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

Abstract

The genotype-specific defense activation in the roots of perennial tree crops to soilborne necrotrophic pathogens remains largely unknown. A recent phenotyping study indicated that the apple rootstock genotypes B.9 and G.935 have contrasting resistance responses to infection by Pythium ultimum. In the current study, a comparative transcriptome analysis by Illumina Solexa HiSeq 3000 platform was carried out to identify the global transcriptional regulation networks between the susceptible B.9 and the resistant G.935 to P. ultimum infection. Thirty-six libraries were sequenced to cover three timepoints after pathogen inoculation, with three biological replicates for each sample. The transcriptomes in the roots of the susceptible genotype B.9 were reflected by overrepresented differentially expressed genes (DEGs) with downregulated patterns and systematic suppression of cellular processes at 48 h post inoculation (hpi). In contrast, DEGs with annotated functions, such as kinase receptors, MAPK signaling, JA biosynthesis enzymes, transcription factors, and transporters, were readily induced at 24 hpi and continued up-regulation at 48 hpi in G.935 roots. The earlier and stronger defense activation is likely associated with an effective inhibition of necrosis progression in G.935 roots. Lack of effector-triggered immunity or existence of a susceptibility gene could contribute to the severely disturbed transcriptome and susceptibility in B.9 roots. The identified DEGs constitute a valuable resource for hypothesis-driven studies to elucidate the resistance/tolerance mechanisms in apple roots and validating their potential association with resistance traits.

Understanding Root Rot Disease in Agricultural Crops

“…This has been observed in various transcriptome analysis studies against root rots [295,296,299,353]. Similar observations were discernible from transcriptomic and microscopic data in the susceptible B.9 roots [27,366,368]. Microscopy data on the pathogen growth progress revealed a swift development of root necrosis in the most susceptible genotypes, with the entire root system becoming necrotic within a period of 24 h after initial infection [368].…”

“…The transcriptomic changes in apple root tissue when infected with P. ultimum were analyzed using tolerant and susceptible rootstock lines [365,366]. The mechanism of defense response involving the recognition of PAMPs, hormone signaling, and synthesis of PR genes was identified.…”

Genes Involved in Stress Response and Especially in Phytoalexin Biosynthesis Are Upregulated in Four Malus Genotypes in Response to Apple Replant Disease

“…They act against pathogens and as scavengers of reactive oxygen species (Börner, 1959;Emmett et al, 2014;Henfrey et al, 2015). An upregulation of flavonol metabolism genes was also found in apple roots under replant conditions (Weiß et al, 2017a;Weiß et al, 2017b) and upon infection with P. ultimum (Shin et al, 2014;Zhu et al, 2014;Shin et al, 2016b;Zhu et al, 2019).…”

“…Further genes upregulated under ARD conditions are involved in auxin, ethylene, jasmonate, and cytokinin biosyntheses and signaling (Shin et al, 2014;Shin et al, 2016b;Weiß et al, 2017a;Zhu et al, 2019). Salicylic acid, ethylene, and jasmonic acid are important signaling compounds in the biotic stress defense response (Glazebrook, 2005;Broekaert et al, 2006).…”

The Function of MAPK Cascades in Response to Various Stresses in Horticultural Plants

“…A comparative transcriptomic analysis was performed using root tissues of equivalent developmental stages between apple replant disease-tolerant Geneva ® 935 (G.935) and susceptible Bud 9 (B.9) apple rootstocks after Pythium ultimum inoculation. A mitogen-activated protein kinase kinase kinase 3-like (MDP0000187103) gene demonstrated specific suppression in B.9, whereas the same gene was consistently upregulated in G.935 ( Zhu et al., 2019 ). MAPK1 , which belongs to group A MAPKs, played an important role in the defense response to two citrus canker pathogens, Xanthomonas citri and X. aurantifolii , in citrus ( de Oliveira et al., 2013 ).…”