2011 Annual Report 1a.Objectives (from AD-416) The purpose of the cooperative agreement is to enable collaboration on developing soybeans with resistance to several important pathogens and pests of soybeans. 1b.Approach (from AD-416) Continue to develop crosses of interests (resistant x susceptible), advance populations of new crosses and work with other already developed populations including recombinant inbred lines. Evaluate these parents and populations for resistance to various pathogens and pests including Sclerotinia stem rot using known techniques developed for greenhouse and/or laboratory use. Genomic DNA from plants in mapping populations of interest will be used for molecular analysis using markers (SSR and/or SNP Golden Gate Assay). Polymorphic SNP markers among parents of mapping populations will be selected to genotype the regions and fine map linked resistance genes. Linkage analysis and composite interval mapping will be performed to identify genes controlling disease resistance in the populations. 3.Progress Report A method to evaluate incomplete and partial resistance to soybean rust, caused by Phakopsora pachyrhizi, using qPCR to measure fungal colonization within infected tissues was developed and proof of concept experiments were conducted. Highly significant differences in the extent of fungal colonization in leaves were found among genotypes expressing complete, incomplete, partial resistance, and susceptible reactions to two fungal isolates, based on visual assessments of signs and symptoms of soybean rust. Phakopsora pachyrhizi colonization in some genotypes with partial resistance was not significantly different from some genotypes with incomplete resistance. The soybean aphid resistance gene Rag2, present in soybean PI 200538, was mapped to within a 54 base pair interval in the soybean genome. Based on the recently published Williams 82 soybean genome sequence assembly, a putative NBS-LRR-type candidate soybean aphid resistance gene was identified within the 54 bp interval. A Golden Gate Assay was performed on genomic DNA from a segregating recombinant inbred line mapping population derived from a cross between sudden death (SDS)-resistant PI 507531 and SDS-susceptible Spencer. At least one new putative quantitative trait locus (QTL) associated with partial resistance to SDS was identified. This project was monitored through electronic messages, phone conferences, and face-to-face meetings.