title: Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing.
abstract: BACKGROUND
  In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elements, and stress response. Extensive studies of miRNAs have been performed in model plants such as rice and Arabidopsis thaliana. In maize, most miRNAs and their target genes were analyzed and identified by clearly different treatments, such as response to low nitrate, salt and drought stress. However, little is known about miRNAs involved in maize ear development. The objective of this study is to identify conserved and novel miRNAs and their target genes by combined small RNA and degradome sequencing at four inflorescence developmental stages.
  
  
  RESULTS
  We used deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four ear developmental stages, which resulted in identification of 22 conserved and 21-maize-specific miRNA families together with their corresponding miRNA*. Comparison of miRNA expression in these developmental stages revealed 18 differentially expressed miRNA families. Finally, a total of 141 genes (251 transcripts) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Moreover, the differentially expressed miRNAs-mediated pathways that regulate the development of ears were discussed.
  
  
  CONCLUSIONS
  This study confirmed 22 conserved miRNA families and discovered 26 novel miRNAs in maize. Moreover, we identified 141 target genes of known and new miRNAs and ta-siRNAs. Of these, 72 genes (117 transcripts) targeted by 62 differentially expressed miRNAs may attribute to the development of maize ears. Identification and characterization of these important classes of regulatory genes in maize may improve our understanding of molecular mechanisms controlling ear development.
authors.forename: Hongjun
authors.initials: H
authors.lastname: Liu
authors.forename: Cheng
authors.initials: C
authors.lastname: Qin
authors.forename: Zhe
authors.initials: Z
authors.lastname: Chen
authors.forename: Tao
authors.initials: T
authors.lastname: Zuo
authors.forename: Xuerong
authors.initials: X
authors.lastname: Yang
authors.forename: Huangkai
authors.initials: H
authors.lastname: Zhou
authors.forename: Meng
authors.initials: M
authors.lastname: Xu
authors.forename: Shiliang
authors.initials: S
authors.lastname: Cao
authors.forename: Yaou
authors.initials: Y
authors.lastname: Shen
authors.forename: Haijian
authors.initials: H
authors.lastname: Lin
authors.forename: Xiujing
authors.initials: X
authors.lastname: He
authors.forename: Yinchao
authors.initials: Y
authors.lastname: Zhang
authors.forename: Lujiang
authors.initials: L
authors.lastname: Li
authors.forename: Haiping
authors.initials: H
authors.lastname: Ding
authors.forename: Thomas
authors.initials: T
authors.lastname: Lübberstedt
authors.affiliation: Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China. zzmmaize@gmail.com.
authors.forename: Zhiming
authors.initials: Z
authors.lastname: Zhang
authors.forename: Guangtang
authors.initials: G
authors.lastname: Pan
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D030541:Databases, Genetic; D055864:Droughts; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D009566:Nitrates / Q000737:chemistry / Q000494:pharmacology; D012275:Oryza / Q000235:genetics / Q000378:metabolism; D059367:RNA Cleavage; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism; D012492:Salts / Q000737:chemistry / Q000494:pharmacology; D059467:Transcriptome; D003313:Zea mays / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D009566:Nitrates; D018749:RNA, Plant; D034741:RNA, Small Interfering; D012492:Salts