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ARS Home » Midwest Area » St. Paul, Minnesota » Cereal Disease Lab » Research » Research Project #426554

Research Project: Fine-scale Dissection of the Host-Pathogen Interaction Landscape Using Genome-Wide Association Scans of the Host and Pathogen Genomes

Location: Cereal Disease Lab

Project Number: 5062-21220-023-04-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Sep 1, 2013
End Date: Aug 31, 2017

Specific objectives are: (a) Investigate genome-wide variation in the diverse panels of wheat (300 accessions) and Pgt (200 isolates) using high-throughput SNP genotyping and next-generation sequencing approaches; (b), Characterize resistance phenotypes of the wheat diversity panel resulting from inoculation with each of the 200 Pgt isolates; (c) Characterize expression variation in the infected leaves of accessions from the wheat diversity panel; (d) Identify the genetic factors controlling the host-pathogen interaction by performing GWAM of resistance to Pgt in rust and wheat simultaneously; (e) Identify the genetic factors controlling pathogen aggressiveness and host quantitative resistance; (f) Develop the database of allelic variants of genes in the host and pathogen (Rust-WheatVDB) that define the outcome of an infection.

We will use advances in next-generation sequencing and publicly available genomic data for the comprehensive analysis of the genetics of the host-pathogen interaction at the whole genome level. ARS will analyze whole genome variation simultaneously in the host and pathogen populations to detect the alleles of interacting genes that define the outcome of infection. A panel of 300 selected wheat accessions and 200 isolates of the wheat stem rust fungus will be genotyped and characterized for resistance phenotype. Transcriptome analysis of bulked susceptible and resistant wheat accessions will be analyzed using an RNA-seq approach to identify transcripts differentiating these two groups. Genome-wide association mapping of both wheat and stem rust fungus will be used to identify genetic factors controlling host-parasite interactions. In addition, genetic factors controlling pathogen aggressiveness will be analyzed by characterizing phenotypic variation in the 200 stem rust fungal isolates.