Deep Sequencing of Maize Small RNAs Reveals a Diverse Set of MicroRNA in Dry and Imbibed Seeds

Abstract

Seed germination plays a pivotal role during the life cycle of plants. As dry seeds imbibe water, the resumption of energy metabolism and cellular repair occur and miRNA-mediated gene expression regulation is involved in the reactivation events. This research was aimed at understanding the role of miRNA in the molecular control during seed imbibition process. Small RNA libraries constructed from dry and imbibed maize seed embryos were sequenced using the Illumina platform. Twenty-four conserved miRNA families were identified in both libraries. Sixteen of them showed significant expression differences between dry and imbibed seeds. Twelve miRNA families, miR156, miR159, miR164, miR166, miR167, miR168, miR169, miR172, miR319, miR393, miR394 and miR397, were significantly down-regulated; while four families, miR398, miR408, miR528 and miR529, were significantly up-regulated in imbibed seeds compared to that in dry seeds. Furthermore, putative novel maize miRNAs and their target genes were predicted. Target gene GO analysis was performed for novel miRNAs that were sequenced more than 50 times in the normalized libraries. The result showed that carbohydrate catabolic related genes were specifically enriched in the dry seed, while in imbibed seed target gene enrichment covered a broad range of functional categories including genes in amino acid biosynthesis, isomerase activity, ligase activity and others. The sequencing results were partially validated by quantitative RT-PCR for both conserved and novel miRNAs and the predicted target genes. Our data suggested that diverse and complex miRNAs are involved in the seed imbibition process. That miRNA are involved in plant hormone regulation may play important roles during the dry-imbibed seed transition.

Genome-Wide Identification of MicroRNAs and Their Targets in the Leaves and Fruits of Eucommia ulmoides Using High-Throughput Sequencing

“…Most miRNA * showed weak expression, and their expression levels were much lower than the expression of their corresponding miRNAs. This is consistent with the idea that miRNA * strands are degraded rapidly during the biogenesis of mature miRNAs (Rajagopalan et al, 2006; Li et al, 2013). Intriguingly, Eu-miR8 * reads were extremely enriched in mature fruits, suggesting that the retention of star strands can occur in a tissue- and stage-specific manner.…”

How membranes organize during seed germination: three patterns of dynamic lipid remodelling define chilling resistance and affect plastid biogenesis

“…This confirmed that plastids rarely developed in the dry seeds. The PA level was 6.38 nmol/mg in dry seeds (Table 1), which was much higher than that previously reported in leaves (Crowe & Crowe, 1992, Li, Wang, Liu, Cui, Chen, Zhang, Jiang, Xu, Li, Li, Zhao & Chen, 2013, Welti et al , 2002). PA levels in leaves are usually around 1 nmol/mg, but can increase 2–10-fold under stress conditions, such as freezing and desiccation (Li et al , 2008, Pagnussat et al , 2012, Welti et al , 2002).…”

DELAY OF GERMINATION1 ( DOG1 ) regulates both seed dormancy and flowering time through microRNA pathways

“…4A), and defects in DOG1 function could result in altered postgerminative plant development and floral transition as well as reduced seed dormancy (SI Appendix, Fig. S5) (32,41,64,65). We also note that a primary phenotype of DOG1 action is an extension of dry after-ripening times required for dormancy alleviation (19).…”

“…S5). miR156 accumulates to high levels during seed development (32,64) and is abundant in young seedlings and decreases as plants age, in association with the transition to adult phase and flowering (30,38,65). This pattern indicates that high miR156 levels are reset during embryogenesis and seed development, as occurs for FLC, a strong floral repressor (7).…”