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.

Genome‐wide identification and characterization of microRNAs responding to ABA and GA in maize embryos during seed germination

“…1; Table S2). The result was consistent with previous reports from maize (Jiao et al 2011;Kang et al 2012;Li et al 2013aLi et al , 2016) and similar to those from A. thaliana (Rajagopalan et al 2006), rice (Morin et al 2008) and peanut (Gao et al 2017).…”

Movement of small RNAs in and between plants and fungi

“…Small RNAs were first discovered in Escherichia coli in 1984 (Mizuno et al, 1984). Subsequently, they have been found in all kingdoms of life operating as noncoding RNA with diverse functions (Wassarman et al, 2001;Saito, Kakeshita, and Nakamura, 2009;Pantaleo et al, 2010;Li et al, 2016). Most small RNAs serve as regulators of gene expression (Hammond et al, 2000;McCaffrey et al, 2002;Paul et al, 2002).…”

Multi-Omics Analysis of Small RNA, Transcriptome, and Degradome in T. turgidum—Regulatory Networks of Grain Development and Abiotic Stress Response

“…Rapid development of NGS techniques has led to the discovery of many conserved and novel miRNA families related to grain development in cereal crops such as bread wheat, maize, rice, and barley [ 36 , 37 , 38 , 39 ]. A previous study in durum also focused on miRNAs related to nitrogen starvation during grain fill, with pooled samples from root, leaf, flag leaf, and spike tissues [ 21 ].…”