Candidate reference genes for quantitative gene expression analysis in Lagerstroemia indica

qRT-PCR Reference Gene Selection for the Discoloration of Tender Leaves in Hawk Tea (Litsea coreana)

To identify stable reference genes for qRT-PCR analysis across different developmental stages and color variations of tender leaves in Litsea coreana, seven candidate reference genes were selected based on existing transcriptome data. qRT-PCR was performed on tender leaves of L. coreana at various stages and under different color conditions. The stability of these genes was evaluated using GeNorm (version 2003), NormFinder (version 0953), BestKeeper (version 2003), and ReFinder software (version 2004). The most stable genes were selected, and the stability of the chosen reference genes was validated. RPL and ACT were the most stable genes across different leaf developmental stages, while ACT and EF1-α showed the highest stability across different leaf colors. Overall, ACT and EF1-α were the most stable reference genes for both developmental stages and color variations. ACT and EF1-α can be used as reliable reference genes for gene expression studies in the color change process of L. coreana tender leaves. This will provide a foundation for further research into the molecular mechanisms of leaf color changes and the development of color regulation genes in L. coreana.

Selection of Reference Genes of Flower Development in Ludisia discolor

Background: RT-qPCR is a powerful strategy for recognizing the most appropriate reference genes, which can successfully minimize experimental mistakes through accurate normalization. Ludisia discolor, recognized for its ornamental value, features little, distinctive blossoms with twisted lips and gynostemium showing chiral asymmetry, together with striking blood-red fallen leaves periodically marked with golden blood vessels. Methods and Results: To ensure the accuracy of qRT-PCR, selecting appropriate reference genes for quantifying target gene expression levels is essential. This study aims to identify stable reference genes during the development of L. discolor. In this study, the entire floral buds, including the lips and gynostemium from different development stages, were taken as materials. Based upon the transcriptome information of L. discolor, nine housekeeping genes, ACT, HIS, EF1-α1, EF1-α2, PP2A, UBQ1, UBQ2, UBQ3, and TUB, were selected in this research study as prospect interior referral genes. The expression of these nine genes were found by RT-qPCR and afterwards comprehensively examined by four software options: geNorm, NormFinder, BestKeeper, and ΔCt. The outcomes of the analysis showed that ACT was the most steady gene, which could be the most effective inner referral gene for the expression evaluation of flower advancement in L. discolor. Conclusions: The results of this study will contribute to the molecular biology research of flower development in L. discolor and closely related species.

DREB1 and DREB2 Genes in Garlic (Allium sativum L.): Genome-Wide Identification, Characterization, and Stress Response

Dehydration-responsive element-binding (DREB) transcription factors (TFs) of the A1 and A2 subfamilies involved in plant stress responses have not yet been reported in Allium species. In this study, we used bioinformatics and comparative transcriptomics to identify and characterize DREB A1 and A2 genes redundant in garlic (Allium sativum L.) and analyze their expression in A. sativum cultivars differing in the sensitivity to cold and Fusarium infection. Eight A1 (AsaDREB1.1-1.8) and eight A2 (AsaDREB2.1-2.8) genes were identified. AsaDREB1.1-1.8 genes located in tandem on chromosome 1 had similar expression patterns, suggesting functional redundancy. AsaDREB2.1-2.8 were scattered on different chromosomes and had organ- and genotype-specific expressions. AsaDREB1 and AsaDREB2 promoters contained 7 and 9 hormone- and stress-responsive cis-regulatory elements, respectively, and 13 sites associated with TF binding and plant development. In both Fusarium-resistant and -sensitive cultivars, fungal infection upregulated the AsaDREB1.1-1.5, 1.8, 2.2, 2.6, and 2.8 genes and downregulated AsaDREB2.5, but the magnitude of response depended on the infection susceptibility of the cultivar. Cold exposure strongly upregulated the AsaDREB1 genes, but downregulated most AsaDREB2 genes. Our results provide the foundation for further functional analysis of the DREB TFs in Allium crops and could contribute to the breeding of stress-tolerant varieties.

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.

Genome-Wide Identification, Expression, and Response to Fusarium Infection of the SWEET Gene Family in Garlic (Allium sativum L.)

Proteins of the SWEET (Sugar Will Eventually be Exported Transporters) family play an important role in plant development, adaptation, and stress response by functioning as transmembrane uniporters of soluble sugars. However, the information on the SWEET family in the plants of the Allium genus, which includes many crop species, is lacking. In this study, we performed a genome-wide analysis of garlic (Allium sativum L.) and identified 27 genes putatively encoding clade I-IV SWEET proteins. The promoters of the A. sativum (As) SWEET genes contained hormone- and stress-sensitive elements associated with plant response to phytopathogens. AsSWEET genes had distinct expression patterns in garlic organs. The expression levels and dynamics of clade III AsSWEET3, AsSWEET9, and AsSWEET11 genes significantly differed between Fusarium-resistant and -susceptible garlic cultivars subjected to F. proliferatum infection, suggesting the role of these genes in the garlic defense against the pathogen. Our results provide insights into the role of SWEET sugar uniporters in A. sativum and may be useful for breeding Fusarium-resistant Allium cultivars.

Transcriptome Approach Reveals the Response Mechanism of Heimia myrtifolia (Lythraceae, Myrtales) to Drought Stress

Drought is a major environmental condition that inhibits the development and cultivation of Heimia myrtifolia. The molecular processes of drought resistance in H. myrtifolia remain unknown, which has limited its application. In our study, transcriptome analyzes were compared across three treatment groups (CK, T1, and T2), to investigate the molecular mechanism of drought resistance. Plant leaves wilted and drooped as the duration of drought stress increased. The relative water content of the leaves declined dramatically, and relative electrolyte leakage rose progressively. Using an RNA-Seq approach, a total of 62,015 unigenes with an average length of 1730 bp were found, with 86.61% of them annotated to seven databases, and 14,272 differentially expressed genes (DEGs) were identified in drought stress. GO and KEGG enrichment analyzes of the DEGs revealed significantly enriched KEGG pathways, including photosynthesis, photosynthetic antenna proteins, plant hormone signal transduction, glutathione metabolism, and ascorbate and aldarate metabolism. Abscisic acid signal transduction was the most prevalent in the plant hormone signal transduction pathway, and other plant hormone signal transductions were also involved in the drought stress response. The transcription factors (including MYB, NAC, WRKY, and bHLH) and related differential genes on significantly enriched pathways all played important roles in the drought process, such as photosynthesis-related genes and antioxidant enzyme genes. In conclusion, this study will provide several genetic resources for further investigation of the molecular processes that will be beneficial to H. myrtifolia cultivation and breeding.

Selection of suitable candidate genes for mRNA expression normalization in bulbil development of Pinellia ternata

Pinellia ternata (Thunb.) Breit. (Abbreviated as P. ternata). It is a commonly prescribed Chinese traditional medicinal herb for the treatment of phlegm, cough, and morning sick. Bulbil reproduction is one of the main reproductive methods of P. ternata. The accurate quantification of gene expression patterns associated with bulbil development might be helpful to explore the molecular mechanism involved in P. ternata reproduction. Quantitative real-time PCR was the most preferred method for expression profile and function analysis of mRNA. However, the reference genes in different tissues of P. ternata in different periods of bulbil development have not been studied in detail. In present study, the expression stability of eight candidate reference genes were determined with programs: geNorm, NormFinder, BestKeeper, and refFinder. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was identified as the top- rated reference gene in all samples of P. ternata, while different combinations of reference gene proved to be the most stable depending on development stage and tissue type. Furthermore, the reliability of GAPDH expression was verified by six P. ternata related genes in hormone and nutrient biosynthesis pathways, and the expression profiles of these genes were agreed with the results of RNA-seq digital gene expression analysis. These results can contribute to studies of gene expression patterns and functional analysis of P. ternata involved in bulbil development.

Stable reference gene selection for quantitative real-time PCR normalization in passion fruit (Passiflora edulis Sims.)

BACKGROUND

Passiflora edulis is a tropical fruit with high nutrient and medicinal values that is widely planted in southern China. However, the molecular biology of P. edulis has not been well studied. There are few reports regarding the choice of reference genes for gene expression studies of passion fruit.

METHODS AND RESULTS

By using three algorithms, implemented in geNorm, NormFinder and BestKeeper, we have selected ten candidate reference genes to explore their transcriptional expression stability in various tissues and under cold stress conditions. EF1 and HIS were stably expressed in five tissues. Ts and OTU were stably in vegetative organs. 50 S and Liom were stably in reproductive organs. The transcriptional abundance of EF1 and UBQ was stable in cold-treated and recovery treated leaf samples of P. edulis. In all samples, EF1 and Ts exhibited the highest expression stability. Evaluation of selected genes using simple statistical methods (ANOVA and post hoc analysis). Overall, EF1 emerged as the optimum reference gene for qRT-PCR normalize in P. edulis. In addition, the qRT-PCR analysis revealed that expression of ICE1 increases with the duration of cold treatment.

CONCLUSIONS

In this study, we successfully screened stable reference genes from 10 candidates in P. edulis and verified the results by analyzing the expression level of ICE1. The results provide reliable and effective reference genes for future research on gene expression analysis in P. edulis, and lay a foundation for follow-up research on functional genes in P. edulis.