Articles
Transcriptome analysis uncovers the genes regulating the apple rootstock response to Phytophthora cactorum
Article number
1439_64
Pages
483 – 490
Language
English
Abstract
Phytophthora cactorum is a polyphagous oomycetal pathogen infecting many host plant species.
It is the principal agent of root rot in the strawberry and collar rot in the apple trunk, causing inhibition of plant growth and root system development.
The motile zoospores are spread through water in soil between the root system of plants, but also through splashing rainfall water on the above ground parts of plants.
Within the research carried out at The National Institute of Horticultural Research (InHort) in Skierniewice, Poland, apple rootstocks M.9, PJ-173/2012, PJ-191/2016, P 59 and P 60 were inoculated with zoospores of P. cactorum. To confirm the effectiveness of inoculation, bait tests were done, for selective detection of the active fungal spore presence in the substrate in which plants were grown.
The presence of the pathogen was confirmed for PJ-173/2012 rootstock.
From infected and control plants of PJ-173/2012 root samples were collected for total RNA isolation addressed for the comparative Next Generation Sequencing analysis.
Apple transcriptome sequencing was performed for both the control and the infected samples.
A total of 34 478 raw reads were obtained and mapped on the reference genome of the cultivar ‘Golden Delicious’. After normalizing the raw data, differentially expressed genes (DEGs) comprising 9 335 upregulated and 9 342 downregulated were identified by comparison assessment of infected and control samples.
Functional Gene Ontology enrichment analysis, allowed to assign the DEG’s into three main functional groups: biological processes (7 681); cellular components (2 724) and molecular function (4 938). Mapping of DEGs confirmed the largest number of genes in the endoplasmic reticulum protein processing pathway (mdm4141). Three of the selected genes, i.e.: BiP, HsP70 (involved in ubiquitin ligase complex formation) and sHSF, were subjected for verification analysis (qRT-PCR) to assess their suitability as candidates for early selection of plants infected by P. cactorum.
It is the principal agent of root rot in the strawberry and collar rot in the apple trunk, causing inhibition of plant growth and root system development.
The motile zoospores are spread through water in soil between the root system of plants, but also through splashing rainfall water on the above ground parts of plants.
Within the research carried out at The National Institute of Horticultural Research (InHort) in Skierniewice, Poland, apple rootstocks M.9, PJ-173/2012, PJ-191/2016, P 59 and P 60 were inoculated with zoospores of P. cactorum. To confirm the effectiveness of inoculation, bait tests were done, for selective detection of the active fungal spore presence in the substrate in which plants were grown.
The presence of the pathogen was confirmed for PJ-173/2012 rootstock.
From infected and control plants of PJ-173/2012 root samples were collected for total RNA isolation addressed for the comparative Next Generation Sequencing analysis.
Apple transcriptome sequencing was performed for both the control and the infected samples.
A total of 34 478 raw reads were obtained and mapped on the reference genome of the cultivar ‘Golden Delicious’. After normalizing the raw data, differentially expressed genes (DEGs) comprising 9 335 upregulated and 9 342 downregulated were identified by comparison assessment of infected and control samples.
Functional Gene Ontology enrichment analysis, allowed to assign the DEG’s into three main functional groups: biological processes (7 681); cellular components (2 724) and molecular function (4 938). Mapping of DEGs confirmed the largest number of genes in the endoplasmic reticulum protein processing pathway (mdm4141). Three of the selected genes, i.e.: BiP, HsP70 (involved in ubiquitin ligase complex formation) and sHSF, were subjected for verification analysis (qRT-PCR) to assess their suitability as candidates for early selection of plants infected by P. cactorum.
Authors
S. Keller-Przybyłkowicz, M.A. Lewandowski, A. Walencik, K. Strojny, M. Michalecka
Keywords
differentially expressed genes, GO enrichment
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