Integration of ATAC-Seq and RNA-Seq Reveals the Role of FaTIP1 in Red Light-Induced Fruit Ripening in Strawberry

Abstract

Light is an important environmental factor affecting the ripening and quality of strawberry fruit. Previous studies have shown that red light treatment can promote strawberry ripening. Gene expression is closely associated with chromatin openness, and changes in chromatin accessibility are crucial for the binding of transcription factors to downstream regulatory sequences. However, the changes in chromatin accessibility in response to different light treatments in octoploid strawberry plants are still unclear. In this study, the landscape of chromatin accessibility of octoploid strawberry under red (R) and yellow–green (YG) light conditions was analyzed by the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Through bioinformatics and Venn diagram analyses, a total of 1456 and 1854 group-specific genes (GSGs) were screened in the R and YG groups, respectively. By using RNA sequencing (RNA-seq), 440 differentially expressed genes (DEGs) were identified. Among these genes, 194 were upregulated under red light treatment. Through joint analysis of ATAC-seq and RNA-seq data, three red group-specific genes with increased expression were identified, namely, FaTIP1, FaQKY and FaLBD1. Through gene expression and transient transformation analyses of strawberry fruit, we further demonstrated that FaTIP1 can respond to red light induction and promote the ripening process of strawberry fruit. Our results provide a reference for the study of chromatin accessibility in octoploid strawberry and reveal new factors involved in the fruit’s response to red light and the regulation of the ripening process of strawberry fruit.