2013 Annual Report
1a.Objectives (from AD-416):
We will use the results of host-parasite investigations, data from the genome sequences of Phytophthora infestans and related species, results of population and epidemiological studies, to improve the practice of late blight management in production systems within the five year scope of the grant (2016). Within the same time-frame, we will test the deployment of superior resistance genes for late blight in both potato and tomato. In addition, a small component of the project will investigate alternative methods of creating resistant plants, and combating the pathogen to enable the next phase of translational research starting in 2016. Objectives have applications for all Oomycetes although most work will focus on P. infestans. P. infestans thus serves as a model organism for management of other Phytophthora species.
1b.Approach (from AD-416):
A multidisciplinary approach will be used to accomplish research goals. These include genetics, structural and functional genomics, bioinformatics, proteomics, epidemiology, population genetics, plant breeding, and biochemistry. To achieve the extension goals, we will use rapid diagnostics tools, a web-based decision support system, GPS, real-time simulation modeling, and innovative methods to communicate with growers. Education aspects of the project will involve growers, extension educators, graduate students, and undergraduates. The latter will include a research experience program for undergraduates at the University of California-Riverside specializing in oomycete genomics. Interns will train in PI labs including participating ARS labs. This $9.5 million NIFA/AFRI CAPS grant is led by scientists at UC Riverside and combines a large, international, interdisciplinary research team at many institutions.
This research was conducted in support of NP303 objective 2C of the parent project. We have received 164 isolates in 2013 from the 2012 field season that are currently have been genotyped to assess genotypic diversity. There is considerably more diversity than observed in 2011.
We are assembling, genotyping and phenotyping a large panel of isolates that are sexual. Isolates are being characterized for fungicide resistance. Other phenotypic assays are in development including tomato/potato specialization, sporulation, lesion area, and more are being considered.
We are determining differences among the genomes of US1, US8, US22 and US23 using genome sequences obtained from UC Riverside. Briefly, we have mapped genomes against the reference genome T30-4 and called SNPs, indels and other features. Indels are being used to develop diagnostic assays. We are also using SNP data to find how US lineages diverged and what their evolutionary history is.
Preliminary results enrichment for heterozygous sites in clonal US lineages (US1, 22, 23, 24) versus sexual isolates from Mexico: PIC99189, MX90128. We have started characterizing diversity of ipiO effectors in US and Mexican populations of the pathogen.
We are evaluating other genetic loci that show potential for markers development including the mitochondrial genome and nuclear regions.