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Transcriptional analysis on the effect of the overexpression of VvSUC11,VvSUC12,or VvSUC27 in tomato on the growth of fruit

ABSTRACT: Purpose: We used transcriptome sequencing to study the regulated mechanism of VvSUC11,VvSUC12,or VvSUC27 on tomato fruit growth. Methods: the 35S:: VvSUC11, VvSUC12, and VvSUC27 constructs were introduced into transgenic tomatoes (Micro-Tom) by the Agrobacterium-mediated transformation, 5 DPA (days after anthesis) fruit was collected, 3 replicates per group. Extract total RNA, detect RNA quality, library preparation, sequencing, and analyze data. Results:Reads were obtained for each sample using Illumina Hiseq X Ten sequencing. After discarding the low-quality reads, corresponding to over 40 million clean reads obtained from sequencing were mapped on the reference genome of Solanum lycopersicum. High Pearson's correlation coefficients of FPKM distribution between the three biological replicates for each sample were detected (1> R2 > 0.99, P < 0.001) , reflecting the robustness of our library preparation from tomato RNA samples. Compared with WT lines, there were 2459 DEGs in the VvSUC11-overexpressing lines, of which 1283 genes were upregulated and 1176 genes were downregulated. Whereas, there were 1369 DEGs in VvSUC12-overexpressing lines, including 544 upregulated and 825 downregulated genes. In the meanwhile,there were 1777 DEGs in VvSUC27-overexpressing lines, including 623 upregulated and 1154 downregulated genes.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE161505 | GEO | 2020/11/16

REPOSITORIES: GEO

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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.

Dataset Information

Transcriptional analysis on the effect of the overexpression of VvSUC11,VvSUC12,or VvSUC27 in tomato on the growth of fruit

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