Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptome analysis of tomato introgression line during fruit development.

ABSTRACT: We performed transcriptome analyses throughout fruit development using the tomato cultivar M82 and its near-isogenic line IL8-3, with interesting and useful traits such as a high content of soluble solids. To identify genes that show differential expression between M82 and IL8-3 fruits, we used a custom microarray containing 43,803 tomato probes. Some genes, such as cell wall invertase and sucrose synthase genes, which are encoded by LIN6 (Solyc10g083290) and TOMSSF (Solyc12g009300) respectively, are well known to play a key role in the sink function of fruit. In this study, the levels of LIN6 and TOMSSF transcripts were higher in IL8-3 than in M82 fruit at 20 and 30 DAF, which are developmental stages for starch accumulation and increased hexose content, respectively, in IL8-3 fruit (Ikeda et al. 2013), and decreased to the level of M82 at ripening stage. Similar patterns were observed in many metabolites of glycolysis and the pentose phosphate pathway as well as metabolites in starch and sucrose metabolism. Gene expressions during fruit development were analyzed. Three biological replicates were prepared for each stage, and a total of 24 samples were analyzed.

ORGANISM(S): Solanum lycopersicum

SUBMITTER: Yoshinori Kanayama

PROVIDER: E-GEOD-78260 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Dynamic Metabolic Regulation by a Chromosome Segment from a Wild Relative During Fruit Development in a Tomato Introgression Line, IL8-3.

Ikeda Hiroki H Shibuya Tomoki T Imanishi Shunsuke S Aso Hisashi H Nishiyama Manabu M Kanayama Yoshinori Y

Plant & cell physiology 20160412 6

We performed comparative metabolome and transcriptome analyses throughout fruit development using the tomato cultivar M82 and its near-isogenic line IL8-3, with interesting and useful traits such as a high content of soluble solids. Marked differences between M82 and IL8-3 were found not only in ripe fruits but also at 20 days after flowering (DAF) in the hierarchical clustering analysis of the metabolome, whereas patterns were similar between the two genotypes at 10 and 30 DAF. Our metabolome a ...[more]

PMID: 27076398

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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.

Dataset Information

Transcriptome analysis of tomato introgression line during fruit development.

Publications

Dynamic Metabolic Regulation by a Chromosome Segment from a Wild Relative During Fruit Development in a Tomato Introgression Line, IL8-3.

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