Abstract:

The E2F/DP gene family plays a significant regulatory role in the growth, development and stress response of plants. The bioinformatics analysis of the E2F/DP gene family in red raspberry (Rubus idaeus) and the expression pattern analysis in different tissues and after exogenous spraying of melatonin lay the foundation for in-depth exploration of the function of E2F/DP genes in red raspberry. In this study, three members of the E2F/DP gene family were obtained from the transcriptome database of ‘Heritage’ red raspberry. The E2F/DP gene family of red raspberry was analyzed by bioinformatics methods. Subsequently, the expression levels of E2F/DP in different tissues and organs, fruits at different developmental stages and fruits after exogenous spraying of melatonin were analyzed by qRT-PCR. The proteins encoded by RuE2F/DPs have a minimum of 243 amino acids and a maximum of 761 amino acids, with a minimum relative molecular mass of 26.88 kDa and a maximum of 82.55 kDa. Their isoelectric points range from 5.69 to 9.07. RuE2F/DP-1 is a stable hydrophilic protein, while RuE2F/DP2-3 is unstable hydrophilic protein. All RuE2F/DPs-encoded proteins are located in the cell nucleus, have no signal peptides, are non-secretory proteins, non-transmembrane proteins, and contain the conserved E2F_TDP domain. Their secondary structures are all composed of four types of structures, including α-helices, β-turns, random coils, and extended strands. The prediction results of their tertiary structures are consistent with their secondary structures. RuE2F/DP-1 and RuE2F/DP-3 have expression correlations. The RuE2F/DP gene family contains 9 to 14 exons and 4 to 10 conserved motifs; phylogenetic analysis indicates that the RuE2F/DP family members belong to different subgroups, and red raspberry is more closely related to strawberry; the cis-acting elements in the promoter suggest that the RuE2F/DP gene family mainly participates in plant growth and development and responses to drought, low temperature and other stress environments; qRT-PCR analysis shows that the expression levels of three members of the RuE2F/DP gene family in young roots and green fruits are higher than those in other tissues; melatonin treatment has a positive regulatory function on RuE2F/DP1-2 and a negative regulatory function on RuE2F/DP-3. The research results reveal that the RuE2F/DP gene family may play a role in the growth of red raspberry roots, the growth and development of fruits, the response to adverse stress during the growth process, and the hormone response to melatonin.

Key words: red raspberry (Rubus idaeus), E2F/DP gene, bioinformatics analysis, expression analysis, RT-qPCR, melatonin, tissue specificity