Systematic analysis and identification of regulators for SRS genes in Capsicum annuum

SHI-related sequence (SRS) transcription factors are essential for plant development and growth regulation, phytohormone biosynthesis and stress response. The SRS gene family was analyzed in several plant species including Arabidopsis and rice, however, a systematic analysis of this family in solanaceous crops remains to be conducted. To identify SRS genes involved in stress tolerance in pepper ( Capsicum annuum ), a systematic analysis of this family was performed. In total, seven SRS family members were found in pepper, which can be divided into four clades. Variation in gene structure and motifs was detected between CaSRS genes and their tomato orthologs, further supported by protein three-dimensional structure prediction. Promoter cis-element analysis suggested that SRS genes may play a critical role in development, phytohormone and stress response in both tomato and pepper. Gene expression profiles also indicated the involvement of CaSRSs in these processes. Weighted correlation network of pepper transcriptomic data from phytohormone and stress treatments revealed a cluster of four CaSRSs that are likely involved in phytohormone and temperature response, as revealed by pathway and Gene Ontology enrichment analyses. Conserved non-coding sequences (CNSs) and available ATAC-seq data analyses suggested that several transcription factors, including a heat sensor in Arabidopsis , can bind to the CNSs of SRS2 and SRS3. Yeast one-hybrid assay confirmed a strong interaction between SlbZIP2 and SlSRS3 promoter. In summary, our comprehensive bioinformatics analysis and experimental evidence support the hypothesis that SRS genes play an important role in temperature and phytohormone responses in pepper. This study provides the molecular basis for further functional characterization of CaSRSs under temperature stress as well as functional analysis of SRS in other solanaceous crops.