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ARS Home » Plains Area » Lincoln, Nebraska » Wheat, Sorghum and Forage Research » Research » Research Project #431803

Research Project: Genetics and Genomics of Pathogen Resistance in Switchgrass

Location: Wheat, Sorghum and Forage Research

Project Number: 3042-21000-032-05-I
Project Type: Interagency Reimbursable Agreement

Start Date: Aug 1, 2016
End Date: Jul 31, 2019

Objective:
1. Understand the genetic and genomic bases of pathogen response in locally adapted upland and lowland switchgrass breeding populations with contrasting disease symptoms under field conditions. 2. Dissect the molecular underpinnings of why cv Kanlow has broad resistance/tolerance to pathogens. 3. Discover the molecular causes that permit systemic viral infections in some switchgrass plants but not in other genetically-related plants.

Approach:
A number of field breeding nurseries have been screened for two years for rust and viral symptoms. These include full-sibs, half-sibs, parents, and a number of unrelated plants for several tetraploid populations including cultivars Kanlow, Summer, and Liberty. These populations will be analyzed using a combination of classical genetics and markers, RNA-Seq, RT-qPCR, immunoblots and limited genomic sequencing to assess plant responses and pathogen loads in diverse tissues. Divergent plants will be selected to generate F1 and advanced generations and hybrids pseudo-F2 seeds for rescreening, QTL mapping, genome-wide selection, transcriptomics, and validation of markers as key selection tools for identifying resistant and tolerant germplasm. This is specifically needed in the upland populations, which have lower apparent resistance to pathogens. The overarching goal will be to identify resistant germplasm for cultivar improvement. Initially, seedlings will be screened against rust and viruses in a greenhouse at the 3-5 leaf stage to principally identify susceptible and resistant genotypes. The pool of genotypes will form the base population for the generation of full-sib families. Genotypes with the most divergent responses will be screened using genomic, functional genomic and physiological assays. Selected plants will be maintained in clonally replicated field nurseries. To aid in these studies, we will attempt to engineer one of these switchgrass-specific viruses to express GFP to monitor viral movement in-situ, generate antibodies to the capsid proteins (which are quite different in primary amino acid sequence) to distinguish between the different viruses, and document which specific viral proteins are required to initiate a host-response. These diagnostics in turn will be used to assess the short (within hours) and longer (days) transcriptomic responses in plants. Within genetically-related switchgrass plants, there are apparent differences in the pathogen loads within tissues and in the systemic infection of plant parts. Using existing field plants and those generated during Objective 1 and 2, we will use a combination of tools (RNA-Seq, qPCR, immunoblots, and other diagnostics (see Objective 2) to understand the transmission of pathogens within a plant and via seeds. At this point, it is not known how effectively/quantitatively systemic infections can affect plant fitness and bioenergy traits. We will have access to a number of plants in the field and greenhouses. Many of these plants have already been scored for viral infection.