Unknown,Transcriptomics,Genomics,Proteomics

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Evidence of developmental escape from transcriptional-gene-silencing in MESSI retrotransposons

ABSTRACT: The intent of the experiment was to infer, from tissue-specific PCR-free whole DNA sequencing analysis, the putative increase in DNA copy number of active LTR retrotransposons in shoot apical meristems of tomato (Solanum lycopersicum). For this, we performed two lanes of Illumina pair-end DNA-seq in meristems and leaves of M82 tomato line.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Solanum lycopersicum

SUBMITTER: Diego Sanchez H.

PROVIDER: E-MTAB-7823 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Tomatoes are one of the valuable sources of antioxidants such as carotenes, ascorbic acid (AsA), and phenolic compounds (flavonoids and hydroxycinnamic acid derivatives). These secondary metabolites have been proved to be beneficial for humans and animals because their involvement in the prevention of many proliferative and degenerative diseases. The aim of this work is to gain greater insights in the genetic control of phenylpropanoid accumulation in tomato fruit by using genomics-based strategies. In order to identify QTLs controlling antioxidant accumulation in tomato fruit we carried out a comparative analysis of Solanum pennellii x S. lycopersicum cv. M82 introgression lines (ILs) over three year trials in greenhouse environment. Among all, IL7-3 showed higher fruit content of total phenolics and the HPLC-UV profile revealed that chlorogenic acid mainly accounted for the higher performance of this line. To investigate in details genetic mechanisms and candidate genes controlling phenols synthesis and accumulation in IL7-3 fruit we performed a comparative transcriptomic analysis in tomato pericarp. In particular, RNA was extracted from percarp of IL7-3 and M82 parental line and hybridized on a 90k Combimatrix TomatArray 1.0. The experiment was repeated over two consecutive years. The transcriptomic approach allowed to identify 291 differentially expressed transcripts, 149 showing up-rgulation and 142 down-regulation. The ethylene signaling pathway has been involved in the modulation of the level of total phenolics in ripe fruit. In particular, an Ethilene Responsive Factor 1 (ERF1) was functionally characterized by TILLING (Targeting Local Lesion IN Genomes) approach. The mutant line expressed lower accumulation of phenolics in the fruit and additional insights on the regulation of phenolics in tomato ripe fruit were provided. Comparative microarray analysis between a tomato introgression line (IL7-3) expressing higher level of fruit total phenolics and its parental cultivar M82 (reference) was performed. In particular, samples were generated by pooling red-ripe fruit from the same plant and discarding the seeds, jelly parenchyma, columella and placenta tissues. Three plant replica were used for each line (IL7-3 and M82) and the experiment was replicated over two consecutive years.