2011 Annual Report 1a.Objectives (from AD-416) Develop SNP markers for soybean aphid resistance genes for marker assisted breeding for Rag3 and Rag4 genes. 1b.Approach (from AD-416) SNP (single nucleotide polymorphism) markers will be identified in the genomic regions of the aphid resistance genes using appropriate RIL mapping populations and near isogenic lines. The Solexa sequencing and Illumina and other genotyping platforms will be used for mapping the SNPs. 3.Progress Report Rag3 was previously mapped between Satt299 and Sat_244 (about 10 cM) and Rag4 was mapped between Satt648 and Satt348 (about 15 cM). To fine map these two genes, we created two large populations, one (050016) has individuals of 386 and another (070070) has individuals of 927. These two populations were genotyped with the closest flanking markers (Satt435 and Satt245 for rag1, and Satt569 and Satt348 for rag4). A total of 77 and 68 lines were selected from population 050016 and 070070. All those lines recombined at one of these two intervals. The phenotype data for those lines have been collected in two years (one in the field cage in 2009 and one in the greenhouse in 2010). To further reduce the intervals where rag1 and rag4 located, we added three more SSR markers (SSR-13-417, SSR-13-392, SSR-13-320) in the rag4 interval and three more markers (SSR-07-282, SSR-07-328, SSR-07-411) in the rag1 interval using 170 lines in population 070070. These rag1 and rag4 intervals were further narrowed down to 7.2 cM and 2.7 cM. Over 4,000 F2 plants or F2:3 families that are segregating for the rag3 gene were evaluated for aphid resistance in our greenhouse. DNA was extracted from these plants and tested with simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers flanking the rag3 gene to identify recombinants between the flanking markers. Twelve recombinants that are homozygous for both flanking markers were identified. About 200 additional recombinants that are homozygous for one flanking marker and heterozygous for the other flanking marker were also identified. This research relates to objective 2A (Characterize and map aphid resistance genes in three soybean plant introductions) of the parent project. Progress is monitored by monthly telephone conversation between the Co-PI and the Authorized Departmental Officer’s Designated Representative (ADODR) and quarterly written progress reports from Co-PI to ADODR. Also, face to face meetings of the Co-PI and ADODR at soybean breeder’s workshop once a year.