Transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings

• Published in: Plant molecular biology Vol. 77; no. 1-2; pp. 129 - 144
• Main Authors: Nanjo, Yohei, Maruyama, Kyonoshin, Yasue, Hiroshi, Yamaguchi-Shinozaki, Kazuko, Shinozaki, Kazuo, Komatsu, Setsuko
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.09.2011; Springer Nature B.V
• Subjects: Acclimation; Acclimatization; Amino acids; Biochemistry; Biodegradation; Biomedical and Life Sciences; Cell death; Cell walls; Chromatin; DNA microarrays; DNA probes; Energy Metabolism - genetics; Flooding; Floods; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Genomes; Glycine max - genetics; Glycine max - metabolism; Glycolysis; Hypocotyl - genetics; Hypocotyl - metabolism; Hypocotyls; Injuries; Life Sciences; Metabolic Networks and Pathways - genetics; Metabolism; Metabolites; Oligonucleotide Array Sequence Analysis; Oligonucleotides; phosphofructokinase; Photosynthesis; Photosynthesis - genetics; Plant biology; Plant Pathology; Plant Proteins - genetics; Plant Proteins - metabolism; Plant Roots - genetics; Plant Roots - metabolism; Plant Sciences; Post-transcription; Protein biosynthesis; Protein synthesis; pyrophosphates; RNA processing; Roots; Seedlings; Seedlings - genetics; Seedlings - metabolism; Soybeans; Stress; Stress response; Stress, Physiological - genetics; Transcription; Transcription, Genetic; Water - metabolism; Seedling; Soybean; Flooding; Transcriptome
• ISSN: 0167-4412; 1573-5028
• DOI: 10.1007/s11103-011-9799-4

To understand the transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings, genome-wide changes in gene expression were analyzed using a soybean microarray chip containing 42,034 60-mer oligonucleotide probes. More than 6,000 of flooding-responsive genes in the roots including hypocotyl of soybean seedlings were identified. The transcriptional analysis showed that genes related to photosynthesis, glycolysis, Ser-Gly-Cys group amino acid synthesis, regulation of transcription, ubiquitin-mediated protein degradation and cell death were significantly up-regulated by flooding. Meanwhile, genes related to cell wall synthesis, secondary metabolism, metabolite transport, cell organization, chromatin structure synthesis, and degradation of aspartate family amino acid were significantly down-regulated. Comparison of the responses with other plants showed that genes encoding pyrophosphate dependent phosphofructokinase were down-regulated in flooded soybean seedlings, however, those in tolerant plants were up-regulated. Additionally, genes related to RNA processing and initiation of protein synthesis were not up-regulated in soybean, however, those in tolerant plants were up-regulated. Furthermore, we found that flooding-specific up-regulation of genes encoding small proteins which might have roles in acclimation to flooding. These results suggest that functional disorder of acclimative responses to flooding through transcriptional and post-transcriptional regulations is involved in occurring flooding injury to soybean seedlings.