Genome-Wide Identification and Expression Analysis of the Aquaporin Gene Family in Plum (Prunus salicina) in Relation to Fruit Cracking

Background: Aquaporins (AQPs) play critical regulatory roles in plant water transport and stress responses. This study aimed to systematically identify the AQP gene family in plum (Prunus salicina), elucidate their evolutionary characteristics, and analyze their expression patterns during fruit cracking, thereby establishing a foundation for further functional characterization. Methods: Utilizing the whole-genome sequences of ‘Sanyueli’ and ‘Wushancuili’, AQP family members were identified through a combined approach of BLAST homology search and HMMER profiling. Bioinformatics analyses were conducted to examine phylogeny, gene structure, and promoter cis-acting elements. Additionally, relative expression levels of candidate genes in different tissues of cracked versus normal fruits were quantified using qRT-PCR. Results: A total of 28 and 31 AQP members were identified in the ‘Sanyueli’ and ‘Wushancuili’ genomes, respectively, which were classified into five evolutionary subfamilies. Promoter analysis revealed significant enrichment of abscisic acid (ABA) and methyl jasmonate (MeJA) responsive elements. qRT-PCR results indicated that AQP members exhibited tissue- and cultivar-specific expression patterns in response to cracking, with notably high expression levels observed in the peel. Conclusions: This study provides the first systematic identification and characterization of the AQP gene family in P. salicina, highlighting their potential regulatory roles in cracking stress. These findings lay a theoretical foundation for further understanding the transcriptional regulatory mechanisms and functional differentiation of plum AQPs.