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ARS Home » Pacific West Area » Wenatchee, Washington » Physiology and Pathology of Tree Fruits Research » Research » Publications at this Location » Publication #303416

Research Project: Integration of Host-Genotype and Manipulation of Soil Biology for Soil-borne Disease Control in Agro-Ecosystems

Location: Physiology and Pathology of Tree Fruits Research

Title: Transcriptome profiling on apple root defense responses to infection by Pythium ultimum

Author
item Zhu, Yanmin
item Zheng, Ping - Washington State University Extension Service
item Shin, Sung
item Fazio, Gennaro
item Mazzola, Mark
item Main, Dorrie - Washington State University Extension Service

Submitted to: Meeting Abstract
Publication Type: Proceedings
Publication Acceptance Date: 3/30/2014
Publication Date: 6/26/2014
Citation: Zhu, Y., Zheng, P., Shin, S.B., Fazio, G., Mazzola, M., Main, D. 2014. Transcriptome profiling on apple root defense responses to infection by Pythium ultimum. Proceedings of 7th International Rosaceae Genomics Conference. 12.

Interpretive Summary:

Technical Abstract: The defense response of apple rootstock to necrotrophic soilborne pathogens inciting replant disease is poorly defined. In this study, apple rootstock seedlings were inoculated with Pythium ultimum, a primary member in replant disease pathogen complex. Root tissues including mock inoculated were sampled at 0, 1, 4, 8, 24, 48, 72 and 96 hour post inoculation (hpi). RNA-Seq based transcriptome profiling was performed with at least 20 million reads per sample. The large gap mapper plugin and the transcript discovery plugin in combination with the existing RNA-Seq tool in the CLC Genomics Workbench were used to map the reads and identify the differentially expressed genes (DEGs); gene ontology analysis and KEGG pathway analysis were applied to annotate DEGs. The peak response is at 48 hpi based on the number of the identified DEGs (1061). Members from gene families functioning in hormone signaling such as ET, JA, GA, CK and auxin, encoding NAC, WRKY, MYB and ERF transcription factors; encoding enzymes in several biosynthesis pathways of potential antimicrobial secondary metabolites and cell wall modification are among the identified DEGs. The results from this study represent a crucial step in dissecting the resistant mechanisms in perennial root system to soilborne pathogens. It seems that the molecular framework of defense responses in perennial root system is largely conserved with that characterized using foliar pathosystem. Further investigation on the defense responses specific to various pathogens and rootstock genotypes (resistant and susceptible) should reveal valuable information for future genomics-assisted breeding of resistant apple rootstock.