Integrated transcriptome and metabolome analyses reveal the mechanism by which bagging treatment affects peel reddening in Orah mandarin

Orah mandarin is a late-ripening citrus variety that is popular with consumers because of its red peel when ripe. However, the Orah mandarin from the Yunnan production area has difficulty reddening its peel. In this study, we applied different bagging treatments to Orah mandarin at the end of fruit expansion, and by analyzing the fruits for color difference values and intrinsic qualities, we found that the white bagging (W) treatment had the best color effect and contributed to the TSS, TA, SAR of the fruits. To further investigate the reasons for the changes in the skin color of Orah mandarin, we conducted a comprehensive analysis of W treatment and unbagging fruits via transcriptomic and metabolomic techniques. Forty-nine carotenoid metabolites, in which violaxanthin laurate, apocarotenal, and β-citraurin were the main substances responsible for the red color of Orah mandarin peels, were detected via UPLC-APCI-MS/MS targeted metabolomics analysis. Eighty-one structural genes related to carotenoid biosynthesis were screened via RNA-Seq, and the transcript levels of LYCB2, LUT5–6, ZEP9, ZEP5, and NXS2 were positively correlated with the red carotenoid content. Correlation analysis revealed that the expression levels of HSF2, MYB2, and WRKY2 were positively correlated with those of genes and metabolites (R² > 0.95). The qRT-PCR results also verified the expression of some of the genes and transcription factors. In addition, we identified a regulatory mechanism that promotes the red color trait in the peel of Orah mandarin, where bagging treatment increased the transcript levels of genes such as LYCB2, LUT5–6, ZEP9, ZEP5, and NXS2, which, in turn, increased the content of apocarotenoids and carotenoids in the peel, and HSF2, MYB2, WRKY2, and other transcription factors (TFs) interact with the above genes and metabolites, which further positively regulate carotenoid biosynthesis. The present study provides new insights into the effects of bagging on Orah mandarin fruits to offer valuable guidance for research on fruit color and carotenoid regulation.