Nutrition metabolism plays an important role in the alternate bearing of the olive tree (Olea europaea L.)
Ontology highlight
ABSTRACT:
ORGANISM(S): Olea europaea Populus trichocarpa
PROVIDER: GSE42950 | GEO | 2012/12/17
SECONDARY ACCESSION(S): PRJNA183935
REPOSITORIES: GEO
Similar Datasets
Project description:We carried out genome wide transcriptome analyses in different organs and developmental stages of the olive tree using the NimbleGen Array oligonucleotide probe sets. Cluster analyses of the genes showed that samples collected from different organs could be sorted into separate groups. The nutritional control had a particularly remarkable impact on the alternate bearing for O. europaea, as shown by the differential expressions of transcripts under different developmental phases and organs Six sample sets were prepared for array analyses: i) unripe fruit (UF); ii) ripe fruit (RF); iii) “on-year” mature leaf (November sample, ON-M); iv) “on-year” juvenile leaf (July sample, ON-J); v) “off-year” mature leaf (November samples, OFF-M); and vi) “off-year” juvenile leaf (July sample, OFF-J).
2012-12-17 | E-GEOD-42950 | biostudies-arrayexpress
Project description:We aimed to identify miRNA regulated by alternate bearing in O. europaea. For this purpose, six olive (Olea europaea L. )(Ayvalık variety) small RNA libraries were constructed from fruits (ripe and unripe) and leaves ("on-year" and "off-year" mature -leaven in November and juvenile - leaven in July plants) and sequenced by high-throughput Illumina sequencing. Bioinformatics analyses of 93,526,915 reads identified 135 conserved miRNA, belonging to 22 miRNA families in olive tree. In addition, 38 novel miRNA were discovered in the datasets. Expression of olive tree miRNA varied greatly among the six libraries, indicating contribution of diverse miRNA in balancing between reproductive and vegetative phases. The differential expression of miRNA was evaluated on the basis of the developmental phase of the samples.
2012-12-18 | GSE42978 | GEO
Project description:We aimed to identify miRNA regulated by alternate bearing in O. europaea. For this purpose, six olive (Olea europaea L. )(Ayvalık variety) small RNA libraries were constructed from fruits (ripe and unripe) and leaves ("on-year" and "off-year" mature -leaven in November and juvenile - leaven in July plants) and sequenced by high-throughput Illumina sequencing. Bioinformatics analyses of 93,526,915 reads identified 135 conserved miRNA, belonging to 22 miRNA families in olive tree. In addition, 38 novel miRNA were discovered in the datasets. Expression of olive tree miRNA varied greatly among the six libraries, indicating contribution of diverse miRNA in balancing between reproductive and vegetative phases. The differential expression of miRNA was evaluated on the basis of the developmental phase of the samples. Sequences of six olive miRNAs (Olea europaea L. )(Ayvalık variety) plants (ripe and unripe fruits, leaves of mature and juvenile plants of both "on-year" and "off-year") were generated by Illumina sequencing
2012-12-18 | E-GEOD-42978 | biostudies-arrayexpress
Project description:This is an RNA-seq study of the transcriptomic activity of different tissues from adult olive tree cv. Picual on field conditions. This analysis unveiled 53,456 genes with expression in at least one tissue; 32,030 of them were expressed in all organs and 19,575 were found to be potential housekeeping genes. In addition, the specific expression pattern in each part of the plant was studied. The flower was clearly the organ with the highest number of exclusive expressed genes, 3,529, and many of them were involved in reproduction. On the contrary, the stem only showed 229 exclusive expressed genes. The gene ontology (GO) terms analysis of these genes in each organ highlighted some tissue-specific pathways. In general, many of these organ-specific genes are involved in regulatory activities and have nuclear protein localization, with the exception of the leave, where there are also many genes whose coded proteins have plastid localization; to a lesser extent, this was also observed in stems. On the other hand, the pathogen defense and immunity pathways are highly represented in the roots. These data show a complex pattern of gene expression in different organs.
2020-05-07 | GSE140648 | GEO
Project description:Gene expression pattern in olive tree organs (Olea europaea L.)
| PRJNA590386 | ENA
Project description:The olive tree (Olea europaea L.) is widely known for its strong tendency for alternate bearing, which severely affects the fruit yield from year to year. Microarray based gene expression analysis using RNA from olive samples (on-off years leaves and ripe-unripe fruits) are particularly useful to understand the molecular mechanisms influencing the periodicity in the olive tree. Thus, we carried out genome wide transcriptome analyses involving different organs and temporal stages of the olive tree using the NimbleGen Array containing 136,628 oligonucleotide probe sets. Cluster analyses of the genes showed that cDNAs originated from different organs could be sorted into separate groups. The nutritional control had a particularly remarkable impact on the alternate bearing of olive, as shown by the differential expression of transcripts under different temporal phases and organs. Additionally, hormonal control and flowering processes also played important roles in this phenomenon. Our analyses provide further insights into the transcript changes between "on year" and "off year" leaves along with the changes from unrpipe to ripe fruits, which shed light on the molecular mechanisms underlying the olive tree alternate bearing. These findings have important implications for the breeding and agriculture of the olive tree and other crops showing periodicity. To our knowledge, this is the first study reporting the development and use of an olive array to document the gene expression profiling associated with the alternate bearing in olive tree.
| S-EPMC3610735 | biostudies-literature
Project description:Cultivated olive tree (Olea europaea L. subsp. europaea var. europaea) is one of most relevant worldwide-extended crops. Since this plant has a huge effect on the economy of several regions, especially in those located in the Mediterranean basin, all efforts focused on its protection have a great relevance in agriculture sustainability. As all extended crops, olive tree cultivars are under the threat of a wide range of pathogens. Among them, Verticillium dahliae has been in the spotlight in the last decades because the disease caused by this soil-borne fungus (Verticillium wilt) is easily spread and can eventually kill the tree. In this line, many different factors have been studied in order to shed some light on the molecular/genetic mechanisms underlying the Olea europaea-Verticillium dahliae interaction, some of them focused on the gene expression pattern of the host. In this study, the expression pattern of roots from thirty-six O. europaea cultivars with different resistance/susceptibility degree to Verticillium wilt has been analyzed by RNA-Seq. As a result, processes involved in plant defense, transcription and root development have emerged as potential players in the differential response to Verticillium wilt of these cultivars. Additionally, a quite interesting set of 421 genes with an opposite expression pattern in those cultivars showing extreme resistance/susceptibility to Verticillium wilt has been discovered, establishing a solid group of candidates to take into account in future genetic improvement programs.
2021-04-07 | GSE152236 | GEO
Project description:A transcriptomics approach was used as a tool to unravel gene regulatory network underlying salinity response in a salt-tolerant olive cultivar (cv. Kalamon) by simulating as much as possible olive growing conditions in the field. A 135 day long salinity experiment was conducted using one year old trees exposed to NaCl stress for 90 days followed by 45 days of post-stress period. Total RNA was extracted from the root samples after 15, 45 and 90 days of NaCl-treated and un-treated olive trees as well as after 15 and 45 days of post-treatment period and used for microarray hybridizations using a loop design. Hierarchical clustering of differentially expressed transcripts revealed two major, distinct clusters. Despite the limited number of probe set, a transcriptional regulatory networks was constructed for the salt-tolerant cultivar.
2012-11-20 | GSE36196 | GEO
Project description:A comparative transcriptomics approach was used as a tool to unravel gene regulatory networks underlying salinity response in olive trees by simulating as much as possible olive growing conditions in the field. Specifically, we investigated the genotype-dependent differences in the transcriptome response of two olive cultivars, a salt tolerant and a salt sensitive. A 135 day long comparative salinity experiment was conducted using one year old trees exposed to NaCl stress for 90 days followed by 45 days of post-stress period. Total RNA was extracted from the root samples after 15, 45 and 90 days of NaCl-treated and un-treated olive trees as well as after 15 and 45 days of post-treatment period and used for microarray hybridizations using a loop design. Hierarchical clustering of differentially expressed transcripts revealed two major, distinct clusters for each cultivar. Despite the limited number of probe set, transcriptional regulatory networks were constructed for the salt-tolerant and salt-sensitive cultivar. The comparison of the salt responsive transcriptional regulatory networks in olive with those reported for Arabidopsis suggests that a tree species might respond in a similar to Arabidopsis way at the transcriptome level under salinity stress.
2012-11-20 | GSE36197 | GEO
Project description:Olive (Olea europaea) cv.Kalamon: Control vs Salt-treated
| PRJNA155753 | ENA