Combined gene expression and QTL analysis of soybean quantitative resistance to Phytophthora sojae

To identify soybean genes and QTLs associated with quantitative resistance to infection by the oomycete pathogen Phytophthora sojae, we conducted a very large-scale microarray experiment using 2522 Affymetrix GeneChips. The experiment involved assaying a total of 298 soybean recombinant inbred lines together with internal checks. A total of 298 soybean recombinant inbred lines (F12 RILs, labeled from R001 to R317) derived from a G. max (V71-370) and G. soja (PI407162) cross were assayed with two experimental replicates. 295 out of the 298 RILs were assayed in experimental replicate I, with the plants organized into 16 blocks, while in experimental replicate II 288 RILs were assayed in 13 blocks. Three soybean genotypes (V71-370, Sloan and VPRIL9) were included within each block as internal controls. Replicates of each set of the three controls, incubated in the same growth chamber, were harvested at three different times (approximately 9 am, 10:30 am, and 12 pm). A P. sojae isolate, PT2004C2.S1, which is virulent to the soybean lines carrying Rps1a, Rps1b, Rps1k, Rps2, Rps3a, Rps3c, Rps4, Rps5, Rps6, or Rps7, was used in this study. For each soybean line, approximately 30 seedlings were inoculated on the roots with P. sojae and after 5 days, 7.5 mm root segments were collected from immediately above and below the upper margin of the visible lesion (referred to as the "Upper" and "Lower" infection courts). From approximately 20 mock-inoculated plants, 15 mm root segments ("Mock") were collected from positions on the roots matching the lesions on the pathogen-inoculated plants.