title: Contribution of transcriptional regulation to natural variations in Arabidopsis.
abstract: BACKGROUND
  Genetic control of gene transcription is a key component in genome evolution. To understand the transcriptional basis of natural variation, we have studied genome-wide variations in transcription and characterized the genetic variations in regulatory elements among Arabidopsis accessions.
  
  
  RESULTS
  Among five accessions (Col-0, C24, Ler, WS-2, and NO-0) 7,508 probe sets with no detectable genomic sequence variations were identified on the basis of the comparative genomic hybridization to the Arabidopsis GeneChip microarray, and used for accession-specific transcriptome analysis. Two-way ANOVA analysis has identified 60 genes whose mRNA levels differed in different accession backgrounds in an organ-dependent manner. Most of these genes were involved in stress responses and late stages of plant development, such as seed development. Correlation analysis of expression patterns of these 7,508 genes between pairs of accessions identified a group of 65 highly plastic genes with distinct expression patterns in each accession.
  
  
  CONCLUSIONS
  Genes that show substantial genetic variation in mRNA level are those with functions in signal transduction, transcription and stress response, suggesting the existence of variations in the regulatory mechanisms for these genes among different accessions. This is in contrast to those genes with significant polymorphisms in the coding regions identified by genomic hybridization, which include genes encoding transposon-related proteins, kinases and disease-resistance proteins. While relatively fewer sequence variations were detected on average in the coding regions of these genes, a number of differences were identified from the upstream regions, several of which alter potential cis-regulatory elements. Our results suggest that nucleotide polymorphisms in regulatory elements of genes encoding controlling factors could be primary targets of natural selection and a driving force behind the evolution of Arabidopsis accessions.
authors.affiliation: Torrey Mesa Research Institute, Syngenta Research and Technology, 3115 Merryfield Row, San Diego, CA 92121, USA. wenchen@diversa.com
authors.forename: Wenqiong J
authors.initials: WJ
authors.lastname: Chen
authors.forename: Sherman H
authors.initials: SH
authors.lastname: Chang
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Hudson
authors.forename: Wai-King
authors.initials: WK
authors.lastname: Kwan
authors.forename: Jingqiu
authors.initials: J
authors.lastname: Li
authors.forename: Bram
authors.initials: B
authors.lastname: Estes
authors.forename: Daniel
authors.initials: D
authors.lastname: Knoll
authors.forename: Liang
authors.initials: L
authors.lastname: Shi
authors.forename: Tong
authors.initials: T
authors.lastname: Zhu
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D035264:Flowers / Q000235:genetics; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation / Q000235:genetics*; D046228:Microarray Analysis; D011110:Polymorphism, Genetic; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012044:Regression Analysis; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D015203:Reproducibility of Results; D013045:Species Specificity; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D012333:RNA, Messenger