Genome-wide identification of the<i>MADS-box</i>transcription factor family in pear (<i>Pyrus bretschneideri</i>) reveals evolution and functional divergence

Abstract

<i>MADS-box</i> transcription factors play significant roles in plant developmental processes such as floral organ conformation, flowering time, and fruit development. Pear (<i>Pyrus</i>), as the third-most crucial temperate fruit crop, has been fully sequenced. However, there is limited information about the <i>MADS</i> family and its functional divergence in pear. In this study, a total of 95 <i>MADS-box</i> genes were identified in the pear genome, and classified into two types by phylogenetic analysis. Type I <i>MADS-box</i> genes were divided into three subfamilies and type II genes into 14 subfamilies. Synteny analysis suggested that whole-genome duplications have played key roles in the expansion of the <i>MADS</i> family, followed by rearrangement events. Purifying selection was the primary force driving <i>MADS-box</i> gene evolution in pear, and one gene pairs presented three codon sites under positive selection. Full-scale expression information for <i>PbrMADS</i> genes in vegetative and reproductive organs was provided and proved by transcriptional and reverse transcription PCR analysis. Furthermore, the <i>PbrMADS11(12)</i> gene, together with partners <i>PbMYB10</i> and <i>PbbHLH3</i> was confirmed to activate the promoters of the structural genes in anthocyanin pathway of red pear through dual luciferase assay. In addition, the <i>PbrMADS11</i> and <i>PbrMADS12</i> were deduced involving in the regulation of anthocyanin synthesis response to light and temperature changes. These results provide a solid foundation for future functional analysis of <i>PbrMADS</i> genes in different biological processes, especially of pigmentation in pear.