Scientia Agricultura Sinica ›› 2022, Vol. 55 ›› Issue (20): 3997-4010.doi: 10.3864/j.issn.0578-1752.2022.20.011

• HORTICULTURE • Previous Articles     Next Articles

Transcriptome and Metabolome Integrated Analysis of Epistatic Genetics Effects on Eggplant Peel Color

SUN BaoJuan1(),WANG Rui2,SUN GuangWen2,WANG YiKui3,LI Tao1,GONG Chao1,HENG Zhou1,YOU Qian1,LI ZhiLiang1()   

  1. 1Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640
    2College of Horticulture, South China Agricultural University, Guangzhou 510642
    3Institute of Vegetable, Guangxi Academy of Agricultural Sciences, Nanning 530007
  • Received:2022-01-20 Accepted:2022-06-06 Online:2022-10-16 Published:2022-10-24
  • Contact: ZhiLiang LI E-mail:sunbaojuan@hotmail.com;vri_li@163.com

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Abstract:

【Objective】Peel color is closely related to the appearance and value of eggplant. Anthocyanin is one of the natural pigments that determines an eggplant’s peel color. Through the comparison of gene expression and metabolites as well as the analysis on the mechanism of epistatic gene interaction and regulation of anthocyanin synthesis in eggplant peel, this paper provided a theoretical basis for eggplant breeding with different peel colors.【Method】The white-peel female parent 19141 with mutation at the structural gene ANS of anthocyanin biosynthesis pathway, white-peel male parent 19147 with mutation at regulatory gene MYB1 of anthocyanin biosynthesis pathway, and their F1 hybrid E3316 with reddish-purple-peel were used as test materials, while transcriptome sequencing and wide-targeted metabolome analysis were performed on peels of commercial eggplant.【Result】The transcriptome sequencing analysis showed that: 19141_vs_19147 had the most differentially expressed genes (DEGs), followed by E3316_vs_19141. The two comparison groups both had the significant enrichment of DEGs in the flavonoid pathway. The DEGs of E3316_vs_19147 were the least and were not enriched in the flavonoid pathway. A total of 218 metabolites were detected by wide-targeted metabolome analysis. A total of 113 differential accumulated metabolites (DAMs) were detected in E3316_vs_19141, and total 98 DAMs were detected in E3316_vs_19147. The combined analysis of transcriptome and metabolome found that the relative expression levels of key structural genes CHS, CHI, F3H, DFR and ANS, key regulatory genes MYB1, AN1 and AN11, modifier genes 3GT, 5GT, AT and OMT, and transporter gene AN9 (GST) involving anthocyanin biosynthesis pathway had the relation of 19141>E3316>19147. The contents of anthocyanin metabolite cyanidin (CAS: 528-58-5) and cyanin (CAS: 20905-74-2) related to peel coloration had the relation of E3316>19147>19141. The combined analysis of transcriptome and metabolome both showed that the difference of E3316_vs_19141 was bigger than E3316_vs_19147. Under the regulation of epistatic genes, F3'H and F3'5'H genes were expressed simultaneously in eggplant peel, but the expression level of F3'H was much higher than that of F3'5'H. The anthocyanin content of E3316 was higher than that of its parents, while the chlorogenic acid content was lower than that of its parents. 【Conclusion】Under the interaction of epistatic genes with controlling the peel color, the locus (type) and mutation mode of mutant gene in parent determined the trend of gene expression in the whole anthocyanin metabolism pathway and the inhibition mode of peel pigmentation. The reddish-purple-peel F1 hybrid of two white-peel parents was the result of the function complementation of two mutated gene involved in anthocyanin biosynthesis pathway. The highly expressed F3'H was the main cause for synthesis of cyanidin, and the relationship between anthocyanin and chlorogenic acid biosynthesis was competitive in peels.

Key words: eggplant, peel color, epistatic genes, anthocyanins, transcriptome, metabolome

Fig. 1

Fruit picture of eggplants used in this study"

Fig. 2

DEGs statistics of different comparison groups"

Fig. 3

Dot map for KEGG pathway enrichment of DEGs in different comparison groups"

Table 1

DEGs enrichment of flavonoid biosynthesis pathway in different comparison groups"

基因ID
Gene ID		 基因注释
Gene annotation		 E3316_vs_19141
log2倍数变化
Log2 fold change		 19141_vs_19147
log2倍数变化
log2 fold change
EGP22200 查尔酮异构酶基因 Chalcone isomerase 1 (CHI1) -3.00 6.94
EGP24232 查尔酮异构酶基因 Chalcone isomerase 3 (CHI3) -2.13 3.59
EGP30923 黄烷酮3-羟化酶基因 Flavanone 3-hydroxylase (F3H) -2.49 2.85
EGP10290 黄酮3′-羟化酶基因 Flavonoid 3′-hydroxylase (F3'H) _ 1.15
EGP32037 黄酮3′,5′-羟化酶基因 Flavonoid 3′5′-hydroxylase (F3′5′H) -4.50 9.32
EGP31017 二氢黄酮醇4-还原酶 Dihydroflavonol 4-reductase (DFR) -1.53 6.93
EGP18904 花青素合成酶基因 Anthocyanidin synthase (ANS) -1.96 7.43
EGP16482 花青素O-甲基转移酶基因 Anthocyanin, O-methyltransferase (OMT) -4.35 8.26
EGP06309 花青素O-甲基转移酶基因 Anthocyanin, O-methyltransferase (OMT) _ -1.91
EGP24021 反式肉桂酸4-单加氧酶基因 cinnamate-4-hydroxylase (C4H) _ 3.31
EGP05102 羟基肉桂酰转移酶基因 Shikimate/quinate hydroxycinnamoyl transferase (HCT) -4.33 2.33
EGP30738 羟基肉桂酰转移酶基因 Shikimate/quinate hydroxycinnamoyl transferase (HCT) -1.24 1.74
EGP01163 羟基肉桂酰转移酶基因 Shikimate/quinate hydroxycinnamoyl transferase (HCT) -1.75 _
EGP02613 羟基肉桂酰辅酶A奎尼羟基肉桂转移酶 Hydroxycinnamoyl coenzyme A-quinate transferase (HQT) -0.98 _
EGP13381 反式肉桂酸4-单加氧酶基因 cinnamate-4-hydroxylase (C4H) 2.20 -1.93
EGP07013 羟基肉桂酰转移酶基因 Shikimate/quinate hydroxycinnamoyl transferase (HCT) 1.59 -0.91
EGP32043 羟基肉桂酰转移酶基因 Shikimate/quinate hydroxycinnamoyl transferase (HCT) 6.12 -7.32
EGP10080 羟基肉桂酰转移酶基因 Shikimate/quinate hydroxycinnamoyl transferase (HCT) 1.16 _

Fig. 4

PCA score of metabolites in eggplant peel of 19141, 19147 and E3316"

Fig. 5

Dot diagram for KEGG pathway enrichment of differential metabolites"

Fig. 6

Heatmap of DAMs in eggplant peel of 19141, 19147 and E3316 The metabolite in the red box was E3116, which was up-regulated compared with the parent; the metabolite in the green box was E3316, which was down regulated compared with the parent"

Fig. 7

Transcriptome and metabolome integrated analysis of peel anthocyanin synthesis controlled by epistatic genes A: The pathway of anthocyanin biosynthesis; B: The heatmap based on FPKM value of genes related to anthocyanin biosynthesis pathway; C: The structure and relative content of metabolites related to anthocyanin biosynthesis detected by wide-target metabolome analysis"

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