Selection of reference genes for quantitative real-time PCR analysis of photosynthesis-related genes expression in Lilium regale

Screening and validation of reference genes in Dracaena cochinchinensis using quantitative real-time PCR

Dragon's blood, the red resin derived from the wounded Dracaena, is a precious traditional medicine used by different culture. Dracaena cochinchinensis is one of the main species of Dracaena, and is the endangered medicinal plants in China. The vulnerable status severely limits the medicinal value and wide application of dragon's blood. Therefore, it's essential to analyze the mechanisms that form dragon's blood in order to increase artificial production. To clarify the mechanisms forming dragon's blood, understanding gene expression in the flavonoid biosynthesis pathway is the foundation. However, reference genes of D. cochinchinensis haven't been analyzed. In this study, expression profiles of seven commonly used housekeeping genes (Actin, α-EF, UBC, β-tubulin, 18S, GAPDH, His) were evaluated by using quantitative real-time PCR combined with the algorithms geNorm, NormFinder, BestKeeper, and RefFinder. On the basis of overall stability ranking, the best reference genes were the combinations β-tubulin +UBC for wounded stems and α-EF +18S + Actin for different organs. Reliability of the recommended reference genes was validated by normalizing relative expression of two key enzyme genes PAL1 and CHI1 in the flavonoid biosynthesis pathway. The results provide a foundation to study gene expression in future research on D. cochinchinensis or other Dracaena.

Screening and Validation of Internal Reference Genes for Quantitative Real-Time PCR Analysis of Leaf Color Mutants in Dendrobium officinale

Leaf color mutants (LCMs) are important resources for studying diverse metabolic processes such as chloroplast biogenesis and differentiation, pigments' biosynthesis and accumulation, and photosynthesis. However, in Dendrobium officinale, LCMs are yet to be fully studied and exploited due to the unavailability of reliable RGs (reference genes) for qRT-PCR (quantitative real-time reverse transcription PCR) normalization. Hence, this study took advantage of previously released transcriptome data to select and evaluate the suitability of ten candidate RGs, including Actin (Actin), polyubiquitin (UBQ), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor 1-α (EF1α), β-tubulin (β-TUB), α-tubulin (α-TUB), 60S ribosomal protein L13-1 (RPL13AD), aquaporin PIP1-2 (PIP1-2), Intima protein (ALB3) and Cyclin (CYCB1-2) for normalizing leaf color-related genes' expression levels via qRT-PCR. Stability rankings analysis via common software Best-Keeper, GeNorm, and NormFinder disclosed that all ten genes met the requirements of RGs. Of them, EF1α exhibited the highest stability and was selected as the most reliable. The reliability and accuracy of EF1α were confirmed through qRT-PCR analysis of fifteen chlorophyll pathway-related genes. The expression patterns of these genes via EF1α normalization were consistent with the results by RNA-Seq. Our results offer key genetic resources for the functional characterization of leaf color-related genes and will pave the way for molecular dissection of leaf color mutations in D. officinale.

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 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.

The identification of key candidate genes mediating yellow seedling lethality in a Lilium regale mutant

Leaf color mutants are ideal materials for exploring plant photosynthesis mechanisms, chlorophyll biosynthetic pathways and chloroplast development. The yellow seedling lethal mutant lrysl1 was discovered from self-bred progenies of Lilium regale; however, the mechanism of leaf color mutation remains unclear. In this study, the ultrastructural and physiological features and de novo RNA-Seq data of a L. regale leaf color mutant and wild-type L. regale were investigated. Genetic analysis indicated that the characteristics of the lrysl1 mutant were controlled by a recessive nuclear gene. The chlorophyll a, chlorophyll b and carotenoid contents in the mutant leaves were lower than those in the wild-type leaves. Furthermore, the contents of the chlorophyll precursors aminolevulinic acid (ALA), porphobilinogen (PBG), protoporphyrin IX (ProtoIX), Mg-protoporphyrin IX (Mg-ProtoIX), and protochlorophyll (Pchl) decreased significantly in mutant leaves. Transcriptome data from the mutant and wild type showed that a total of 892 differentially expressed genes were obtained, of which 668 and 224 were upregulated genes and downregulated genes in the mutant, respectively. Almost all genes in the photosynthesis pathway and chlorophyll biosynthetic pathway were downregulated in the mutant, which corroborated the differences in the physiological features mentioned above. Further research indicated that the chloroplasts of the mutant leaves exhibited an abnormal morphology and distribution and that the expression of a gene related to chloroplast development was downregulated. It was concluded that abnormal chloroplast development was the main cause of leaf color mutation in the mutant lrysl1 and that LrGLK was a gene related to chloroplast development in L. regale. This research provides a foundation for further research on the mechanism by which LrGLK regulates chloroplast development in L. regale.