Identification and characterization of novel microRNAs for fruit development and quality in hot pepper (Capsicum annuum L.)

Liu, Zhoubin; Zhang, Yuping; Ou, Lijun; Kang, Linyu; Liu, Yuhua; Lv, Junheng; Ge, Wei; Yang, Bo‐Yi; Yang, Sha; Chen, Wenchao; Dai, Xiang; Li, Xuefeng; Zhou, Shudong; Zhang, Zhuqing; Ma, Yanqing; Zou, Xuexiao

doi:10.1016/j.gene.2017.01.020

Cited by 43 publications

(37 citation statements)

References 36 publications

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“…The distribution of various size of sRNAs showed that 24 nt sRNAs are the most abundant, accounting for 49.5% (4RTR) to 39.2% (7RTR), following by 22 nt sRNAs (Additional le: Fig.1). The distribution is consistent with previous reports in various plants (Liu et al 2017). To verify the results, we analyzed the Pearson correlation coe cients of the miRNA expression between the biological duplicates (Additional le: Figure S1), and the Pearson r value of miRNA expression were about 0.8.…”

Section: Resultssupporting

confidence: 86%

Identification of cold stress responsive microRNAs in cold tolerant and susceptible Hemerocallis fulva by high throughput sequencing

Huang

Jiang

Jin

et al. 2020

Preprint

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Background:Hemerocallis fulva is a perennial herb belonging to Hemerocallis of Hemerocallis. Because of the large and bright colors, it is often used as a garden ornamental plant. But most varieties of H. fulva on the market will wither in winter, which will affect their beauty. It is very important to study the effect of low temperature stress on the physiological indexes of H. fulva and understand the cold tolerance of different H. fulva. MiRNA is a kind of endogenous non coding small molecular RNA with length of 21-24nt. It mainly inhibits protein translation by cutting target genes, and plays an important role in the development of organisms, gene expression and biological stress. Low temperature is the main abiotic stress affecting the production of H. fulva in China, which hinders the growth and development of plants. A comprehensive understanding of the expression pattern of microRNA in H. fulva under low temperature stress can improve our understanding of microRNA mediated stress response. Although there are many studies on miRNAs of various plants under cold stress at home and abroad, there are few studies on miRNAs related to cold stress of H. fulva. It is of great significance to explore the cold stress resistant gene resources of H. fulva, especially the identification and functional research of miRNA closely related to cold stress, for the breeding of excellent H. fulva.Results A total of 5619 cold-responsive miRNAs, 315 putative novel and 5 304 conserved miRNAs, were identified from the leaves and roots of two different varieties ‘Jinyan’ (cold-tolerant) and ‘Lucretius ’ (cold-sensitive), which were stressed under -4 oC for 24 h. Twelve conserved and three novel miRNAs (novel-miR10, novel-miR19 and novel-miR48) were differentially expressed in leaves of ‘Jinyan’ under cold stress. Novel-miR19, novel-miR29 and novel-miR30 were up-regulated in roots of ‘Jinyan’ under cold stress. Thirteen and two conserved miRNAs were deferentially expressed in leaves and roots of ‘Lucretius’ after cold stress. The deferentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR156, miR166 and miR319 families. A total of 6 598 target genes for 6 516 known miRNAs and 82 novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Ten differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR(q-PCR), and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR156a-3-p, miR319a, and novel-miR19) may play important roles in plant response to cold stress.Conclusions Our study indicates that some putative target genes and miRNA mediated metabolic processes and stress responses are significant to cold tolerance in H. fulva.

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Section: Resultssupporting

confidence: 86%

Identification of cold stress responsive microRNAs in cold tolerant and susceptible Hemerocallis fulva by high throughput sequencing

Huang

Jiang

Jin

et al. 2020

Preprint

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“…In plants, miRNAs regulate gene expression mainly by cleaving the targeted mRNAs 13 , 53 . Many other miRNAs also participated in disease resistance by targeting defense genes or TFs.…”

Section: Discussionmentioning

confidence: 99%

Integrated mRNA and microRNA transcriptome analysis reveals miRNA regulation in response to PVA in potato

Liu

Chen

et al. 2017

Sci Rep

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Potato (Solanum tuberosum L.) is the fourth most important crop worldwide. Potato virus A (PVA) is one of the most harmful viruses infecting potatoes. However, the molecular mechanisms governing the responses to PVA infection in potato at the transcriptional and post-transcriptional levels are not well understood. In this study, we performed both mRNA and small RNA sequencing in potato leaves to identify the genes and miRNAs involved in the response to PVA infection. A total of 2,062 differentially expressed genes (DEGs) and 201 miRNAs (DEMs) were identified, respectively. Gene ontology (GO) and KEGG analysis revealed that these DEGs were involved in the transduction of pathogen signals, transcriptional reprogramming, induction of hormone signaling, activation of pathogenesis-related (PR) genes, and changes in secondary metabolism. Small RNA sequencing revealed 58 miRNA-mRNA interactions related to PVA infection. Some of the miRNAs (stu-miR482d-3p, stu-miR397-5p, etc) which target PR genes showed negative correlations between the DEMs and DEGs. Eight of the DEGs and three DEMs with their target genes were further validated by quantitative real time-PCR (qRT-PCR). Overall, this study provides a transcriptome-wide insight into the molecular basis of resistance to PVA infection in potato leaves and potenital candidate genes for improving resistance cultivars.

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“…However, even though considerable attention has been given to the molecular mechanism of pepper fruit development (Jang et al, 2015; Liu et al, 2017), the RGs in pepper fruit have not yet been characterized. Only a small number of the previous related studies focused on the identification of the optimal RGs for qPCR analysis under various stress conditions, or in different pepper tissues, and these studies were mainly based on the evaluation or validation of some previously reported candidate RGs (for example, house-keeping genes) under various conditions (Wan et al, 2011; Wang et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Identification of Optimal Reference Genes for Normalization of qPCR Analysis during Pepper Fruit Development

et al. 2017

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Due to its high sensitivity and reproducibility, quantitative real-time PCR (qPCR) is practiced as a useful research tool for targeted gene expression analysis. For qPCR operations, the normalization with suitable reference genes (RGs) is a crucial step that eventually determines the reliability of the obtained results. Although pepper is considered an ideal model plant for the study of non-climacteric fruit development, at present no specific RG have been developed or validated for the qPCR analyses of pepper fruit. Therefore, this study aimed to identify stably expressed genes for their potential use as RGs in pepper fruit studies. Initially, a total of 35 putative RGs were selected by mining the pepper transcriptome data sets derived from the PGP (Pepper Genome Platform) and PGD (Pepper Genome Database). Their expression stabilities were further measured in a set of pepper (Capsicum annuum L. var. 007e) fruit samples, which represented four different fruit developmental stages (IM: Immature; MG: Mature green; B: Break; MR: Mature red) using the qPCR analysis. Then, based on the qPCR results, three different statistical algorithms, namely geNorm, Normfinder, and boxplot, were chosen to evaluate the expression stabilities of these putative RGs. It should be noted that nine genes were proven to be qualified as RGs during pepper fruit development, namely CaREV05 (CA00g79660); CaREV08 (CA06g02180); CaREV09 (CA06g05650); CaREV16 (Capana12g002666); CaREV21 (Capana10g001439); CaREV23 (Capana05g000680); CaREV26 (Capana01g002973); CaREV27 (Capana11g000123); CaREV31 (Capana04g002411); and CaREV33 (Capana08g001826). Further analysis based on geNorm suggested that the application of the two most stably expressed genes (CaREV05 and CaREV08) would provide optimal transcript normalization in the qPCR experiments. Therefore, a new and comprehensive strategy for the identification of optimal RGs was developed. This strategy allowed for the effective normalization of the qPCR analysis of the pepper fruit development at the whole pepper genome level. This study not only explored the optimal RGs specific for studying pepper fruit development, but also introduced a referable strategy of RG mining which could potentially be implicated in other plant species.

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Identification and characterization of novel microRNAs for fruit development and quality in hot pepper (Capsicum annuum L.)

Cited by 43 publications

References 36 publications

Identification of cold stress responsive microRNAs in cold tolerant and susceptible Hemerocallis fulva by high throughput sequencing

Identification of cold stress responsive microRNAs in cold tolerant and susceptible Hemerocallis fulva by high throughput sequencing

Integrated mRNA and microRNA transcriptome analysis reveals miRNA regulation in response to PVA in potato

Identification of Optimal Reference Genes for Normalization of qPCR Analysis during Pepper Fruit Development

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