Genome-wide identification of B3 superfamily in pecan (Carya illinoensis): In silico and experimental analyses

Abstract

The B3 superfamily comprises a class of transcription factors containing B3 functional domains that play crucial roles in plant growth and development. However, the identification and analysis of the B3 superfamily have not been reported in pecans. In this study, 75 B3 superfamily members were identified and divided into four families, namely ARF (31), RAV (10), LAV (8), and REM (26). The gene structure, conserved motifs and domain analysis indicated that each family was highly similar. The Ka/Ks results indicated that the CiB3s underwent purifying selection. Several growth- and development-related cis-elements, such as Box 4, GATA-motif, and G-Box, were found in the promoter of the B3 transcription factor. The results obtained from the transcriptomic analysis of different kernel development stages and different tissues of pecan and qRT-PCR, indicated that several transcription factors, particularly CiABI3, CiFUS3, and CiLEC2, were involved in regulating kernel development. In particular, the expression of CiFUS3 changed significantly between S3 and S5. Additionally, CiFUS3 is localized in the nucleus and has no self-transcriptional activity. A yeast one-hybrid experiment showed that CiFUS3 could bind to the RY-motif related to seed development. Overall, our study provides a reference for the role of CiFUS3 in oil synthesis and the functional study of B3 genes in pecan.