Integrate Transcriptomic and Metabolomic Analysis of Fruits Quality Differences between ‘Guiyou No. 1’ and ‘Shatianyou’ Pomelo （Citrus maxima）

doi:10.13560/j.cnki.biotech.bull.1985.2025-0279

Abstract

Abstract:

Objective This study aims to elucidate the differences of fruit qualities and metabolic regulation between the self-pollinated cultivar pomelo ‘Guiyou No. 1’ and its female parent ‘Shatianyou’, it will provide a theoretical basis for future comprehensive research on the mechanisms of fruit quality formation and the metabolic regulation in pomelo. Method Based on physicochemical parameter measurements, transcriptomics, and widely targeted metabolomics, the fruit qualities, gene expression levels, and metabolite profiles were systematically analyzed in mature fruits of ‘Guiyou No.1’ and ‘Shatianyou’ pomelo. Result There were no significant differences in fruit weight, soluble solids content, titratable acidity, and vitamin C content between pomelo ‘Guiyou No.1’ and ‘Shatianyou’. Fruit shape index in ‘Guiyou No.1’ was significantly greater than that in ‘Shatianyou’, while the total amino acid content was significantly less than that in ‘Shatianyou’. Compared to ‘Shatianyou’, the 285 differentially expressed genes (DEGs) were screened, including 190 up-regulated genes and 95 down-regulated genes, respectively. These DEGs were primarily enriched in metabolic pathways, such as arginine and proline metabolism, fatty acid metabolism, and phenylpropanoid biosynthesis. Metabolome profiling suggested that a total of 90 differential metabolites were detected in ‘Guiyou No.1’, with 17 up-regulated and 30 down-regulated ones, compared with pomelo ‘Shatianyou’. Upregulated metabolites were mainly alkaloids and coumarins, while downregulated ones included amino acids, flavonoids, and phenolic acids. The differences of fruit quality between ‘Guiyou No.1’ and ‘Shatianyou’ were primarily influenced by the pathways of amino acids, alkaloids, and phenylpropanoids. Key genes such as GOT2, COMT, UGT73C, CYP71A and PAIC were identified as potentially playing crucial roles in the quality formation of pomelo fruits. Conclusion No significant differences in general qualities, are detected between mature fruits of ‘Guiyou No.1’ and ‘Shatianyou’ pomelo; however, there are obvious differences in terms of amino acids, flavonoids, phenolic acids, and alkaloids. The differential genes and metabolites between the two cultivars are mainly enriched in the metabolic pathways of amino acid and phenylpropanoid.

Key words: Guiyou No.1, Shatianyou, fruit qualities, transcriptome, metabolomics, amino acids, flavonoids, alkaloids

LIU Jian-guo, LIU Ge-er, GUO Ying-xin, WANG Bin, WANG Yu-kun, LU Jin-feng, HUANG Wen-ting, ZHU Yun-na. Integrate Transcriptomic and Metabolomic Analysis of Fruits Quality Differences between ‘Guiyou No. 1’ and ‘Shatianyou’ Pomelo （Citrus maxima）[J]. Biotechnology Bulletin, 2025, 41(9): 168-181.

Figures/Tables 10

Table 1 RT-qPCR validation gene and primer information

基因序号 Gene ID	基因名称 Gene name	上游引物序列 Forward primers sequence （5′-3′）	下游引物序列 Reverse primers sequence （5′-3′）	用途 Usage
Cg8g019990	PAL	GAAAGTCCTGACGATGGGGG	GCATCAACGGGTAAGTTGCG	荧光定量PCR Quantitative real-time PCR
Cg2g026340	4CL	GGCTGCTTGCATTTTTCGGA	AGGCAGCACACATAGGATCG
Cg4g020580	C4H	CTGAGGAGTTTCGGCCAGAG	TGCAATCACAAGCCCCAAGA
Cg1g010540	GPPK	GGAAGCCGAAGAGATGGAGG	TGAGGGGTTTGTTGTGGCAA
Cg7g018290	CYP71A	TCTGGGCAATGTCAGAGCTA	GTCTTGGGAGTAGCATCGGG
Cg7g005510	CSE	CTCCACGGCGAAGAGGATAA	GTGCCACATCCCCTCGTAAA
Cg4g014720	CAD	GCTCGGATTGACCCAAGAAG	AGCTTCTTTTGGAATTGGCTCTATC
Cg3g013930	CER	CCTGATCTCGCATTCTCCCC	GGCTCGTGTAGAGACTTCGG
Cg6g013340	HCT	CCCTTCGCCGAATCATCAGT	ACACGTTCGCCTTTGCATTC
Cg5g006480	GAPC	GGTGGCAGGGCTGCTTCATT	AGCGTCCTTCTCCAGCCTCA	荧光定量PCR内参基因 Reference gene for RT-qPCR

Fig. 1 Phenotypes (A) and quality indexes (B-G) of 'Guiyou No.1' and 'Shatianyou' fruits* indicates significant differences at P < 0.05 level, ns indicates no significant differences

Fig. 2 Volcano of 'Guiyou No.1' and 'Shatianyou' fruits

Fig. 3 GO enrichment analysis (A), KEGG analysis of differentially expressed genes (B), and expressed heatmap involved in metabolites pathways in (C) 'Guiyou No.1' and 'Shatianyou' fruits

Fig. 4 RT-qPCR verification of differentially expressed genes in 'Guiyou No.1' and 'Shatianyou' fruits

Fig. 5 Pie chart of metabolite category composition in 'Guiyou No.1' and 'Shatianyou'

Fig. 6 Principal components analysis (A) and hierarchical clustering analysis (B) of metabolites in 'Guiyou No.1' and 'Shatianyou' fruits

Fig. 7 OPLS-DA score diagram and verification diagram of model of metabolites in 'Guiyou No.1' and 'Shatianyou' fruits, as well as analysis of differential metabolitesA: OPLS-DA score diagram. B: Verification diagram of model. C: Volcano plot. D: Classification of differential metabolites. E: The heatmap of differential metabolites

Fig. 8 Metabolic pathway enrichment analysis of differential metabolites between 'Guiyou No.1' and 'Shatianyou' fruitsA: KEGG classification plot. B: Differential abundance score plot

Fig. 9 Main common mapping pathways of transcription and metabolism in 'Guiyou No.1' and 'Shatianyou' fruitsA: Scatter plot of 9-quadrant associate analyses. B: KEGG enrichment analysis. C: Differential metabolites and genes analysis in major metabolic pathways

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