title: Analysis of integrated multiple 'omics' datasets reveals the mechanisms of initiation and determination in the formation of tuberous roots in Rehmannia glutinosa.
abstract: All tuberous roots in Rehmannia glutinosa originate from the expansion of fibrous roots (FRs), but not all FRs can successfully transform into tuberous roots. This study identified differentially expressed genes and proteins associated with the expansion of FRs, by comparing the tuberous root at expansion stages (initiated tuberous root, ITRs) and FRs at the seedling stage (initiated FRs, IFRs). The role of miRNAs in the expansion of FRs was also explored using the sRNA transcriptome and degradome to identify miRNAs and their target genes that were differentially expressed between ITRs and FRs at the mature stage (unexpanded FRs, UFRs, which are unable to expand into ITRs). A total of 6032 genes and 450 proteins were differentially expressed between ITRs and IFRs. Integrated analyses of these data revealed several genes and proteins involved in light signalling, hormone response, and signal transduction that might participate in the induction of tuberous root formation. Several genes related to cell division and cell wall metabolism were involved in initiating the expansion of IFRs. Of 135 miRNAs differentially expressed between ITRs and UFRs, there were 27 miRNAs whose targets were specifically identified in the degradome. Analysis of target genes showed that several miRNAs specifically expressed in UFRs were involved in the degradation of key genes required for the formation of tuberous roots. As far as could be ascertained, this is the first time that the miRNAs that control the transition of FRs to tuberous roots in R. glutinosa have been identified. This comprehensive analysis of 'omics' data sheds new light on the mechanisms involved in the regulation of tuberous roots formation.
authors.affiliation: College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, 350002.
authors.forename: Mingjie
authors.initials: M
authors.lastname: Li
authors.affiliation: College of Bioengineering, Henan University of Technology, Zhengzhou, China, 450001.
authors.forename: Yanhui
authors.initials: Y
authors.lastname: Yang
authors.affiliation: College of Life Sciences, Henan Agricultural University, Zhengzhou, China, 450002.
authors.forename: Xinyu
authors.initials: X
authors.lastname: Li
authors.affiliation: College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, 350002.
authors.forename: Li
authors.initials: L
authors.lastname: Gu
authors.affiliation: College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, 350002.
authors.forename: Fengji
authors.initials: F
authors.lastname: Wang
authors.affiliation: College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, 350002.
authors.forename: Fajie
authors.initials: F
authors.lastname: Feng
authors.affiliation: College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, 350002.
authors.forename: Yunhe
authors.initials: Y
authors.lastname: Tian
authors.affiliation: College of Life Sciences, Henan Agricultural University, Zhengzhou, China, 450002.
authors.forename: Fengqing
authors.initials: F
authors.lastname: Wang
authors.affiliation: College of Life Sciences, Henan Agricultural University, Zhengzhou, China, 450002.
authors.forename: Xiaoran
authors.initials: X
authors.lastname: Wang
authors.affiliation: College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, 350002.
authors.forename: Wenxiong
authors.initials: W
authors.lastname: Lin
authors.affiliation: College of Life Sciences, Henan Agricultural University, Zhengzhou, China, 450002 zyzhang@fafu.edu.cn xinjian1@yahoo.com.
authors.forename: Xinjian
authors.initials: X
authors.lastname: Chen
authors.affiliation: College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, 350002 zyzhang@fafu.edu.cn xinjian1@yahoo.com.
authors.forename: Zhongyi
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D018506:Gene Expression Regulation, Plant; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D032267:Rehmannia / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D036226:Seedlings / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant
keywords: Degradome; RNA-Seq; fibrous roots; iTRAQ; initiation; miRNAs; transition; tuberous roots.