title: Expression profiling reveals functionally redundant multiple-copy genes related to zinc, iron and cadmium responses in Brassica rapa.
abstract: Genes underlying environmental adaptability tend to be over-retained in polyploid plant species. Zinc deficiency (ZnD) and iron deficiency (FeD), excess Zn (ZnE) and cadmium exposure (CdE) are major environmental problems for crop cultivation, but little is known about the differential expression of duplicated genes upon these stress conditions. Applying Tag-Seq technology to leaves of Brassica rapa grown under FeD, ZnD, ZnE or CdE conditions, with normal conditions as a control, we examined global gene expression changes and compared the expression patterns of multiple paralogs. We identified 812, 543, 331 and 447 differentially expressed genes under FeD, ZnD, ZnE and CdE conditions, respectively, in B. rapa leaves. Genes involved in regulatory networks centered on the transcription factors bHLH038 or bHLH100 were differentially expressed under (ZnE-induced) FeD. Further analysis revealed that genes associated with Zn, Fe and Cd responses tended to be over-retained in the B. rapa genome. Most of these multiple-copy genes showed the same direction of expression change under stress conditions. We conclude that the duplicated genes involved in trace element responses in B. rapa are functionally redundant, making the regulatory network more complex in B. rapa than in Arabidopsis thaliana.
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Southern Street 12, 100081, Beijing, China; Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands.
authors.forename: Jimeng
authors.initials: J
authors.lastname: Li
authors.forename: Bo
authors.initials: B
authors.lastname: Liu
authors.forename: Feng
authors.initials: F
authors.lastname: Cheng
authors.forename: Xiaowu
authors.initials: X
authors.lastname: Wang
authors.forename: Mark G M
authors.initials: MG
authors.lastname: Aarts
authors.forename: Jian
authors.initials: J
authors.lastname: Wu
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D029741:Brassica rapa / Q000235:genetics* / Q000378:metabolism; D002104:Cadmium / Q000378:metabolism*; D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D020131:Genes, Duplicate; D017343:Genes, Plant; D006706:Homeostasis; D007501:Iron / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015032:Zinc / Q000378:metabolism*
chemical_list: D002104:Cadmium; D007501:Iron; D015032:Zinc
keywords: Brassica rapa; Tag-Seq; cadmium (Cd); differentially expressed gene (DEG); gene expression profile; iron (Fe); zinc (Zn)