Genome-wide identification and molecular characterization of the MAPK family members in sand pear (Pyrus pyrifolia).

Background: 'Whangkeumbae', a highly regarded variety of sand pear, is celebrated in the market for its distinctive and superior flavor. However, the rapid production of ethylene after harvest significantly shortens its shelf life, becoming a major limiting factor for enhancing its commercial value. Mitogen-activated protein kinases (MAPKs) are a highly conserved family of transferases in eukaryotes. Although the importance of this family has been extensively studied in other plants, the precise composition and functional mechanisms of MAPK members in sand pear remain elusive. A genome-wide identification and molecular characterization of the MAPK gene family were conducted in Pyrus pyrifolia. This comprehensive analysis aimed to elucidate the genomic distribution, evolutionary relationships, and potential biological roles of MAPK genes in fruit senescence.

Results: Four PpMAPKs were identified from our transcriptome data of sand pear, and 22 PpMAPK proteins were identified from the sand pear genome. Specifically, the transcriptomic PpMAPK3-L (GenBank accession number: PP992971), PpMAPK7-L (GenBank accession number: PP992972), PpMAPK10-L (GenBank accession number: PP992973), and PpMAPK16-L (GenBank accession number: PP992974) exhibited sequence homology values of 99.19%, 100%, 94.51%, and 95.75%, respectively, with their corresponding genomic counterparts (EVM0007944.1, EVM0004426.1, EVM0023771.1, EVM0027166.1). These findings indicate that the integrated analysis of transcriptomic and genomic data provides critical genetic insights into the MAPK genes in sand pear, culminating in the identification of a total of 25 PpMAPK genes in this species. Further phylogenetic analysis classified these genes into four subfamilies (A, B, C, and D), with subfamilies A and B each comprising six members, subfamily C with four members, and subfamily D with nine members. The potential functional differences among the gene members of each subfamily provide valuable clues for future research into MAPK signaling pathways. Further analysis by qRT-PCR revealed that the expression of four PpMAPK genes was positively correlated with fruit senescence in Pyrus pyrifolia. Additionally, interaction analysis revealed a significant interaction between PpMAPK3-L and PpbZIP2, which coordinatively regulate the senescence traits of fruits in sand pear through their joint influence during the senescence process.

Conclusion: The results of this study suggest that PpMAPK3-L, PpMAPK7-L, PpMAPK10-L, and PpMAPK16-L are likely to play pivotal roles in the maturation and senescence of sand pear fruit. Specifically, the interaction between PpMAPK3-L and PpbZIP2 could play a key role in the regulation of fruit senescence, indicating that the MAPK signaling pathway may modulate the fruit's physiological state through interactions with transcription factors. This finding offers significant insights for further investigation into the functions of MAPK genes in the maturation and senescence of sand pear fruit and provides a new direction for investigating biotechnological approaches for delaying senescence and prolonging shelf life.