Comparative transcriptome analysis of leaf color in 'Shine Muscat' and 'ZhongShan-HongYu' hybrids

• Transcriptome analysis revealed the molecular mechanism of the different leaf color of the hybrid offspring of 'Shine Muscat' and 'ZhongShan-HongYu'. • The phenylalanine metabolism and flavonoid biosynthesis, etc. were significantly enriched. • WGCNA identified a significant correlation between the cyan module and the colour transition stage of R-type leaf. The colour of plant leaves undergoes changes during different growth stages, with anthocyanins playing a pivotal role in this process. 'Shine Muscat' (MS) is a white-flesh green-leaf variety, while 'ZhongShan-HongYu' (ZS-HY) is a red-flesh red-leaf variety. The leaves of their hybrid offspring show different colour in autumn. However, the anthocyanin biosynthetic pathway in these varieties remains poorly understood. In this study, we present the results of the transcriptomic analysis of the hybrid progeny of 'MS' and 'ZS-HY' indicated that the red-fleshed progeny (R-type) exhibited a significantly enhanced capacity for anthocyanin accumulation in their leaves compared to the white-fleshed progeny (L-type). The transcriptomic analysis identified 639 and 3885 differentially expressed genes (DEGs) when comparing GGR (red leaf stage G) vs GGL (green leaf stage G) and GGR (red leaf stage G) vs GCR (red leaf stage C), respectively. The KEGG analysis revealed that the DEGs were predominantly enriched in the metabolism of tryptophan and the biosynthesis of flavonoids. Furthermore, the analysis identified a number of key genes involved in anthocyanin synthesis, including LDOX, CHS, FLS1, CHS3, LAR1, F3H, ANR, DFR, F3′5′H, UFGT, LAR2, CHI, F3′H, and so forth. WGCNA revealed that the cyan module correlates with the transition in leaf colour in red-leaf plants, thus unravelling the complex network of genes and transcription factors involved in anthocyanin biosynthesis. Transcriptomic analysis demonstrated that the significant differential expression of VvHY5, VvWRKY44 and VvMYBA6 is crucial for the synthesis of R-type anthocyanins.