Transcriptome analysis in buds of peach trees treated with hydrogen cyanamide that advanced bud break
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PROVIDER: PRJNA526626 | ENA |
REPOSITORIES: ENA
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Project description:To determine how dormancy breaking agent, hydrogen cyanamide (HC) advances bud break in peach (Prunus persica), this research compared the transcriptome of buds of low-chill ‘TropicBeauty’ peach trees treated with 1% (v/v) HC and that of non-treated trees at 3 and 7 days after treatment (DAT), respectively, using RNA sequencing analysis. The peak of total bud break occurred 6 weeks earlier in the HC treated trees (at 32 DAT) than the non-treated trees (at 74 DAT). There were 1312 and 1095 differentially expressed genes (DEGs) at 3 and 7 DAT, respectively. At 3 DAT, DEGs related to oxidative stress, including response to hypoxia, lipid oxidation, and reactive oxygen species (ROS) metabolic process, were up regulated in HC-treated buds. Additionally, DEGs encoding enzymes for ROS scavenging and pentose phosphate pathway were up regulated at 3 DAT but were not differently expressed at 7 DAT, indicating a temporary demand for defense mechanisms against HC-triggered oxidative stress. Up regulation of DEGs for cell division and development at 7 DAT, which were down regulated at 3 DAT, suggests cell activity was initially suppressed but enhanced within 7 days following the treatment. At 7 DAT, DEGs related to cell wall degradation and modification were up-regulated, possibly responsible for the burst of buds. The results of this study strongly suggest that HC induces transient oxidative stress shortly after application leading to the release of bud dormancy and, subsequently, causes an increase in cell activity and cell wall loosening, thereby accelerating bud break in peach.
2020-03-12 | GSE128158 | GEO
Project description:Perennial plants, like fruit trees grown in temperate regions, are characterized by bud dormancy, a rest state that protects the bud from cold during winter. At the same time, these plants have developed a requirement for winter chill for correct flowering. However, winters are becoming increasingly warm in temperate regions, resulting in dramatic effects on the flowering output and therefore crop yield. A compound that successfully compensates for missing winter chill is hydrogen cyanamide, which has been used to synchronize and advance flowering time in a range of commercially important fruit crops. Hydrogen cyanamide also represents a unique tool for researchers to study controlled endodormancy release. Here, we treated dormant sweet cherry flower buds with hydrogen cyanamide, sampling flower buds at different time points after treatment. RNAseq revealed more than 6,000 hydrogen cyanamide-responsive genes. In accordance with these results, hydrogen cyanamide treatment increased the levels of jasmonoyl-isoleucine (JA-Ile) and the cytokinins trans-zeatin riboside (tZR), dihydrozeatin (DZ) and dihydrozeatin riboside (DZR). Furthermore, hydrogen cyanamide affected the expression of antioxidant- and cell wall loosening-associated transcripts. These results suggest a complex mechanism of action for hydrogen cyanamide-induced endodormancy release, including key roles for JA-Ile, zeatin-type cytokinins and hydrogen cyanide.
2017-06-01 | GSE94290 | GEO
Project description:Microarray analysis revealed specific alterations in gene expression in dormancy breaking buds induced by pruning (P), hydrogen cyanamide (HC), pruning plus hydrogen cyanamide (PHC) after 24 h of treatment. PHC treatment altered the expression of the largest number of genes and rapid accumulation of a sublethal level of reactive oxygen species and reactive nitrogen species subsequently induces cell wall loosening and expansion for bud sprouting
2016-08-30 | GSE86163 | GEO
Project description:In deciduous fruit trees, entrance into dormancy occurs in later summer/fall, concomitantly with the shortening of day length and decrease in temperature. Generally speaking, dormancy can be divided into endodormancy, ecodormancy and paradormancy. In Prunus species flower buds, entrance into the dormant stage occurs when the apical meristem is partially differentiated; during dormancy, flower verticils continue their growth and differentiation. In this work we focused our attention on flower bud development during winter in peach. In order to understand how bud development progress is regulated during winter we integrated cytological epigenetic and chromatin genome wide data with transcriptional outputs to obtained a complete picture of the main regulatory pathways involved in endodormancy.
2022-04-06 | GSE190586 | GEO
Project description:In deciduous fruit trees, entrance into dormancy occurs in later summer/fall, concomitantly with the shortening of day length and decrease in temperature. Generally speaking, dormancy can be divided into endodormancy, ecodormancy and paradormancy. In Prunus species flower buds, entrance into the dormant stage occurs when the apical meristem is partially differentiated; during dormancy, flower verticils continue their growth and differentiation. In this work we focused our attention on flower bud development during winter in peach. In order to understand how bud development progress is regulated during winter we integrated cytological epigenetic and chromatin genome wide data with transcriptional outputs to obtained a complete picture of the main regulatory pathways involved in endodormancy.
2022-04-06 | GSE189882 | GEO
Project description:Devastating citrus disease Huanglongbing (HLB) is without existing cures. Herein, we present results demonstrating the possible mechanisms (hypoxia stress) behind HLB-triggered shoot dieback by comparing the transcriptomes, hormone profiles, and key enzyme activities in buds of severely and mildly symptomatic ‘Hamlin’ sweet orange (Citrus sinensis). Within six months (October – May) in field conditions, severe trees had 23% bud dieback, greater than mild trees (11%), with a concomitant reduction in canopy density. In February, differentially expressed genes (DEGs) associated with responses to osmotic stress, low oxygen levels, and cell death were upregulated, with those for photosynthesis and cell cycle downregulated in severe versus mild trees. For severe trees, not only were the key markers for hypoxia, including anaerobic fermentation, reactive oxygen species (ROS) production, and lipid oxidation, transcriptionally upregulated, but also alcohol dehydrogenase activity was significantly greater compared to mild trees, indicating a link between bud dieback and hypoxia. Tricarboxylic acid cycle revival, given the upregulation of glutamate dehydrogenase and alanine aminotransferase DEGs, suggests that ROS may also be generated during hypoxiareoxygenation. Greater (hormonal) ratios of abscisic acid to cytokinins and jasmonates and upregulated DEGs encoding NADPH oxidases in severe versus mild trees indicate additional ROS production under limited oxygen availability due to stomata closure. Altogether, our results provided evidence that as HLB progresses, excessive ROS produced in response to hypoxia and during hypoxia-reoxygenation likely intensify the oxidative stress in buds leading to cell death, contributing to marked bud and shoot dieback and decline of the severely symptomatic sweet orange trees.
2023-04-03 | GSE228890 | GEO
Project description:Correlation analysis of the expression of bud dormancy-related genes in 10 peach cultivars, with different chilling requirements for dormancy release.
2012-01-15 | E-MEXP-3201 | biostudies-arrayexpress
Project description: Not available
| S-EPMC7475240 | biostudies-literature
Project description:Virus elimination is indispensable for the maintenance of stone fruit plantations, because these pathogens can cause serious crop damage and crop losses. Currently we do not possess efficient plant protection methods against viruses therefore prevention has a prominent role. In order to prevent infections, pathogen-free propagation material production and application of effective diagnostic methods have essential role. Our examined peach samples derived from isolator houses and stock nurseries of Fruitculture Research Institute of NARIC. With the help of highly sensitive metagenomic diagnostic methods: such as next generation sequencing of small RNAs, we are able to detect all of the presenting pathogens within our samples. During preparation steps, total RNA was isolated from leaf samples, RNA pools were made from the varieties, and then small RNA libraries were prepared. Sequencing was performed on Illumina platform and we used CLC Genomics Workbench for the bioinformatics evaluation. Results were verified by RT-PCR and Northern-blot. PCR products were cloned into pJET vector and Sanger sequenced. As a result, we detected nectarine stem pitting-associated virus (NSPaV), peach associated luteovirus (PaLV) and also peach latent mosaic viroid (PLMVd) which presence has to be checked regularly. Moreover we proved the incidence of PLMVd and PaLV first time in Hungary. We suspect, that the source of the viral infection might be the propagation material, which was used as a base for the variety collection in this isolator house.
2022-06-29 | GSE130859 | GEO
Project description:Plant shoots typically grow upward in opposition to the pull of gravity. However, exceptions exist throughout the plant kingdom. Most conspicuous are trees with weeping or pendulous branches. While such trees have long been cultivated and appreciated for their ornamental value, the molecular basis behind the weeping habit is not known. Here, we characterized a weeping tree phenotype in Prunus persica (peach) and identified the underlying genetic mutation using a genomic sequencing approach. Weeping peach tree shoots exhibited a downward elliptical growth pattern and did not exhibit an upward bending in response to 90° reorientation. The causative allele was found to be an uncharacterized gene, Ppa013325, having a 1.8-Kb deletion spanning the 5′ end. This gene, dubbed WEEP, was predominantly expressed in phloem tissues and encodes a highly conserved 129-amino acid protein containing a sterile alpha motif (SAM) domain. Silencing WEEP in the related tree species Prunus domestica (plum) resulted in more outward, downward, and wandering shoot orientations compared to standard trees, supporting a role for WEEP in directing lateral shoot growth in trees. This previously unknown regulator of branch orientation, which may also be a regulator of gravity per- ception or response, provides insights into our understanding of how tree branches grow in opposition to gravity and could serve as a critical target for manipulating tree architecture for improved tree shape in agricultural and horticulture applications.
2018-03-21 | GSE112080 | GEO