Identification of reliable reference genes for quantitative real-time PCR normalization in pitaya

Identification and validation of qRT-PCR reference genes for analyzing grape infection with gray mold

BACKGROUND

Grapes are highly valued for their nutritional and economic benefits, and have been widely studied for their biological attributes such as fruit development, quality formation, and stress resistance. One significant threat to grape quality is gray mold, caused by Botrytis cinerea, which can infect the flowers, fruits, leaves, and stems. The quantitative real-time PCR (qRT-PCR), known for its high sensitivity and quantitative accuracy, is an essential tool for analyzing gene expression related to the pathogenesis of gray mold, thereby providing deeper insights into the disease.

RESULT

In this study, we aim to identify stable internal reference genes crucial for accurate gene expression analysis via qRT-PCR. Utilizing transcriptome data from grapes under various disease stresses, we identified twelve candidate reference genes with consistently high expression levels. The stability of these genes was assessed through delta-CT, geNorm, NormFinder, BestKeeper, and RefFinder analyses after establishing the cycling thresholds (Ct) in different grape varieties treated with Botrytis cinerea.

CONCLUSIONS

Our findings reveal that VIT-17s0000g02750 and VIT-06s0004g04280 exhibit stable expression and are suitable as new reference genes. This foundational work supports further research into the molecular mechanisms of grape biological processes.

Transcriptome-guided selection of stable reference genes for expression analysis in spinach

Accurate measurement of gene expression levels is vital for advancing plant biology research. This study explores the identification and validation of stable reference genes (RGs) for gene expression analysis in Spinacia oleracea. Leveraging transcriptome data from various developmental stages, we employed rigorous statistical analyses to identify potential RGs. A total of 1196 candidate genes were initially screened based on expression variability, with subsequent refinement using criteria such as low variance and stability. Among 12 commonly used candidate RGs, EF1α and H3 emerged as the most stable across diverse experimental conditions, while GRP and PPR exhibited lower stability. These findings were further validated through qRT-PCR assays and comprehensive statistical analyses, including geNorm, NormFinder, BestKeeper, and RefFinder. Our study underscores the importance of systematic RG selection to ensure accurate normalization in gene expression studies, particularly in the context of S. oleracea developmental stages and physiological processes like flowering. These validated RGs provide a robust foundation for future gene expression analysis in S. oleracea and contribute to the advancement of molecular research in plant biology.

Selection and Validation of Reference Genes in Dendrocalamus brandisii for Quantitative Real-Time PCR

Dendrocalamus brandisii (Munro) Kurz is a sympodial bamboo species with a wide distribution in tropical and subtropical regions. Due to its remarkable regenerative ability and exceptional flavor, this species plays a pivotal role in bolstering the economies of numerous nations across these regions. We recently published a high-quality genome of this species. To date, no study results have identified the optimal reference genes for quantitative real-time polymerase chain reaction (qRT-PCR) normalization in Dendrocalamus brandisii. qRT-PCR offers a highly accurate and effective approach to analyzing gene expression. However, the precision of the resulting quantitative data hinges on the correct choice of reference genes. Twenty-one potential reference genes were identified from the D. brandisii transcriptomes. Their expression in 23 samples, including 8 different tissue organs and 15 samples of D. brandisii under various treatment conditions, were evaluated through qRT-PCR. Subsequently, four software programs-Delta CT, geNorm, NormFinder, and RefFinder-were employed to compare their expression stability. The results revealed that the selection of optimal reference genes varied based on the particular organ and condition being examined. EF-1-α-2 consistently exhibits the most stable expression across diverse tissues, while ACTIN-1, TUBULIN-1, and EF-1-α-2 were the most consistent reference genes in roots, culms, and leaves under various treatments, respectively. In this study, we identified and characterized appropriate internal genes utilized for calibrating qRT-PCR analyses of D. brandisii across different tissue organs and under various treatments. This research will provide key insights for advancing the study of gene functionality and molecular biology in D. brandisii and related species.

Novel systems biology experimental pipeline reveals matairesinol's antimetastatic potential in prostate cancer: an integrated approach of network pharmacology, bioinformatics, and experimental validation

Matairesinol (MAT), a plant lignan renowned for its anticancer properties in hormone-sensitive cancers like breast and prostate cancers, presents a promising yet underexplored avenue in the treatment of metastatic prostate cancer (mPC). To elucidate its specific therapeutic targets and mechanisms, our study adopted an integrative approach, amalgamating network pharmacology (NP), bioinformatics, GeneMANIA-based functional association (GMFA), and experimental validation. By mining online databases, we identified 27 common targets of mPC and MAT, constructing a MAT-mPC protein-protein interaction network via STRING and pinpointing 11 hub targets such as EGFR, AKT1, ERBB2, MET, IGF1, CASP3, HSP90AA1, HIF1A, MMP2, HGF, and MMP9 with CytoHuba. Utilizing DAVID, Gene Ontology (GO) analysis highlighted metastasis-related processes such as epithelial-mesenchymal transition, positive regulation of cell migration, and key Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including cancer, prostate cancer, PI3K-Akt, and MAPK signaling, while the web resources such as UALCAN and GEPIA2 affirmed the clinical significance of the top 11 hub targets in mPC patient survival analysis and gene expression patterns. Our innovative GMFA enrichment method further enriched network pharmacology findings. Molecular docking analyses demonstrated substantial interactions between MAT and 11 hub targets. Simulation studies confirmed the stable interactions of MAT with selected targets. Experimental validation in PC3 cells, employing quantitative real-time reverse-transcription PCR and various cell-based assays, corroborated MAT's antimetastatic effects on mPC. Thus, this exhaustive NP analysis, complemented by GMFA, molecular docking, molecular dynamics simulations, and experimental validations, underscores MAT's multifaceted role in targeting mPC through diverse therapeutic avenues. Nevertheless, comprehensive in vitro validation is imperative to solidify these findings.

Identifying Core Genes Related to Low-Temperature Stress Resistance in Quinoa Seedlings Based on WGCNA

Quinoa is a nutritious crop that is tolerant to extreme environmental conditions; however, low-temperature stress can affect quinoa growth, development, and quality. Considering the lack of molecular research on quinoa seedlings under low-temperature stress, we utilized a Weighted Gene Co-Expression Network Analysis to construct weighted gene co-expression networks associated with physiological indices and metabolites related to low-temperature stress resistance based on transcriptomic data. We screened 11 co-expression modules closely related to low-temperature stress resistance and selected 12 core genes from the two modules that showed the highest associations with the target traits. Following the functional annotation of these genes to determine the key biological processes and metabolic pathways involved in low-temperature stress, we identified four important transcription factors involved in resistance to low-temperature stress: gene-LOC110731664, gene-LOC110736639, gene-LOC110684437, and gene-LOC110720903. These results provide insights into the molecular genetic mechanism of quinoa under low-temperature stress and can be used to breed lines with tolerance to low-temperature stress.

Identification and validation of stable reference genes for RT-qPCR analyses of Kobresia littledalei seedlings

BACKGROUND

Kobreisa littledalei, belonging to the Cyperaceae family is the first Kobresia species with a reference genome and the most dominant species in Qinghai-Tibet Plateau alpine meadows. It has several resistance genes which could be used to breed improved crop varieties. Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR) is a popular and accurate gene expression analysis method. Its reliability depends on the expression levels of reference genes, which vary by species, tissues and environments. However, K.littledalei lacks a stable and normalized reference gene for RT-qPCR analysis.

RESULTS

The stability of 13 potential reference genes was tested and the stable reference genes were selected for RT-qPCR normalization for the expression analysis in the different tissues of K. littledalei under two abiotic stresses (salt and drought) and two hormonal treatments (abscisic acid (ABA) and gibberellin (GA)). Five algorithms were used to assess the stability of putative reference genes. The results showed a variation amongst the methods, and the same reference genes showed tissue expression differences under the same conditions. The stability of combining two reference genes was better than a single one. The expression levels of ACTIN were stable in leaves and stems under normal conditions, in leaves under drought stress and in roots under ABA treatment. The expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expression was stable in the roots under the control conditions and salt stress and in stems exposed to drought stress. Expression levels of superoxide dismutase (SOD) were stable in stems of ABA-treated plants and in the roots under drought stress. Moreover, RPL6 expression was stable in the leaves and stems under salt stress and in the stems of the GA-treated plants. EF1-alpha expression was stable in leaves under ABA and GA treatments. The expression levels of 28 S were stable in the roots under GA treatment. In general, ACTIN and GAPDH could be employed as housekeeping genes for K. littledalei under different treatments.

CONCLUSION

This study identified the best RT-qPCR reference genes for different K. littledalei tissues under five experimental conditions. ACTIN and GAPDH genes can be employed as the ideal housekeeping genes for expression analysis under different conditions. This is the first study to investigate the stable reference genes for normalized gene expression analysis of K. littledalei under different conditions. The results could aid molecular biology and gene function research on Kobresia and other related species.

Advances in the Understanding of Postharvest Physiological Changes and the Storage and Preservation of Pitaya

Highly prized for its unique taste and appearance, pitaya is a tasty, low-calorie fruit. It has a high-water content, a high metabolism, and a high susceptibility to pathogens, resulting in an irreversible process of tissue degeneration or quality degradation and eventual loss of commercial value, leading to economic loss. High quality fruits are a key guarantee for the healthy development of economic advantages. However, the understanding of postharvest conservation technology and the regulation of maturation, and senescence of pitaya are lacking. To better understand the means of postharvest storage of pitaya, extend the shelf life of pitaya fruit and prospect the postharvest storage technology, this paper analyzes and compares the postharvest quality changes of pitaya fruit, preservation technology, and senescence regulation mechanisms. This study provides research directions for the development of postharvest storage and preservation technology.

Selection and Validation of qRT-PCR Internal Reference Genes to Study Flower Color Formation in Camellia impressinervis

Real-time quantitative PCR (qRT-PCR) is a pivotal technique for gene expression analysis. To ensure reliable and accurate results, the internal reference genes must exhibit stable expression across varied experimental conditions. Currently, no internal reference genes for Camellia impressinervis have been established. This study aimed to identify stable internal reference genes from eight candidates derived from different developmental stages of C. impressinervis flowers. We employed geNorm, NormFinder, and BestKeeper to evaluate the expression stability of these candidates, which was followed by a comprehensive stability analysis. The results indicated that CiTUB, a tubulin gene, exhibited the most stable expression among the eight reference gene candidates in the petals. Subsequently, CiTUB was utilized as an internal reference for the qRT-PCR analysis of six genes implicated in the petal pigment synthesis pathway of C. impressinervis. The qRT-PCR results were corroborated by transcriptome sequencing data, affirming the stability and suitability of CiTUB as a reference gene. This study marks the first identification of stable internal reference genes within the entire genome of C. impressinervis, establishing a foundation for future gene expression and functional studies. Identifying such stable reference genes is crucial for advancing molecular research on C. impressinervis.

Identification and Validation of Reference Genes for qRT-PCR Analysis of Petal-Color-Related Genes in Rosa praelucens

The flower's color is regarded as one of the most outstanding features of the rose. Rosa praelucens Byhouwer, an endemic and critically endangered decaploid wild rose species, is abundant in phenotypic diversity, especially in flower color variation, from white to different degrees of pink. The mechanism underlying this variation, e.g., the level of petal-color-related genes, is worth probing. Seven candidate reference genes for qRT-PCR analysis, including tubulin α chain (TUBA), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone H2B (Histone2A), eukaryotic translation elongation factor 1-α (EEF1A), 60S ribosomal protein (RPL37), eukaryotic translation initiation factor 1-α (EIF1A), and aquaporins (AQP), were detected from the transcriptome datasets of full blooming flowers of white-petaled and pink-petaled individuals, and their expression stabilities were evaluated through qRT-PCR analysis. According to stability rankings analysis, EEF1A showed the highest stability and could be chosen as the most suitable reference gene. Moreover, the reliability of EEF1A was demonstrated via qRT-PCR analysis of six petal-color-related target genes, the expression patterns of which, through EEF1A normalization, were found to be consistent with the findings of transcriptome analysis. The result provides an optimal reference gene for exploring the expression level of petal-color-related genes in R. praelucens, which will accelerate the dissection of petal-color-variation mechanisms in R. praelucens.

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.

Transcriptome-Based Identification of the Optimal Reference Genes for Quantitative Real-Time Polymerase Chain Reaction Analyses of Lingonberry Fruits throughout the Growth Cycle

(1) Background: Vaccinium vitis-idaea is a nutritionally and economically valuable natural wild plant species that produces berries useful for treating various diseases. There is growing interest in lingonberry, but there is limited information regarding lingonberry reference genes suitable for gene expression analyses of different tissues under various abiotic stress conditions. The objective of this study was to identify stable reference genes suitable for different lingonberry tissues in response to abiotic stress. (2) Methods: The delta Ct method and the GeNorm v3.5 and NormFinder v20 programs were used to comprehensively analyze gene expression stability. (3) Results: Actin Unigene23839 was the best reference gene for analyzing different cultivars, whereas Actin CL5740.Contig2 was the most suitable reference gene for analyzing different tissues and alkali stress. In contrast, 18S rRNA CL5051.Contig1 was the most stable reference gene under drought conditions. (4) Conclusions: These suitable reference genes may be used in future qRT-PCR analyses of different lingonberry tissues and the effects of abiotic stresses. Furthermore, the study data may be useful for functional genomics studies and the molecular breeding of lingonberry. In summary, internal reference genes or internal reference gene combinations should be carefully selected according to the experimental conditions to ensure that the generated gene expression data are accurate.

Identification of HuSWEET Family in Pitaya (Hylocereus undatus) and Key Roles of HuSWEET12a and HuSWEET13d in Sugar Accumulation

The sugar composition and content of fruit have a significant impact on their flavor and taste. In pitaya, or dragon fruit, sweetness is a crucial determinant of fruit taste and consumer preference. The sugars will eventually be exported transporters (SWEETs), a novel group of sugar transporters that have various physiological functions, including phloem loading, seed filling, nectar secretion, and fruit development. However, the role of SWEETs in sugar accumulation in pitaya fruit is not yet clear. Here, we identified 19 potential members (HuSWEET genes) of the SWEET family in pitaya and analyzed their conserved motifs, physiochemical characteristics, chromosomal distribution, gene structure, and phylogenetic relationship. Seven highly conserved α-helical transmembrane domains (7-TMs) were found, and the HuSWEET proteins can be divided into three clades based on the phylogenetic analysis. Interestingly, we found two HuSWEET genes, HuSWEET12a and HuSWEET13d, that showed strong preferential expressions in fruits and an upward trend during fruit maturation, suggesting they have key roles in sugar accumulation in pitaya. This can be further roughly demonstrated by the fact that transgenic tomato plants overexpressing HuSWEET12a/13d accumulated high levels of sugar in the mature fruit. Together, our result provides new insights into the regulation of sugar accumulation by SWEET family genes in pitaya fruit, which also set a crucial basis for the further functional study of the HuSWEETs.

Screening of Reference miRNA of Different Early- and Late-Flowering Tree Peony Varieties

miRNA plays an important role in plant growth and development and in response to various stresses. Quantitative real-time PCR (qRT-PCR) technology is often used to detect the expression level of miRNAs and genes by comparing with reference genes. In order to screen out the optimal reference miRNAs in different tree peony varieties, the petals of 42 different early- and late-flowering tree peony varieties were used as experimental materials, and geNorm, NormFinder, Bestkeeper, and RefFinder software were used to evaluate the stability of 16 candidate reference miRNAs. The results showed that the average Ct values of all candidate reference miRNAs were between 15.34 ± 0.29 and 32.64 ± 0.38. The optimal number of reference miRNAs was four, which were PsPC-5p-19095, PsPC-3p-51259, PsmiR159a, and PsPC-3p-6660 in geNorm. The stability of PsPC-3p-6660 was the highest in the analysis results of NormFinder software. Among the analysis results of Bestkeeper software, PsMIR319-p5 has the highest stability. Among the results of comprehensive evaluation and analysis of several software using RefFinder, the candidate reference miRNA with the highest stability was PsPC-3p-6660. When PsPC-3p-6660 was used as the reference miRNA, the expression of PomiR171 and PomiR414 in response to different flowering times of tree peony was relatively stable in 42 tree peony varieties, indicating that PsPC-3p-6660 was stable and reliable. The results of this study provide a reference miRNA for studying the expression changes of miRNA in different tree peony varieties and further exploring the regulatory mechanism of miRNA in different peony varieties.

The effect of Cissus quadrangularis Salisb. extract on maturation of rat mesenchymal stem cells

Degenerative diseases, such as osteoporosis, could be treated by stem cells. The aim of this study was to identify the gene expression of bone marrow mesenchymal stem cells (BM-MSC) derived from Sprague Dawley rats and to assess the effect of Cissus quadrangularis Salisb. extract on their maturation into bone cells. The BM-MSC were divided into three groups: (a) BM-MSCs + osteoblast cell growth basal medium as the positive control; (b) BM-MSCs + Dulbecco's modified eagle's medium (DMEM) + 0.3 mg/mL methanol extract of C. quadrangularis as methanol group; and (c) BM-MSC + DMEM + 0.3 mg/mL ethyl acetate extract of C. quadrangularis as ethyl acetate group. A relative quantification approach using was used to analyze the expression of the alp (alkaline phosphatase) gene, with the beta-actin gene was used to normalize the expression of the alp gene. The intra-assay variation was calculated to validate the RT-qPCR data. Our study found that the intra-assay variation value was acceptable, with most of the coefficients of variability (CV) value <5. Ethyl acetate solvent outperformed methanol solvent in extracting the active compound C. quadrangularis. In the ethyl acetate extract group, the expression of the alp gene increased three times compared to the positive control. In methanol extract group, the expression of alp gene was lower six times compared to positive control. This study suggests that C. quadrangularis extracts using ethyl acetate could induce the maturation of BM-MSCs. However, further studies are warrant to confirm this effect using different indicators.

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 of reference genes for qRT-PCR studies in the colchicine producing Gloriosa superba L

The flame lily, Gloriosa superba L., is one of the two primary sources of the anti-inflammatory drug, colchicine. Previous studies have shown that a higher level of colchicine production occurs in the rhizomes than in leaves and roots. Earlier precursor feeding and transcriptome analysis of G. superba have provided a putative pathway and candidate genes involved in colchicine biosynthesis. Comparative analysis of expression levels of candidate pathway genes in different tissues of G. superba using quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) can reveal highly expressed genes in the rhizome compared to other tissues which could suggest roles of the gene products in colchicine biosynthesis. Normalization is an important step in effectively analyzing differential gene expression by qRT-PCR with broader applications. The current study selected candidate reference genes from the transcriptome datasets and analyzed them to determine the most stable genes for normalization of colchicine biosynthesis-related genes. Using RefFinder, one stable reference gene, UBC22, was selected to normalize gene expression levels of candidate methyltransferase (MT) genes in the leaves, roots, and rhizomes of G. superba. With UBC22 as reference gene, the methyltransferases, GsOMT1, GsOMT3, and GsOMT4 showed significantly higher expression levels in the rhizome of G. superba, while MT31794 was more highly expressed in the roots. In conclusion, the current results showed a viable reference gene expression analysis system that could help elucidate colchicine biosynthesis and its exploitation for increased production of the drug in G. superba.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11816-023-00840-x.

Unraveling molecular mechanisms underlying low-temperature adaptation in Laguncularia racemosa

Laguncularia racemosa (L.) C.F. Gaertn is a controversial species in China, in terms of being a pioneer species for mangrove restoration and a putative invasive species occupying natural habitats. The tolerance to chilling stress allows L. racemosa to adapt to extreme climate change. However, little is known about the molecular-level chilling resistance mechanisms in L. racemosa, which restricts our understanding of its biological features and invasion potential. In this study, L. racemosa seedlings were treated with freezing temperature (0 °C) at four durations (0 h, 3 h, 12 h and 24 h of recovery after treatment), and both physiological and transcriptional regulations underlying chilling stress resistance were investigated. Chilling stress caused damage to the cell membrane system and reduced photosynthesis efficiency of L. racemosa seedlings. To combat the adverse impacts, plasma membrane biosynthesis and antioxidant processes were substantially enhanced. After 24 h of recovery, the seedlings nearly recovered to normal growth condition, except for the processes related to photosynthesis, indicating their vigorous adaptation to short-term chilling stress. Importantly, the individuals from higher latitude displayed better adaptation to chilling injury than those from lower latitude, highlighting the role of long-term heredity × environment interactions in promoting the chilling resistance capacity of L. racemosa. These features allow L. racemosa to survive in extremely cold weather, but may also increase its risk of invasion into intertidal ecosystems. Together, our findings present a comprehensive view of the chilling-adaptative mechanisms of L. racemosa, which provide clues for better evaluating the invasive potential of L. racemosa.

Identification of HubHLH family and key role of HubHLH159 in betalain biosynthesis by activating the transcription of HuADH1, HuCYP76AD1-1, and HuDODA1 in pitaya

Basic helix-loop-helix (bHLH) proteins are dimeric transcription factors (TFs) involved in various plant physiological and biological processes. Despite this, little is known about the molecular properties and roles of bHLH TFs in pitaya betalain biosynthesis. Here we report the identification of 165 HubHLH genes in H. undantus genome, their chromosomal distribution, physiochemical characteristics, conserved motifs, gene structure, phylogeny and synteny of HubHLH genes. Based on phylogenetic relationship analysis, the 165 HubHLHs were divided into 26 subfamilies and unequally distributed on the 11 chromosomes of pitaya. Based on the pitaya transcriptome data, a candidate gene HubHLH159 was obtained, and the real-time quantitative PCR analysis confirmed that HubHLH159 showed a high expression level in 'Guanhuahong' pitaya (red-pulp) at mature stage, indicating its role in betalain biosynthesis. HubHLH159 is a Group II protein and contains a bHLH domain. It is a nuclear protein with transcriptional activation activity. Dual luciferase reporter assays and virus-induced gene silencing (VIGS) experiments showed that HubHLH159 promotes betalain biosynthesis by activating the expression of HuADH1, HuCYP76AD1-1, and HuDODA1. The results of the present study lay a new theoretical reference for the regulation of pitaya betalain biosynthesis and also provides as essential basis for the future analysis of the functions of HubHLH gene family.

Betalain biosynthesis in red pulp pitaya is regulated via HuMYB132: a R-R type MYB transcription factor

BACKGROUND

Multiple MYB transcription factors (TFs) are involved in the regulation of plant coloring. Betalain is a kind of natural plant pigment and its biosynthesis is regulated by a number of enzymes. Despite this, little is known about the molecular properties and roles of MYB TFs in pitaya betalain biosynthesis.

RESULTS

In the present study, we identified a 1R-MYB gene, HuMYB132, which is preferentially expressed in red-pulp pitaya at the mature stage. It was clustered with Arabidopsis R-R-type genes and had two DNA-binding domains and a histidine-rich region. The expression assays in N. benthamiana and yeast indicated that HuMYB132 is a nucleus-localized protein with transcriptional activation activity. Dual luciferase reporter assay and electrophoretic mobility shift assays (EMSA) demonstrated that HuMYB132 could promote the transcriptional activities of HuADH1, HuCYP76AD1-1, and HuDODA1 by binding to their promoters. Silencing HuMYB132 reduced betalain accumulation and the expression levels of betalain biosynthetic genes in pitaya pulps.

CONCLUSIONS

According to our findings, HuMYB132, a R-R type member of 1R-MYB TF subfamily, positively regulates pitaya betalain biosynthesis by regulating the expression of HuADH1, HuCYP76AD1-1, and HuDODA1. The present study provides a new theoretical reference for the management of pitaya betalain biosynthesis and also provides an essential basis for future regulation of betalain biosynthesis in Hylocereus.

Identification of RT-qPCR reference genes suitable for gene function studies in the pitaya canker disease pathogen Neoscytalidium dimidiatum

Neoscytalidium dimidiatum is the main causal agent of pitaya canker. Most studies of virulence and pathogenicity genes have measured expression levels using real-time quantitative polymerase chain reaction (RT-qPCR). Suitable reference genes are essential for ensuring that estimates of gene expression levels by RT-qPCR are accurate. However, no reference genes can be robustly applied across all contexts and species. No studies to date have evaluated the most effective reference genes for normalizing gene expression levels estimated by RT-qPCR in N. dimidiatum. In this study, RT-qPCR data for individual candidate reference genes were analyzed using four different methods: the delta Ct method and the geNorm, NormFinder, and BestKeeper algorithms. We evaluated the utility of eight candidate reference genes (18S rRNA, Actin (1), Actin (2), Actin, GAPDH (1), GAPDH (2), UBQ, and Tubulin) for normalizing expression levels estimated by RT-qPCR in N. dimidiatum at different developmental stages, at different temperatures, and during interaction with pitaya. All candidate reference genes were suitable for gene expression analysis except for Actin (2). Tubulin and Actin (1) were the most stably expressed reference genes under different temperatures. Actin (1) and Actin were the most stably expressed reference genes in N. dimidiatum at different developmental stages. Tubulin and UBQ were the most stably expressed reference genes during interaction with pitaya. Actin and 18s rRNA were the most stably expressed across all experimental conditions. Subsequently, Tubulin and UBQ were further investigated in analyses of pectinase expression during the pitaya-N. dimidiatum interaction. Our results provide insights that will aid future RT-qPCR studies of gene expression in N. dimidiatum.

Global transcriptome dissection of pollen-pistil interactions induced self-incompatibility in dragon fruit (Selenicereus spp.)

Self-incompatibility (SI) is a major issue in dragon fruit (Selenicereus spp.) breeding and production. Therefore, a better understanding of the dragon fruit SI mechanism is needed to improve breeding efficiency and ultimate production costs. To reveal the underlying mechanisms of SI in dragon fruit, plant anatomy, de novo RNA sequencing-based transcriptomic analysis, and multiple bioinformatic approaches were used to analyze gene expression in the pistils of the self-pollinated and cross-pollinated dragon fruit flowers at different intervals of time after pollination. Using fluorescence microscopy, we observed that the pollen of 'Hongshuijing', a self-incompatible dragon fruit variety (S. monacanthus), germinated on its own stigma. However, the pollen tube elongation has ceased at 1/2 of the style, confirming that dragon fruit experiences gametophyte self-incompatibility (GSI). We found that the pollen tube elongation in vitro was inhibited by self-style glycoproteins in the SI variety, indicating that glycoproteins were involved in SI. That is to say the female S factor should be homologous of S-RNase or PrsS (P. rhoeas stigma S factor), both of which are glycoproteins and are the female S factors of the two known GSI mechanism respectively. Bioinformatics analyses indicated that among the 43,954 assembled unigenes from pistil, there were six S-RNase genes, while 158 F-box genes were identified from a pollen transcriptomic dataset. There were no P. rhoeas type S genes discovered. Thus, the identified S-RNase and F-box represent the candidate female and male S genes, respectively. Analysis of differentially expressed genes (DEGs) between the self and cross-pollinated pistils at different time intervals led to the identification of 6,353 genes. We then used a weighted gene co-expression network analysis (WGCNA) to find some non-S locus genes in SI responses in dragon fruit. Additionally, 13 transcription factors (TFs) (YABBY4, ANL2, ERF43, ARF2, BLH7, KNAT6, PIF3, two OBF1, two HY5 and two LHY/CCA) were identified to be involved in dragon fruit GSI. Thus, we uncovered candidate S and non-S genes and predicted more SI-related genes for a more detailed investigation of the molecular mechanism of dragon fruit SI. Our findings suggest that dragon fruit possesses a GSI system and involves some unique regulators. This study lays the groundwork for future research into SI mechanisms in dragon fruit and other plant species.

Reference Gene Selection for qPCR Analysis in Schima superba under Abiotic Stress

Quantitative real-time PCR (qPCR) is an indispensable technique for gene expression analysis in modern molecular biology. The selection and evaluation of suitable reference genes is a prerequisite for accurate gene expression analysis. Schimasuperba is a valuable tree species that is environmentally adaptable and highly fire-resistant. In this study, 12 candidate reference genes were selected to check their stability of gene expression in different tissues under abiotic stresses: cold stress, salt stress, and drought stress by ΔCt, geNorm, NormFinder, BestKeeper, and RefFinder. The results indicated that AP-2 was the most stably expressed overall and for the cold stress and drought stress. eIF-5α gene expression was the most stable under the salt stress treatment, while UBQ expression was the most stable across mature leaves, shoots, stems, and roots. In contrast, UBC20, GAPDH, and TUB were the least stably expressed genes tested. This study delivers valid reference genes in S. superba under the different experimental conditions, providing an important resource for the subsequent elucidation of the abiotic stress adaptation mechanisms and genes with biological importance.

Physiological, Agronomical, and Proteomic Studies Reveal Crucial Players in Rice Nitrogen Use Efficiency under Low Nitrogen Supply

Excessive use of nitrogenous fertilizers to enhance rice productivity has become a significant source of nitrogen (N) pollution and reduced sustainable agriculture. However, little information about the physiology of different growth stages, agronomic traits, and associated genetic bases of N use efficiency (NUE) are available at low-N supply. Two rice (Oryza sativa L.) cultivars were grown with optimum N (120 kg ha-1) and low N (60 kg ha-1) supply. Six growth stages were analyzed to measure the growth and physiological traits, as well as the differential proteomic profiles, of the rice cultivars. Cultivar Panvel outclassed Nagina 22 at low-N supply and exhibited improved growth and physiology at most of the growth stages and agronomic efficiency due to higher N uptake and utilization at low-N supply. On average, photosynthetic rate, chlorophyll content, plant biomass, leaf N content, and grain yield were decreased in cultivar Nagina 22 than Panvel was 8%, 11%, 21%, 19%, and 22%, respectively, under low-N supply. Furthermore, proteome analyses revealed that many proteins were upregulated and downregulated at the different growth stages under low-N supply. These proteins are associated with N and carbon metabolism and other physiological processes. This supports the genotypic differences in photosynthesis, N assimilation, energy stabilization, and rice-protein yield. Our study suggests that enhancing NUE at low-N supply demands distinct modifications in N metabolism and physiological assimilation. The NUE may be regulated by key identified differentially expressed proteins. These proteins might be the targets for improving crop NUE at low-N supply.

Breeding an underutilized fruit crop: a long-term program for Hylocereus

This review describes three decades of introduction, agro-technology development, breeding and selection of Hylocereus species, known as pitaya or dragon fruit, as an example of a holistic program aimed to develop the horticultural potential of a perennial underutilized fruit crop. Interspecific homoploid and interploid crosses and embryo rescue procedures produced improved hybrids, some of which have been released to farmers. Molecular tools and morphological and phenological comparisons between the parental species and the resulting hybrids provided valuable information on dominant/recessive traits and on genetic relationships that could be exploited for further hybridizations. In addition, Hylocereus were crossed with species of the closely related genus Selenicereus, producing valuable intergeneric hybrids. In situ chromosome doubling resulted in the production of autopolyploid lines, from which an understanding of the effect of increased ploidy on fruit traits and metabolomic profiles was obtained. Gamete-derived lines were produced, adding to our biobank homozygote lines that were subsequently used for further hybridization. Spontaneous chromosome doubling occurred in haploid gamete-derived Hylocereus monacanthus lines and in interspecific interploid Hylocereus megalanthus × H. undatus hybrids obtained from an embryo rescue procedure, resulting in plants with double the expected ploidy. Challenging technical problems were addressed by the development of protocols for DNA isolation, flow cytometry, in situ chromosome doubling, androgenesis, gynogenesis and embryo rescue following interspecific and interploidy crosses. Current research leading to the development of genomics and molecular tools, including a draft genome of H. undatus, is also presented. Perspectives for further development of Hylocereus species and hybrids are discussed.

Identification of Suitable Reference Genes for qRT-PCR Normalization in Kiwifruit

Reference genes are used for the correction of qRT-PCR data, and it is necessary to investigate the optimum reference gene under certain conditions. The expression levels of seven traditional reference genes ACT1, ACT2, GAPDH, 18S rRNA, UBQ, TUB and CYP were analyzed using qRT-PCR in different varieties, tissues, developmental stages and hormone (or pollen polysaccharide) treatments in kiwifruit. Gene expression stability was assessed with the help of three common software (geNorm, NormFinder, BestKeeper), and the minimum number of reference genes necessary for normalization was also determined. GAPDH, ACT1 and ACT2 were selected as reference genes for different genotypes of kiwifruit. GAPDH and UBQ were the best combinations of reference genes for root, stem, leaf, flower and fruit. GAPDH and ACT1 could be the preferred reference genes for normalization of qRT-PCR data during fruit development. The pairing of ACT1 and UBQ constituted the optimal combination of reference genes in kiwifruit treated with different hormones (or pollen polysaccharide). This study provides a new and reliable option for the use of reference genes in the analysis of gene expression patterns of interest in kiwifruit.

Metabolic Profiling of Organic Acids Reveals the Involvement of HuIPMS2 in Citramalic Acid Synthesis in Pitaya

Pitayas are rich in organic acids, especially citramalic acid, which is significantly higher than the plants. However, the mechanism of citramalic acid biosynthesis remains to be fully elucidated. In this study, organic acid compositions and contents, as well as expression patterns of key genes related to organic acid metabolism were analyzed during fruit maturation of four different pitaya cultivars i.e., ‘Guanhuabai’ (GHB), ‘Guanhuahong’ (GHH), ‘Wucihuanglong’ (WCHL), and ‘Youcihuanglong’ (YCHL). The total organic acid contents increased first and then declined during fruit maturation. The main organic acids were citramalic acid during the early stages of GHB, GHH, and WCHL pitayas, and dominated by malic acid as fruit maturation. In comparison, citric acid and malic acid were main organic acid for ‘YCHL’ pitaya. Citramalate synthase (IPMS) was involved in the synthesis of citramalic acid, and three types of HuIPMS i.e., HuIPMS1, HuIPMS2, and HuIPMS3, were obtained in our study. Highest expression levels of HuIPMS1 were detected in sepals, while HuIPMS2 and HuIPMS3 exhibited preferential expression in tender stems and ovaries. The expression levels of HuIPMS2 and HuIPMS3 were positively correlated with the content of citramalic acid in the four pitaya cultivars. HuIPMS2 was a chloroplast-localized protein, while HuIPMS3 presented a cytoplasmic-like and nuclear subcellular localization. These findings provide an important basis for further understanding of the molecular mechanism that leads to citramalic acid metabolism during pitaya fruit maturation.

HuNAC20 and HuNAC25, Two Novel NAC Genes from Pitaya, Confer Cold Tolerance in Transgenic Arabidopsis

NAC transcription factors are one of the largest families of transcriptional regulators in plants, and members of the gene family play vital roles in regulating plant growth and development processes including biotic/abiotic stress responses. However, little information is available about the NAC family in pitaya. In this study, we conducted a genome-wide analysis and a total of 64 NACs (named HuNAC1-HuNAC64) were identified in pitaya (Hylocereus). These genes were grouped into fifteen subgroups with diversities in gene proportions, exon–intron structures, and conserved motifs. Genome mapping analysis revealed that HuNAC genes were unevenly scattered on all eleven chromosomes. Synteny analysis indicated that the segmental duplication events played key roles in the expansion of the pitaya NAC gene family. Expression levels of these HuNAC genes were analyzed under cold treatments using qRT-PCR. Four HuNAC genes, i.e., HuNAC7, HuNAC20, HuNAC25, and HuNAC30, were highly induced by cold stress. HuNAC7, HuNAC20, HuNAC25, and HuNAC30 were localized exclusively in the nucleus. HuNAC20, HuNAC25, and HuNAC30 were transcriptional activators while HuNAC7 was a transcriptional repressor. Overexpression of HuNAC20 and HuNAC25 in Arabidopsis thaliana significantly enhanced tolerance to cold stress through decreasing ion leakage, malondialdehyde (MDA), and H₂O₂ and O₂⁻ accumulation, accompanied by upregulating the expression of cold-responsive genes (AtRD29A, AtCOR15A, AtCOR47, and AtKIN1). This study presents comprehensive information on the understanding of the NAC gene family and provides candidate genes to breed new pitaya cultivars with tolerance to cold conditions through genetic transformation.

A Genome-Wide Identification Study Reveals That HmoCYP76AD1, HmoDODAα1 and HmocDOPA5GT Involved in Betalain Biosynthesis in Hylocereus

Betalains are water-soluble nitrogen-containing pigments with multiple bioactivities. Pitayas are the only at large-scale commercially grown fruit containing abundant betalains for consumers. Currently, the key genes involved in betalain biosynthesis remain to be fully elucidated. Moreover, genome-wide analyses of these genes in betalain biosynthesis are not available in betalain-producing plant species. In this study, totally 53 genes related to betalain biosynthesis were identified from the genome data of Hylocereus undatus. Four candidate genes i.e., one cytochrome P-450 R gene (HmoCYP76AD1), two L-DOPA 4,5-dioxygenase genes (HmoDODAα1 and HmoDODAα2), and one cyclo-DOPA 5-O glucosyltransferase gene (HmocDOPA5GT) were initially screened according to bioinformatics and qRT-PCR analyses. Silencing HmoCYP76AD1, HmoDODAα1, HmoDODAα2 or HmocDOPA5GT resulted in loss of red pigment. HmoDODAα1 displayed a high level of L-DOPA 4,5-dioxygenase activity to produce betalamic acid and formed yellow betaxanthin. Co-expression of HmoCYP76AD1, HmoDODAα1 and HmocDOPA5GT in Nicotiana benthamiana and yeast resulted in high abundance of betalain pigments with a red color. These results suggested that HmoCYP76AD1, HmoDODAα1, and HmocDOPA5GT play key roles in betalain biosynthesis in Hylocereus. The results of the present study provide novel genes for molecular breeding programs of pitaya.

Selection and validation of reference genes for qRT-PCR analysis during fruit ripening of red pitaya (Hylocereus polyrhizus)

Red pitaya (Hylocereus polyrhizus) is widely cultivated in southern and southwestern China. To provide a basis for studying the molecular mechanisms of the ripening of this fruit, we carried out RNA sequencing (RNA-seq) analysis to identify differentially and stably expressed unigenes. The latter may serve as a resource of potential reference genes for normalization of target gene expression determined using quantitative real-time PCR (qRT-PCR). We selected 11 candidate reference genes from our RNA-seq analysis of red pitaya fruit ripening (ACT7, EF-1α, IF-4α, PTBP, PP2A, EF2, Hsp70, GAPDH, DNAJ, TUB and CYP), as well as β-ACT, which has been used as a reference gene for pitayas in previous studies. We then comprehensively evaluated their expression stability during fruit ripening using four statistical methods (GeNorm, NormFinder, BestKeeper and DeltaCt) and merged the four outputs using the online tool RefFinder for the final ranking. We report that PTBP and DNAJ showed the most stable expression patterns, whereas CYP and ACT7 showed the least stable expression patterns. The relative gene expression of red pitaya sucrose synthase and 4, 5-dihydroxyphenylalanine-extradiol-dioxygenase as determined by quantitative real-time PCR and normalized to PTBP and DNAJ was consistent with the RNA-seq results, suggesting that PTBP and DNAJ are suitable reference genes for studies of red pitaya fruit ripening.

Reference gene selection for real-time quantitative PCR assays in different tissues of Huperzia serrata based on full-length transcriptome sequencing

Huperzia serrata (H. serrata) produces various types of effective lycopodium alkaloids, especially Huperzine A (HupA), which is a promising drug for the treatment of Alzheimer's disease. Numerous studies focused on the chemistry, bioactivities, toxicology, and clinical trials of HupA; however, the public genomic and transcriptomic resources are very limited for H. serrata research, especially for the selection of optimum reference genes. Based on the full-length transcriptome datasets and previous studies, 10 traditional and three new candidate reference genes were selected in different tissue of H. serrata. Then, two optimal reference genes GAPDHB and HisH2A were confirmed by four analysis methods. In order to further verify the accuracy of the two reference genes, they were used to analyze the expression patterns of four HupA-biosynthetic genes (lysine decarboxylas, RS-norcoclaurine 6-O-methyltransferase, cytochrome P45072A1, and copper amine oxidase). The data suggested that the expression pattern of HupA-biosynthetic genes was consistent with them in transcriptome sequencing in different tissue of H. serrata. This study identified that GAPDHB and HisH2A provides the reliable normalization for analyzing the HupA biosynthetic gene expression in different tissues of H. serrata on the transcriptional level.

Maintenance of Postharvest Quality and Reactive Oxygen Species Homeostasis of Pitaya Fruit by Essential Oil p-Anisaldehyde Treatment

The performance of p-Anisaldehyde (PAA) for preserving pitaya fruit quality and the underpinning regulatory mechanism were investigated in this study. Results showed that PAA treatment significantly reduced fruit decay, weight loss and loss of firmness, and maintained higher content of total soluble solids, betacyanins, betaxanthins, total phenolics and flavonoids in postharvest pitaya fruits. Compared with control, the increase in hydrogen peroxide (H₂O₂) content and superoxide anion (O₂^•−) production was inhibited in fruit treated with PAA. Meanwhile, PAA significantly improved the activity of antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT). Moreover, PAA-treated pitaya fruit maintained higher ascorbic acid (AsA) and reduced-glutathione (GSH) content but lower dehydroascorbate (DHA) and oxidized glutathione (GSSG) content, thus sustaining higher ratio of AsA/DHA and GSH/GSSG. In addition, activities of ascorbate peroxidase (APX), glutathione reductase (GR), monodehydroascorbate reductase (MDHAR) and dehydrogenation ascorbic acid reductase (DHAR), as well as the expression of HpSOD, HpPOD, HpCAT, HpAPX, HpGR, HpDHAR and HpMDHAR, were enhanced after PAA treatment. The findings suggest that postharvest application of PAA may be a reliable method to control postharvest decay and preserve quality of harvested pitaya fruit by enhancing the antioxidant potential of the AsA-GSH cycle and activating an antioxidant defense system to alleviate reactive oxygen species (ROS) accumulation.

Genome-Wide Characterization of R2R3-MYB Transcription Factors in Pitaya Reveals a R2R3-MYB Repressor HuMYB1 Involved in Fruit Ripening through Regulation of Betalain Biosynthesis by Repressing Betalain Biosynthesis-Related Genes

The MYB (myeloblastosis) superfamily constitutes one of the most abundant transcription factors (TFs) regulating various biological processes in plants. However, the molecular characteristics and functions of MYB TFs in pitaya remain unclear. To date, no genome-wide characterization analysis of this gene family has been conducted in the Cactaceae species. In this study, 105 R2R3-MYB members were identified from the genome data of Hylocereus undatus and their conserved motifs, physiological and biochemical characteristics, chromosome locations, synteny relationship, gene structure and phylogeny were further analyzed. Expression analyses suggested that three up-regulated HuMYBs and twenty-two down-regulated HuMYBs were probably involved in fruit ripening of pitaya. Phylogenetic analyses of R2R3-MYB repressors showed that seven HuMYBs (HuMYB1, HuMYB21, HuMYB48, HuMYB49, HuMYB72, HuMYB78 and HuMYB101) were in clades containing R2R3-MYB repressors. HuMYB1 and HuMYB21 were significantly down-regulated with the betalain accumulation during fruit ripening of ‘Guanhuahong’ pitaya (H. monacanthus). However, only HuMYB1 had R2 and R3 repeats with C1, C2, C3 and C4 motifs. HuMYB1 was localized exclusively to the nucleus and exhibited transcriptional inhibition capacities. Dual luciferase reporter assay demonstrated that HuMYB1 inhibited the expression of betalain-related genes: HuADH1, HuCYP76AD1-1 and HuDODA1. These results suggested that HuMYB1 is a potential repressor of betalain biosynthesis during pitaya fruit ripening. Our results provide the first genome-wide analyses of the R2R3-MYB subfamily involved in pitaya betalain biosynthesis and will facilitate functional analysis of this gene family in the future.

Genome-Wide Identification of Aquaporin Gene Family in Pitaya Reveals an HuNIP6;1 Involved in Flowering Process

Aquaporins (AQPs) are essential membrane proteins involved in seed maturation and germination, stomata movement, photosynthesis, and regulation of plant flowering processes. Pitaya flowers are open at night and wither at daybreak, which shows an obvious circadian rhythm. In this study, a comprehensive genome-wide analysis of AQPs in Hylocereus undantus was conducted to screen key genes associated with flowering processes. A total of 33 HuAQP genes were identified from the H. undantus genome. The 33 HuAQPs were grouped into four subfamilies: 10 PIPs, 13 TIPs, 8 NIPs, and 2 SIPs, which were distributed on 9 out of 11 pitaya chromosomes (Chr) (except for Chr7 and Chr10). Results from expression profiles showed that HuNIP6;1 may be involved in pitaya's floral opening. HuNIP6;1 was localized exclusively in the cell membrane. Overexpression of HuNIP6;1 in Arabidopsis thaliana significantly promoted early flowering through regulating negative flowering regulators of MJM30, COL9, and PRR5, suggesting that HuNIP6;1 plays key roles in regulating flowering time. The present study provides the first genome-wide analysis of the AQP gene family in pitaya and valuable information for utilization of HuAQPs.

Selection and validation reference genes for qRT-PCR normalization in different cultivars during fruit ripening and softening of peach (Prunus persica)

Quantitative real-time PCR (qRT-PCR) has been emerged as an effective method to explore the gene function and regulatory mechanisms. However, selecting appropriate reference gene (s) is a prerequisite for obtaining accurate qRT-PCR results. Peach is one of important fruit in Rosaceae and is widely cultivated worldwide. In this study, to explore reliable reference gene (s) in peach with different types during fruit ripening and softening (S1-S4), nine candidate reference genes (EF-1α, GAPDH, TBP, UBC, eIF-4α, TUB-A, TUB-B, ACTIN, and HIS) were selected from the whole-genome data. Then, the expression levels of the nine selected genes were detected using qRT-PCR in three peach types, including 'Hakuho' (melting type), 'Xiacui' (stony hard type), 'Fantasia' and 'NJC108' (non-melting type) cultivars were detected using qRT-PCR. Four software (geNorm, NormFinder, BestKeeper and RefFinder) were applied to evaluate the expression stability of these candidate reference genes. Gene expression was characterized in different peach types during fruit ripening and softening stages. The overall performance of each candidate in all samples was evaluated. The Actin gene (ACTIN) was a suitable reference gene and displayed excellent stability in 'Total' set, 'Hakuho' samples, S3 and S4 fruit developmental stages. Ubiquitin C gene (UBC) showed the best stability in most independent samples, including 'Fantasia', 'NJC108', S2 sets. Elongation factor-1α gene (EF-1α) was the most unstable gene across the set of all samples, 'NJC108' and S2 sets, while showed the highest stability in 'Xiacui' samples. The stability of candidate reference genes was further verified by analyzing the relative expression level of ethylene synthase gene of Prunus persica (PpACS1) in fruit ripening and softening periods of 'Hakuho'. Taken together, the results from this study provide a basis for future research on the mining of important functional genes, expression patterns and regulatory mechanisms in peach.

Selection and Validation of Reference Genes for qRT-PCR Analysis in the Oil-Rich Tuber Crop Tiger Nut (Cyperus esculentus) Based on Transcriptome Data

Tiger nut (Cyperus esculentus), a perennial C₄ plant of the Cyperaceae family, is an unconventional crop that is distinguished by its oil-rich tubers, which also possesses the advantages of strong resistance, wide adaptability, short life periods, and large biomass. To facilitate studies on gene expression in this species, we identified and validated a series of reference genes (RGs) based on transcriptome data, which can be employed as internal controls for qRT-PCR analysis in tiger nut. Fourteen putative candidate RGs were identified and evaluated across nine different tissues of two cultivars, and the RGs were analyzed using three different algorithms (geNorm, NormFinder, and BestKeeper). The stability rankings of the candidate RGs were merged into consensus lists with RankAggreg. For the below-ground storage organ of tiger nut, the optimal RGs were TUB4 and UCE2 in different developmental stages of tubers. UCE2 and UBL5 were the most stably expressed RGs among all tissues, while Rubisco and PGK exhibited the lowest expression stability. UCE2, UBL5 and Rubisco were compared to normalize the expression levels of the caleosin (CLO) and diacylglycerol acyltransferase 2-2 (DGAT2-2) genes across the same tissues. Our results showed that the RGs identified in this study, which exhibit more uniform expression patterns, may be utilized for the normalization of qRT-PCR results, promoting further research on gene expression in various tissues of tiger nut.

Systematic selection and validation of suitable reference genes for quantitative real-time PCR normalization studies of gene expression in Nitraria tangutorum

Suitable reference genes can be used to calibrate the error in quantitative real-time PCR (qPCR) experiments, making the results more credible. However, there are no reference genes suitable for multiple species and under different experimental conditions. Nitraria tangutorum Bobr. is a typical plant native to desert areas. It is drought-resistant, saline-alkali resistant, extreme temperatures-resistant, and has strong adaptability. To date, the importance of this germplasm has not been sufficiently understood; therefore, it is still unclear which genes can be used as reference genes to calibrate qPCR data of N. tangutorum. In this study we analyzed the expression levels of 10 candidate reference genes (ACT, GAPDH, TUA, TUB, CYP, UBC, His, PP2A, HSP, and EF1-α) in N. tangutorum seedlings under a series of experimental conditions, including in different organs (root, stem, and leaf) and under abiotic stresses (salt, drought, heat, and cold) and hormone stimuli (abscisic acid) by qPCR. Three software programs (geNorm, NormFinder, and BestKeeper) were used to evaluate the expression stability of the ten genes. Comprehensive analysis showed that EF1-α and His had the best expression stability, whereas HSP was the least suitable as a reference gene. The expression profile of NtCER7, a gene related to the regulation of cuticular wax biosynthesis in N. tangutorum, verified the accuracy of the experimental results. Based on this study, we recommend EF1-α and His as suitable reference genes for N. tangutorum. This paper provides the first data on stable reference genes in N. tangutorum, which will be beneficial to studying the gene expression of N. tangutorum and other Nitraria species in the future.

Integrated sRNAome and RNA-Seq analysis reveals miRNA effects on betalain biosynthesis in pitaya

BACKGROUND

MicroRNAs (miRNAs) and their regulatory functions in anthocyanin, carotenoid, and chlorophyll accumulation have been extensively characterized in many plant species. However, the miRNA regulatory mechanism in betalain biosynthesis remains mostly unknown.

RESULTS

In this study, 126 conserved miRNAs and 41 novel miRNAs were first isolated from Hylocereus monacanthus, among which 95 conserved miRNAs belonged to 53 miRNA families. Thirty-four candidate miRNAs related to betalain biosynthesis were differentially expressed. The expression patterns of those differential expressed miRNAs were analyzed in various pitaya tissues by RT-qPCR. A significantly negative correlation was detected between the expression levels of half those miRNAs and corresponding target genes. Target genes of miRNAs i.e. Hmo-miR157b-HmSPL6-like, Hmo-miR160a-Hpcyt P450-like3, Hmo-miR6020-HmCYP71A8-like, Hmo-novel-2-HmCYP83B1-like, Hmo-novel-15-HmTPST-like, Hmo-miR828a-HmTT2-like, Hmo-miR858-HmMYB12-like, Hmo-miR858-HmMYBC1-like and Hmo-miR858-HmMYB2-like were verified by 5'RACE and transient expression system in tobacco.

CONCLUSIONS

Hmo-miR157b, Hmo-miR160a, Hmo-miR6020 Hmo-novel-2, Hmo-novel-15, Hmo-miR828a and Hmo-miR858 play important roles in pitaya fruit coloration and betalain accumulation. Our findings provide new insights into the roles of miRNAs and their target genes of regulatory functions involved in betalain biosynthesis of pitaya.

Transcriptomics-based identification and characterization of glucosyltransferases involved in betalain biosynthesis in Hylocereus megalanthus

Pitaya (Hylocereus spp.) is the only commercial cultivation of fruit containing abundant betalains for consumer. Betalains are water-soluble nitrogen-containing pigments with high nutritional value and bioactivities. In this study, contents of betaxanthins and betacyanins were compared between 'Guanhuabai' (H. undatus) and 'Huanglong' (H. megalanthus) pitayas and key genes involved in betalain biosynthesis were screened from 'Huanglong' pitaya by RNA-Seq technology. Twenty-nine candidate genes related to betalain biosynthesis were obtained from the transcriptome data. Based on expression characteristics and sequence analyses, HmB5GT1 and HmHCGT2 were further analyzed. HmB5GT1 and HmHCGT2 were both conserved in 'PSPG-box' and localized in nucleus. Silencing of HmB5GT1 and HmHCGT2 resulted in a significant reduction in betacyanin and betaxanthin contents. Those results suggested that HmB5GT1 and HmHCGT2 are possibly involved in betalain biosynthesis in H. megalanthus. The present work provides new information on betalain biosynthesis in Hylocereus at the transcriptional level.

Evaluation of duplicated reference genes for quantitative real-time PCR analysis in genome unknown hexaploid oat (Avena sativa L.)

BACKGROUND

Oat (Avena sativa L.), a hexaploid crop with unknown genome, has valuable nutritional, medicinal and pharmaceutical uses. However, no suitable RGs (reference genes) for qPCR (quantitative real-time PCR) has been documented for oat yet. Single-copy gene is often selected as RG, which is challengeable or impactable in unexplored polyploids.

RESULTS

In this study, eleven candidate RGs, including four duplicated genes, were selected from oat transcriptome. The stability and the optimal combination of these candidate RGs were assessed in 18 oat samples by using four statistical algorithms including the ΔCt method, geNorm, NormFinder and BestKeeper. The most stable RGs for "all samples", "shoots and roots of seedlings", "developing seeds" and "developing endosperms" were EIF4A (Eukaryotic initiation factor 4A-3), UBC21 (Ubiquitin-Conjugating Enzyme 21), EP (Expressed protein) and EIF4A respectively. Among these RGs, UBC21 was a four-copy duplicated gene. The reliability was validated by the expression patterns of four various genes normalized to the most and the least stable RGs in different sample sets.

CONCLUSIONS

Results provide a proof of concept that the duplicated RG is feasible for qPCR in polyploids. To our knowledge, this study is the first systematic research on the optimal RGs for accurate qPCR normalization of gene expression in different organs and tissues of oat.