Genome-wide identification of the class III peroxidase gene family and its association with fruit rind cracking in Cucumis melo

Peroxidase activity and lignin accumulation were significantly higher in cracking-susceptible cultivars compared to cracking-resistant cultivars, with cracked rinds displaying elevated levels relative to intact rinds. Sixty-four <i>PRX</i> genes were identified in the melon genome, and phylogenetic analysis categorized them into six subgroups. The <i>CmPRX</i> genes were unevenly distributed across 12 chromosomes, and collinearity analysis uncovered eight duplicated gene pairs within the melon genome. Comparative synteny analysis revealed that the number of collinear <i>PRX</i> gene pairs between melon and other Cucurbitaceae species, specially cucumber and watermelon, was greater than that observed with the more distantly related <i>Arabidopsis</i>. Promoter <i>cis-</i>acting element examination revealed that the 64 <i>CmPRX</i> genes harbored 25 classes of elements associated with hormones, stress responses, and growth and development. Transcriptome data from melon rinds revealed that the <i>CmPRX</i> genes could be clustered into six groups based on expression patterns across different rind types. Among these, <i>CmPRX</i> genes in clusters 1 and 6 exhibited higher transcript levels in cracked rinds compared to non-cracked rinds. Moreover, quantitative real-time polymerase chain reaction analyses confirmed that <i>CmPRX39</i>, <i>CmPRX48</i>, and <i>CmPRX51</i> were expressed at significantly elevated levels in cracked rinds compared with those of non-cracked rinds. Protein interaction network prediction showed that these three candidate genes interacted with multiple proteins involved in the lignin synthesis pathway, suggesting their potential regulatory roles in rind cracking of melon through mediating lignin polymerization. These findings identified candidate genes influencing rind cracking in melon, thereby offering potential molecular targets for the breeding of cracking-resistant cultivars.