Tissue-specific transcriptomic insights into peel thickness in muscadine (Muscadinia rotundifolia)

The genetic and developmental basis of muscadine peel development remains unknown. To address this, we conducted the first tissue-specific, cross-cultivar transcriptomic analysis of the muscadine berry, profiling gene expression across four fruit layers (epidermis, hypodermis, mesocarp, and endocarp) in three cultivars with contrasting peel characteristics.

Transcriptome comparisons revealed conserved enrichment of cuticle- and cell wall- related pathways in outer fruit tissues, along with cultivar-specific differences in gene expression. We identified several genes and pathways associated peel thickness, as well as candidate genes that may contribute to slippery texture characteristic of muscadine berry. Loss-of-function mutants for PAL1 and XTH7 exhibited a significant reduction in silique valve thickness relative to wild-type controls, suggesting a role in regulating cuticle deposition.