Discovery of Relevant Response in Infected Potato Plants from Time Series of Gene Expression Data

Dragan Gamberger,Dragana Miljkovic,Kristina Gruden,Nada Lavrač,Tjaša Stare

doi:10.3390/make1010023

Abstract

The paper presents a methodology for analyzing time series of gene expression data collected from the leaves of potato virus Y (PVY) infected and non-infected potato plants, with the aim to identify significant differences between the two sets of potato plants’ characteristic for various time points. We aim at identifying differentially-expressed genes whose expression values are statistically significantly different in the set of PVY infected potato plants compared to non-infected plants, and which demonstrate also statistically significant changes of expression values of genes of PVY infected potato plants in time. The novelty of the approach includes stratified data randomization used in estimating the statistical properties of gene expression of the samples in the control set of non-infected potato plants. A novel estimate that computes the relative minimal distance between the samples has been defined that enables reliable identification of the differences between the target and control datasets when these sets are small. The relevance of the outcomes is demonstrated by visualizing the relative minimal distance of gene expression changes in time for three different types of potato leaves for the genes that have been identified as relevant by the proposed methodology.

Highlights

Potato (Solanum tuberosum L.) is the most widely grown tuber crop in the world, and the fourth largest food crop in terms of fresh produce, after rice, wheat, and tomato
We aim at identifying differentially-expressed genes whose expression values are statistically significantly different in the set of potato virus Y (PVY) infected potato plants compared to non-infected plants, and which demonstrate statistically significant changes of expression values of genes of PVY infected potato plants in time
This paper proposes a methodology aimed at systematic identification of genes that have statistically significant differences of gene expression values between the PVY infected samples and the non-infected samples at various time points of the recorded time series data

Summary

Introduction

Potato (Solanum tuberosum L.) is the most widely grown tuber crop in the world, and the fourth largest food crop in terms of fresh produce, after rice, wheat, and tomato. Salicylic acid (SA) has shown to mediate resistance in many compatible plant-virus interactions and its deficiency leads to impairment of the defense responses and increased susceptibility to pathogen attacks [6,7]. We performed a time series analysis of defense responses in compatible potato-PVYNTN interaction using the tolerant cultivar Désirée [4]. The SA-deficient transgenic NahG-Désirée showed a greater susceptibility to PVYNTN. The appearance of the symptoms in NahG-Désirée corresponded to the first detection of viral multiplication at 4 dpi [4]. The dynamics of whole transcriptome changes of cultivar Désirée and NahG-Désirée was analysed in inoculated and systemically infected leaves following 0, 1, 3, 4, 5, and 7 dpi

Methods

Results

Conclusion