Use of High Resolution Spatiotemporal Gene Expression Data to Uncover Novel Tissue-Specific Promoters in Tomato

Lulu Chen,Wenzhen Li,Yuhang Li,Yuting Wang,Lingxia Zhao,Xuechao Feng

doi:10.3390/agriculture11121195

Lulu Chen, Wenzhen Li + Show 4 more

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https://doi.org/10.3390/agriculture11121195

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Abstract

Genetic modification can be an effective strategy for improving the agronomic traits of tomato (Solanum lycopersicum) to meet demands for yield, quality, functional components, and stress tolerance. However, limited numbers of available tissue-specific promoters represent a bottleneck for the design and production of transgenic plants. In the current study, a total of 25 unigenes were collected from an RNA-sequence dataset based on their annotation as being exclusively expressed in five type of tissues of tomato pericarp (outer and inner epidermis, collenchyma, parenchyma, and vascular tissues), and every five unigenes, was respectively selected from each tissue based on transcription expression. The 3-kb 5′ upstream region of each unigene was identified from the tomato genome sequence (SL2.50) using annotated unigene sequences, and the promoter sequences were further analyzed. The results showed an enrichment in T/A (T/A > 70%) in the promoter regions. A total of 15 putative tissue-/organ-specific promoters were identified and analyzed by real-time (RT) quantitative (q) PCR analysis, of which six demonstrated stronger activity than widely used tissue-specific tomato promoters. These results demonstrate how high spatiotemporal and high throughput gene expression data can provide a powerful means of identifying spatially targeted promoters in plants.

Highlights

Tomato (Solanum lycopersicum) is at most a dual-purpose crop for vegetable and fruit worldwide, and it has served as a model plant in many aspects of fruit physiology, development, and metabolism, as well as genetics, evolutionary biology, and developmental biology [1]
The authors found that the tissue-specific unigenes were mostly distributed in both tissues of the oep and vas (501/624)
We found that there was a low level of DNA sequence homology in the promoters by cluster tissue-specific promoters, one to four copies of the downstream promoter element (DPE) were found in these cases (Figure 5 and Supplementary file S7)

Summary

Introduction

Tomato (Solanum lycopersicum) is at most a dual-purpose crop for vegetable and fruit worldwide, and it has served as a model plant in many aspects of fruit physiology, development, and metabolism, as well as genetics, evolutionary biology, and developmental biology [1]. The progress of tomato breeding was prompted by molecular maker-assisted breeding techniques with molecular biology developments, and efficiency and the predicted breeding was sharply rapid with the biotechnological development and dissection of several metabolic pathways It especially concerned the medical industry when tomato was used as a model system to express therapeutic proteins [2,3,4]. The content of the foreign protein was limited to a low-activity promoter that controls gene expression encoding. This limits tomato application as an expression system for the development of molecular farming. Thereafter, a large number of promoters have been identified by

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