Ontology highlight
ABSTRACT:
PROVIDER: PRJEB54712 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| CTLL_repository.vcf.csi | Other | |||
| CTLL_repository.vcf.gz | Vcf |
Items per page: 5 1 - 2 of 2 |
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Project description:Morphological and molecular characterization of tomato landraces from Lazio region in central Italy
2022-07-16 | PRJEB54712 | EVA
Project description:Fruit taste is determined by sugars, acids and in some species, bitter chemicals. Attraction of seed-dispersing organisms in nature and breeding for consumer preferences requires reduced fruit bitterness. A key metabolic shift during ripening prevents tomato fruit bitterness by eliminating α-tomatine, a renowned defence-associated Solanum alkaloid. Here, we combined fine mapping with information from 150 re-sequenced genomes and genotyping a 650 tomato core collection to identify nine bitter-tasting accessions including the ‘high α-tomatine’ Peruvian landraces reported by Rick and colleagues (1994). These ‘bitter’ accessions contain a deletion in GORKY, a nitrate/peptide family (NPF) transporter mediating α-tomatine subcellular localization during fruit ripening. GORKY exports α-tomatine and its derivatives from the vacuole to the cytosol and this facilitates the conversion of the entire α-tomatine pool to non-bitter forms, rendering the fruit palatable. Hence, GORKY activity was a significant innovation in the process of tomato fruit domestication and breeding. The experiment was carried out to further prove that GORKY is localized to tonoplast in ripe fruit.
2021-01-04 | PXD023289 | Pride
Project description:Transcriptional profiling of three mexican maize landraces under 10, and 17 days stress and recovery irrigation A dye balanced modified loop design was implemented. Two biological replicates (pooling five representative plants) representing each sampling point for each genotype were obtained for purified RNA from 120 randomly chosen seedlings. This experiment involved a total of forty-eight (24 sets) of microarray hybridizations, including direct and dye swap comparisons between treatments as well as across the three landraces. This design allowed us to determine differences in gene expression between the three different landraces under drought stress (10 and 17 days) and at recovery irrigation compared to irrigated controls.
2010-05-16 | E-GEOD-14728 | biostudies-arrayexpress
Project description:To investigate the involvement of arbuscular mycorrhizal symbiosis in the moleular regulation in foxtail millet roots and the effects of genetic variation on AMS-mediated molecular regulation, we isolated total RNA from the roots of 3 different landraces for comprehensive transcriptomic analysis. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different landraces (Hanevalval, TT8, ICE36) after 6-week mock or arbuscular mycorrhizal fungi treatments.
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Project description:Transcriptional profiling of three mexican maize landraces under 10, and 17 days stress and recovery irrigation
2010-01-01 | GSE14728 | GEO
Project description:Tomato seeds (S. lycopersicum ‘Fl Lanai’) were germinated under greenhouse conditions maintained at 24°C-29°C in flat trays (BWI Apopka, Catalog Number GPPF72S7X) filled with Sungro Horticulture soil (Metro-mix 830, BWI Apopka, Cat# TX830). Two weeks post emergence seedlings were transplanted to 4” pots using the same soil and transferred to a Conviron walk-in growth chamber (CMP6060) for the remainder of the experiment. Conviron conditions include a 14h/10h light/dark cycle maintained at 28°C, and plants were fertilized weekly (20-20-20). To prevent cross contamination, tomato plants were confined to insect proof cages at all times (BioQuip 1450NS68). Four weeks after transplanting, 40 whiteflies (B. tabaci MEAM1) were collected from virus free or Tomato Mottle Virus (ToMoV) established colonies via aspiration and moved into a clip cage placed on the 4th true leaf of each tomato plant as previously described38. Whiteflies were reared cabbage (Brassica oleracea), while viruliferous whiteflies were reared on ToMoV infected tomato from colonies established in the Polston lab. For all plants in this study, feeding was halted after 3 days of whitefly feeding (3 DPI) by gentle removal of clip cages and whitefly termination using insecticidal soap (Garden Safe, 1% of potassium salts of fatty acids). For the samples referred to as “local”, the tomato leaf bound within the clip cages was immediately removed and snap frozen for protein extraction. For the samples designated “systemic”, the plants were allowed to continue growing for 7 additional days after clip cage removal and whitefly termination, at which point the 9th leaf was excised and snap frozen. Plants used for collection of local leaves at 3 DPI were not used for the collection of systemic leaves 10 DPI. For both local and systemic leaves collected, we also included a no treatment control (NTC) that was subjected identically to clip cage and insecticidal soap applications, but without the addition of whitefly or ToMoV. Our experiment therefore consists of a no-treatment control (NTC), a whitefly treatment (+WF), and a viruliferous whitefly (+WFV) treatment for both local (4th true leaf, 3 DPI) and systemic leaves (9th true leaf, 10 DPI). The presence of ToMoV in all infected plants was confirmed via Nanopore sequencing. Briefly, Tomato genomic DNA was extracted from five systemic leaf samples using the PureGene tissue DNA isolation kit (product # 158667; QIAGEN, Valencia, CA, USA), following the manufacturer’s protocol and stored at -80°C until needed. Library preparation was performed using the Rapid Sequencing Kit RBK004 protocol (Oxford Nanopore Technologies) and loaded onto a 9.4.1 flow cell in a MinION connected to a MinIT with live base calling enabled. Resulting sequencing reads for each sample were mapped to both ToMoV A component (GenBank accession: L14460) and ToMoV B component (GenBank accession: L14461) sequences.
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Project description:RNA interference (RNAi) is a widely-used approach to generate virus-resistant transgenic crops. However, durability of RNAi-mediated resistance under extreme field conditions and side-effects of stable RNAi expression have not been thoroughly investigated. Here we performed field trials and molecular characterization of two RNAi-transgenic Solanum lycopersicum lines resistant to Tomato yellow leaf curl virus (TYLCV) disease, the major constraint for tomato cultivation in Cuba and worldwide. In order to determine potential impact of the hairpin RNA transgene expression on tomato genome expression and development, differences in the phenotypes and the transcriptome profiles between the transgenic and non-transgenic plants were examined. Transcriptome profiling revealed a common set of up- and down-regulated tomato genes, which correlated with slight developmental abnormalities in both transgenic lines.
2014-11-29 | GSE63708 | GEO