2008 Annual Report 1a.Objectives (from AD-416) The overall objective of this research is the creation of single nucleotide polymorphism (SNP) or SSR DNA markers in soybean and wheat, the development of genetic maps and the application of these markers to existing mapping populations and to newly developed populations that have been developed and extensively characterized by the University of Maryland. The specific objective of this research is the genetic mapping of the DNA markers for the discovery of quantitative trait loci (QTL)/genes that are useful for the genetic improvement of soybean and wheat. 1b.Approach (from AD-416) Polymerase chain reaction (PCR) primers will be designed to soybean and wheat DNA sequence obtained from plasmid clones and from other existing sources of DNA sequence data such as GenBank at the National Center for Biotechnology Information. The PCR primers will be tested via the analysis of the resulting PCR products. Finally, the DNA sequence of PCR products will be determined from a small group of soybean or wheat genotypes and compared using PolyBayes SNP discovery software. In the case of soybean, the resulting sequence will also be compared with the newly developed whole genome sequence of Williams 82 soybean. SNP DNA marker discovery will be followed by the development of single base extension assays or Illumina GoldenGate assays that allow the detection of the SNP DNA markers. Alternatively, existing SSR markers for soybean and wheat will be made available. Both the SNP and SSR markers will be used to genotype the members of existing mapping populations or new populations that have been created by the University of Maryland and for which the University has developed extensive phenotypic information. 3.Progress Report This agreement is with the Department of Plant Science and Landscape Architecture, University of Maryland, College Park and is funded by appropriated funds with the objective of discovering molecular genetic markers targeted at genes/quantitative trait loci (QTL) for various traits in wheat including cold tolerance and disease resistance. In addition this agreement is funded as a subcontract derived from funding derived from a grant from United Soybean Board. Research was conducted to validate quantitative trait loci (QTLs) for Fusarium head blight resistance in the novel wheat germplasm CJ-9306. A study was conducted to validate QTLs contributing to resistance to deoxynivalenol (DON) accumulation as well as to grain yield loss in a population of 152 F7 recombinant inbred lines (RILs) derived from the cross of Veery x CJ9306, and to determine the source of identified QTLs. Of 192 simple sequence repeat (SSR) markers screened on the parents, a total of 72 SSRs were polymorphic. A total of 39 of the SSR markers were used to analyze 152 recombinant inbred lines from Veery x CJ 9306 RILs and ten donor parents of CJ9306. These were in the regions of the three novel QTL on chromosomes 2D, 1A and 5A. This work is still in progress. In other work, a novel approach for the targeted development of new SSR markers in soybean was evaluated. The source sequences of existing SSR and SNP markers that have been genetically mapped were positioned on the soybean whole genome sequence from the Department of Energy, Joint Genome Institute (soy7x.release.fasta.gz). Through this sequence alignment, a total of 2820 sequence scaffolds were not anchored with the existing SSR or SNP loci. These “floating scaffolds” required markers in order to anchor them to the soybean genetic map. The DNA sequence of the floating scaffolds was searched for the presence of tri- and di-nucleotide SSRs motifs. Subsequently, a total of 384 polymerase chain reaction (PCR) primer sets were designed for each of the floating scaffolds and were verified to be unique in the soybean genome using electronic-PCR. Primer sets were evaluated on eight soybean genotypes: Williams82, Noir 1, Minsoy, Archer, Evans, Peking, PI468916, and Essex. Preliminary results indicated that 80% of the primer sets amplified polymorphic PCR products between at least two of the eight genotypes i.e., they will serve as useful DNA markers. A total of 69% of the primer sets were polymorphic between Williams 82 and PI468916. These SSR markers provide a resource of new markers for soybean breeders and geneticists and also assist in anchoring the new Whole Soybean Genome Sequence. Quarterly meetings with the collaborator at the University of Maryland as well as continuous contact with the collaborator via e-mail are used to monitor project progress.