title: Genome-Wide Identification and Characterization of microRNAs in Developing Grains of Zea mays L.
abstract: The development and maturation of maize kernel involves meticulous and fine gene regulation at transcriptional and post-transcriptional levels, and miRNAs play important roles during this process. Although a number of miRNAs have been identified in maize seed, the ones involved in the early development of grains and in different lines of maize have not been well studied. Here, we profiled four small RNA libraries, each constructed from groups of immature grains of Zea mays inbred line Chang 7-2 collected 4-6, 7-9, 12-14, and 18-23 days after pollination (DAP). A total of 40 known (containing 111 unique miRNAs) and 162 novel (containing 196 unique miRNA candidates) miRNA families were identified. For conserved and novel miRNAs with over 100 total reads, 44% had higher accumulation before the 9th DAP, especially miR166 family members. 42% of miRNAs had highest accumulation during 12-14 DAP (which is the transition stage from embryogenesis to nutrient storage). Only 14% of miRNAs had higher expression 18-23 DAP. Prediction of potential targets of all miRNAs showed that 165 miRNA families had 377 target genes. For miR164 and miR166, we showed that the transcriptional levels of their target genes were significantly decreased when co-expressed with their cognate miRNA precursors in vivo. Further analysis shows miR159, miR164, miR166, miR171, miR390, miR399, and miR529 families have putative roles in the embryogenesis of maize grain development by participating in transcriptional regulation and morphogenesis, while miR167 and miR528 families participate in metabolism process and stress response during nutrient storage. Our study is the first to present an integrated dynamic expression pattern of miRNAs during maize kernel formation and maturation.
authors.affiliation: China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China.
authors.forename: Dandan
authors.initials: D
authors.lastname: Li
authors.affiliation: China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China.
authors.forename: Zongcai
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America.
authors.forename: Lei
authors.initials: L
authors.lastname: Gao
authors.affiliation: China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China.
authors.forename: Lifang
authors.initials: L
authors.lastname: Wang
authors.affiliation: China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China.
authors.forename: Meijuan
authors.initials: M
authors.lastname: Gao
authors.affiliation: China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China.
authors.forename: Zhujin
authors.initials: Z
authors.lastname: Jiao
authors.affiliation: China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China.
authors.forename: Huili
authors.initials: H
authors.lastname: Qiao
authors.affiliation: China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China.
authors.forename: Jianwei
authors.initials: J
authors.lastname: Yang
authors.affiliation: China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China.
authors.forename: Min
authors.initials: M
authors.lastname: Chen
authors.affiliation: China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China.
authors.forename: Lunguang
authors.initials: L
authors.lastname: Yao
authors.affiliation: Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America.
authors.forename: Renyi
authors.initials: R
authors.lastname: Liu
authors.affiliation: China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China.
authors.forename: Yunchao
authors.initials: Y
authors.lastname: Kan
mesh_terms: D002523:Edible Grain / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D012639:Seeds / Q000235:genetics / Q000254:growth & development; D003313:Zea mays / Q000235:genetics* / Q000254:growth & development*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant