title: Regulatory modules controlling early shade avoidance response in maize seedlings.
abstract: BACKGROUND
  Optimization of shade avoidance response (SAR) is crucial for enhancing crop yield in high-density planting conditions in modern agriculture, but a comprehensive study of the regulatory network of SAR is still lacking in monocot crops.
  
  
  RESULTS
  In this study, the genome-wide early responses in maize seedlings to the simulated shade (low red/far-red ratio) and also to far-red light treatment were transcriptionally profiled. The two processes were predominantly mediated by phytochrome B and phytochrome A, respectively. Clustering of differentially transcribed genes (DTGs) along with functional enrichment analysis identified important biological processes regulated in response to both treatments. Co-expression network analysis identified two transcription factor modules as potentially pivotal regulators of SAR and de-etiolation, respectively. A comprehensive cross-species comparison of orthologous DTG pairs between maize and Arabidopsis in SAR was also conducted, with emphasis on regulatory circuits controlling accelerated flowering and elongated growth, two physiological hallmarks of SAR. Moreover, it was found that the genome-wide distribution of DTGs in SAR and de-etiolation both biased toward the maize1 subgenome, and this was associated with differential retention of various cis-elements between the two subgenomes.
  
  
  CONCLUSIONS
  The results provide the first transcriptional picture for the early dynamics of maize phytochrome signaling. Candidate genes with regulatory functions involved in maize shade avoidance response have been identified, offering a starting point for further functional genomics investigation of maize adaptation to heavily shaded field conditions.
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
authors.forename: Hai
authors.initials: H
authors.lastname: Wang
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
authors.forename: Guangxia
authors.initials: G
authors.lastname: Wu
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
authors.forename: Binbin
authors.initials: B
authors.lastname: Zhao
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
authors.forename: Baobao
authors.initials: B
authors.lastname: Wang
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Lang
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China. zhangchunyi@caas.cn.
authors.forename: Chunyi
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China. wanghaiyang@caas.cn.
authors.forename: Haiyang
authors.initials: H
authors.lastname: Wang
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D017360:Arabidopsis / Q000235:genetics; D016000:Cluster Analysis; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D018745:Genome, Plant; D008027:Light; D051942:Phytochrome A / Q000235:genetics; D051939:Phytochrome B / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid; D036226:Seedlings / Q000235:genetics / Q000254:growth & development*; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome; D003313:Zea mays / Q000235:genetics*
chemical_list: D051942:Phytochrome A; D018749:RNA, Plant; D014157:Transcription Factors; D051939:Phytochrome B
keywords: Maize; Phytochrome; Regulatory module; Shade; Transcriptome