Transcriptomic Profiling Uncovers Molecular Basis for Major Color Metabolism During Fruit Development in Red-Skinned Cultivar ‘Taishanhong’ and Green-Skinned Cultivar ‘Luqing 1’ Pomegranates in Shandong Province, China

Fruit peel color is a key quality trait of pomegranate that influences consumer preference and market value. However, the pigmentation patterns and underlying molecular mechanisms in red- and green-skinned cultivars remain incompletely understood. This study aimed to elucidate the transcriptional basis of peel color variation between the red-skinned cultivar ‘Taishanhong’ (TSH) and the green-skinned cultivar ‘Linqing1’ (LQ1). Pigment contents were determined in fruit peels at three developmental stages, and RNA-seq was performed to identify key genes regulating peel coloration. The results show that anthocyanin content increased progressively during fruit development in both cultivars, whereas chlorophyll and carotenoid contents declined gradually. TSH accumulated significantly more anthocyanins but contained markedly lower levels of chlorophyll and carotenoids than LQ1. The S1_vs_S3 comparison yielded the largest number of differentially expressed genes (DEGs) in both cultivars, which were enriched in phenylalanine metabolism, flavonoid biosynthesis, photosynthesis, and carotenoid biosynthesis pathways. Twenty-four DEGs related to anthocyanin metabolism were identified, among which chalcone isomerase (PgCHI4), Flavonol synthase (PgFLS1), and UDP-glucose: flavonoid 3-O-glucosyltransferase (PgUFGT1) were strongly correlated with anthocyanin accumulation. Twenty-eight DEGs associated with carotenoid metabolism were detected; geranylgeranyl pyrophosphate synthase (PgGGPS1, PgGGPS2) and zeaxanthin epoxidase (PgZEP1) were closely linked to carotenoid biosynthesis, whereas carotenoid cleavage dioxygenase (PgCCD2) and 9-cis-epoxycarotenoid dioxygenase 2 (PgNCED2) were associated with carotenoid degradation. Chlorophyll metabolism was potentially regulated by multiple genes, including fructose-1,6-bisphosphate aldolase (PgFBA1), glyceraldehyde-3-phosphatedehydrogenase (PgGAPDH1, PgGAPDH4). Furthermore, 78 transcription factors from the MYB (myeloblastosis), ERF (ethylene response factor), bHLH (basic helix-loop-helix), NAC (NAM, ATAF1/2 and CUC2), ARF (auxin response factor) families were identified as candidate regulators of pigment metabolism. Collectively, this study delineates a cultivar-specific transcriptional program underlying peel color differentiation in pomegranate and identifies candidate structural genes and transcription factors that can serve as targets for functional validation and marker-assisted breeding of fruit color traits.