Pei Cao1, Wenjuan Fan1,2, Pengjia Li1,2, Yuxin Hu3,4. 1. Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China. 2. University of Chinese Academy of Sciences, 100049, Beijing, China. 3. Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China. huyuxin@ibcas.ac.cn. 4. National Center for Plant Gene Research, 100093, Beijing, China. huyuxin@ibcas.ac.cn.
Abstract
BACKGROUND: Long noncoding RNAs (lncRNAs) have been shown to play important roles in the regulation of plant growth and development. Recent transcriptomic analyses have revealed the gene expression profiling in wheat spike development, however, the possible regulatory roles of lncRNAs in wheat spike morphogenesis remain largely unclear. RESULTS: Here, we analyzed the genome-wide profiling of lncRNAs during wheat spike development at six stages, and identified a total of 8,889 expressed lncRNAs, among which 2,753 were differentially expressed lncRNAs (DE lncRNAs) at various developmental stages. Three hundred fifteen differentially expressed cis- and trans-regulatory lncRNA-mRNA pairs comprised of 205 lncRNAs and 279 genes were predicted, which were found to be mainly involved in the stress responses, transcriptional and enzymatic regulations. Moreover, the 145 DE lncRNAs were predicted as putative precursors or target mimics of miRNAs. Finally, we identified the important lncRNAs that participate in spike development by potentially targeting stress response genes, TF genes or miRNAs. CONCLUSIONS: This study outlines an overall view of lncRNAs and their possible regulatory networks during wheat spike development, which also provides an alternative resource for genetic manipulation of wheat spike architecture and thus yield.
BACKGROUND: Long noncoding RNAs (lncRNAs) have been shown to play important roles in the regulation of plant growth and development. Recent transcriptomic analyses have revealed the gene expression profiling in wheat spike development, however, the possible regulatory roles of lncRNAs in wheat spike morphogenesis remain largely unclear. RESULTS: Here, we analyzed the genome-wide profiling of lncRNAs during wheat spike development at six stages, and identified a total of 8,889 expressed lncRNAs, among which 2,753 were differentially expressed lncRNAs (DE lncRNAs) at various developmental stages. Three hundred fifteen differentially expressed cis- and trans-regulatory lncRNA-mRNA pairs comprised of 205 lncRNAs and 279 genes were predicted, which were found to be mainly involved in the stress responses, transcriptional and enzymatic regulations. Moreover, the 145 DE lncRNAs were predicted as putative precursors or target mimics of miRNAs. Finally, we identified the important lncRNAs that participate in spike development by potentially targeting stress response genes, TF genes or miRNAs. CONCLUSIONS: This study outlines an overall view of lncRNAs and their possible regulatory networks during wheat spike development, which also provides an alternative resource for genetic manipulation of wheat spike architecture and thus yield.
Authors: Philip A Wigge; Min Chul Kim; Katja E Jaeger; Wolfgang Busch; Markus Schmid; Jan U Lohmann; Detlef Weigel Journal: Science Date: 2005-08-12 Impact factor: 47.728
Authors: Lin Li; Steven R Eichten; Rena Shimizu; Katherine Petsch; Cheng-Ting Yeh; Wei Wu; Antony M Chettoor; Scott A Givan; Rex A Cole; John E Fowler; Matthew M S Evans; Michael J Scanlon; Jianming Yu; Patrick S Schnable; Marja C P Timmermans; Nathan M Springer; Gary J Muehlbauer Journal: Genome Biol Date: 2014-02-27 Impact factor: 13.583