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.
Highlights
Maize kernel is one of the most important global staple foods
Our results show a dynamic expression profile of miRNAs during maize seed development, giving us insight into the roles of miRNAs during the formation and maturation of maize kernel
Our results show that miR167 has higher accumulation during the stage of nutrient storage, indicating that miR167 might be involved in the metabolism regulation of seed maturity by regulating the expression of the monocopper oxidase (MCO) gene
Summary
Maize kernel is one of the most important global staple foods. Elucidation of the molecular mechanism of maize kernel development will be helpful to the production of PLOS ONE | DOI:10.1371/journal.pone.0153168 April 15, 2016microRNAs in Developing Grains of Maize improved varieties of maize, and for providing insight into seed development of other crop angiosperms. Elucidation of the molecular mechanism of maize kernel development will be helpful to the production of PLOS ONE | DOI:10.1371/journal.pone.0153168. Many genes are involved in the process of kernel maturation: ZmHOX, ZmOCL1, KN1, ESR, BETL, and BAP are associated with the development of embryos and endosperms [1, 2]; BT, DU, SH, SU, and WX are involved in starch synthesis [3]; while O2, FL2, and MC participate in storage proteins formation [4,5,6,7]. Development and maturation of maize kernel involves meticulous and fine gene regulation at transcriptional and post-transcriptional levels. Genome-wide analysis of gene expression profiles during maize kernel development has been performed, and different categories of genes have been identified at various developmental stages, the mechanisms of kernel maturation remains elusive [8,9,10,11,12,13,14,15]
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