Metabolomic and transcriptomic analyses reveal the effects of grafting on blood orange quality

Identification of key genes controlling anthocyanin biosynthesis in the fruits of a bud variety of Tarocco blood-orange

Tarocco is a prevalent blood-orange variety in China, has a bud variant identified in Wenzhou City. To characterize the quality traits and molecular mechanisms underlying inhibition of anthocyanin synthesis in this variety, we collected fruits of Tarocco (WT) and the bud variant Ouya (MT) at nine developmental stages. Their anthocyanin, soluble sugar, and organic acid profiles were examined, and transcriptomes and metabolites were analyzed at three developmental stages. The results revealed that MT is a new blood orange variety with weak anthocyanins and a better sugar-acid ratio than the WT. The content of anthocyanin in MT fruits were significantly lower than those in WT fruits, especially cyanidin-like anthocyanins, while the flavone contents exhibited no remarkable variation. A total of 64 differentially expressed genes (DEGs), including five transcription factors (TFs), five methylation-related genes, and one flavonoid biosynthesis gene, were identified between WT and MT at three fruit developmental stages. The potential regulatory networks of these TFs were further constructed using weighted gene co-expression network analysis.Furthermore, in MT fruit treated with the 5-azacytidine, we observed hypomethylation of anthocyanins accumulated in the pulp and the promoters and genebodies of some anthocyanin synthesis-related genes. These results provide new insights into the influence of DNA methylation on anthocyanin accumulation in MT and also provide support for the promotion of MT as a new variety.

Comparative Transcriptome Analysis Reveals Potential Molecular Regulation of Organic Acid Metabolism During Fruit Development in Late-Maturing Hybrid Citrus Varieties

Late-maturing hybrid citrus is a significant fruit that combines the best traits of both parents and is highly prized for its unique flavor. Not only can organic acids alter the flavor of citrus pulp, but they are also essential for cellular metabolism, energy conversion, and maintaining the acidbase balance in plant tissues. Although organic acids play a key role in the quality formation of citrus fruits, there is still insufficient research on the metabolic processes of organic acids in late-maturing hybrid citrus varieties. In this study, three late-maturing citrus varieties with different acidity levels, namely 'Huangjinjia' (HJ), 'Kiyomi' (QJ), and 'Harumi' (CJ), were selected to systematically investigate the metabolic regulation mechanism of organic acids in late-maturing citrus through transcriptome sequencing technology, combined with physiological and biochemical analyses. This study revealed gene expression differences related to organic acid synthesis and degradation. Through gene expression profiling, several genes closely associated with organic acid metabolism were identified, and a preliminary gene network related to the regulation of organic acid metabolism was constructed. The results showed that there were significant differences in the organic acid metabolic pathways between different varieties and growth stages of the fruit. Specifically, HJ had a higher TA content than QJ and CJ, primarily due to the significantly higher citric acid and malic acid contents in HJ compared to the other two varieties. Further analysis revealed that four gene modules showed a high correlation with the levels of major organic acids in the fruits. The genes involved in these modules are closely related to organic acid synthesis, degradation, and transport. Additionally, we also identified several key genes (AS1, BZP44, COL4, TCP4, IDD10, YAB2, and GAIPB) that might be involved in the regulation of organic acid metabolism. The functions of these genes could have a significant impact on the expression levels changes of enzymes related to organic acid metabolism. This study provides a foundation for exploring the intrinsic mechanisms regulating the organic acid content in late-maturing hybrid citrus fruits and contributes to the functional research of organic acids in late-maturing hybrid citrus and the molecular design of high-quality varieties.

Combined Metabolomics and Network Pharmacology Analysis Reveal the Effect of Rootstocks on Anthocyanins, Lipids, and Potential Pharmacological Ingredients of Tarroco Blood Orange (Citrus sinensis L. Osbeck)

The benefits of citrus fruits are strongly associated with their secondary metabolites. In this study, we conducted widely targeted metabolomics analyses to compare the variability of the ingredients in four scion-rootstock combinations. A total of 376 differential metabolites were obtained by a multivariate statistical analysis, and a KEGG pathway analysis showed that the enriched metabolic pathways were mainly related to the biosynthesis of flavonoids as well as lipid metabolism. The anthocyanin-targeted metabolomic features showed that cyanidin 3-O-glucoside, cyanidin 3-O-(6-O-malonyl-beta-D-glucoside), cyanidin 3-O-sophoroside, and cyanidin 3-O-xyloside were the pigments responsible for the red color of Tarocco. A lipid metabolomics analysis revealed that when Tarocco was hetero-grafted with rootstock H, there was an increase in the content of each lipid subclass, accompanied by an increase in the levels of unsaturated fatty acids, including polyunsaturated linoleic and linolenic acids, thus impacting the ratio of unsaturated fatty acids to saturated fatty acids. Additionally, we determined their antioxidant capacity ('Trifoliate orange' (Z) > 'Citrange' (ZC) > 'Hongju' (H) > 'Ziyang Xiangcheng' (X)) using in vitro assays. Finally, we utilized a network pharmacology analysis to explore the antioxidant mechanisms and potential pharmacological ingredients; we obtained 26 core targets proteins and 42 core metabolites associated with oxidative damage, providing a basis for future preventive and therapeutic applications of these metabolites.

Widely Targeted Metabolomic Analysis Provides New Insights into the Effect of Rootstocks on Citrus Fruit Quality

The use of different rootstocks has a significant effect on the content of flavor components and overall fruit quality. However, little information is available about the metabolic basis of the nutritional value of citrus plants. In this study, UPLC-MS/MS (ultra-performance liquid chromatography-tandem mass spectrometry) was performed to analyze the metabolites of three late-maturing hybrid mandarin varieties ('Gold Nugget', 'Tango' and 'Orah') grafted on four rootstocks ('Trifoliate orange', 'Carrizo citrange', 'Red tangerine' and 'Ziyang Xiangcheng'). A total of 1006 metabolites were identified through OPLS-DA (Orthogonal Partial Least Squares-Discriminant Analysis) analysis. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis revealed the most critical pathways among the different pathways associated with genes grafted on the four rootstocks that were differentially activated, including tryptophan metabolism and sphingolipid metabolism in 'Gold Nugget'; tryptophan metabolism, phenylpropanoid biosynthesis and sphingolipid metabolism in 'Tango'; and pantothenate and CoA biosynthesis- and photosynthesis-related biosynthesis in 'Orah'. A considerable difference between the different rootstocks was also observed in the accumulation of lipids, phenolic acids and flavonoids; further analysis revealed that the rootstocks regulated specific metabolites, including deacetylnomylinic acid, sudachinoid A, amoenin evodol, rutaevin, cyclo (phenylalanine-glutamic acid), cyclo (proline-phenylalanine), 2-hydroxyisocaproic acid, and 2-hydroxy-3-phenylpropanoic acid. The results of this study provide a useful foundation for further investigation of rootstock selection for late-maturation hybrid mandarin varieties.