Comparative Transcriptome Analysis of Phytophthora blight Resistance of Pepper at Seedling Stage

doi:10.7668/hbnxb.201751450

Abstract

Abstract: The objective of this study was to study the molecular mechanism of pepper phytophthora blight and to explore the functional genes related to phytophthora blight resistance. Based on the identification of phytophthora blight resistance in 114 natural populations of pepper, one resistant material and three susceptible materials were selected as materials to perform high-throughput transcriptome sequencing by means of Illumina RNA-seq sequencing platform. The clean reads were selected to map the reference sequences of Pepper_Zunla_1_Ref_v1.0. The results showed that 78.95%-85.11% clean reads could be matched to unique genome locus. The gene expression level was calculated using RPKM method. The false discovery rate ≤ 0.001 and the absolute value of|log₂ Ratio| ≥ 1 were used as the threshold to judge the significance of gene expression differences. Finally, the functions and pathways of differentially expressed genes(DEGs) were annotated by comparing them with the Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG). According to the top 10 GO classification, the main functions included the oxidoreductase activity, carboxylolyase activity, peroxidase activity, metabolic process and adverse reaction etc. Among them, 117 DEGs could be classified into the KEGG pathway, including 25 up-regulated DEGs and 92 down-regulated DEG. These pathways were associated with the ubiquitin-mediated proteolysis, oxidative phosphorylation, plant hormone signaling, phospholipase D signaling, and phosphatidylinoinositol signaling systems. The disease resistance of pepper was mainly related to enzymatic activity, stress response, protein metabolism pathway, plant hormones and other regulations. It was found that the disease resistance of pepper was a highly complex process, which was composed of multiple cross channel regulation, including metabolic processes, defense responses and hormone regulation, etc. The results laid the foundation for further studying the molecular mechanism of pepper disease resistance.

Key words: Pepper, Phytophthora blight, Transcriptome, Differentially expressed genes, Function

CLC Number:

S641.3

LEI Yang, CHENG Yan, QIAO Ning, JIAO Yansheng, MIAO Ruyi, YANG Yuhua. Comparative Transcriptome Analysis of Phytophthora blight Resistance of Pepper at Seedling Stage[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2019, 34(3): 194-202. doi: 10.7668/hbnxb.201751450.

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References

[1] Zhang Y L,Jia Q L,Li D W,Wang J E,Yin Y X,Gong Z H. Characteristic of the pepper CaRGA2 gene in defense responses against Phytophthora capsici Leonian[J]. International Journal of Molecular Sciences,2013,14:8985-9004.doi:10.3390/ijms14058985.
[2] Naegele R P,Ashrafi H,Hill T A,Chinwo S R,Van Deynze A E, Hausbeck M K. QTL mapping of fruit rot resistance to the plant pathogen Phytophthora capsici in a recombinant inbred line Capsicum annuum population[J]. Phytopathology,2014,104(5):479-83.doi:10.1094/PHYTO-05-13-0143-R.
[3] Ristiano J B,Johnston S A. Ecologically based approaches to management of Phytophthora blight on bell pepper[J]. Plant Disease,1999,83:1080-1089.doi:10.1094/PDIS.1999.83.12.1080.
[4] 杨学辉,肖崇刚,袁洁. 贵州辣椒疫病病原鉴定及生物学特性研究[J]. 西南大学学报(自然科学版),2004,26(4):413-416.doi:10.3969/j.issn.1673-9868.2004.04.010.
Yang X H,Xiao C G,Yuan J. Studies on identification of Phytophthora capsici in guizhou province and on its biological characteristics[J]. Journal of Southwest Agricultural University(Natural Science),2004,26(4):413-416.
[5] 冯宝珍. 辣椒疫霉(Phytophthora capsici) 诱导坏死蛋白基因克隆及功能研究[D]. 泰安:山东农业大学,2011.doi:10.7666/d.d143924.
Feng B Z. Cloning and functional analysis of NPP(Necrosis Phytophythora Protein) genes from Phytophthora capsici[D]. Taian:Shandong Agricultural University,2011
[6] Lamour K H,Mudge J,Gobena D,Hurtadogonzales O P,Schmutz J,Kuo A,Miller N A,Rice B J,Raffaele S,Cano L M. Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici[J]. Molecular Plant-microbe Interactions,2012,25:1350.doi:10.1094/MPMI-02-12-0028-R.
[7] Chen L,Ning M,Wang P Y,Nan F,Shen H L. Transcriptome sequencing and De Novo analysis of a cytoplasmic male sterile line and its Near-isogenic restorer line in Chili Pepper(Capsicum annuum L.) [J]. PLoS One,2013,8:e65209.doi:10.1371/journal.pone.0065209.
[8] 刘峰,谢玲玲,弭宝彬,欧阳娴,茆振川,谢丙炎. 辣椒转录组SNP挖掘及多态性分析[J]. 园艺学报,2014,41(2):343-348.doi:10.3969/j.issn.0513-353X.2014.02.016.
Liu F,Xie L L,Mi B B,Ouyang X,Mao Z C,Xie B Y. SNP Mining in pepper transeriptome and the polymorphism analysis[J]. Acta Horticulturae Sinica,2014,41(2):343-348.
[9] Wang P,Wang L,Guo J,Yang W,Shen H. Molecular mapping of a gene conferring resistance to Phytophthora capsici Leonian race 2 in pepper line PI201234(Capsicum annuum L.) [J]. Molecular Breeding,2016,36(6):66.doi:10.1007/s11032-016-0464-0.
[10] Kim H J,Nahm S H,Lee H R,Yoon G B,Kim K T,Kang B C,Choi D,Kweon O Y,Cho M C,Kwon J K. BAC-derived markers converted from RFLP linked to Phytophthora capsici resistance in pepper(Capsicum annuum L.) [J]. Theoretical and Applied Genetics,2008,118:15.doi:10.1007/s00122-008-0873-5.
[11] Sy O,Steiner R,Bosland P W. Recombinant inbred line differential identifies race-specific resistance to phytophthora root rot in Capsicum annuum[J]. Phytopathology,2008,98:867-870.doi:10.1094/PHYTO-98-8-0867.
[12] Lee Y K,Hippe-Sanwald S,Jung H W,Hong J K,Hause B,Hwang B K. In situ localization of chitinase mRNA and protein in compatible and incompatible interactions of pepper stems with Phytophthora capsic[J]. Protoplasma,2000,211:64-75.doi:10.1007/BF01279900.
[13] Cheng C M,Palloix A,Lefebvre V. Isolation,mapping and characterization of allelic polymorphism of Chi3-P1,a class Ⅲ chitinase of Capsicum annuum L[J]. Plant Science,2002,163:481-489.doi:10.1016/S0168-9452(02) 00151-6.
[14] Yoo T H,Park C J,Ham B K,Kim K J,Paek K H. Ornithine decarboxylase gene(CaODC1) is specifically induced during TMV-mediated but salicylate-independent resistant response in hot pepper[J]. Plant and Cell Physiology,2004,45:1537-1542.doi:10.1093/pcp/pch176.
[15] Wang J E,Li D W,Gong Z H,Zhang Y L. Optimization of virus-induced gene silencing in pepper(Capsicum annuum L.) [J]. Genetics and Molecular Research,2013,12:2492-2506.doi:10.4238/2013.July.24.4.
[16] Orłowska E,Fiil A,Kirk H G,Llorente B,Cvitanich C. Differential gene induction in resistant and susceptible potato cultivars at early stages of infection by Phytophthora infestans[J]. Plant Cell Reports,2012,31(1):187-203.doi:10.1007/s00299-011-1155-2.
[17] Yogendra K N,Kumar A,Sarkar K,Li Y,Pushpa D,Mosa K A,Duggavathi R,Kushalappa A C. Transcription factor StWRKY1 regulates phenylpropanoid metabolites conferring late blight resistance in potato[J]. Journal of Experimental Botany,2015,66:7377-7389.doi:10.1093/jxb/erv434.
[18] Studham M E,Macintosh G C. Phytohormone signaling pathway analysis method for comparing hormone responses in plant-pest interactions[J]. BMC Research Notes,2012,5:1-7.doi:10. 1186/1756-0500-5-392.
[19] Wang B,Liu J,Tian Z,Song B,Xie C. Monitoring the expression patterns of potato genes associated with quantitative resistance to late blight during Phytophthora infestans infection using cDNA microarrays[J]. Plant Science,2005,169:1155-1167.doi:10.1016/j.plantsci.2005.07.020.
[20] Alcázar M D,Egea C,Espín A,Candela M E. Peroxidase isoenzymes in the defense response of Capsicum annuum to Phytophthora capsici[J]. Physiologia Plantarum,2010,94:736-742.doi:10.1111/j.1399-3054.1995.tb00992.x.
[21] Mozzetti C,Ferraris L,Tamietti G,Matta A. Variation in enzyme activities in leaves and cell suspension as markers of incompatibility in different Phytophthora-pepper interactions[J]. Physiological and Molecular Plant Pathology,1995,46:95-107.doi:10.1051/litt/201113003.
[22] Nú n ez-Pastrana R,Arcos-Ortega G F,Souza-Perera R A,Sánchez-Borges C A,Nakazawa-Ueji Y E,Guzmán-Antonio A A,Zúñiga-Aguilar J J. Ethylene,but not salicylic acid or methyl jasmonate,induces a resistance response against Phytophthora capsici in Habanero pepper[J]. European Journal of Plant Pathology,2011,131:669-683.doi:10.1007/s10658-011-9841-z.
[23] Kang D S, Min K J, Kwak A M, Lee S Y, Kang H W. Defense response and suppression of Phytophthora blight disease of pepper by water extract from spent mushroom substrate of Lentinula edodes[J]. The Plant Pathology Journal, 2017, 33(3):264-275.doi:10.5423/ppj.oa.02.2017.0030.
[24] Rookes J E,Wright M L,Cahill D M. Elucidation of defence responses and signalling pathways induced in Arabidopsis thaliana following challenge with Phytophthora cinnamomi[J]. Physiological and Molecular Plant Pathology,2008,72:151-161.doi:10.1016/j.pmpp.2008.08.005.
[25] Ueeda M,Kubota M,Nishi K. Contribution of jasmonic acid to resistance against Phytophthora blight in Capsicum annuum cv. SCM334[J]. Physiological and Molecular Plant Pathology,2005,67:149-154.doi:10.1016/j.pmpp.2005.12.002.
[26] Maksimov I V,Sorokan' A V,Chereoanova E A,Surina O B,Troshina N B,Yarullina L G. Effects of salicylic and jasmonic acids on the components of pro/antioxidant system in potato plants infected with late blight[J]. Russian Journal of Plant Physiology,2011,58(2):299-306.doi:10.1134/s1021443711010109.
[27] Boevink P C,Wang X,Hazel M L,He Q,Shaista N,Armstrong M R,Zhang W,Ingo H,Gilroy E M,Tian Z. A Phytophthora infestans RXLR effector targets plant PP1c isoforms that promote late blight disease[J]. Nature Communications,2016,7:10311.doi:10.1038/ncomms10311.
[28] 王妮妍,蒋德安. 茉莉酸及其甲酯与植物诱导抗病性[J]. 植物生理学报,2002,38:279-284.doi:10.13592/j.cnki.ppj.2002.03.033.
Wang N Y,Jiang D A. The role of Jasmonic acid and methyl jasmonate in plant induced disease resistance[J]. Plant Physiology Journal,2002,38:279-284.
[29] Birch P R,Armstrong M,Bos J,Boevink P,Gilroy E M,Taylor R M,Wawra S,Pritchard L,Conti L,Ewan R. Towards understanding the virulence functions of RXLR effectors of the oomycete plant pathogen Phytophthora infestans[J]. Journal of Experimental Botany,2009,60:1133.doi:10.1093/jxb/ern353.
[30] Balaji V,Sessa G,Smart C D. Silencing of host basal defense response-related gene expression increases susceptibility of Nicotiana benthamiana to Clavibacter michiganensis subsp. michiganensis[J]. Phytopathology,2011,101:349-357.doi:10.1094/PHYTO-05-10-0132.
[31] 胡婷丽,李魏,刘雄伦,戴良英. 泛素化在植物抗病中的作用[J]. 微生物学通报,2014,41:1175-1179.doi:10.13344/j.microbiol.china.140148.
Hu T L,Li W,Liu Xi L,Dai L Y. The role of ubiquitination in plant disease resistance[J]. Microbiology China,2014,41:1175-1179.
[32] Vierstra R D. The ubiquitin-26S proteasome system at the nexus of plant biology[J]. Nature Reviews Molecular Cell Biology,2009,10(6):385-397.doi:10.1038/nrm2688.
[33] Spoel S H,Mou Z,Tada Y. Proteasome-mediated turnover of the transcription coactivator NPR1 plays dual roles in regulating plant immunity[J]. Cell,2009,137(5):860-872.doi:10.1016/j.cell.2009.03.038.
[34] Backer R,Mahomed W,Reeksting B J,Engelbrecht J,Ibarralaclette E,Berg N V D. Phylogenetic and expression analysis of the NPR1-like gene family from Persea americana (Mill.) [J]. Frontiers in Plant Science,2015,6:300.doi:10.3389/fpls.2015.00300.
[35] Liu X Y,Wang J Y,Fan B L,Shang Y T,Sun Y F,Dang C,Xie C J,Wang Z Y,Peng Y K. A coi1 gene in wheat contributes to the early defence response against wheat powdery mildew[J]. Journal of Phytopathology,2018,166(2):116-122.doi:10.1111/jph.12667.
[36] Zhou J,Lu D,Xu G,Finlayson S A,He P,Shan L. The dominant negative arm domain uncovers multiple functions of pub13 in arabidopsis immunity,flowering,and senescence[J]. Journal of Experimental Botany,2015,66(11):3353.doi:10.1093/jxb/erv148.

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