Differential expression of genes in soybean in response to the causal agent of Asian soybean rust (Phakopsora pachyrhizi Sydow) is soybean growth stage-specific

• Published in: Theoretical and applied genetics 2009, Vol.118 (2), p.359-370, Article 359
• Main Authors: Panthee, Dilip R, Marois, James J, Wright, David L, Narváez, Dario, Yuan, Joshua S, Stewart, C. Neal Jr
• Format: Article
• Language: English
• Subjects: Agriculture; Basidiomycota; Biochemistry; Biological and medical sciences; Biomedical and Life Sciences; Biotechnology; Classical genetics, quantitative genetics, hybrids; Cluster Analysis; Crop diseases; Fundamental and applied biological sciences. Psychology; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes, Plant; Genetics of eukaryotes. Biological and molecular evolution; Genomes; Glycine max - genetics; Glycine max - growth & development; Glycine max - microbiology; Horticulture; Immunity, Innate - genetics; Life Sciences; Oligonucleotide Array Sequence Analysis; Original Paper; Pathogens; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Diseases - microbiology; Plant Genetics and Genomics; Plant Proteins - genetics; Plant Proteins - metabolism; Plant sciences; Pteridophyta, spermatophyta; Reverse Transcriptase Polymerase Chain Reaction; RNA, Messenger - metabolism; Software; Soybeans; Vegetals
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-008-0905-1

Understanding plant host response to a pathogen such as Phakopsora pachyrhizi, the causal agent of Asian soybean rust (ASR), under different environmental conditions and growth stages is crucial for developing a resistant plant variety. The main objective of this study was to perform global transcriptome profiling of P. pachyrhizi-exposed soybean (Glycine max) with susceptible reaction to the pathogen from two distinct developmental growth stages using whole genome Affymetrix microarrays of soybean followed by confirmation using a resistant genotype. Soybean cv. 5601T (susceptible to ASR) at the V₄ and R₁ growth stages and Glycine tomentella (resistant to ASR) plants were inoculated with P. pachyrhizi and leaf samples were collected after 72 h of inoculation for microarray analysis. Upon analyzing the data using Array Assist software at 5% false discovery rate (FDR), a total of 5,056 genes were found significantly differentially expressed at V₄ growth stage, of which 2,401 were up-regulated, whereas 579 were found differentially expressed at R₁ growth stage, of which 264 were up-regulated. There were 333 differentially expressed common genes between the V₄ and R₁ growth stages, of which 125 were up-regulated. A large difference in number of differentially expressed genes between the two growth stages indicates that the gene expression is growth-stage-specific. We performed real-time RT-PCR analysis on nine of these genes from both growth stages and both plant species and found results to be congruent with those from the microarray analysis.