Genotype-specific suppression of multiple defense pathways in apple root during infection by Pythium ultimum

Authors: Zhu, Yanmin; Shao, Jonathan; ZHOU, ZHE - Chinese Academy Of Agricultural Sciences; Davis, Robert

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/10/2018
Publication Date: 1/1/2019
Citation: Zhu, Y., Shao, J.Y., Zhou, Z., Davis, R.E. 2019. Genotype-specific suppression of multiple defense pathways in apple root during infection by Pythium ultimum. Horticulture Research. 6:10. https://doi.org/10.1038/s41438-018-0087-1.
DOI: https://doi.org/10.1038/s41438-018-0087-1

Interpretive Summary: The behaviors of plant genes, namely their gene expression patterns, are commonly utilized to infer their function for a biological process. To elucidate the global gene expression networks over the biology of interest, the currently available RNA-sequencing based transcriptome analysis is the most powerful tool, which can identify and quantify all expressed genes in a specific tissues type. Illumina Solexa HiSeq-3000 represent one of the most current sequencing platform, which can produce billion of 150 bp paired-end reads to cover each and every expressed gene in a tissue. To uncover the mechanisms of apple roots responding to infection from soilborne necrotrophic pathogens, comparative transcriptome analyses were performed on two apple rootstock genotypes, the susceptible B.9 and the resistant G.935. to P. ultimum infection. Analysis of the obtained mega dataset revealed the distinct patterns of genotype-specific molecular defense activation during the early pathogenesis at 24, 48 and 72 hpi (hour post inoculation). Differentially expressed genes (DEGs) were identified by comparing the same genes expressed between mock inoculated and P. ultimum infected tissues. Our results clearly demonstrated that the susceptible genotype B.9 exhibited the more dramatically disturbed transcriptomes and systematic suppression of many cellular processes in its root tissues, especially at 48 hpi. In contrast, G.935 roots showed the less-disturbed transcriptomes under the attack from the same pathogen. Sharp differences were observed at the intensity and number of genes functioning at multiple phases of defense activation between these two genotypes. DEGs with annotated functions including kinase receptors, MAPK signaling, Jasmonate biosynthesis enzymes, defense related transcription factor, transporters were readily induced at 24 dpi and with continuing up-regulation at 48 hpi in G.935 roots; in contrast, delayed and interrupted induction of these genes occurred in B.9 roots under the pathogenic pressure. These identified DEGs constitute a valuable resource for hypothesis-driven studies to validate the roles of these candidate genes conferring resistance/tolerance to infection by P. ultimum in apple roots.

Technical Abstract: Background: Global transcriptional networks regulating defense responses in roots of tree crops to soilborne necrotrophic pathogens are poorly elucidated. Contrasting resistance responses between susceptible B.9 and resistant G.935 were observed for their overall survival rates and necrotic progression patterns to P. ultimum infection. To identify the mechanism underlying their resistance responses, a synchronized micropropagation procedure was applied to generate comparable apple plants for both genotypes and simultaneous inoculation procedure. Comparative transcriptomic analyses were carried out to unravel the genotype-specific regulation patterns of molecular defense activation during the early pathogenesis at 24, 48 and 72 hpi (hour post inoculation). Results: A total of 426,001,826 paired-end reads of 150 bp were generated by Illumina Solexa HiSeq 3000 platform per genotype/treatment/timepoint with three biological replicates. Differentially expressed genes (DEGs) were identified by mapping the reads to 95332 gene models from apple draft genome sequences v3.01a. The more dramatically disturbed transcriptomes in the root of a susceptible genotype B.9 were reflected by overrepresented downregulated DEGs and systematic suppression of many cellular processes, especially at 48 hpi. In contrast, most DEGs were up-regulated from the less-disturbed transcriptome of G.935 roots. DEGs with annotated functions including kinase receptors, MAPK signaling, JA biosynthesis enzymes, TFs, transporters were readily induced at 24 dpi and with continuing up-regulation at 48 hpi in G.935 roots; but delayed and interrupted induction of these genes occurred in B.9 roots. The data demonstrated that an earlier and stronger defense activation is directly associated with the effective deterrence of necrosis progression in the resistant G.935 roots. Lack of effector triggered immunity or existence of a susceptibility gene in B.9 roots could contribute to the severely disturbed transcriptome and ineffective defense activation. Conclusions: Genotype-specific suppression of multiple defense pathways at 48 hpi likely determine the outcome of interactions between apple roots and invading P. ultimum. The identified DEGs constitute a valuable resource for hypothesis-driven studies to validate the candidate genes and elucidate the resistance/tolerance mechanisms in apple roots to infection by P. ultimum.