Abstract Cold stress acclimation (CS-ACC) makes plant acquire CS-memory and enhances cold tolerance. However, the transcriptional mechanism during recovery after CS-ACC is rarely reported. Here, we found that CsRBOH5.1 was essential for global genes to rebuild histone H3 lysine 4 trimethylation (H3K4me3) deposition during recovery after CS-ACC, and the necessity was more obvious with the extension of recovery time. CsRBOH5.1 knockout completely destroyed CS transcriptional memory (CS-TM) and disrupted most of cold-responsive gene transcription during recovery after CS-ACC. We also found that deposition pattern of H3K4me3/H3K27me3 on CS-memory genes contributed to CS-TM while that on CS-induction genes (up-down and down-up regulated) went against their transcription pattern formation, showing a natural inherent property even after CS-ACC. Moreover, CsRBOH5.1 knockout did not change this conservative property. In summary, we for the first time in plants found that CsRBOH5.1 , a non-typical-histone methylation regulatory gene, regulated global genes’ H3K4me3 during recovery after CS-ACC.
Abstract MicroRNAs (miRNAs) are 19–24 nucleotide (nt) noncoding RNAs that play important roles in abiotic stress responses in plants. High temperatures have been the subject of considerable attention due to their negative effects on plant growth and development. Heat-responsive miRNAs have been identified in some plants. However, there have been no reports on the global identification of miRNAs and their targets in tomato at high temperatures, especially at different elevated temperatures. Here, three small-RNA libraries and three degradome libraries were constructed from the leaves of the heat-tolerant tomato at normal, moderately and acutely elevated temperatures (26/18 °C, 33/33 °C and 40/40 °C, respectively). Following high-throughput sequencing, 662 conserved and 97 novel miRNAs were identified in total with 469 conserved and 91 novel miRNAs shared in the three small-RNA libraries. Of these miRNAs, 96 and 150 miRNAs were responsive to the moderately and acutely elevated temperature, respectively. Following degradome sequencing, 349 sequences were identified as targets of 138 conserved miRNAs, and 13 sequences were identified as targets of eight novel miRNAs. The expression levels of seven miRNAs and six target genes obtained by quantitative real-time PCR (qRT-PCR) were largely consistent with the sequencing results. This study enriches the number of heat-responsive miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in tomatoes at elevated temperatures.
Abstract Background Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks. Results Here, RNA expression in 0 h, 8 h and 30 h saturated irrigation-treated fruits from two contrasting tomato genotypes, ‘LA1698’ (cracking-resistant, CR) and ‘LA2683’ (cracking-susceptible, CS), was analysed by mRNA and lncRNA sequencing. The GO pathways of the differentially expressed mRNAs were mainly enriched in the ‘hormone metabolic process’, ‘cell wall organization’, ‘oxidoreductase activity’ and ‘catalytic activity’ categories. According to the gene expression analysis, significantly differentially expressed genes included Solyc02g080530.3 ( Peroxide, POD ), Solyc01g008710.3 ( Mannan endo-1,4-beta-mannosidase, MAN ), Solyc08g077910.3 ( Expanded, EXP ), Solyc09g075330.3 ( Pectinesterase , PE ), Solyc07g055990.3 ( Xyloglucan endotransglucosylase-hydrolase 7, XTH7 ), Solyc12g011030.2 ( X yloglucan endotransglucosylase-hydrolase 9 , XTH9 ), Solyc10g080210.2 ( Polygalacturonase-2, PG2 ), Solyc08g081010.2 ( Gamma-glutamylcysteine synthetase, gamma-GCS ), Solyc09g008720.2 ( Ethylene receptor , ER ), Solyc11g042560.2 ( Ethylene-responsive transcription factor 4, ERF4 ) etc. In addition, the lncRNAs (XLOC_134491 and XLOC_036966) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking. Conclusions This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H 2 O 2 ) signal transduction and many cell wall-related mRNAs (EXP, PG, XTH), as well as some lncRNAs ( XLOC_134491 and XLOC_104931, etc.). Keywords Tomato, LncRNA, mRNA, Transcriptome, Network, Fruit cracking
Abstract Background: Low temperature seriously depressed the uptake, translocation from root to shoot and metabolism of nitrate and ammonium in thermophilic plants such as cucumber, and the growth of plant was inhibited accordingly. However, there was no breakthrough in the effect of low temperature on nitrogen transport over the years. Results: By using the non-invasive micro-test technology the net NO 3 - and NH 4 + fluxes rate in root hair zone and vascular bundles of main root, stem, petiole, midrib, lateral vein, and shoot tip of cucumber seedlings under normal temperature (NT) and low temperature (LT) treatment were tested, respectively. Under LT treatment, the net NO 3 - flux rate in root hair zone and vascular bundles of cucumber seedlings decreased, while the net NH 4 + flux rate in vascular bundles of midribs, lateral veins and shoot tips increased. In accordance with this, the relative expression of CsNRT1.4a in petioles and midribs was down-regulated, while the expressions of CsAMT1.2a ~ 1.2c in midribs were up-regulated. The results of 15 N isotope tracing showed that compared with NT treatment, NO 3 - -N and NH 4 + -N uptake of the seedlings under LT treatment decreased 78.1% and 58.8%, respectively, and the concentration and proportion of both NO 3 - -N and NH 4 + -N distributed in the shoot decreased. Under LT treatment, the actual nitrate reductase activity (NRA act ) in roots didn’t change significantly, while NRA act in stems and petioles of LT treatment increased by 113.2% and 96.2%, respectively. Conclusion: In summary, the higher net NH 4 + flux rate in leaves and young tissues may be due to the higher NR act in stems and petioles, which could reduce more NO 3 - to NH 4 + so as to reduce the energy consumption in nitrogen transportation under low temperature.
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