title: Genome-wide transcriptome analysis of two contrasting Brassica rapa doubled haploid lines under cold-stresses using Br135K oligomeric chip.
abstract: Genome wide transcription analysis in response to stresses is important to provide a basis of effective engineering strategies to improve stress tolerance in crop plants. We assembled a Brassica rapa oligomeric microarray (Br135K microarray) using sequence information from 41,173 unigenes and analyzed the transcription profiles of two contrasting doubled haploid (DH) lines, Chiifu and Kenshin, under cold-treatments. The two DH lines showed great differences in electrolyte leakage below -4°C, but similar patterns from 4°C to -2°C. Cold-treatments induced 885 and 858 genes in Chiifu and Kenshin, respectively. Overall, 134, and 56 genes showed an intrinsic difference in expression in Chiifu and Kenshin, respectively. Among 5,349 genes that showed no hit found (NHF) in public databases, 61 and 24 were specifically expressed in Chiifu and Kenshin, respectively. Many transcription factor genes (TFs) also showed various characteristics of expression. BrMYB12, BrMYBL2, BrbHLHs, BrbHLH038, a C2H2, a WRKY, BrDREB19 and a integrase-type TF were induced in a Chiifu-specific fashion, while a bHLH (Bra001826/AT3G21330), bHLH, cycling Dof factor and two Dof type TFs were Kenshin specific. Similar to previous studies, a large number of genes were differently induced or regulated among the two genotypes, but many genes, including NHFs, were specifically or intrinsically expressed with genotype specificity. Expression patterns of known-cold responsive genes in plants resulted in discrepancy to membrane leakage in the two DH lines, indicating that timing of gene expression is more important to conferring freezing tolerance rather than expression levels. Otherwise, the tolerance will be related to the levels of transcripts before cold-treatment or regulated by other mechanisms. Overall, these results indicate common signaling pathways and various transcriptional regulatory mechanisms are working together during cold-treatment of B. rapa. Our newly developed Br135K oligomeric microarray will be useful for transcriptome profiling, and will deliver valuable insight into cold stresses in B. rapa.
authors.affiliation: Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea.
authors.forename: Hee-Jeong
authors.initials: HJ
authors.lastname: Jung
authors.affiliation: Department of Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea.
authors.forename: Xiangshu
authors.initials: X
authors.lastname: Dong
authors.affiliation: Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea.
authors.forename: Jong-In
authors.initials: JI
authors.lastname: Park
authors.affiliation: Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea.
authors.forename: Senthil Kumar
authors.initials: SK
authors.lastname: Thamilarasan
authors.affiliation: Department of Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea.
authors.forename: Sang Sook
authors.initials: SS
authors.lastname: Lee
authors.affiliation: GreenGene Biotech Inc., Genomics and Genetics Institute, Yongin, Republic of Korea.
authors.forename: Yeon-Ki
authors.initials: YK
authors.lastname: Kim
authors.affiliation: Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea.
authors.forename: Yong-Pyo
authors.initials: YP
authors.lastname: Lim
authors.affiliation: Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea.
authors.forename: Ill-Sup
authors.initials: IS
authors.lastname: Nou
authors.affiliation: Department of Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea.
authors.forename: Yoonkang
authors.initials: Y
authors.lastname: Hur
mesh_terms: D029741:Brassica rapa / Q000235:genetics* / Q000502:physiology; D003080:Cold Temperature; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D005838:Genotype; D006238:Haploidy; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010940:Plant Proteins / Q000235:genetics*; D013312:Stress, Physiological
chemical_list: D010940:Plant Proteins