Genome-Wide Identification of the PME Gene Family in Plum and Its Potential Roles in Fruit Texture Formation

Fruit texture is a major component of plum quality, affecting both consumer acceptance and postharvest behavior. Pectin methylesterases (PMEs) play important roles in cell-wall pectin modification and are therefore likely to contribute to plum fruit texture development and ripening-associated softening. However, the PME gene family has not yet been comprehensively investigated in plum (Prunus salicina L.).

In the present study, a chromosome-level plum genome was used to survey this gene family at the whole-genome scale. Phylogenetic relationships, chromosomal positions, exon-intron organization, conserved motifs, domain architectures, gene duplication, and cis-elements were analyzed. Four flesh texture traits were measured in 55 plum accessions to characterize texture variation and select two representative cultivars with contrasting flesh textures for further molecular analysis. Based on the clustering results, 'WSCL' and 'FR' were selected for expression profiling during fruit development and subsequent correlation analysis with texture traits.

A total of 46 PsPME genes were identified. Phylogenetic analysis classified them into four major subgroups. Structural analyses indicated an overall conserved family framework, although noticeable variation was retained among individual members. Dispersed duplication made the largest contribution to family expansion, and most duplicated pairs appeared to have evolved under purifying selection. Correlation analysis showed that PsPME20, PsPME22, and PsPME25 were significantly negatively correlated with flesh firmness, while PsPME20 was additionally linked to flesh compactness and flesh fragility.

Overall, this study clarifies the structural and evolutionary characteristics of the PsPME family and identifies candidate genes that may contribute to texture differences in plum, offering a basis for future functional studies and breeding programs.