Transcriptome-level analysis of gene expressions in different tissues of tomato and key gene identifications during seed germination

Abstract

Exploring the spatiotemporal expression patterns of genes is the foundation for studying their functions and molecular mechanisms. Genes with stable spatiotemporal expression patterns are often used as reference genes for quantitative real-time polymerase chain reaction (qRT-PCR) and genes are significantly highly expressed in a specific tissue or stage often represent their unique biological functions. Tomato is an important economic crop and a model plant for scientific researches. However, the existing reference genes in tomatoes are not stable enough and researches on tissue-specific genes have been more focused on flowers and fruits, with less emphasis on studying the seed germination process. In this study, a total of 26 tissue/organ samples from the entire growth cycle of tomatoes were collected from Micro-Tom (Solanum lycopersicum cv. Micro-Tom). After RNA sequencing, a transcriptome database of the entire growth cycle of tomatoes was constructed. Solyc01g107870.3 gene was identified as a novel reference gene through systematic analysis and validated by qRT-PCR. Moreover, tissue-specific genes in seed and 8 days past germination (DPG) seedlings are screened. Among them, SlLEA16 gene belongs to late embryogenesis abundant protein (LEA) gene family, having subcellular localization in the nucleus and cytoplasm, and playing important roles in seed germination initiation. The above experimental results provide data support for studying tomato gene spatiotemporal expression patterns and can also serve as an experimental basis for investigating the deeper mechanisms of tomato seed germination processes.