Transcriptomic Analysis Reveals the Impact of Interstock on Vesicle Granulation in ‘Hainan Qingyou’ Pomelo (Citrus maxima) Fruit

‘Hainan Qingyou’ (Citrus maxima) Pomelo is one of the predominant local cultivars cultivated in Hainan Province, renowned for its high economic value and strong market competitiveness. However, during cultivation, it was observed that the fruit quality of ‘Hainan Qingyou’ grafted onto a ‘Sanhong’ interstock deteriorated, predominantly manifesting as vesicle granulation. This study was therefore conducted to investigate this phenomenon using ‘Sanhong’ Honey Pomelo as the interstock. Fruit quality indicators were measured, and pulp transcriptomic analysis was performed during the expansion and maturation stages. The results indicated that fruits grafted onto ‘Sanhong’ interstock (SHZ) exhibited increased peel thickness, yellower peel, reduced edible rate, higher pulp firmness, decreased total soluble solids (TSS), increased total acid content, and reduced total antioxidant capacity at maturity, all contributing to diminished fruit quality. Additionally, SHZ fruit accumulated higher lignin content in the pulp, leading to vesicle granulation, which severely compromised marketability. Transcriptomic analysis identified 42 structural genes involved in lignin biosynthesis in ‘Hainan Qingyou’ pulp, including 5 PAL, 2 C4H, 2 4CL, 6 CAD, 15 PER, 2 HCT, 1 C3′H, 1 CCoAOMT, 1 CCR, 1 COMT, 2 CSE, and 1 F5H genes. Most of these genes were highly expressed in SHZ fruit at maturity, with expression levels significantly higher than those in fruit grafted onto ‘Hainan Qingyou’ interstock (QYZ). The interstock also affected hormone signaling pathways. Weighted gene co-expression network analysis (WGCNA) identified transcription factors such as MYB, MIKC, ERF, and bZIP as key regulators involved in pulp lignin biosynthesis. This study provides insights into the effects of rootstocks on citrus fruit quality and offers valuable information for cultivar improvement in pomelo orchards.