Genome-Wide Identification, Evolution, and Expression Analysis of the MAPK Gene Family in Rosaceae Plants

Mitogen-activated protein kinases (MAPKs) are crucial regulators in coping with abiotic and biotic stresses, including drought, salinity, fungi, and pathogens. However, little is known about the characteristics, evolution process, and functional divergence of the MAPK gene family in Rosaceae plants. A total of 97 MAPK members were identified in six Rosaceae species, including 12 genes in Fragaria vesca, 22 genes in Malus domestica, 23 genes in Pyrus bretschneideri, 12 genes in Prunus mume, 14 genes in Prunus persica, and 14 genes in Rosa chinensis. All MAPK members of six Rosaceae plants were categorized into four clusters by the phylogenetic relationship analysis. Collinearity analysis discovered that both segmental duplication and tandem duplication contributed to the expansion of MAPK family genes in Rosaceae plants. And the analysis of motifs and gene structures indicated that the evolution of the MAPK gene family was highly conserved among phylogenetic clusters in Rosaceae species. In addition, the dN/dS rates of MAPK paralogous gene pairs were below one, suggesting the MAPK gene family in Rosaceae was driven by purifying selective pressure. Furthermore, functional divergence analysis discovered that 14 amino acid residues were detected as potentially key sites for functional divergence of MAPK family genes between different cluster pairs, specifically Type I functional divergence. The analysis of functional distance indicated that cluster C retained more of the original functional features, while cluster B exhibited functional specialization. Moreover, the expression profiles revealed that PmMAPK8, PmMAPK9, and PmMAPK10 were both highly expressed under drought stress and low temperature conditions. This study aims to comprehensively analyze the evolutionary process and functional analyses of the MAPK gene family in Rosaceae plants, which will lay the foundation for future studies into MAPK genes of Rosaceae in response to drought and cold stress.