2010 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 Rag1 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. The rag3 gene was previously mapped between Sat_339 and Satt414 (about 20 cM) using 249 lines from a large population (050017), which has a total of 797 lines. All these 797 lines have been phenotyped in 2008 in the greenhouse. From that experiment, we also selected 19 pairs of isogenic lines, each pair had opposite phenotypes and derived from a same line. To narrow down the interval, we added seven more SSR markers (SSR-16-418, SSR-16-444, SSR-16-467, SSR-16-486, SSR-16-538, SSR-16-507, and SSR-16-549) in that interval using those 249 lines. The interval was narrowed down to about 13 cM. The progress is monitored by monthly telephone conversations between the Co-PI and the 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.