RNA sequencing analysis provides new insights into dynamic molecular responses to Valsa mali pathogenicity in apple ‘Changfu No. 2’
- 31 Downloads
Valsa canker caused by the necrotrophic pathogen Valsa mali (Vm) severely affects apple production in Eastern Asia. The molecular basis underlying the apple response to Vm infection is poorly understood. Hence, we performed RNA sequencing (RNA-seq) to investigate the dynamic gene expression profiles of a major apple cultivar, ‘Changfu No.2’, during Vm infection. Compared with the control (C), 104, 313, and 1059 differentially expressed genes (DEGs) were detected from the phloem tissue within the range of 0.9–1.3 cm (T1), 0.5–0.9 cm (T2), and 0.1–0.5 cm (T3) beyond the lesion periphery, respectively. Gene ontology (GO) enrichment analysis revealed that the DEGs associated with plant growth and development were down-regulated, whereas those related to defense responses were up-regulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that hormonal and Ca2+ signaling and phenylpropanoid biosynthesis were involved in the defense responses. In conclusion, multiple defense responses associated with ABA, JA, ET, Ca2+, and cell wall signals contributed to the defense against Vm infection in ‘Changfu No.2’. In contrast, the DEGs with inhibited expression were involved in plant growth and development; auxin signaling and several resistance genes might weaken the resistance of ‘Changfu No.2’ to pathogens. Our results offer a new insight into plant responses against necrotrophs and could benefit programs aimed at breeding for Vm resistance.
KeywordsValsa canker Apple Hormone Ca2+-signal Defense responses
Cell wall degrading enzymes
Differentially expressed genes
Methyl salicylic acid
Pathogen-associated molecular pattern
Real-time quantitative PCR
Systemic acquired resistance
We would like to thank Ph.D Lijun Bai (GeneBang Inc., Chengdu, China, www.genebang.com) for technical assistance with RNA sequencing and bioinformatic analysis.
ZC and CB conceived, designed, and coordinated the study. ZC, MJ, CM, and DH performed the experiments and collected, analyzed, and deposited the data. CZ proofread the final draft and revised the manuscript. All authors have read and approved the manuscript.
This work was supported by the Talent introduction Project of Gansu Agricultural University (GSAU-RCZX201712) and the Natural Science Foundation of China No. 31501728.
Compliance with ethical standards
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
This article does not contain any studies with human participants performed by any of the authors.
Data Archiving Statement
The raw data has been deposited in the National Center for Biotechnology information (NCBI) Short Read Archive (SPA) under accession number SRP160545.
- Cao K, Guo L, Li B, Sun G, Chen H (2009) Investigations on the occurrence and control of apple canker in China. Plant Prot 35:114–116 (In Chinese)Google Scholar
- Daccord N, Celton JM, Linsmith G, Becker C, Choisne N, Schijlen E, Geest H, Bianco L, Micheletti D, Velasco R, Pierro E, Gouzy J, Rees D, Guérif P, Muranty H, Durel CE, Laurens F, Lespinasse Y, Gaillard S, Aubourg S, Quesneville H, Weigel D, Weg E, Troggio M, Bucher E (2017) High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet 49:1099–1106CrossRefPubMedGoogle Scholar
- Harwood J (2012) Lipids in plants and microbes. Springer Science & Business Media, BerlinGoogle Scholar
- Kepley JB, Jacobi WR (2000) Pathogenicity of Cytospora fungi on six hardwood species. J Arboric 26:326–332Google Scholar
- Kidd BN, Kadoo NY, Dombrecht B, Tekeoglu M, Gardiner DM, Thatcher LF, Aitken E, Schenk P, Manners J, Kazan K (2011) Auxin signaling and transport promote susceptibility to the root-infecting fungal pathogen Fusarium oxysporum in Arabidopsis. Mol Plant Microbe Interact 24:733–748CrossRefPubMedGoogle Scholar
- Magnin-Robert M, Le BD, Markham J, Dorey S, Clément C, Baillieul F, Dhondt-Cordelier S (2015) Modifications of sphingolipid content affect tolerance to hemibiotrophic and necrotrophic pathogens by modulating plant defense responses in arabidopsis. Plant Physiol 169:2255–2274PubMedPubMedCentralGoogle Scholar
- Sasabe M, Takeuchi K, Kamoun S, Ichinose Y, Govers F, Toyoda K, Shiraishi T, Yamada T (2000) Independent pathways leading to apoptotic cell death, oxidative burst and defense gene expression in response to elicitin in tobacco cell suspension culture. FEBS J 267:5005–5013Google Scholar
- Tarazona S, García F, Ferrer A, Dopazo J, Conesa A (2012) Noiseq: a rna-seq differential expression method robust for sequencing depth biases. University of Southampton 17:18Google Scholar
- Tsegaye Y, Richardson CG, Bravo JE, Mulcahy BJ, Lynch DV, Markham JE, Jaworski JG, Chen M, Cahoon EB, Dunn TM (2007) Arabidopsis mutants lacking long chain base phosphate lyase are fumonisin-sensitive and accumulate trihydroxy-18:1 long chain base phosphate. J Biol Chem 282:28195–28206CrossRefPubMedGoogle Scholar
- Tsuda K, Katagiri F, Parker J E, Ellis J G (2010) Comparing signaling mechanisms engaged in patterntriggered and effector-triggered immunity. Curr Opin Plant Biol 13:459-465Google Scholar
- Wei J, Huang L, Gao Z, Ke X, Kang Z (2010) Laboratory evaluation methods of apple Valsa canker disease caused by Valsa ceratosperma sensu Kobayashi. Acta Phytopathologica Sinica 40:14–20 (In Chinese)Google Scholar
- Zuo C, Zhang W, Mao J, Jiang X, Ma Z, Su J, Chen B (2017a) Genome wide identification and expression analysis of LysM receptor like kinase in apple. Acta Horticulturae Sinica 44:733–742 (In Chinese)Google Scholar
- Zuo C, Zhang W, Chen Z, Chen B, Huang Y (2017b) RNA sequencing reveals that endoplasmic reticulum stress and disruption of membrane integrity underlie dimethyl Trisulfide toxicity against Fusarium oxysporum f. sp. cubense tropical race 4. Front Microbiol 8:1365CrossRefPubMedPubMedCentralGoogle Scholar