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

RichHTML

33

PDF

93

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"

[1] 于可可, 杨英军, 郭大龙, 刘海楠, 裴茂松, 韦同路, 边璐, 余义和. 葡萄VlCKX8基因克隆与植物生长调节剂响应分析. 植物生理学报, 2021, 57(1): 85-93. doi: 10.13592/j.cnki.ppj.2020.0427.
doi: 10.13592/j.cnki.ppj.2020.0427
YU K K, YANG Y J, GUO D L, LIU H N, PEI M S, WEI T L, BIAN L, YU Y H. Cloning and plant growth regulator response analysis of Vl CKX8 in grape. Plant Physiology Journal, 2021, 57(1): 85-93. doi: 10.13592/j.cnki.ppj.2020.0427. (in Chinese)
doi: 10.13592/j.cnki.ppj.2020.0427
[2] GUO D L, XI F F, YU Y H, ZHANG X Y, ZHANG G H, ZHONG G Y. Comparative RNA-Seq profiling of berry development between table grape ‘Kyoho’ and its early-ripening mutant ‘Fengzao’. BMC Genomics, 2016, 17(1): 795. doi: 10.1186/s12864-016-3051-1.
doi: 10.1186/s12864-016-3051-1
[3] FRANCK J, LATORRE B A, TORRES R, ZOFFOLI J P. The effect of preharvest fungicide and postharvest sulfur dioxide use on postharvest decay of table grapes caused by Penicillium expansum. Postharvest Biology and Technology, 2005, 37(1): 20-30.
doi: 10.1016/j.postharvbio.2005.02.011
[4] GABLER F M, MERCIER J, JIMÉNEZ J I, SMILANICK J L. Integration of continuous biofumigation with Muscodor albus with pre-cooling fumigation with ozone or sulfur dioxide to control postharvest gray mold of table grapes. Postharvest Biology and Technology, 2009, 55(2): 78-84.
doi: 10.1016/j.postharvbio.2009.07.012
[5] ZUTAHY Y, LICHTER A, KAPLUNOV T, LURIE S. Extended storage of ‘Red Globe’ grapes in modified SO2 generating pads. Postharvest Biology and Technology, 2008, 50(1): 12-17.
doi: 10.1016/j.postharvbio.2008.03.006
[6] CHEN R C, WU P W, CAO D Y, TIAN H Q, CHEN C K, ZHU B Z. Edible coatings inhibit the postharvest berry abscission of table grapes caused by sulfur dioxide during storage. Postharvest Biology and Technology, 2019, 152: 1-8.
doi: 10.1016/j.postharvbio.2019.02.012
[7] ZHAO W, BALDWIN E A, BAI J H, PLOTTO A, IREY M. Comparative analysis of the transcriptomes of the calyx abscission zone of sweet orange insights into the Huanglongbing-associated fruit abscission. Horticulture Research, 2019, 6: 71. doi: 10.1038/s41438-019-0152-4.
doi: 10.1038/s41438-019-0152-4
[8] PATHARKAR O R, WALKER J C. Advances in abscission signaling. Journal of Experimental Botany, 2018, 69(4): 733-740. doi: 10.1093/jxb/erx256.
doi: 10.1093/jxb/erx256
[9] ZHAO M L, LI C Q, MA X S, XIA R, CHEN J Y, LIU X C, YING P Y, PENG M J, WANG J, SHI C L, LI J G. KNOX protein KNAT1 regulates fruitlet abscission in litchi by repressing ethylene biosynthetic genes. Journal of Experimental Botany, 2020, 71(14): 4069-4082. doi: 10.1093/jxb/eraa162.
doi: 10.1093/jxb/eraa162
[10] ESTORNELL L H, AGUSTÍ J, MERELO P, TALÓN M, TADEO F R. Elucidating mechanisms underlying organ abscission. Plant Science, 2013, 199/200: 48-60. doi: 10.1016/j.plantsci.2012.10.008.
doi: 10.1016/j.plantsci.2012.10.008
[11] PATTERSON S E, BLEECKER A B. Ethylene-dependent and -independent processes associated with floral organ abscission in Arabidopsis. Plant Physiology, 2004, 134(1): 194-203.
doi: 10.1104/pp.103.028027
[12] BOTTON A, RUPERTI B. The yes and no of the ethylene involvement in abscission. Plants, 2019, 8(6): 187.
doi: 10.3390/plants8060187
[13] LIU D M, LI J N, LI Z W, PEI Y X. Hydrogen sulfide inhibits ethylene-induced petiole abscission in tomato (Solanum lycopersicum L.). Horticulture Research, 2020, 7: 14. doi: 10.1038/s41438-019- 0237-0.
doi: 10.1038/s41438-019- 0237-0
[14] KUANG J F, WU J Y, ZHONG H Y, LI C Q, CHEN J Y, LU W J, LI J G. Carbohydrate stress affecting fruitlet abscission and expression of genes related to auxin signal transduction pathway in litchi. International Journal of Molecular Sciences, 2012, 13(12): 16084-16103. doi: 10.3390/ijms131216084.
doi: 10.3390/ijms131216084
[15] LI C Q, ZHAO M L, MA X S, WEN Z X, YING P Y, PENG M J, NING X P, XIA R, WU H, LI J G. The HD-Zip transcription factor LcHB2 regulates litchi fruit abscission through the activation of two cellulase genes. Journal of Experimental Botany, 2019, 70(19): 5189-5203. doi: 10.1093/jxb/erz276.
doi: 10.1093/jxb/erz276
[16] WU P W, XIN F Y, XU H J L, CHU Y Y, Du Y L, TIAN H Q, ZHU B Z. Chitosan inhibits postharvest berry abscission of ‘Kyoho’ table grapes by affecting the structure of abscission zone, cell wall degrading enzymes and SO2 permeation. Postharvest Biology and Technology, 2021, 176: 111507.
doi: 10.1016/j.postharvbio.2021.111507
[17] CHANG Y M, LIN H H, LIU W Y, YU C P, CHEN H J, WARTINI P P, KAO Y Y, WU Y H, LIN J J, LU M Y J, TU S L, WU S H, SHIU S H, KU M S B, LI W H. Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes. PNAS, 2019, 116(8): 3091-3099. doi: 10.1073/pnas.1817621116.
doi: 10.1073/pnas.1817621116
[18] CHEN C J, CHEN H, ZHANG Y, THOMAS H R, FRANK M H, HE Y H, XIA R. TBtools: An integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 2020, 13(8): 1194-1202. doi: 10.1016/j.molp.2020.06.009.
doi: 10.1016/j.molp.2020.06.009
[19] KUANG J F, WU C J, GUO Y F, WALTHER D, SHAN W, CHEN J Y, CHEN L, LU W J. Deciphering transcriptional regulators of banana fruit ripening by regulatory network analysis. Plant Biotechnology Journal, 2021, 19(3): 477-489. doi: 10.1111/pbi.13477.
doi: 10.1111/pbi.13477
[20] NI P Y, JI X R, GUO D L. Genome-wide identification, characterization, and expression analysis of GDSL-type esterases/ lipases gene family in relation to grape berry ripening. Scientia Horticulturae, 2020, 264: 109162.
doi: 10.1016/j.scienta.2019.109162
[21] 房经贵, 朱旭东, 贾海锋, 王晨. 植物蔗糖合酶生理功能研究进展. 南京农业大学学报, 2017, 40(5): 759-768.
FANG J G, ZHU X D, JIA H F, WANG C. Research advances on physiological function of plant sucrose synthase. Journal of Nanjing Agricultural University, 2017, 40(5): 759-768. (in Chinese)
[22] YI J W, WANG Yi, MA X S, ZHANG J Q, ZHAO M L, HUANG X M, LI J G, HU G B, WANG H C. LcERF2 modulates cell wall metabolism by directly targeting a UDP-glucose-4-epimerase gene to regulate pedicel development and fruit abscission of litchi. The Plant Journal, 2021, 106(3): 801-816.
doi: 10.1111/tpj.15201
[23] CHEZEM W R, MEMON A, LI F S, WENG J K, CLAY N K. SG2-type R2R3-MYB transcription factor MYB15 controls defense-induced lignification and basal immunity in Arabidopsis. The Plant Cell, 2017, 29(8): 1907-1926. doi: 10.1105/tpc.16.00954.
doi: 10.1105/tpc.16.00954
[24] JIANG Y J, LIANG G, YANG S Z, YU D Q. Arabidopsis WRKY57 functions as a node of convergence for jasmonic acid- and auxin- mediated signaling in jasmonic acid-induced leaf senescence. The Plant Cell, 2014, 26(1): 230-245. doi: 10.1105/tpc.113.117838.
doi: 10.1105/tpc.113.117838
[25] 陈清帅. 拟南芥糖信号快速响应的机理研究[D]. 泰安: 山东农业大学, 2019.
CHEN Q S. Studies on mechanism of the rapid response to sugar signal in Arabidopsis thaliana[D]. Tai’an: Shandong Agricultural University, 2019. (in Chinese)
[26] KUBO H, HAYASHI K. Characterization of root cells of anl2 mutant in Arabidopsis thaliana. Plant Science, 2011, 180(5): 679-685.
doi: 10.1016/j.plantsci.2011.01.012
[27] RUSCONI F, SIMEONI F, FRANCIA P, COMINELLI E, CONTI L, RIBONI M, SIMONI L, MARTIN C R, TONELLI C, GALBIATI M. The Arabidopsis thaliana MYB60 promoter provides a tool for the spatio-temporal control of gene expression in stomatal guard cells. Journal of Experimental Botany, 2013, 64(11): 3361-3371. doi: 10.1093/jxb/ert180.
doi: 10.1093/jxb/ert180
[28] LECHNER E, LEONHARDT N, EISLER H, PARMENTIER Y, ALIOUA M, JACQUET H, LEUNG J, GENSCHIK P. MATH/BTB CRL 3 receptors target the homeodomain-leucine zipper ATHB6 to modulate abscisic acid signaling. Developmental Cell, 2011, 21(6): 1116-1128. doi: 10.1016/j.devcel.2011.10.018.
doi: 10.1016/j.devcel.2011.10.018
[29] 赵洪梅, 安利佳, 马有会. 同源域-亮氨酸拉链蛋白ATHB6的研究进展. 中国农学通报, 2006, 22(8): 77-82. doi: 10.3969/j.issn.1000-6850.2006.08.020.
doi: 10.3969/j.issn.1000-6850.2006.08.020
ZHAO H M, AN L J, MA Y H. The progress of HD-zip ATHB6. Chinese Agricultural Science Bulletin, 2006, 22(8): 77-82. doi: 10.3969/j.issn.1000-6850.2006.08.020. (in Chinese)
doi: 10.3969/j.issn.1000-6850.2006.08.020
[30] WANG L, QIU T Q, YUN J R, GUO N N, HE Y J, HAN X P, WANG Q Y, JIA P F, WANG H D, LI M Z, WANG C, WANG X L. Arabidopsis ADF1 Regulated by MYB73 is involved in response to salt stress via affecting actin filaments organization. Plant & cell physiology, 2021, 62(9): 1387-1395.
[1] ZHANG KeKun,CHEN KeQin,LI WanPing,QIAO HaoRong,ZHANG JunXia,LIU FengZhi,FANG YuLin,WANG HaiBo. Effects of Irrigation Amount on Berry Development and Aroma Components Accumulation of Shine Muscat Grape in Root-Restricted Cultivation [J]. Scientia Agricultura Sinica, 2023, 56(1): 129-143.
[2] LI XuFei,YANG ShengDi,LI SongQi,LIU HaiNan,PEI MaoSong,WEI TongLu,GUO DaLong,YU YiHe. Analysis of VlCKX4 Expression Characteristics and Prediction of Transcriptional Regulation in Grape [J]. Scientia Agricultura Sinica, 2023, 56(1): 144-155.
[3] LÜ XinNing,WANG Yue,JIA RunPu,WANG ShengNan,YAO YuXin. Effects of Melatonin Treatment on Quality of Stored Shine Muscat Grapes Under Different Storage Temperatures [J]. Scientia Agricultura Sinica, 2022, 55(7): 1411-1422.
[4] SONG SongQuan,LIU Jun,TANG CuiFang,CHENG HongYan,WANG WeiQing,ZHANG Qi,ZHANG WenHu,GAO JiaDong. Research Progress on the Physiology and Its Molecular Mechanism of Seed Desiccation Tolerance [J]. Scientia Agricultura Sinica, 2022, 55(6): 1047-1063.
[5] GUO ZeXi,SUN DaYun,QU JunJie,PAN FengYing,LIU LuLu,YIN Ling. The Role of Chalcone Synthase Gene in Grape Resistance to Gray Mold and Downy Mildew [J]. Scientia Agricultura Sinica, 2022, 55(6): 1139-1148.
[6] FANG HaoYuan, YANG Liang, WANG HongZhuang, CAO JinCheng, REN WanPing, WEI ShengJuan, YAN PeiShi. Effects of Cross-Ventilation System on Physiology and Production Performance of Beef Cattle in Summer [J]. Scientia Agricultura Sinica, 2022, 55(5): 1025-1036.
[7] WANG HuiLing, YAN AiLing, SUN Lei, ZHANG GuoJun, WANG XiaoYue, REN JianCheng, XU HaiYing. eQTL Analysis of Key Monoterpene Biosynthesis Genes in Table Grape [J]. Scientia Agricultura Sinica, 2022, 55(5): 977-990.
[8] YOU YuWan,ZHANG Yu,SUN JiaYi,ZHANG Wei. Genome-Wide Identification of NAC Family and Screening of Its Members Related to Prickle Development in Rosa chinensis Old Blush [J]. Scientia Agricultura Sinica, 2022, 55(24): 4895-4911.
[9] ZHANG Jie,JIANG ChangYue,WANG YueJin. Functional Analysis of the Interaction Between Transcription Factors VqWRKY6 and VqbZIP1 in Regulating the Resistance to Powdery Mildew in Chinese Wild Vitis quinquangularis [J]. Scientia Agricultura Sinica, 2022, 55(23): 4626-4639.
[10] WANG Bo,QIN FuQiang,DENG FengYing,LUO HuiGe,CHEN XiangFei,CHENG Guo,BAI Yang,HUANG XiaoYun,HAN JiaYu,CAO XiongJun,BAI XianJin. Difference in Flavonoid Composition and Content Between Summer and Winter Grape Berries of Shine Muscat Under Two-Crop-a-Year Cultivation [J]. Scientia Agricultura Sinica, 2022, 55(22): 4473-4486.
[11] LIU Xin,ZHANG YaHong,YUAN Miao,DANG ShiZhuo,ZHOU Juan. Transcriptome Analysis During Flower Bud Differentiation of Red Globe Grape [J]. Scientia Agricultura Sinica, 2022, 55(20): 4020-4035.
[12] MA YuQuan,WANG XiaoLong,LI YuMei,WANG XiaoDi,LIU FengZhi,WANG HaiBo. Differences in Nutrient Absorption and Utilization of 87-1 Grape Variety Under Different Rootstock Facilities [J]. Scientia Agricultura Sinica, 2022, 55(19): 3822-3830.
[13] PANG HaoWan,FU QianKun,YANG QingQing,ZHANG YuanYuan,FU FengLing,YU HaoQiang. Maize Transcription Factor ZmEREB93 Negatively Regulates Kernel Development [J]. Scientia Agricultura Sinica, 2022, 55(19): 3685-3696.
[14] YaTing JIA,HuiHui HU,YaJun ZHAI,Bing ZHAO,Kun HE,YuShan PAN,GongZheng HU,Li YUAN. Molecular Mechanism of Regulation by H-NS on IncFⅡ Plasmid Transmission of Multi-drug Resistant Chicken Escherichia coli [J]. Scientia Agricultura Sinica, 2022, 55(18): 3675-3684.
[15] ZHANG YunXiu,JIANG Xu,WEI ChunXue,JIANG XueQian,LU DongYu,LONG RuiCai,YANG QingChuan,WANG Zhen,KANG JunMei. The Functional Analysis of High Mobility Group MsHMG-Y Involved in Flowering Regulation in Medicago sativa L. [J]. Scientia Agricultura Sinica, 2022, 55(16): 3082-3092.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备09089781号-30
Copyright 2018 © Editorial office of Scientia Agricultura Sinica
Tel: 86-010-82106279    E-mail: zgnykx@mail.caas.net.cn
Supported by Beijing Magtech Co.Ltd