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Open Access Highly Accessed Research article

Insights into organ-specific pathogen defense responses in plants: RNA-seq analysis of potato tuber-Phytophthora infestans interactions

Liangliang Gao1, Zheng Jin Tu2, Benjamin P Millett1 and James M Bradeen1*

Author Affiliations

1 Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA

2 Biomedical Statistics and Informatics Division, Mayo Clinic, Rochester, MN, 55905, USA

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BMC Genomics 2013, 14:340  doi:10.1186/1471-2164-14-340

Published: 23 May 2013

Abstract

Background

The late blight pathogen Phytophthora infestans can attack both potato foliage and tubers. Although interaction transcriptome dynamics between potato foliage and various pathogens have been reported, no transcriptome study has focused specifically upon how potato tubers respond to pathogen infection. When inoculated with P. infestans, tubers of nontransformed ‘Russet Burbank’ (WT) potato develop late blight disease while those of transgenic ‘Russet Burbank’ line SP2211 (+RB), which expresses the potato late blight resistance gene RB (Rpi-blb1), do not. We compared transcriptome responses to P. infestans inoculation in tubers of these two lines.

Results

We demonstrated the practicality of RNA-seq to study tetraploid potato and present the first RNA-seq study of potato tuber diseases. A total of 483 million paired end Illumina RNA-seq reads were generated, representing the transcription of around 30,000 potato genes. Differentially expressed genes, gene groups and ontology bins that exhibited differences between the WT and +RB lines were identified. P. infestans transcripts, including those of known effectors, were also identified.

Conclusion

Faster and stronger activation of defense related genes, gene groups and ontology bins correlate with successful tuber resistance against P. infestans. Our results suggest that the hypersensitive response is likely a general form of resistance against the hemibiotrophic P. infestans—even in potato tubers, organs that develop below ground.

Keywords:
Solanum tuberosum; Next-generation sequencing (NGS); RNA-seq; Phytophthora infestans; FPKM (fragments per kilobase of exon per million mapped reads); JA (jasmonic acid); SA (salicylic acid); ET (Ethylene); qRT-PCR