Scientia Agricultura Sinica ›› 2022, Vol. 55 ›› Issue (11): 2214-2226.doi: 10.3864/j.issn.0578-1752.2022.11.011

• HORTICULTURE • Previous Articles     Next Articles

Co-Expression Network and Transcriptional Regulation Analysis of Sulfur Dioxide-Induced Postharvest Abscission of Kyoho Grape

YANG ShengDi(),MENG XiangXuan,GUO DaLong,PEI MaoSong,LIU HaiNan,WEI TongLu,YU YiHe()   

  1. College of Horticulture and Plant Protection, Henan University of Science and Technology/Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471000, Henan
  • Received:2021-09-28 Accepted:2021-12-13 Online:2022-06-01 Published:2022-06-16
  • Contact: YiHe YU E-mail:yangshengdi2050@163.com;yuyihe@haust.edu.cn

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Abstract:

【Objective】 Sulfur dioxide (SO2) treatment can effectively prevent Botrytis cinerea and postharvest decay, but it can lead to berry abscission, the purpose of this study was to explore the molecular mechanism of grape berry abscission induced by SO2. 【Method】 Kyoho grapes were treated with SO2, samples were collected at 2, 4 and 6 d, respectively, and the grape berry abscission rates of the control group (CK) and SO2 treatment group. The samples of ‘Kyoho’ grapes under CK control and SO2-treated were sequenced at 2, 4 and 6 d after harvest by high-throughput sequencing technique, the grape genome was used as the reference genome for sequence alignment, and the gene expression was calculated by TPM algorithm, the transcriptome data were systematically analyzed by gene set enrichment analysis (GSEA), gene co-expression network (GCN) and transcription regulation network prediction, and the expression was verified by using quantitative real-time fluorescence PCR (qRT-PCR). 【Result】 SO2 treatment could significantly induce grape berry abscission, the grape berry abscission treated with SO2 was 9.88% at 2 d and 19.24% at 4 d, which were significantly higher than those in the control group, the abscission rate reached 38.25% at 6 d, while the abscission rate of the control group was only 11.85%. GSEA analysis showed that the GO biological process enriched in CK group was mainly related to oxidative stress response, cell wall metabolism and phenylalanine metabolic pathway, and CK group was enriched in plant cell wall tissue, pectin metabolism, cell wall modification, polygalacturonic acid and other pathways. The GO biological process enriched in SO2 group is mainly related to energy metabolism pathway, and it is enriched to photosynthesis, tetrapyrrole metabolism, precursor metabolite and energy production, glucose metabolism and other pathways in SO2 group at 2 d. The KEGG metabolic pathways enriched in CK group mainly include the mutual conversion of pentose and glucuronic acid, galactose metabolism, plant hormone signal transduction, citric acid cycle (TCA cycle), etc. SO2 group includes photosynthesis, citric acid cycle (TCA cycle), glycolysis, etc. GCN divided the leading genes in GSEA analysis into 12 levels: level 4-9 were enriched in energy metabolism and glucose metabolism-related pathways, while level 4 was enriched in hormone response and oxidative stress response. The transcriptional regulation prediction analysis of GCN key level gene promoter sequences showed that there were 987 pairs of regulatory relationships among 95 transcription factors (TFs). WRKY14, WOX8, KUA1 were continuously downregulated under SO2 treatment, wihle MYB60, MYB73, ANL2, ERF2, DOF3.6, GATA25, WRKY57, KAN2, ATHB6 were continuously upregulated under SO2 treatment. In addition, MYB15, WRKY11, WRKY33, WRKY40, WRK75 were first adjusted upwards and then downwards. The transcriptional regulatory networks of ERF2, MYB60 and WRKY40 revealed that the regulated target genes were involved in cell wall metabolism, sugar metabolism and other related pathways. The qRT-PCR results showed that the up-regulated expression trend of PME36 and ERF2 was similar, and GAUT7, MYB60 and UGE3 had similar up-regulated expression trends. In addition, WRKY40 was induced to be up-regulated at 2 and 4 d of SO2 treatment, PPME1 and COMT1 expression was consistently down-regulated, and LAC15 was significantly up-regulated at 4 d of SO2 treatment. 【Conclusion】 SO2 induced the expression of genes related to nutrient metabolism, energy metabolism and cell wall metabolism pathway, which was regulated by a variety of transcription factors, and eventually leads to the grape berry abscission.

Key words: grape, abscission, GCN, transcription factor, regulation

Table 1

The sequences of the primers used in this experiment"

基因名称 Gene name 上游引物Primer sequence (5′-3′) 下游引物 Primer sequence (5′-3′)
Vitvi18g03065:LAC15 CCGAGCCACTGTTCATGGAG AGCACTTCATCTCGAACCGC
Vitvi11g00034:PPME1 GTGATCACAGCTCAGGCAAG TGAGAGTGCCCATGTAGGTG
Vitvi09g01122:WRKY40 CTGCCCTGTCAAGAAGAAGG TGAGCTGAGTGAGGATGCAC
Vitvi16g02061:COMT1 CGAAGGGCCGGCCAC CAGGGGAGGGGATGTCTCTT
Vitvi16g00349:ERF2 CAGTCTGATGCCGTTCTTGA CCTAGGCTCCTCCTTCACCT
Vitvi15g00703:PME36 GAAGGAAGTGCAACCGACAT TATGGACCATGCGGGTTAGT
Vitvi01g01838:UPTG2 CTGGCAAGAAGAGCTGATCC AATCTCCAGCAGATGGGTTG
Vitvi08g00069:MYB60 CAGGCCTAAGTTGGAGCAAG GGAGGGTTGTGCTTCTTCTG
Vitvi15g00687:UGE3 GTGGGCTTCTTCGAGTTCAG CCAGTAAGCGAAAGGCCATA
Vitvi08g00009:GAUT7 CATTGCCTCAGGAGTTTCGT CCCAACCTCACCCTACAGAA
ubiqutin1 GTGGTATTATTGAGCCATCCTT AACCTCCAATCCAGTCATCTAC

Fig. 1

Postharvest grape abscission due to SO2 A: Abscission in SO2-treated and CK groups at 0-6 d postharvest storage; B: Abscission rate during storages"

Fig. 2

Enrichment analysis of GSEA gene set based on GO biological process A: GO biological process enriched in the CK group; B: GO biological process enriched in the SO2 group; C: Distribution of partial GO term alignments of gene set members enriched in the CK group; D: Distribution of partial GO biological process alignments of gene set members enriched in the SO2 group"

Fig. 3

Enrichment analysis of GSEA gene set based on KEGG pathway A: KEGG pathway enriched by GSEA; B: Distribution of partial KEGG pathway alignments of gene set members enriched in the CK group; C: Distribution of partial KEGG pathway alignments of gene set members enriched in the SO2 group"

Fig. 4

Analysis of gene co-expression network A: Gene co-expression network, different Levels (Abbreviated as L) are represented by different coloured circles; B: The distributions of PCC values and P value between genes; C: Heat map of GCN network nodes"

Fig. 5

Enrichment analysis at level 4 to 9"

Fig. 6

Regulatory network predictions of transcription factor A: Transcription factor regulatory predictions for different 水平gene sets (correlation>0.7, Padj≤0.05 and “level” is abbreviated as “L”); B: Types and proportions of transcription factors in regulatory networks; C: log2 FC (SO2 vs CK) values for TFs"

Fig. 7

Regulatory network of key transcription factor Rectangles represent transcription factors and circles represent targeted genes, and the larger the circle size is, the stronger the correlation is with the expression of corresponding transcription factors A: WRKY40 transcription factor regulatory network; B: ERF2 transcription factor regulatory network; C: MYB60 transcription factor regulatory network"

Fig. 8

Identification of key genes by qRT-PCR and correlation analysis with RNA-seq A: qRT-PCR of key genes, B: Correlation analysis of qRT-PCR with RNA-seq"

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