Assessment of miRNA expression profile and differential expression pattern of target genes in cold-tolerant and cold-sensitive tomato cultivars

Koç, İbrahim; Filiz, Ertuğrul; Tombuloğlu, Hüseyin

doi:10.1080/13102818.2015.1061447

Cited by 29 publications

(17 citation statements)

References 69 publications

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“…In this study, miR167 and miR393 were upregulated in both cultivars, while miR160 was upregulated in FN39 (relative cold tolerance cultivar) and downregulated in ROC22 (relative cold sensitivity cultivar). In Lycopersicon esculentum Mill studies using stem-loop RT-qPCR, miR167 and miR393 increased at 4 °C at early time points (0, 1, 4 and 16 h) [ 53 ]. In 2-week-old Arabidopsis seedlings, miR393 was strongly induced by cold, NaCl, dehydration and ABA treatments [ 54 ].…”

Section: Discussionmentioning

confidence: 99%

miRNA alteration is an important mechanism in sugarcane response to low-temperature environment

Yang

Zhang

et al. 2017

BMC Genomics

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BackgroundCold is a major abiotic stress limiting the production of tropical and subtropical crops in new production areas. Sugarcane (Saccharum spp.) originates from the tropics but is cultivated primarily in the sub-tropics where it frequently encounters cold stress. Besides regulating plant growth, miRNAs play an important role in environmental adaption.ResultsIn this study, a total of 412 sugarcane miRNAs, including 261 known and 151 novel miRNAs, were obtained from 4 small RNA libraries through the Illumina sequencing method. Among them, 62 exhibited significant differential expression under cold stress, with 34 being upregulated and 28 being downregulated. The expression of 13 miRNAs and 12 corresponding targets was validated by RT-qPCR, with the majority being consistent with the sequencing data. GO and KEGG analysis indicated that these miRNAs were involved in stress-related biological pathways. To further investigate the involvement of these miRNAs in tolerance to abiotic stresses, sugarcane miR156 was selected for functional analysis. RT-qPCR revealed that miR156 levels increased in sugarcane during cold, salt and drought stress treatments. Nicotiana benthamiana plants transiently overexpressing miR156 exhibited better growth status, lower ROS levels, higher anthocyanin contents as well as the induction of some cold-responsive genes, suggesting its positive role in the plant cold stress response.ConclusionsThis study provides a global view of the association of miRNA expression with the sugarcane response to cold stress. The findings have enriched the present miRNA resource and have made an attempt to verify the involvement of miR156 in plant response to cold stress.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4231-3) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

miRNA alteration is an important mechanism in sugarcane response to low-temperature environment

Yang

Zhang

et al. 2017

BMC Genomics

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“…The important role of miRNAs in response to different environmental stresses has been verified in previous studies [ 21 , 15 , 31 – 35 ]. Several works have introduced cold stress responsive miRNAs in different plant species such as Arabidopsis [ 7 , 16 ], tea [ 14 ], tomato [ 36 , 37 ], rice [ 38 ], wheat [ 39 , 40 ], peach [ 12 ], Populus [ 41 ] and Brachypodium [ 6 ]. No study has been done on the miRNAs regulatory response to cold stress in almond.…”

Section: Discussionmentioning

confidence: 99%

“…The identified roles of this group of proteins include polar auxin transport, lipid catabolism, xenobiotic detoxification through transporting toxic compounds from cytosol into the vacuole [ 73 ] disease resistance, and stomatal function [ 71 ]. The induction of this ABC transporter in cold-tolerant tomato cultivar has been reported [ 37 ]. In our study, the significant up-regulation of ABC transporter in the H genotype, and not in the Sh12 genotype, revealed the involvement of this gene in cold tolerance, possibly through different processes such as detoxification mechanisms.…”

Section: Discussionmentioning

confidence: 99%

The Small-RNA Profiles of Almond (Prunus dulcis Mill.) Reproductive Tissues in Response to Cold Stress

et al. 2016

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Spring frost is an important environmental stress that threatens the production of Prunus trees. However, little information is available regarding molecular response of these plants to the frost stress. Using high throughput sequencing, this study was conducted to identify differentially expressed miRNAs, both the conserved and the non-conserved ones, in the reproductive tissues of almond tolerant H genotype under cold stress. Analysis of 50 to 58 million raw reads led to identification of 174 unique conserved and 59 novel microRNAs (miRNAs). Differential expression pattern analysis showed that 50 miRNA families were expressed differentially in one or both of almond reproductive tissues (anther and ovary). Out of these 50 miRNA families, 12 and 15 displayed up-regulation and down-regulation, respectively. The distribution of conserved miRNA families indicated that miR482f harbor the highest number of members. Confirmation of miRNAs expression patterns by quantitative real- time PCR (qPCR) was performed in cold tolerant (H genotype) alongside a sensitive variety (Sh12 genotype). Our analysis revealed differential expression for 9 miRNAs in anther and 3 miRNAs in ovary between these two varieties. Target prediction of miRNAs followed by differential expression analysis resulted in identification of 83 target genes, mostly transcription factors. This study comprehensively catalogued expressed miRNAs under different temperatures in two reproductive tissues (anther and ovary). Results of current study and the previous RNA-seq study, which was conducted in the same tissues by our group, provide a unique opportunity to understand the molecular basis of responses of almond to cold stress. The results can also enhance the possibility for gene manipulation to develop cold tolerant plants.

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“…Some miRNAs related to low-temperature stress in plants have been studied and verified, and the regulatory mechanisms of plant responses to low-temperature stress is also well understood [ 9 ]. Many studies have been carried out using Solanaceae plants [ 10 – 18 ], however, few studies focus on the miRNAs of eggplant, especially wild eggplant species.…”

Section: Introductionmentioning

confidence: 99%

Cold-responsive miRNAs and their target genes in the wild eggplant species Solanum aculeatissimum

Liu

Zhang

et al. 2017

BMC Genomics

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BackgroundLow temperature is an important abiotic stress in plant growth and development, especially for thermophilic plants. Eggplants are thermophilic vegetables, although the molecular mechanism of their response to cold stress remains to be elucidated. MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play an essential role during plant development and stress responses. Although the role of many plant miRNAs in facilitating chilling tolerance has been verified, little is known about the mechanisms of eggplant chilling tolerance.ResultsHere, we used high-throughput sequencing to extract the miRNA and target genes expression profiles of Solanum aculeatissimum (S. aculeatissimum) under low temperature stress at different time periods(0 h, 2 h, 6 h, 12 h, 24 h). Differentially regulated miRNAs and their target genes were analyzed by comparing the small RNA (sRNA) and miRBase 20.0 databases using BLAST or BOWTIE, respectively. Fifty-six down-regulated miRNAs and 28 up-regulated miRNAs corresponding to 220 up-regulated mRNAs and 94 down-regulated mRNAs, respectively, were identified in S. aculeatissimum. Nine significant differentially expressed miRNAs and twelve mRNAs were identified by quantitative Real-time PCR and association analysis, and analyzed for their GO function enrichment and KEGG pathway association.ConclusionsIn summary, numerous conserved and novel miRNAs involved in the chilling response were identified using high-throughput sequencing, which provides a theoretical basis for the further study of low temperature stress-related miRNAs and the regulation of cold-tolerance mechanisms of eggplant at the miRNA level.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4341-y) contains supplementary material, which is available to authorized users.

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Assessment of miRNA expression profile and differential expression pattern of target genes in cold-tolerant and cold-sensitive tomato cultivars

Cited by 29 publications

References 69 publications

miRNA alteration is an important mechanism in sugarcane response to low-temperature environment

miRNA alteration is an important mechanism in sugarcane response to low-temperature environment

The Small-RNA Profiles of Almond (Prunus dulcis Mill.) Reproductive Tissues in Response to Cold Stress

Cold-responsive miRNAs and their target genes in the wild eggplant species Solanum aculeatissimum

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