Identification of microRNAs in developing wheat grain that are potentially involved in regulating grain characteristics and the response to nitrogen levels

Abstract

Background: MicroRNAs (miRNAs) play crucial roles in the regulation of plant development and growth, but little information is available concerning their roles during grain development under different nitrogen (N) application levels. Our objective was to identify miRNAs related to the regulation of grain characteristics and the response to different N fertilizer conditions. Results: A total of 79 miRNAs (46 known and 33 novel miRNAs) were identified that showed significant differential expression during grain development under both high nitrogen (HN) and low nitrogen (LN) treatments. The miRNAs that were significantly upregulated early in grain development target genes involved mainly in cell differentiation, auxin-activated signaling, and transcription, which may be associated with grain size; miRNAs abundant in the middle and later stages target genes mainly involved in carbohydrate and nitrogen metabolism, transport, and kinase activity and may be associated with grain filling. Additionally, we identified 50 miRNAs (22 known and 28 novel miRNAs), of which 11, 9, and 39 were differentially expressed between the HN and LN libraries at 7, 17, and 27 days after anthesis (DAA). The miRNAs that were differentially expressed in response to nitrogen conditions target genes involved mainly in carbohydrate and nitrogen metabolism, the defense response, and transport as well as genes that encode ubiquitin ligase. Only one novel miRNA (PC-5p-2614_215) was significantly upregulated in response to LN treatment at all three stages, and 21 miRNAs showed significant differential expression between HN and LN conditions only at 27 DAA. We therefore propose a model for target gene regulation by miRNAs during grain development with N-responsive patterns. Conclusions: The potential targets of the identified miRNAs are related to various biological processes, such as carbohydrate/nitrogen metabolism, transcription, cellular differentiation, transport, and defense. Our results indicate that miRNA-mediated networks, via posttranscriptional regulation, play crucial roles in grain development and the N response, which determine wheat grain weight and quality. Our study provides useful information for future research of regulatory mechanisms that focus on improving grain yield and quality.

Potassium Deficiency Significantly Affected Plant Growth and Development as Well as microRNA-Mediated Mechanism in Wheat (Triticum aestivum L.)

“…K + deficiency affected root development in a wide range of plant species (Jia et al, 2008;Maathuis, 2009;Zhang et al, 2009;Hafsi et al, 2014;Guo et al, 2019). To study the potential miRNA-mediated mechanism in which plant responds to K + deficiency, we have selected and tested a total of 20 miRNAs that are associated with root development (Khan et al, 2011;Couzigou and Combier, 2016;Li and Zhang, 2016) and responses to nutrients (Maathuis, 2009;Kulcheski et al, 2015) including nitrogen and phosphorus deficiency (Bao et al, 2019;Filina et al, 2019;Yang et al, 2019;Asefpour Vakilian, 2020;Hou et al, 2020;Liu et al, 2020;Lv et al, 2020;Tiwari et al, 2020). These 20 miRNAs were miR160, miR164, miR165, miR166, miR167, miR169, miR171, miR172, miR390, miR393, miR396, miR847, miR857, miR156, miR162, miR319, miR395, miR778, miR399, and miR827.…”

Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat (Fagopyrum tataricum)

“…An increasing body of evidence shows that miRNAs participate in the regulation of seed development in crop plants. To date, thousands miRNAs have been identified in the development of seed in multiple crop plants including rice [ 19 , 20 ], maize [ 21 , 22 ], wheat [ 23 , 24 ], barley [ 25 , 26 ], soybean [ 27 , 28 ], peanut [ 18 ], Brassica napus [ 29 , 30 ], narrow-leafed lupin [ 6 ], and common buckwheat [ 4 ] by using a high-throughput sequencing approach. These studies found that the expression of various miRNAs is extremely dynamic during seed development and some miRNAs are specifically expressed in seed, implying that miRNAs have very vital regulatory roles in seed development.…”

Roles of Non-Coding RNAs in Response to Nitrogen Availability in Plants

“…Further to the plant species described above, N-responsive miRNAs have also been identified from dicot crop species including soybean ( Glycine max ) [ 118 ], potato (Indian potato variety Kufri Jyoti ) [ 119 ], tea plant ( Camellia sinensis ) [ 120 ], and from other monocot species such as barley ( Hordeum vulgare ) [ 121 ] and wheat ( Triticum aestivum and Triticum turgidum ) [ 122 , 123 , 124 , 125 ], while N-responsive lncRNAs have yet to be systematically explored.…”