Ribo-seq and RNA-seq analysis enrich the regulatory network of tomato fruit cracking

Abstract

Abstract Tomato (Solanum lycopersicum), one of the most widely grown vegetable crops in the world, faces cracking problems before and after harvest. Fruit cracking reduces the commercial value and seriously affects the economic performance of the fruits through affecting the appearance and quality of the fruit. Clarifying the molecular mechanism underlying tomato fruit cracking is of great importance for the selection and breeding of crack- resistantvarieties. At present, research on the molecular mechanism of tomato fruit cracking has made progress, but few studies have been conducted to explore the genes related to fruit cracking regulation using combined multi-omics analysis. We applied Ribo-seq (ribosome analysis sequencing) and RNA-seq (RNA-sequencing) techniques to uncover potential fruit cracking regulatory genes and improve the regulatory network of fruit cracking using extremely cracking-resistant (CR) and cracking-susceptible (CS) tomato genotypes. Combining these two sets of histological data and translation efficiency, 41 genes were identified to be associated with fruit cracking. The genes played functions on hormone synthesis (Solyc09g089580.4, Solyc07g049530.3, etc.), cell wall metabolism (Solyc04g071070.2, Solyc03g123630.4, etc.), mineral (Solyc10g006660.3, Solyc01g057770.3, etc.), while 10 of them were transcription factors (Solyc05g015850.4, Solyc08g078190.2, etc.).Based on the investigation of interaction relationship between these genes, the synergistic regulation of multi-gene tomato fruit cracking was predicted. Finally, uORFs (upstream open reading frame) in the 5’ UTR region, which may affect the translation efficiency of downstream mORFs (main open reading frame), were analyzed. This study suggests that the synergistic action of transcription and translation is an important molecular mechanism in regulating tomato fruit cracking.