Identification of four novel stu-miR169s and their target genes in Solanum tuberosum and expression profiles response to drought stress

Yang, Jie; Zhang, Ning; Zhou, Xuyang; Wang, Di

doi:10.1007/s00606-015-1242-x

Cited by 14 publications

(10 citation statements)

References 67 publications

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“…The same gene, StNF-YA8, studied previously was reported to be induced by drought stress (Yang et al, 2016). Similarly, PtNF-YA9 has been demonstrated to regulate seed germination, abiotic stress responses, and plant growth and development (Lian et al, 2018).…”

Section: Stnf-ymentioning

confidence: 75%

Genome-Wide Analysis of NF-Y Genes in Potato and Functional Identification of StNF-YC9 in Drought Tolerance

Zhang

Zhu

et al. 2021

Front. Plant Sci.

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The nuclear factor Y (NF-Y) family is comprised of transcription factors that have been implicated in multiple plant biological processes. However, little is known about this family in potato. In the present study, a total of 41 StNF-Y genes were identified in the potato genome. In addition, the phylogenetic, gene structure, motif, and chromosomal location of this family were analyzed. The tissue expression profiles based on RNA-seq data showed that 27 StNF-Y genes had tissue-specific expression, while the remaining 14 had low expression in all tissues. Publicly available transcriptomics data from various abiotic stresses revealed several stress-responsive StNF-Y genes, which were further verified via quantitative real-time polymerase chain reaction experiments. Furthermore, the StNF-YC9 gene was highly induced by dehydration and drought treatments. StNF-YC9 protein was mainly localized in the nucleus and cytoplasmic membrane. Overexpressing StNF-YC9 potato lines (OxStNF-YC9) had significantly increased in root length and exhibited stronger stomatal closure in potato treated by polyethylene-glycol and abscisic acid. In addition, OxStNF-YC9 lines had higher photosynthetic rates and decreased water loss under short-term drought stress compared to wild-type plants. During long-term drought stress, OxStNF-YC9 lines had higher proline levels, lower malondialdehyde content, and increased activity of several antioxidant enzymes, including superoxide dismutase, catalase, and peroxidase. This study increased our understanding of the StNF-Y gene and suggested that StNF-YC9 played an important role in drought tolerance by increased the photosynthesis rate, antioxidant enzyme activity, and proline accumulation coupled to lowered malondialdehyde accumulation in potato.

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Section: Stnf-ymentioning

confidence: 75%

Genome-Wide Analysis of NF-Y Genes in Potato and Functional Identification of StNF-YC9 in Drought Tolerance

Zhang

Zhu

et al. 2021

Front. Plant Sci.

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“…Consistently, miR156 and miR172 affect not only flowering time, but also the timing of tuberization in potato. Similarly, miR169 is conserved related with salt stress in potato and other species ( Yang et al, 2016 ; Zhao et al., 2009 ; Luan et al, 2015 ). Indeed, it has been reported that both TOR and miRNAs are involved in many different signaling pathways to regulate plant growth and development in previous studies ( Jones-Rhoades, Bartel & Bartel, 2006 ; Shi, Wu & Sheen, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

“…Nevertheless, the number of the potato miRNAs (219) deposited in miRBase ( http://www.mirbase.org/ ) was still less than that of rice (1519), Arabidopsis (664), cotton ( Gossypium spp L.) (539) and maize (404). The function of some potato miRNAs were also confirmed, for example, miR172 could induce the potato tuberization ( Martin et al, 2009 ), miR396 , miR156a , miR157a and four miR169s were drought-induced ( Yang et al., 2016 ; Hwang, Shin & Kwon, 2011 ), miR156 could modulate potato architecture and tuberization ( Bhogale et al, 2014 ), miR166 and miR159 were responding to salinity ( Kitazumia et al, 2015 ), miR482e could enhance plant sensitivity to Verticillium dahliae infection ( Yang et al, 2015 ), miR397-5P was involved in the PVA infection ( Li et al, 2017 ), miR164 could mediate the lateral root development ( Zhang et al, 2018 ), and miR160 was associated with local defense and systemic acquired resistance against Phytophthora infestans ( Natarajan et al, 2018 ). Herein, a large number of miRNAs have yet to be discovered, and the functions of most miRNAs remain to be investigated in potato.…”

Section: Introductionmentioning

confidence: 90%

“…As one of the world’s most important staple food, potato ( Solanum tuberosum L.) is essential to food security and human health all over the world, especially in solving the poverty ( Zhang et al., 2017a ). In the last decade, a fast increasing number of potato miRNAs were identified using comprehensive bioinformatic analysis of EST data, comparative genome strategy, computational prediction, and high-throughput sequencing ( Zhang et al., 2013 ; Zhang et al., 2009b ; Yang et al., 2016 ; Yang et al, 2010 ). Nevertheless, the number of the potato miRNAs (219) deposited in miRBase ( http://www.mirbase.org/ ) was still less than that of rice (1519), Arabidopsis (664), cotton ( Gossypium spp L.) (539) and maize (404).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide miRNA expression profiling in potato (Solanum tuberosum L.) reveals TOR-dependent post-transcriptional gene regulatory networks in diverse metabolic pathway

Deng

Yin

Xiong

et al. 2021

PeerJ

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Target of rapamycin (TOR) operates as a hub of the signal transduction that integrates nutrient and energy signaling to promote cell proliferation and growth through mediating the transcriptional and post- transcriptional regulator networks in all eukaryotic species. MicroRNAs (miRNAs) are widespread classes of small, single-stranded, non-coding endogenous RNAs and are widely found in eukaryotes, which play a vital role in regulating gene expression by degrading targeted mRNAs or translational repression at post-transcriptional level. Recent studies found that there were necessarily close connections between miRNA and TOR pathways in mammals. However, there is little information about the interplay between the miRNA and TOR in plants. Thus, the aim of this study was to identify potential TOR-miRNA-mRNA regulatory networks in TOR signaling through global mRNA and microRNA expression profiling in potato. Based on the previous high-throughput transcriptome sequencing and filtering, a total of 2,899 genes were significantly differentially expressed in potato under TOR inhibitors treatment. Pathway analysis revealed that these genes were significantly enriched in multiple metabolic processes. Similarly, in the present study, suppression of TOR resulted in 41 miRNAs up-regulated and 45 down-regulated, revealing that TOR plays a crucial role in the regulation of miRNA regulatory network. Furthermore, integrated mRNA and miRNA expression profiling uncovered that these miRNAs participated in large-scale metabolic process in the TOR signal pathway in potato, such as regulation of autophagy and ubiquitination, and biosynthesis of secondary metabolites. Overall, the results shed new insight into TOR related post-transcriptional gene regulatory networks in potato and suggesting TOR-miRNA-targeting genes relevant networks as a potential genetic resource for potato improvement.

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“…The decreased expression of miR169 might drive the over‐expression of NF‐YA family members in S . tuberosum (Yang et al ). In A .…”

Section: Discussionmentioning

confidence: 99%

Small RNA and degradome profiling reveals important roles for microRNAs and their targets in tea plant response to drought stress

Liu

et al. 2016

Physiologia Plantarum

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Tea (Camellia sinensis) is a popular beverage worldwide. Drought stress (DS) is a major constraint on the growth, yield and quality of tea plants. MicroRNAs (miRNAs) play important roles in plant responses to DS. We constructed eight small RNA libraries from the drought-tolerant 'Ningzhou 2' (NZ2) and drought-susceptible 'Zhuyeqi' (ZYQ) cultivars during four stages [control (CK), the fourth day of DS, the eighth day of DS and after recovery (RC)]. A total of 268 conserved and 62 novel miRNAs were identified using small RNA sequencing. In total, 139 (52.9%) and 96 (36.0%) conserved miRNAs were differentially expressed during the four stages (P ≤ 0.05) in NZ2 and ZYQ, respectively. A total of 814 predicted target genes were identified as differentially regulated by 199 miRNAs through degradome sequencing. Among them, 201 and 218 genes were specific to the NZ2 and ZYQ cultivars, respectively, and 395 were common to both cultivars. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed the biological roles of these targets and showed that some of the targets responded to DS in a stress- and cultivar-dependent manner. Correlated expression patterns between miRNA and their targets showed that specific miRNAs target the miRNA effector Argonaute 1 (AGO1), drought signaling-related receptors and enzymes, transcription factors, and other structural and functional proteins. The predicted regulatory networks provide insights into a potential miRNA-mediated regulatory mechanism. These results will contribute to the breeding of drought-tolerant tea plants and to elucidating miRNA regulation in response to drought.

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Identification of four novel stu-miR169s and their target genes in Solanum tuberosum and expression profiles response to drought stress

Cited by 14 publications

References 67 publications

Genome-Wide Analysis of NF-Y Genes in Potato and Functional Identification of StNF-YC9 in Drought Tolerance

Genome-Wide Analysis of NF-Y Genes in Potato and Functional Identification of StNF-YC9 in Drought Tolerance

Genome-wide miRNA expression profiling in potato (Solanum tuberosum L.) reveals TOR-dependent post-transcriptional gene regulatory networks in diverse metabolic pathway

Small RNA and degradome profiling reveals important roles for microRNAs and their targets in tea plant response to drought stress

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