Identification of genes associated with tolerance to apple canker by genome-wide transcriptome analysis

Abstract

Objective

Neonectria ditissima, the causal agent of fruit tree canker, is one of most destructive diseases of apple trees in producing countries with cool weather. Since it is difficult to control this disease due to the presence of the pathogenic fungus throughout the year, for better understanding of this host–pathogen interaction in order to improve management strategies, a transcriptional analysis of apple gene expression in response to N. ditissima was conducted.

Materials and methods

In the present study, we evaluated transcriptome responses to N. ditissima by selecting the partially resistant cultivar “Jonathan”. The leaf scars of apple trees were artificially inoculated with suspension of N. ditissima and water as control. Then the samples were taken for RNA extraction at three different time points, 5, 15, and 30 days after inoculation. The quality and quantity of the extracted RNA were checked and total RNA was sequenced using Illumina paired-end sequencing and Hiseq2000 sequencer. The quality of the sequence data was done by FastQC software. Then the reads were mapped to apple reference genome by TopHat2 software. Normalization and differential expression analysis of genes were performed with DESeq2. Enrichment analysis of DEGs pathways was done through KEGG software.

Results

Based on GO enrichment and KEGG pathway analyses, it was found that some of the defense response genes were differentially expressed between control and treatment groups. The data provides evidence that apple cultivars inoculated with N. ditissima exhibit significant upregulation of defense-related genes and genes involved in detoxification, peroxidase related reactions, phenylpropanoid metabolism. The highest expression level of genes related to defense was observed 30 days after inoculation. It shows that the pathogen needs time to cause infection and cannot spread quickly in the plant tissue.

Conclusion

Identification of candidate genes involved in pathogenicity of N. ditissima are involved in lignification, detoxification, phosphorylation and pathogen defense. They are a valuable resource in genetic research and allow us to better understand interaction of fungus and the apple defense system, and may assists in apple canker breeding programs.

Keywords

Defense Response; Next-Generation Sequencing (NGS); Malus × Domestica; RNA-Seq

Published in

Journal of agricultural biotechnology
2024, volume: 16, number: 2, pages: 131-152

SLU Authors

• Nybom, Hilde

  • Department of Plant Breeding, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Genetics and Breeding
Botany

Permanent link to this page (URI)

https://res.slu.se/id/publ/139606