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Solanum lycopersicum strain:Micro-Tom, Regina, Ailsa Craig, M82, Moneymaker, San Marzano, and a F2 mapping population (RMF2, n=96)

ABSTRACT: RAD-Seq for tomato

PROVIDER: PRJDB3918 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	DRR035775_1.fastq.gz	Fastqsanger.gz
	DRR035775_2.fastq.gz	Fastqsanger.gz
	DRR035776_1.fastq.gz	Fastqsanger.gz
	DRR035776_2.fastq.gz	Fastqsanger.gz
	DRR035777_1.fastq.gz	Fastqsanger.gz

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Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants.

Project description:Application of mass spectrometry enables the detection of metabolic differences between groups of related organisms. Differences in the metabolic fingerprints of wild-type Solanum lycopersicum and three monogenic mutants, ripening inhibitor (rin), non-ripening (nor) and Colourless non-ripening (Cnr), of tomato are captured with regard to ripening behaviour. A high-resolution tandem mass spectrometry system coupled to liquid chromatography produced a time series of the ripening behaviour at discrete intervals with a focus on changes post-anthesis. Internal standards and quality controls were used to ensure system stability. The raw data of the samples and reference compounds including study protocols have been deposited in the open metabolomics database MetaboLights via the metadata annotation tool Isatab to enable efficient re-use of the datasets, such as in metabolomics cross-study comparisons or data fusion exercises.

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Effect of Low Light on Photosynthetic Performance of Tomato Plants-Ailsa Craig and Carotenoid Mutant <i>Tangerine</i>.

Project description:The effects of a five-day treatment with low light intensity on tomato plants-Ailsa Craig and tangerine mutant-at normal and low temperatures and after recovery for three days under control conditions were investigated. The tangerine tomato, which has orange fruits, yellowish young leaves, and pale blossoms, accumulates prolycopene rather than all-trans lycopene. We investigated the impact of low light at normal and low temperatures on the functioning and effectiveness of photosynthetic apparatuses of both plants. The photochemical activities of Photosystem I (PSI) and Photosystem II (PSII) were assessed, and the alterations in PSII antenna size were characterized by evaluating the abundance of PSII-associated proteins Lhcb1, Lhcb2, CP43, and CP47. Alterations in energy distribution and interaction of both photosystems were analyzed using 77K fluorescence. In Aisla Craig plants, an increase in thylakoid membrane fluidity was detected during treatment with low light at a low temperature, while for the tangerine mutant, no significant change was observed. The PSII activity of thylakoids from mutant tangerine was more strongly inhibited by treatment with low light at a low temperature while low light barely affected PSII in Aisla Craig. The obtained data indicated that the observed differences in the responses of photosynthetic apparatuses of Ailsa Craig and tangerine when exposed to low light intensity and suboptimal temperature were mainly related to the differences in sensitivity and antenna complexes of PSII.

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Color Mutations Alter the Biochemical Composition in the San Marzano Tomato Fruit.

Project description:San Marzano (SM) is a traditional Italian landrace characterized by red elongated fruits, originating in the province of Naples (Italy) and cultivated worldwide. Three mutations, yellow flesh (r), green flesh (gf) and colorless fruit epidermis (y) were introduced into SM by backcross and the resulting introgression lines (ILs) produced the expected yellow, brown and pink fruit variants. In addition, ILs carrying double combinations of those mutations were obtained. The six ILs plus the SM reference were analyzed for volatile (VOC), non-polar (NP) and polar (P) metabolites. Sixty-eight VOCs were identified, and several differences evidenced in the ILs; overall gf showed epistasis over r and y and r over y. Analysis of the NP component identified 54 metabolites; variation in early carotenoids (up to lycopene) and chlorophylls characterized respectively the ILs containing r and gf. In addition, compounds belonging to the quinone and xanthophyll classes were present in genotypes carrying the r mutation at levels higher than SM. Finally, the analysis of 129 P metabolites evidenced different levels of vitamins, amino acids, lipids and phenylpropanoids in the ILs. A correlation network approach was used to investigate metabolite-metabolite relationships in the mutant lines. Altogether these differences potentially modified the hedonistic and nutritional value of the berry. In summary, single and combined mutations in gf, r and y generated interesting visual and compositional diversity in the SM landrace, while maintaining its original typology.

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Project description:BackgroundInvestigation of tomato genetic resources is a crucial issue for better straight evolution and genetic studies as well as tomato breeding strategies. Traditional Vesuviano and San Marzano varieties grown in Campania region (Southern Italy) are famous for their remarkable fruit quality. Owing to their economic and social importance is crucial to understand the genetic basis of their unique traits.ResultsHere, we present the draft genome sequences of tomato Vesuviano and San Marzano genome. A 40x genome coverage was obtained from a hybrid Illumina paired-end reads assembling that combines de novo assembly with iterative mapping to the reference S. lycopersicum genome (SL2.40). Insertions, deletions and SNP variants were carefully measured. When assessed on the basis of the reference annotation, 30% of protein-coding genes are predicted to have variants in both varieties. Copy genes number and gene location were assessed by mRNA transcripts mapping, showing a closer relationship of San Marzano with reference genome. Distinctive variations in key genes and transcription/regulation factors related to fruit quality have been revealed for both cultivars.ConclusionsThe effort performed highlighted varieties relationships and important variants in fruit key processes useful to dissect the path from sequence variant to phenotype.

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Project description:Two tomato genotypes with constitutively different ABA level, flacca mutant and wild type of Ailsa Craig cv. (WT), were subjected to three repeated drought cycles, with the aim to reveal the role of the abscisic acid (ABA) threshold in developing drought tolerance. Differential responses to drought of two genotypes were obtained: more pronounced stomatal closure, ABA biosynthesis and proline accumulation in WT compared to the mutant were compensated by dry weight accumulation accompanied by transient redox disbalance in flacca. Fourier-transform infrared (FTIR) spectra analysis of isolated cell wall material and morphological parameter measurements on tomato leaves indicated changes in dry weight accumulation and carbon re-allocation to cell wall constituents in flacca, but not in WT. A higher proportion of cellulose, pectin and lignin in isolated cell walls from flacca leaves further increased with repeated drought cycles. Different ABA-dependent stomatal closure between drought cycles implies that acquisition of stomatal sensitivity may be a part of stress memory mechanism developed under given conditions. The regulatory role of ABA in the cell wall restructuring and growth regulation under low leaf potential was discussed with emphasis on the beneficial effects of drought priming in developing differential defense strategies against drought.

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