Genome-Wide Characterization of MADS-Box Transcription Factor Family Reveals Structural Distinctness and Functional Divergence in Pear (Pyrus × bretschneideri)

MADS-box transcription factors play significant roles in plant development processes, such as floral organ conformation, flowering time, and fruit development. Pear (Pyrus × bretschneideri), as the third-most crucial temperate fruit crop, has been fully sequenced. However, there is limited information about the MADS family and its functional divergence in pear. In this study, a total of 95 MADS-box genes were identified in the pear genome, and classified into two types by phylogenetic analysis. Type I MADS-box genes were divided into 3 subfamilies and type II genes into 14 subfamilies. Within type II, 23 proteins without K domain with conserved MADS domains and similarities to structural features of type I proteins were identified. Synteny analysis suggested that WGD duplications have played key roles in the expansion of MADS family, followed by rearrangement events. Purifying selection was the primary force driving MADS-box gene evolution in pear, and four gene pairs presented 1 to 22 codon sites under positive selection. Full-scale expression information for PbrMADS genes in vegetative and reproductive organs was provided by transcriptional analysis. Based on gene family analysis and excavation of putative genes related to anthocyanin accumulation, PbrMADS11 and PbrMADS12 were identified as important candidate genes in anthocyanin biosynthesis regulation. These results provide a solid foundation for future functional analysis of PbrMADS genes in different biological processes, especially the study of pigmentation in pear.