Infection and genotype remodel the entire soybean transcriptome

BMC Genomics

Table 1 Linear mixed-model analysis (LMMA) of soybean gene expression changes under infection by P. sojae.

^aModel: y = Genotype + Treatment + Time + Genotype × Treatment + Block + Block × Genotype + Block × Treatment + Block × Time + Block × Genotype × Treatment + Error, where y refers to the log2 scale median polish summarized gene expression values, the main factors (Genotype, Treatment and Time) and the interaction Genotype × Treatment were fixed factors while all the remaining terms were random factors. GC-RMA background correction and quantile normalization were performed prior to median polish summarization. LMMA was carried out using Proc Mixed of SAS v9. ^bThe p-values for each of the fixed factors were computed based on normality assumption and adjusted for multiple testing using BH, TST and q-value methods at levels from 0.0001 to 0.05. ^cNumbers of detectable genes significant for each factor at the indicated adjusted p value, and percentages of the total number of detectable genes. ^dGenotypes were V71-370, Sloan and VPRIL9. ^eTreatments include Upper, Lower, and Mock. ^fTime refers to sample harvest time window at 9:00 am, 10:30 am, and 12:00 pm.

ISSN: 1471-2164