Achieving the objectives:
• Bulk segregant analysis to look for SNPs linked to virulence on the PI88788 source of resistance resulted in identification of 4 SNPs with reproducible shifts in allelic frequency correlating with virulence. In each of the SNP regions, a candidate virulence gene with coding region sequence variation has been found. Two of the genes have predicted enzymatic functions; while the functions of other two are unclear they have predicted protein domains consistent with a role in virulence. An assay has been developed to identify 3 of the 4 genes from infective and non-infective SCN.
• Several additional tests have been conducted to assess whether these gene variants truly correlate to infectivity or not. In one case when the putative virulence gene was silenced in nematodes prior to allowing them to infect plants, twice as many cysts formed compared to the unsilenced nematodes.
• In another set of tests, nematodes unrelated to TN20- the virulent line used to isolate the putative virulence genes, were screened for the virulent or nonvirulent genes. Screening the unrelated line (OP50) showed the same virulence alleles as were present in TN20.
• The next step is collecting SCN isolated from fields and testing them in the SNP assay as well as the traditional plant based assays to see if the results are the same. The SNP assay has been completed and the plant based assays are underway.
• The researchers continue to work with the Joint Genome Institute to annotate and improve the SCN genome; this is slow going because there is no dedicated funding for this part of the project. All data collected in this project will be deposited in GenBank as it becomes available.
• We have also obtained the genome sequence of a bacterial endosymbiont of SCN and seven RNA viruses. The endosymbiont and viruses appear to be only present in our avirulent SCN inbred strain, so we are interested in determining if these microorganisms alter SCN virulence.
Not achieving the objectives:
• The objectives were all achieved and additional progress was made towards the long term goal