The primary deliverables for this project are:

Rhg1 marker tests/copy-number tests are used to characterize diverse soybean germplasm and within- variety variation for Rhg1 copy number.

At least one soybean line identified that carries more than ten copies of the Rhg1 locus.

At least one soybean line identified that exhibits higher levels of expression of Rhg1 genes than are present in the Fayette cultivar (Fayette carries PI 88788-source Rhg1).

Replicated SCN resistance testing completed for at least one soybean line that exhibits higher copy number and/or higher expression of Rhg1, to reveal the level of resistance to SCN (Hg Type 0) relative to a known SCN-resistant and a known SCN-susceptible control.

If improved resistance compared to lines with 10 Rhg1 copies was confirmed in two separate resistance tests. Initiated use as a parent in breeding for one or more lines with more than 10 Rhg1 copies,

At least two populations developed by crossing genotypes that vary for Rhg1 copy number tested for resistance to two or more SCN populations that differ in Hg Type, to determine how Rhg1 copy number and copy source impacts resistance.

Experiments completed and analyzed that use comparative mass spectrometry (non-targeted metabolome) data for soybean roots differing in their Rhg1 genotypes, to reveal specific chemical differences between those roots.

SCN resistance testing completed on one or more soybean families segregating for a chromosome with a crossover event tightly linked to cqSCN006 or cqSCN007 from G. soja PI 468916, to further define the boundaries of the genetic interval that carries the gene(s) determining SCN resistance.

Functional testing of at least five candidate genes from the cqSCN006 or cqSCN007 genetic intervals completed, to determine if reduction or elevation of expression of those genes causes a change in the SCN resistance phenotype of soybean roots.

Updated November 8, 2017:
• Research on the impact of copy number was accomplished with four plant populations.
• Experiments were completed that revealed the role of Rhg1 gene copy number and type in determining soybean resistance to soybean cyst nematode. Lines with increased copy number were isolated and are being integrated into breeding programs and are available to the community.
• A new marker technology was developed to allow for accurate genotyping of Rhg1 repeats in a single tube, and breeder-friendly markers are now available for the community. The cost of this assay is approximately $0.19 per sample, which is less than half the cost of a recent published method. These markers and technology have been published (Lee et al. 2016, Plant J., 88 143-153) and a patent application for the markers and the new technology for repeat analysis has been filed (US20160265070 A1).

• KPI met through alternative means of isolating natural populations with increased copy numbers.

• Experiments were initiated to assess expression differences for lines with different copy number and types of Rhg1, these are ongoing.
• Investigations into chemical changes caused by the Rhg1 locus in soybean plants were conducted but the researchers were unable to identify the differences in the plant metabolomes. This work is in its infancy and the majority of the most significant differences detected by the metabolomics analysis were "unknown" compounds.

• Research into the two QTL responsible for novel SCN resistance in Glycine soja PI468916 resulted in putative identification of the gene in QTL cqSCN-006 and narrowed the region in resistance QTL cqSCN-007 to 7 possible genes.

The knowledge that the number of copies of the gene Rhg1 may have bearing on the magnitude of SCN resistance within a variety will make a difference in the future of how varieties are bred for improved SCN resistance.