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. 2023 Jun 1:14:1169220.
doi: 10.3389/fpls.2023.1169220. eCollection 2023.

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

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

Lei Yang et al. Front Plant Sci. .

Abstract

Introduction: Blood orange (Citrus sinensis L.) is a valuable source of nutrition because it is enriched in anthocyanins and has high organoleptic properties. Grafting is commonly used in citriculture and has crucial effects on various phenotypes of the blood orange, including its coloration, phenology, and biotic and abiotic resistance. Still, the underlying genetics and regulatory mechanisms are largely unexplored.

Methods: In this study, we investigated the phenotypic, metabolomic, and transcriptomic profiles at eight developmental stages of the lido blood orange cultivar (Citrus sinensis L. Osbeck cv. Lido) grafted onto two rootstocks.

Results and discussion: The Trifoliate orange rootstock provided the best fruit quality and flesh color for Lido blood orange. Comparative metabolomics suggested significant differences in accumulation patterns of metabolites and we identified 295 differentially accumulated metabolites. The major contributors were flavonoids, phenolic acids, lignans and coumarins, and terpenoids. Moreover, transcriptome profiling resulted in the identification of 4179 differentially expressed genes (DEGs), and 54 DEGs were associated with flavonoids and anthocyanins. Weighted gene co-expression network analysis identified major genes associated to 16 anthocyanins. Furthermore, seven transcription factors (C2H2, GANT, MYB-related, AP2/ERF, NAC, bZIP, and MYB) and five genes associated with anthocyanin synthesis pathway (CHS, F3H, UFGT, and ANS) were identified as key modulators of the anthocyanin content in lido blood orange. Overall, our results revealed the impact of rootstock on the global transcriptome and metabolome in relation to fruit quality in lido blood orange. The identified key genes and metabolites can be further utilized for the quality improvement of blood orange varieties.

Keywords: blood orange; flavonoids; gene expression; pigmentation; quality improvement.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Overview of metabolic profile of lido blood orange on two rootstocks (X and Z) at eight developmental stages (1-8) (A) Pictorial description of lido blood orange fruit with rootstocks Z (Trifoliate orange) and X (Ziyang Xiangcheng) (B) Identification of metabolites and share of each subclass (C) Overview of differentially expressed metabolites between samples at 8 time points (T1-T8) in Lido blood orange with rootstock Z and X (D) Upset plot depicting conserved DAMs between different comparisons.
Figure 2
Figure 2
Differential landscape of metabolites in lido blood orange with two rootstocks Z and X (A) Metabolic profile of 149 differentially accumulated flavonoids (B) Metabolic profile of 34 differentially accumulated phenolic acids (C) Metabolic profile of 47 differentially accumulated lignans and coumarins (D) Metabolic profile of 17 differentially accumulated terpenoids.
Figure 3
Figure 3
Overview of the transcriptomic profile of lido blood orange on two rootstocks (X and Z) at eight developmental stages (T1-T8) (A) Principal component analysis based on FPKM values of fruit samples of lido blood orange with rootstock Z and X at eight time-points (B) Overview of differentially expressed genes between samples at different stages (C) Upset plot depicting conserved DEGs between different comparisons.
Figure 4
Figure 4
Identification and characterization of DEGs associated with Flavonoid biosynthesis (A) Expression profile of 47 DEGs associated with flavonoid biosynthesis and pigmentation at 8 time points (T1-T8) (B) GO term enrichment for DEGs associated with flavonoid biosynthesis and pigmentation. The y-axis indicates the GO pathways and associated genes.
Figure 5
Figure 5
Transcript profiles for genes in the anthocyanin biosynthetic pathway. PAL, phenylalanine ammonia-lyase; 4CH, cinnamic acid 4-hydroxylase; 4CL, 4-coumarate CoA ligase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavanone 3-hydroxylase; F3’5’H, flavonoid 3’,5’ hydroxylase; DFR, dihydroflavonol 4-reductase; UFGT, UDP-glucose: flavonoid-3-O-glucosyltransferase; ANS, anthocyanidin synthase; FLS, flavonol synthase. Green and purple represent samples from Z and X, where left to right is the time point from T1 to T8.
Figure 6
Figure 6
Identification and characterization of DEGs associated with Vitamin C biosynthesis (A) Expression profile of 12 DEGs associated with VC biosynthesis at 8 time points (T1-T8) (B) GO term enrichment for DEGs associated with vitamin C The y-axis indicates the GO pathways and associated genes.
Figure 7
Figure 7
Weighted gene co-expression network analysis for gene mining (A) Module/trait correlations and corresponding p values. (B) Pathway enrichment analysis of genes in ME-purple module (C) The network of the highly connected genes in the ME-purple module. Pink represents transcription factors, and gene names in blue represent the hub genes associated with anthocyanin biosynthesis.
Figure 8
Figure 8
qRT-PCR based expression analysis of selected genes in flavonoid biosynthesis genes at 8 time points (T1-T8) in Lido blood orange with rootstock Z and X. Where PAL: Phenylalanine ammonia-lyase, C4H: Cinnamate 4-hydroxylase, 4CL: 4-Coumarate, CHS: Chalcone synthase, CHI: Chalcone isomerase, F3H: Flavanone 3-hydroxylase, F3’5’H: Flavonoid 3’,5’-hydroxylase, DFR: Dihydroflavonol 4-reductase, ANS: Anthocyanidin synthase, WD40: WD40 repeat-containing protein, UFGT: UDP-glucose: flavonoid 3-O-glucosyltransferase, GST: Glutathione S-transferase, Ruby: Gene involved in cotton fiber development, MYBF1: Myeloblastosis transcription factor 1, NAC: NAM, ATAF, and CUC transcription factor family, FLS: flavonol synthase, and BD-NbHLH: Basic-helix-loop-helix.

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Grants and funding

This work was funded by Chongqing academy of agricultural sciences performance incentive guide project (cqaas2021jxjl01), Chongqing academy of agricultural sciences municipal financial special project (NKY-2022AB005).