Transcriptome Profiling of Abscisic Acid-Related Pathways in SNAC4/9-Silenced Tomato Fruits

Abstract

The NAC (NAM, ATAF, and CUC) family is considered one of the largest families of plant transcription factor, and its members are involved in fruit ripening. Abscisic acid (ABA) has been demonstrated to modulate the fruit ripening process. By applying the virus-induced gene silencing method and next-generation sequencing technology, we conducted a comparative analysis of the effects of SNAC4 (SlNAC48, accession number: NM 001279348.2) and SNAC9 (SlNAC19, accession number: XM 004236996.2) on tomato fruit ripening. The results of high-throughput sequencing identified 1262 significant (p < 0.05) differentially expressed genes (DEGs) in SNAC4-silenced fruit compared to control fruit, while 655 DEGs were identified in SNAC9-silenced fruit. In addition, we selected 26 and 30 significant DEGs (p < 0.05 and log₂-fold change > 1.0) related to ABA in SNAC4-silenced and SNAC9-silenced tomatoes, respectively, for further analysis. The XET gene and two other genes (E8 and EXP1) were significantly down and upregulated in SNAC4-silenced tomatoes, respectively. However, the PYL9 gene and four other genes (PP2C, CYP707A2, EXPA6, and ACS6) were significantly down and upregulated in SNAC9-silenced tomatoes, respectively. In addition, ten DEGs were selected for use in tests to confirm the accuracy of the transcriptomic results by quantitative real-time polymerase chain reaction (qRT-PCR). Our results highlight the relationship between SNAC4/9 and ABA in the regulation of tomato ripening, which may help provide a theoretical basis for further research on the mechanisms of tomato fruit ripening and senescence.

Keywords

Tomato / RNA sequencing / NAC transcription factor / Virus-induced gene silencing / Abscisic acid

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