Systematic identification and prediction of sex-specific MADS-box genes in Zanthoxylum armatum during flower development

Zanthoxylum armatum, as a vital economic tree species serving both as a food source and medicinal plant, it stands as one of the key industries supporting rural revitalization in southwestern China, offered significant economic, ecological, and social benefits. In recent years, there has been a significant increase in the occurrence of male flowers being sterile, which has greatly impeded the industrial development of Z. armatum. In this study, we investigated the MADS-box gene as a pivotal transcription factor (TFs) influencing flower development. To gain a comprehensive understanding of the evolutionary dynamics of MADS-box genes in Z. armatum and establish a solid foundation for future research on this significant gene family, we conducted a genome-wide investigation and analyzed the expression patterns of MADS-box genes. The present study identified a total of 72 MADS-box genes (ZaMADS1–72) from Z. armatum and proposed that the ZaMADS41 gene is pivotal candidate gene influencing the female-to-male transformation. Phylogenetic analysis revealed that these genes can be categorized into two types: Type I (29 genes) and Type II (43 genes), with the latter exhibiting more complex protein domains and motifs compared to the former. Protein-protein interactions were observed among members of the ZaMADS-box gene family, while their promoter regions contained cis-acting elements associated with light response, hormone response, and plant growth and development. Expression profiling during different stages of male and female flower development demonstrated distinct high expression patterns for certain genes specifically in mature male or female flowers. Furthermore, the determination of endogenous hormone content indicated a potential correlation between iP9G and MEJA with sex transformation, while iP9G exhibited a significantly negative association with ZaMADS33 expression. This comprehensive study on MADS-box genes in Z. armatum combined with changes in endogenous hormone levels during male and female flower development, provides a solid theoretical foundation for investigating bud differentiation mechanisms and regulatory techniques in this species.