Determining and validating of chilling responsive microRNAs associated with leaf growth of hybrid maize (Zea mays L.) ADA313
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PROVIDER: PRJNA524353 | ENA |
REPOSITORIES: ENA
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Project description:The exxpression profilling of chilling responsive and growth regulated microRNAs of maize hybrid ADA313 was conducted. Maize seedling were subjected to chilling temperature then meristem, elongation and mature growth zones were sampled. 321 known maize microRNA expression level were determined and compared between meristem, elongation and mature zones. Determining and validating of chilling responsive microRNAs associated with leaf growth of hybrid maize (Zea mays L.) ADA313
2021-02-01 | GSE127219 | GEO
Project description:Chilling stress is a major factor limiting the yield and quality of vegetable soybean (Glycine max L.) on a global scale. Systematic identification and function analysis of miRNA under chilling stress could be helpful to clarify the molecular mechanism of chilling resistance. In the present study, two independent small RNA libraries from leaves of vegetable soybean were constructed, and sequenced with the high-throughput Illumina Solexa system. A total of 434 known miRNAs and three novel miRNAs were identified. Moreover, the expression patterns of these miRNAs have been verified by qRT-PCR analysis. Furthermore, we identified their gene targets by high-throughput degradome sequencing and validated using 5'-RACE. A total of 898 transcripts were targeted by 54 miRNA families attributed to five categories. More importantly, we identified 55 miRNAs that differentially expressed between chilling stress and the control. The targets of these miRNAs were enriched in oxidation-reduction, signal transduction, and metabolic process functional categories. The qRT-PCR confirmed that there was a negative relationship among the miRNAs and their targets under chilling stress. Our work provides comprehensive molecular evidence for the possible involvement of miRNAs in the process of chilling-stress responses in vegetable soybean.
2016-12-28 | GSE76435 | GEO
Project description:Chilling is a major stress to plants of subtropical and tropical origins including maize. To reveal molecular mechanisms underlying chilling tolerance and chilling survival, we investigated maize transcriptome responses to chilling stress in differentiated leaves and roots as well as in crowns with meristem activity for survival. Chilling stress on maize shoots and roots is found to each contribute to seedling lethality in maize. Comparison of maize lines with different chilling tolerance capacity reveals that chilling survival in maize is highly associated with upregulation in leaves and crowns of abscisic acid response pathway, transcriptional regulators and cold response as well as downregulation of heat response in crowns. Comparison of chilling treatment on whole and part of the plants reveals that response to distal-chilling is very distinct from, and sometimes opposite to, response to local- or whole-plant chilling in both leaves and roots, suggesting a communication between shoots and roots in environmental perception. In sum, this study details chilling responses in leaves, roots and crowns and reveals potential chilling survival mechanism in maize, which lays ground for further understanding survival and tolerance mechanisms under low but non-freezing temperatures in tropical and subtropical plants.
2023-07-14 | GSE167881 | GEO
Project description:Two inbred lines with different resistance, which are chilling tolerant KR701 and chilling sensitive hei8834, to undergo quantitative proteomics analysis under chilling stress at the one- and three-leaf stages, respectively.
2022-05-19 | PXD023426 | Pride
Project description:To identify tomato miRNAs involved in chilling response, two small RNA libraries and two degradome libraries from chilling-treated(4°C/4°C for 1h，4h, 8h, 12h, 24h and 48h) and non-chilling-treated (25°C/20°C for 1h，4h, 8h, 12h, 24h and 48h)leaves of LA1777’ (S. habrochaites) seedlings were constructed. A total of 4342604 and 7231609 clean reads were obtained by high-throughput sequencing of the two libraries, respectively. 161 conserved miRNAs and 236 novel miRNAs were identified in the two librayies. Of these miRNAs, 192 were upregulated, whereas 205 were downregulated in response to chilling stress. Among these, 23 miRNAs and 26 miRNAs were significantly upregulated and downregulated in response to chilling stress, respectively.Through degradome sequencing,62 target genes were cleaved by 42 conserved miRNAs, while nine target genes were cleaved by nine novel miRNAs. Target gene functional analysis revealed that most target genes played positive role in the chilling response, primarily by regulating the expression of anti-stress proteins, antioxidant enzymes and genes involved in cell wall formation.
2015-03-03 | GSE57335 | GEO
Project description:Purpose: The goal of this analysis is that to reveal the different expression pattern in chilling-tolerant and chilling susceptible lines under chilling stress.Chilling is a major stress to plants of subtropical and tropical origins including maize. To reveal molecular mechanisms underlying chilling tolerance and chilling survival, we investigated maize transcriptome responses to chilling stress in differentiated leaves and roots as well as in crowns with meristem activity for survival. Chilling stress on maize shoots and roots is found to each contribute to seedling lethality in maize. Comparison of maize lines with different chilling tolerance capacity reveals that chilling survival in maize is highly associated with upregulation in leaves and crowns of abscisic acid response pathway, transcriptional regulators and metal ion transporters as well as downregulation of heat response in crowns. Comparison of chilling treatment on whole and part of the plants reveals that response to distal-chilling is very distinct from, and sometimes opposite to, response to local- or whole-plant chilling in both leaves and roots, suggesting a communication between shoots and roots in environmental perception. In sum, this study details chilling responses in leaves, roots and crowns and reveals potential chilling survival mechanism in maize, which lays ground for further understanding survival and tolerance mechanisms under low but non-freezing temperatures in tropical and subtropical plants.
2023-02-19 | GSE167156 | GEO
Project description:To identify tomato miRNAs involved in chilling response, two small RNA libraries and two degradome libraries from chilling-treated(4M-BM-0C/4M-BM-0C for 1hM-oM-<M-^L4h, 8h, 12h, 24h and 48h) and non-chilling-treated (25M-BM-0C/20M-BM-0C for 1hM-oM-<M-^L4h, 8h, 12h, 24h and 48h)leaves of LA1777M-bM-^@M-^Y (S. habrochaites) seedlings were constructed. A total of 4342604 and 7231609 clean reads were obtained by high-throughput sequencing of the two libraries, respectively. 161 conserved miRNAs and 236 novel miRNAs were identified in the two librayies. Of these miRNAs, 192 were upregulated, whereas 205 were downregulated in response to chilling stress. Among these, 23 miRNAs and 26 miRNAs were significantly upregulated and downregulated in response to chilling stress, respectively.Through degradome sequencing,62 target genes were cleaved by 42 conserved miRNAs, while nine target genes were cleaved by nine novel miRNAs. Target gene functional analysis revealed that most target genes played positive role in the chilling response, primarily by regulating the expression of anti-stress proteins, antioxidant enzymes and genes involved in cell wall formation. tomato miRNA-seq and Degradome-seq after chilling
2015-03-03 | E-GEOD-57335 | biostudies-arrayexpress
Project description:We investigated chilling response of seedlings of three inbred maize lines: chilling tolerant S68911, chilling-sensitive S160 and moderate chilling-sensitive S50676. Kernels were germinated in wet sand in darkness at 25C. Seedlings were transferred to growth chamber (photoperiod 14/10h, temperature 24, light 250 umol quanta x m-2 x s-1), grown till the third-leaf stage and used in experiment. Chilling treatment started at the start of the dark period and lasted 38h (10h dark, 14h light,10h dark, 4h light). Growth conditions was as previously described but temperature was set to 14 (light/dark). At the same time control plants were grown as previously described. There were three biological replications of hybridization scheme.
2016-02-14 | E-MEXP-3508 | biostudies-arrayexpress
Project description:To understand the molecular mechanisms underlying chilling tolerance in rice, transcriptomic deep sequencing was performed to reveal the differentially expressed genes between chilling tolerance chromosome substitution line (CSL), DC90 and its chilling-sensitive recurrent parent 9311 under early chilling stress events. Our results revealed a set of DEGs with higher basal expression in DC90 by comparison with 9311. They were functionally enriched in GO terms, such as, response to stress, response to stimulus, and response to abiotic stimulus, suggesting their positive role in intrinsic chilling tolerance. Common up-regulated and down-regulated DEGs were enriched in 26 and 34 GO terms, including response to stimulus, response to stress, and response to abiotic stimulus, respectively. Furthermore, comparative transcriptomic analysis between DC90 and 9311 in response to early chilling stress revealed 502 DEGs specifically identified in DC90. Most of gene loci were located beyond introgressed regions, implying that the introgression led to reprogramming of transcriptome in response to early chilling stress. CARMO platform analysis of these DEGs presented a complex regulatory network, including phytohormone signaling, photosynthesis pathway, that coordinately involved in chilling tolerance response of DC90. Here, the unveiled molecular regulatory network shed light on deep understanding the mechanisms of rice chilling tolerance. As well, chilling tolerant-QTLs and co-localized DEGs in introgressed fragments, will be focused for further functional investigation of the molecular mechanisms of early chilling stress response in rice.
2017-06-25 | GSE76415 | GEO
Project description:BackgroundMicroRNAs (miRNAs) are small RNAs (sRNAs) approximately 21 nucleotides in length that negatively control gene expression by cleaving or inhibiting the translation of target gene transcripts. Within this context, miRNAs and siRNAs are coming to the forefront as molecular mediators of gene regulation in plant responses to annual temperature cycling and cold stress. For this reason, we chose to identify and characterize the conserved and non-conserved miRNA component of peach (Prunus persica (L.) Batsch) focusing our efforts on both the recently released whole genome sequence of peach and sRNA transcriptome sequences from two tissues representing non-dormant leaves and dormant leaf buds. Conserved and non-conserved miRNAs, and their targets were identified. These sRNA resources were used to identify cold-responsive miRNAs whose gene targets co-localize with previously described QTLs for chilling requirement (CR).ResultsAnalysis of 21 million peach sRNA reads allowed us to identify 157 and 230 conserved and non-conserved miRNA sequences. Among the non-conserved miRNAs, we identified 205 that seem to be specific to peach. Comparative genome analysis between peach and Arabidopsis showed that conserved miRNA families, with the exception of miR5021, are similar in size. Sixteen of these conserved miRNA families are deeply rooted in land plant phylogeny as they are present in mosses and/or lycophytes. Within the other conserved miRNA families, five families (miR1446, miR473, miR479, miR3629, and miR3627) were reported only in tree species (Populustrichocarpa, Citrus trifolia, and Prunus persica). Expression analysis identified several up-regulated or down-regulated miRNAs in winter buds versus young leaves. A search of the peach proteome allowed the prediction of target genes for most of the conserved miRNAs and a large fraction of non-conserved miRNAs. A fraction of predicted targets in peach have not been previously reported in other species. Several conserved and non-conserved miRNAs and miRNA-regulated genes co-localize with Quantitative Trait Loci (QTLs) for chilling requirement (CR-QTL) and bloom date (BD-QTL).ConclusionsIn this work, we identified a large set of conserved and non-conserved miRNAs and describe their evolutionary footprint in angiosperm lineages. Several of these miRNAs were induced in winter buds and co-localized with QTLs for chilling requirement and bloom date thus making their gene targets potential candidates for mediating plant responses to cold stress. Several peach homologs of genes participating in the regulation of vernalization in Arabidopsis were identified as differentially expressed miRNAs targets, potentially linking these gene activities to cold responses in peach dormant buds. The non-conserved miRNAs may regulate cellular, physiological or developmental processes specific to peach and/or other tree species.
| S-EPMC3463484 | biostudies-literature