Solanum pimpinellifolium
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ABSTRACT:
PROVIDER: PRJNA115951 | ENA |
REPOSITORIES: ENA
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Project description:Universally accepted landmark stages are necessary to highlight key events in tomato reproductive development. In this study, we provide a description of floral and fruit development in a red-fruited closely related wild relative of tomato, Solanum pimpinellifolium accession LA1589. We use established and propose new landmarks as the framework for the characterization of the tomato fruit shape gene SUN in fruit development. SUN controls fruit shape predominantly after fertilization and its effect reaches a maximum at 8 days post anthesis coinciding with fruit landmark 4 representing the globular embryo stage of seed development. We also analyzed gene expression profiles of floral buds 10 days before anthesis (floral landmark 7), anthesis-stage flowers (floral landmark 10 and fruit landmark 1), and 5 days post anthesis fruit (fruit landmark 3). The expression profiles of the NILs that differ at sun showed that 34 genes were differentially expressed and most of them at a less than 2-fold difference. However, many genes were differentially expressed between the developmental times points, including many genes involved in phytohormone biosynthesis or signaling as well as organ identity and patterning of tomato fruit. Three biological replicates were conducted with three sets of LA1589 sun NILs that differ at sun growing during different time periods resulting in 3 time points x 2 genotypes x 3 replicates = 18 array hybridizations.
2010-05-18 | E-GEOD-15453 | biostudies-arrayexpress
Project description:Universally accepted landmark stages are necessary to highlight key events in tomato reproductive development. In this study, we provide a description of floral and fruit development in a red-fruited closely related wild relative of tomato, Solanum pimpinellifolium accession LA1589. We use established and propose new landmarks as the framework for the characterization of the tomato fruit shape gene SUN in fruit development. SUN controls fruit shape predominantly after fertilization and its effect reaches a maximum at 8 days post anthesis coinciding with fruit landmark 4 representing the globular embryo stage of seed development. We also analyzed gene expression profiles of floral buds 10 days before anthesis (floral landmark 7), anthesis-stage flowers (floral landmark 10 and fruit landmark 1), and 5 days post anthesis fruit (fruit landmark 3). The expression profiles of the NILs that differ at sun showed that 34 genes were differentially expressed and most of them at a less than 2-fold difference. However, many genes were differentially expressed between the developmental times points, including many genes involved in phytohormone biosynthesis or signaling as well as organ identity and patterning of tomato fruit.
2009-05-21 | GSE15453 | GEO
Project description:In this study, we explored the metabolome and transcriptome of the ripe fruit in nine landrace accessions representing the seven genetic groups and compared them to the mature fruit of the wild progenitor S. pimpinellifolium. The goal is to shed light in understanding the factors responsible for acquiring tomato fruit quality (taste and flavour) at molecular level during the domestication process.
2019-09-10 | GSE125476 | GEO
Project description:To provide insights into how SUN regulates shape and whether this is accompanied with shifts in transcript profiles, we identified differentially expressed genes in eight pairwise comparisons of SUN and wild-type fruit tissues and time points. Lines nearly isogenic for SUN in the cultivated background Solanum lycopersicum c.v. SUN1642 were grown in the greenhouse in a completely randomized design. SA4 is like SUN1642 and SA3 is like WT LA1589 at SUN locus. Flowers at anthesis were tagged and self-pollinated on successive days. Anthesis is defined as when the flower opens. Pollination of flowers was staggered so fruit of all developmental stages would be harvested on the same day. Fruits at stage four, seven, and ten days post anthesis (dpa) were harvested and brought back to the laboratory. Septum, seed, and pericarp tissue were isolated and frozen in liquid nitrogen. Four dpa septum tissues is a mixture of septum and seed tissue. Four dpa pericarp is a mixture of pericarp and exocarp tissue due to small size of four dpa fruits. Seven and 10 dpa pericarp dont contain the exocarp (epidermal) tissues. Four replicates were collected. RNA was extracted using Trizol and Stand-specific libraries were prepared from total RNA and sequences of 51 bp were generated on an Illumina HiSeq2000.
2013-12-10 | E-MTAB-4837 | biostudies-arrayexpress
Project description:This study is to decipher the effect of SUN overexpressed NIL on gene expression during fruit development in tomato. RNA libraries were sequenced through Illumina Nextseq500 at Georgia Genomics and Bioinformatics Core (GGBC) of University of Georgia for 75 bp single end sequencing. Clean reads were mapped to ITAG3.2. Processed data are normalized into TPM.
2019-08-14 | GSE135764 | GEO
Project description:The Zinc Finger Transcription Factor SlZFP2 Negatively Regulates Abscisic Acid Biosynthesis and Fruit Ripening in Tomato
| PRJNA269239 | ENA
Project description:Transcriptome analysis of 7 tissues of commercial tomato (S. lycopersicum cv MoneyMaker) and its wild red-fruited ancestor (S. pimpinellifolium LA0722) genotypes performed to assess expression level of tomato transcriptome and to aid whole genome annotation. Sequencing of fruit at 3 different developmental stages will help to assess gene regulation through ripening.
2012-05-08 | GSE33507 | GEO
Project description:Transcriptome analysis of Eggplant cv. PPL during fruit development at 0, 5, 10, 20 and 50 dpa. Eggplant is third most important solanaceae crop species after potato and tomato. It is a versatile crop adapted to different agro-climatic regions and can be grown throughout the year. Unripe eggplant fruit is consumed as cooked vegetable in various ways. It is low in calories and fats, contains mostly water, some protein, fibre and carbohydrates. To decipher molecular mechanisms involved in fruit development eggplant fruit were collected at 0, 5, 10, 20 and 50 dpa and gene expression profiles were analyzed using Affymetrix tomato GeneChip Genome array.
2014-02-14 | GSE44182 | GEO
Project description:In the present study, we demonstrated that application of CaCl2 to ‘Micro Tom’ tomato fruit (mature green stage) delayed fruit senescence and mature.
2017-09-28 | GSE73520 | GEO
Project description:Background: Tomato (Solanum lycopersicum) self-compatibility (SC) is defined as self-pollen tubes that can penetrate their own stigma, elongate in the style and fertilize their own ovules. Self-incompatibility (SI) is defined as self-pollen tubes that are prevented from developing in the style. To determine the influence of gene expression on style self-pollination, a transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles was performed using RNA-sequencing (RNA-seq) data. Results: Transcriptome profiles of 24-h unpollination (UP) and self-pollination (P) styles from SC and SI tomato species were generated using high-throughput next generation sequencing. From the comparison of SC self-pollinated and unpollinated styles, 1341 differentially expressed genes (DEGs) were identified, of which 753 were downregulated and 588 were upregulated. From the comparison of SI self-pollinated and unpollinated styles, 804 DEGs were identified, of which 215 were downregulated and 589 were upregulated. Nine gene ontology (GO) terms were enriched significantly in SC and 78 GO terms were enriched significantly in SI. A total of 105 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified in SC and 80 enriched KEGG pathways were identified in SI, among which “Cysteine and methionine metabolism pathway” and “Plant hormone signal transduction pathway” were significantly enriched in SI. Conclusions: This study is the first global transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles. Advanced bioinformatic analysis of DEGs uncovered the pathways of “Cysteine and methionine metabolism” and “Plant hormone signal transduction”, which are likely to play important roles in the control of pollen tubes growth in SI species. 24-h unpollination (UP) and self-pollination (P) styles mRNA profiles from SC and SI tomato species were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 platform.
2015-04-09 | E-GEOD-67654 | biostudies-arrayexpress