported. This study intends to screen the applicable compound housekeeping genes in rat fetal kidney. In this study, eight housekeeping genes used in kidney studies based on literature reports (GAPDH, ACTB, 18S, HPRT, YWHAZ, HMBS, PPIA, and TBP) were selected as the research object. Their expression levels in the rat fetal kidney in physiological condition and the intrauterine growth retardation (IUGR) model induced by prenatal dexamethasone exposure (PDE) (0.2 mg/kg·day from gestation Days 9 to 20) was measured. Furthermore, these eight housekeeping genes were used to conduct relative quantitative analysis of nephrin expression in the fetal kidney in PDE-induced IUGR model, to compare the influence of choosing different housekeeping gene on data analysis of nephrin expression and to verify the reliability of selected compound housekeeping genes. In this study, stable housekeeping genes of fetal kidney tissues in PDE-induced IUGR model were identified: ACTB, GAPDH, TBP, and HMBS for males; ACTB, YWHAZ, and GAPDH for females. Besides, our results suggest that ACTB + GAPDH were the best compound housekeeping genes for normalization analysis in male fetal kidney studies, and ACTB + YWHAZ in females. This study will provide an experimental evidence basis for the selection of housekeeping genes in the RT-qPCR experiment in renal development toxicology-related models.

Transcriptome-based selection and validation of optimal house-keeping genes for skin research in goats (Capra hircus)

BACKGROUND

In quantitative real-time polymerase chain reaction (qRT-PCR) experiments, accurate and reliable target gene expression results are dependent on optimal amplification of house-keeping genes (HKGs). RNA-seq technology offers a novel approach to detect new HKGs with improved stability. Goat (Capra hircus) is an economically important livestock species and plays an indispensable role in the world animal fiber and meat industry. Unfortunately, uniform and reliable HKGs for skin research have not been identified in goat. Therefore, this study seeks to identify a set of stable HKGs for the skin tissue of C. hircus using high-throughput sequencing technology.

RESULTS

Based on the transcriptome dataset of 39 goat skin tissue samples, 8 genes (SRP68, NCBP3, RRAGA, EIF4H, CTBP2, PTPRA, CNBP, and EEF2) with relatively stable expression levels were identified and selected as new candidate HKGs. Commonly used HKGs including SDHA and YWHAZ from a previous study, and 2 conventional genes (ACTB and GAPDH) were also examined. Four different experimental variables: (1) different development stages, (2) hair follicle cycle stages, (3) breeds, and (4) sampling sites were used for determination and validation. Four algorithms (geNorm, NormFinder, BestKeeper, and ΔCt method) and a comprehensive algorithm (ComprFinder, developed in-house) were used to assess the stability of each HKG. It was shown that NCBP3 + SDHA + PTPRA were more stably expressed than previously used genes in all conditions analysis, and that this combination was effective at normalizing target gene expression. Moreover, a new algorithm for comprehensive analysis, ComprFinder, was developed and released.

CONCLUSION

This study presents the first list of candidate HKGs for C. hircus skin tissues based on an RNA-seq dataset. We propose that the NCBP3 + SDHA + PTPRA combination could be regarded as a triplet set of HKGs in skin molecular biology experiments in C. hircus and other closely related species. In addition, we also encourage researchers who perform candidate HKG evaluations and who require comprehensive analysis to adopt our new algorithm, ComprFinder.

Identification and evaluation of reference genes for quantitative real-time PCR analysis in Passiflora edulis under stem rot condition

Passion fruit (Passiflora edulis), an important tropical and subtropical fruit, has a high edible and medicinal value. Stem rot disease is one of the most important diseases of passion fruit. An effective way for control and prevention of this disease is to identify the genes associated with resistance to this disease. Quantitative real-time PCR (RT-qPCR) has mainly been widely applied to detect gene expression because of its simplicity, fastness, low cost and high sensitivity. One of the requirements for RT-qPCR is the availability of suitable reference genes for normalization of gene expression. However, currently, no Passiflora edulis reference genes have been identified andthus it has hindered the gene expression studies in this plant. The present study aimed to address this issue. We analyzed sixteen candidate reference genes, including nine common (GAPDH, UBQ, ACT1, ACT2, EF-1α-1, EF-1α-2, TUA, NADP, and GBP) and seven novel genes (C13615, C24590, C27182, C10445, C21209, C22199, and C22526), in different tissues (stem, leaf, flower and fruit) of two accessions under stem rot condition. We calculated the expression stability in twenty-four samples using the ΔCt, GeNorm, NormFinder, BestKeeper and RefFinder. The results showed that both C21209 and EF-1α-2 were sufficient to normalize gene expression under stem rot, whereas the commonly used reference genes, GAPDH and UBQ, were the least stable ones. The expression patterns of PeUFC under stem rot condition normalized by stable and unstable reference genes indicated the suitability of using the optimal reference genes. To our knowledge, this is the first systematic study of reference genes in Passiflora edulis, which identified a number of reliable reference genes suitable for gene expression studies in Passiflora edulis by RT-qPCR.