Evaluation of putative reference genes for quantitative real-time PCR normalization in Lilium regale during development and under stress

Screening and validating of endogenous reference genes in Chlorella sp. TLD 6B under abiotic stress

Chlorella sp. TLD 6B, a microalgae growing in the Taklamakan Desert, Xinjiang of China, is a good model material for studying the physiological and environmental adaptation mechanisms of plants in their arid habitats, as its adaptation to the harsh desert environment has led to its strong resistance. However, when using real-time quantitative polymerase chain reaction (RT-qPCR) to analyze the gene expression of this algae under abiotic stress, it is essential to find the suitable endogenous reference genes so to obtain reliable results. This study assessed the expression stability of 9 endogenous reference genes of Chlorella sp. TLD 6B under four abiotic stresses (drought, salt, cold and heat). These genes were selected based on the analysis results calculated by the three algorithmic procedures of geNorm, NormFinder, and BestKeeper, which were ranked by refinder. Our research showed that 18S and GTP under drought stress, 18S and IDH under salt stress, CYP and 18S under cold stress, GTP and IDH under heat stress were the most stable endogenous reference genes. Moreover, UBC and 18S were the most suitable endogenous reference gene combinations for all samples. In contrast, GAPDH and α-TUB were the two least stable endogenous reference genes in all experimental samples. Additionally, the selected genes have been verified to be durable and reliable by detecting POD and PXG3 genes using above endogenous reference genes. The identification of reliable endogenous reference genes guarantees more accurate RT-qPCR quantification for Chlorella sp. TLD 6B, facilitating functional genomics studies of deserts Chlorella as well as the mining of resistance genes.

Effects of Polyploidization on Morphology, Photosynthetic Parameters and Sucrose Metabolism in Lily

Polyploidization is widely used in ornamental plant breeding. The polyploids usually produce greater amounts of biomass. However, the alternations to sucrose metabolism that occur in lily during development after polyploidization induced using colchicine are poorly understood. In this study, compared with their allodiploid counterparts, allotetraploid lilies presented a larger total leaf area per plant and slightly delayed flowering time. Moreover, photosynthetic parameter measurements revealed a higher net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and maximum Pn for allotetraploids than for allodiploids. Compared with allodiploids, allotetraploids also showed higher nonstructural carbohydrate (NSC) contents during development according to HILIC-CAD results. The expression levels of sucrose metabolism-related genes were higher in allotetraploids than in allodiploids at the same time points. The expression profiles of several target genes in allotetraploids were distinctly different from those in allodiploids. Susy2/3 exhibited opposite expression profiles in allotetraploids and allodiploids, and the expression profiles of SPS3 and Susy2 were significantly correlated with sucrose content change trends in allodiploids and allotetraploids, respectively.

Transcriptome Analysis Reveals that Exogenous Melatonin Confers Lilium Disease Resistance to Botrytis elliptica

Leaf blight, caused by Botrytis elliptica (Berk.) Cooke, is a devastating disease that limits the production of Lilium in China and in other countries worldwide. Numerous studies have indicated that plants have evolved sophisticated and effective signal transduction and defense-related pathways in response to pathogen invasion. Recently, particular attention has been given to the action(s) of melatonin in plants in response to biotic stress, and the role of melatonin in plant–pathogen interactions has also been discussed. In this study, RNA-seq was applied to analyze the transcriptomic changes in Lilium leaves that were pre-treated and post-treated with melatonin after B. elliptica infection for 0, 12, 24, 36, and 72 h and then compare those changes with those of the control. Treatment with exogenous melatonin and infection with B. elliptica caused differential expression of a large number of genes in Lilium leaves. KEGG pathway analysis showed that, after melatonin treatment, the defense-related DEGs were mainly enriched in plant–pathogen interactions, plant hormone signal transduction, MAPK signaling pathways, phenylpropanoid biosynthesis, and phenylalanine metabolism. RT–qPCR was used to verify the expression changes of 12 DEGs, the results of which were consistent with the RNA-seq analysis results. The expression of DEGs related to the MAPK pathway were significantly different between the MB group and the HB group, suggesting that, via the MAPK signaling cascade, melatonin may play a role in the disease resistance of Lilium to B. elliptica. This study provides a new perspective and information for molecular-based breeding of Lilium disease resistance.

Analyses of Botrytis cinerea-responsive LrWRKY genes from Lilium regale reveal distinct roles of two LrWRKY transcription factors in mediating responses to B. cinerea

Botrytis cinerea induced expression of 15 LrWRKY genes; overexpression of LrWRKY39 and LrWRKY41a increased resistance and susceptibility, respectively, to B. cinerea in a manner related to SA and JA signaling. WRKY transcription factors (TFs), a large family, play important roles in coping with biotic stresses. Lilium regale Wilson is a lily species with strong resistance to fungi and viruses; however, functional characterization of LrWRKY TFs remains very limited. Here, a total of 25 LrWRKY members were identified from the L. regale transcriptome, and 15 LrWRKY genes were significantly induced by Botrytis cinerea. Based on their structural features, B. cinerea-responsive LrWRKY genes could be classified into six subgroups (Groups I, IIa-d, and III), and sequence alignment showed that 12 LrWRKY proteins have a well-conserved WRKYGQK domain, while 3 LrWRKYs have a variant sequence (WRKYGKK or WRMYEQK). Quantitative RT-PCR analysis revealed tissue-specific expression of B. cinerea-responsive LrWRKY genes and their expression profiles in response to defense-related hormones salicylic acid (SA), methyl jasmonate (MeJA) and hydrogen peroxide. LrWRKY39 and LrWRKY41a, which encode two LrWRKY TFs with different three-dimensional (3D) models of the WRKY domain, were cloned, and both proteins were targeted to the nucleus. Overexpression of LrWRKY39 and LrWRKY41a in Arabidopsis thaliana increased the resistance and susceptibility to B. cinerea, respectively, compared to the wild type. Similar results were also observed in tobacco and lily (L. longiflorum 'Snow Queen') by transient transformation analyses. Their distinct roles may be related to changes in the transcript levels of SA-/JA-responsive genes. Our results provide new insights into B. cinerea-responsive LrWRKY members and the biological functions of two different 3D models of LrWRKY TFs in defense responses to B. cinerea infection.

Degradation of oxalic acid produced by Botrytis elliptica infection in two ploidy levels of Lilium rosthornii Diels

Oxalic acid (OA) is a crucial pathogenic factor for Sclerotinia spp. fungi, which is closely related to Botrytis spp. fungi. Whether OA is a pathogenic factor for the causal agent of grey mould in lily, Botrytis elliptica, and the response of lily to OA are poorly understood. To address these questions, lesion tissues and deposition of calcium oxalate (CaOX) and callose were observed in diploid and tetraploid leaves of L. rosthornii after inoculation with B. elliptica. Oxalate oxidase (OXO) activity and the transcript levels of some genes related to OA degradation (LrGLP1, LrGLP2 and LrWRKY4), reactive oxygen species (ROS) production/scavenging systems (LrRBOHD, LrGST, LrPOD and LrAPX1) and pathogen-related protein (PR) synthesis (LrCHI, LrBGL and LrPR10) were compared. After diploid and tetraploid leaves inoculation, lesion tissue and callose and CaOX were separately observed around in guard cells and stomata rather than the epidermis in the infected area. OXO activity was triggered at 2 h post-inoculation (hpi) in both ploidy leaves, and it was higher in the latter from 12-48 hpi. Expression of LrGLP1, LrGLP2, LrRBOHD, LrGST, LrPOD, LrCHI, LrBGL and LrPR10 was higher in tetraploids than in diploids from 24(12)-36(48) hpi. In conclusion, for B. elliptica, OA mainly chelates Ca²⁺ from the stomata cell wall. The strong capability to degrade OA and higher expression levels of some genes related to ROS accumulation/scavenging and PR synthesis may partially explain the relatively higher grey mould resistance of tetraploid L. rosthornii.

Hormonal Regulatory Patterns of LaKNOXs and LaBEL1 Transcription Factors Reveal Their Potential Role in Stem Bulblet Formation in LA Hybrid Lily

In lily reproduction, the mechanism of formation of bulbs has been a hot topic. However, studies on stem bulblet formation are limited. Stem bulblets, formed in the leaf axils of under- and above-ground stems, provide lilies with a strong capacity for self-propagation. First, we showed that above-ground stem bulblets can be induced by spraying 100 mg/L 6-BA on the LA hybrid lily 'Aladdin', with reduced endogenous IAA and GA₄ and a higher relative content of cytokinins. Then, expression patterns of three potential genes (two KNOTTED1-like homeobox (KNOX) and one partial BEL1-like homeobox (BELL)), during stem bulblet formation from our previous study, were determined by RT-qPCR, presenting a down-up trend in KNOXs and a rising tendency in BELL. The partial BELL gene was cloned by RACE from L. 'Aladdin' and denoted LaBEL1. Physical interactions of LaKNOX1-LaBEL1 and LaKNOX1-LaKNOX2 were confirmed by yeast two-hybrid and bimolecular fluorescence complementation assays. Furthermore, hormonal regulatory patterns of single LaKNOX1, LaKNOX2, LaBEL1, and their heterodimers, were revealed in transgenic Arabidopsis, suggesting that the massive mRNA accumulations of LaKNOX1, LaKNOX2 and LaBEL1 genes during stem bulblet formation could cause the dramatic relative increase of cytokinins and the decline of GAs and IAA. Taken together, a putative model was proposed that LaKNOX1 interacts with LaKNOX2 and LaBEL1 to regulate multiple phytohormones simultaneously for an appropriate hormonal homeostasis, which suggests their potential role in stem bulblet formation in L. 'Aladdin'.

Analysis of miRNA-mediated regulation of flowering induction in Lilium × formolongi

BACKGROUND

MicroRNAs play pivotal roles in plant vegetative phase change and flowering induction via integrating into multiple flowering pathways. Lilium × formolongi is an important ornamental lily cultivar that can flower within one year after sowing. However, it remains unresolved how miRNA-mediated regulation networks contribute to the L. × formolongi characteristics of a short vegetative growth period and rapid flowering.

RESULTS

In this study, the small RNA libraries and one degradome library were constructed for L. × formolongi during vegetative growth and flowering initiation, and 366 conserved miRNAs and 32 novel miRNAs were identified. Additionally, 84 miRNAs were significantly differentially expressed during development. A total of 396 targets of 185 miRNAs were identified and validated through degradome sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that functions of the targets were top enriched in the cold and cadmium ion responses, pentose phosphate pathway and carbon fixation in photosynthetic organisms. Furthermore, among 23 differentially expressed miRNA-target pairs, the miR156s-LfSPL2, miR172a-LfAP2 and miR164a-LfNAC pairs as well as miR159a-LfSPL2 were found to be relevant to flowering based on the correlation analysis of expression profiles in the miRNA libraries, degradome and transcriptome. A coexpression regulatory network focused on differentially expressed pairs was also constructed by WGCNA, and 14 miRNAs were considered putative key miRNAs during vegetative development and flowering induction. miR156a/ d/ e showed particularly strong relationships with other miRNAs in the coexpression network.

CONCLUSIONS

This study provides cues for the further exploration of the regulatory mechanisms of short vegetative development and flowering in L. × formolongi.

Isolation and functional identification of a Botrytis cinerea-responsive caffeoyl-CoA O-methyltransferase gene from Lilium regale wilson

In plants, genes involved in the Phenylpropanoid/monolignol pathway play important roles in lignin biosynthesis and plant immunity. However, their biological function in Lilium remains poorly characterized. Comparative RNA sequencing of the expression profiles of the monolignol pathway genes from fungi-resistant species Lilium regale after inoculation with Botrytis cinerea was performed. One upregulated caffeoyl-CoA O-methyltransferase gene, LrCCoAOMT, was cloned for functional characterization by reverse genetic methods. LrCCoAOMT encodes a putative protein of 246 amino acids and is highly expressed in stem tissues and responsive to salicylic acid (SA) signaling and B. cinerea infection. LrCCoAOMT was largely directed to the cytoplasm. LrCCoAOMT overexpression in Arabidopsis resulted in an increased lignin deposition in vascular tissues and conferred resistance to B. cinerea infection in transgenic plants. Transient transformation of LrCCoAOMT in nonresistant Lilium sargentiae leaves also identified the defense function to B. cinerea. In addition, transcript levels of genes involved in the monolignol and SA-dependent signaling pathways were altered in transgenic Arabidopsis, suggesting that LrCCoAOMT might play vital roles in the resistance of L. regale to B. cinerea related to the levels of lignin and the regulation of SA signaling. This is the first report to functionally characterize a CCoAOMT gene in Lilium, a potential molecular target for lily molecular improvement.

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

Photosynthesis is closely related to the growth of plants. A stable reference gene is fundamental for studies of the molecular mechanism of photosynthesis in Lilium regale. Therefore, it is very important to select a suitable reference gene for qRT-PCR analysis on genes of photosynthetic system, chlorophyll biosynthetic pathway and chloroplast development in Lilium regale. Three kinds of tissues, leaves and bulbs (abnormal leaves) of tissue culture plantlets and cotyledons of seedlings of the wild-type and mutant Lilium regale were selected as materials for qRT-PCR. Six housekeeping genes were selected as candidate genes from transcriptome sequencing data of the wild-type and yellow seedling lethal mutant of Lilium regale. Finally, the expression stability of six candidate reference genes was analyzed using geNorm, NormFinder, and BestKeeper software, the comparative ∆Ct method, and the RefFinder program. The results showed that LrActin2 was the best reference gene for qRT-PCR analysis of photosynthesis-related genes expression in leaves of tissue culture plantlets and seedlings of Lilium regale. This study provided useful data for further research on molecular mechanism of photosynthesis in the Lilium.

Selección de genes de referencia para análisis transcripcionales en el modelo clavel (Dianthus caryophyllus L.) - Fusarium oxysporum f. sp. dianthi

En el presente trabajo se seleccionaron y validaron genes de referencia para estudios transcripcionales en el modelo clavel - Fusarium oxysporum f. sp. dianthi. Para ello, se seleccionaron genes asociados a procesos básicos celulares que han sido usados como genes de referencia en otros modelos planta-patógeno y se determinó el efecto de la inoculación del patógeno sobre su expresión. Se realizó un diseño de cebadores para los diferentes genes candidatos con el fin de verificar tanto su presencia en el genoma de claveles cultivados en Colombia, como su transcripción constitutiva en los diferentes tejidos por medio de la técnica de transcripción reversa y posterior reacción en cadena de la polimerasa (RT-PCR por sus siglas en ingles). Posteriormente, se evaluaron los niveles transcripcionales de los genes candidatos usando RT-qPCR en tallos y raíces de dos variedades con diferentes niveles de resistencia a la enfermedad, que fueron inoculados con este patógeno. La validación estadística realizada, usando ANOVA y los programas GeNorm y Normfinder, determinó que los genes codificantes para una histona H3 y el ARNr18S no presentan variación en sus niveles de expresión por efecto de la inoculación, permitiendo su uso como genes de referencia en estudios transcripcionales en esta interacción planta-patógeno.

Selection and validation of suitable reference genes for qRT-PCR analysis in pear leaf tissues under distinct training systems

Training systems generally alter tree architecture, which modulates light microclimate within the canopy, for the purpose of improving photosynthetic efficiency and fruit quality. Gene expression quantification is one of the most important methods for exploring the molecular mechanisms underlying the influence of training systems on pear photosynthesis, and suitable reference genes for gene expression normalization are a prerequisite for this method. In this study, the expression stability of nine common and four novel candidate genes were evaluated in 14 different pear leaf samples in two training systems, including those at four developmental stages (training_period) and from different parts of the trees (training_space), using two distinct algorithms, geNorm and NormFinder. Our results revealed that SKD1 (Suppressor of K⁺Transport Growth Defect1)/ YLS8 (Yellow Leaf Specific 8) and ARM (Armadillo) were the most stable single reference genes for the ‘training_period’ and ‘training_space’ subsets, respectively, although these single genes were not as stable as the optimal pairs of reference genes, SKD1+YLS8 and ARM+YLS8, respectively. Furthermore, the expression levels of the PpsAPX (Ascorbate peroxidase) gene showed that the arbitrary use of reference genes without previous testing could lead to misinterpretation of data. This work constitutes the first systematic analysis regarding the selection of superior reference genes in training system studies, facilitating the elucidation of gene function in pear and providing valuable information for similar studies in other higher plants.

Reference Gene Selection for qRT-PCR Normalization Analysis in kenaf (Hibiscus cannabinus L.) under Abiotic Stress and Hormonal Stimuli

Kenaf (Hibiscus cannabinus L.), an environmental friendly and economic fiber crop, has a certain tolerance to abiotic stresses. Identification of reliable reference genes for transcript normalization of stress responsive genes expression by quantitative real-time PCR (qRT-PCR) is important for exploring the molecular mechanisms of plants response to abiotic stresses. In this study, nine candidate reference genes were cloned, and their expression stabilities were assessed in 132 abiotic stress and hormonal stimuli samples of kenaf using geNorm, NormFinder, and BestKeeper algorithms. Results revealed that HcPP2A (Protein phosphatase 2A) and HcACT7 (Actin 7) were the optimum reference genes across all samples; HcUBC (Ubiquitin-conjugating enzyme like protein) was the worst reference gene for transcript normalization. The reliability of the selected reference genes was further confirmed by evaluating the expression profile of HcWRKY28 gene at different stress durations. This work will benefit future studies on discovery of stress-tolerance genes and stress-signaling pathways in this important fiber crop.

Transcriptome-Wide Analysis of Botrytis elliptica Responsive microRNAs and Their Targets in Lilium Regale Wilson by High-Throughput Sequencing and Degradome Analysis

MicroRNAs, as master regulators of gene expression, have been widely identified and play crucial roles in plant-pathogen interactions. A fatal pathogen, Botrytis elliptica, causes the serious folia disease of lily, which reduces production because of the high susceptibility of most cultivated species. However, the miRNAs related to Botrytis infection of lily, and the miRNA-mediated gene regulatory networks providing resistance to B. elliptica in lily remain largely unexplored. To systematically dissect B. elliptica-responsive miRNAs and their target genes, three small RNA libraries were constructed from the leaves of Lilium regale, a promising Chinese wild Lilium species, which had been subjected to mock B. elliptica treatment or B. elliptica infection for 6 and 24 h. By high-throughput sequencing, 71 known miRNAs belonging to 47 conserved families and 24 novel miRNA were identified, of which 18 miRNAs were downreguleted and 13 were upregulated in response to B. elliptica. Moreover, based on the lily mRNA transcriptome, 22 targets for 9 known and 1 novel miRNAs were identified by the degradome sequencing approach. Most target genes for elliptica-responsive miRNAs were involved in metabolic processes, few encoding different transcription factors, including ELONGATION FACTOR 1 ALPHA (EF1a) and TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR 2 (TCP2). Furthermore, the expression patterns of a set of elliptica-responsive miRNAs and their targets were validated by quantitative real-time PCR. This study represents the first transcriptome-based analysis of miRNAs responsive to B. elliptica and their targets in lily. The results reveal the possible regulatory roles of miRNAs and their targets in B. elliptica interaction, which will extend our understanding of the mechanisms of this disease in lily.

Validation of Reference Genes for Quantitative Real-Time PCR during Bicolor Tepal Development in Asiatic Hybrid Lilies (Lilium spp.)

Quantitative real-time PCR (qRT-PCR) is a reliable and high-throughput technique for gene expression studies, but its accuracy depends on the expression stability of reference genes. To date, several reliable reference gene identifications have been reported in Lilium spp., but none has been obtained for lily tepals at different developmental stages. In this study, ten candidate reference genes were selected and evaluated for their expression stability in Lilium 'Tiny Padhye' during the process of bicolor tepal development. The expression stability of these candidates was evaluated by three software programs (geNorm, NormFinder, and BestKeeper) and the comparative ΔCt method, and comprehensive stability rankings were generated by RefFinder. As a result, TIP41-like family gene (TIP41) and actin (ACT) were the best combination of reference genes for tepals at different developmental stages; TIP41 and F-box family gene (F-box) for tepals under shading treatment; ACT, actin11 (ACT11), and elongation factor 1-α (EF1-α) for different tissues; and ACT, TIP41, and ACT11 for all samples. The selected optimal reference genes were further verified by analyzing the expression levels of flavonoid 3'-hydroxylase (LhF3'H) and anthocyanidin 3-O-glucosyltransfersae (LhUFGT) in tepals at different developmental stages. This study provides useful information for gene expression characterization in lilies under different experimental conditions, and can serve as a basis for similar research in other closely related species.

Validation of Reference Genes for RT-qPCR Studies of Gene Expression in Preharvest and Postharvest Longan Fruits under Different Experimental Conditions

Reverse transcription quantitative PCR (RT-qPCR) as the accurate and sensitive method is use for gene expression analysis, but the veracity and reliability result depends on whether select appropriate reference gene or not. To date, several reliable reference gene validations have been reported in fruits trees, but none have been done on preharvest and postharvest longan fruits. In this study, 12 candidate reference genes, namely, CYP, RPL, GAPDH, TUA, TUB, Fe-SOD, Mn-SOD, Cu/Zn-SOD, 18SrRNA, Actin, Histone H3, and EF-1a, were selected. Expression stability of these genes in 150 longan samples was evaluated and analyzed using geNorm and NormFinder algorithms. Preharvest samples consisted of seven experimental sets, including different developmental stages, organs, hormone stimuli (NAA, 2,4-D, and ethephon) and abiotic stresses (bagging and girdling with defoliation). Postharvest samples consisted of different temperature treatments (4 and 22°C) and varieties. Our findings indicate that appropriate reference gene(s) should be picked for each experimental condition. Our data further showed that the commonly used reference gene Actin does not exhibit stable expression across experimental conditions in longan. Expression levels of the DlACO gene, which is a key gene involved in regulating fruit abscission under girdling with defoliation treatment, was evaluated to validate our findings. In conclusion, our data provide a useful framework for choice of suitable reference genes across different experimental conditions for RT-qPCR analysis of preharvest and postharvest longan fruits.