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. 2020 Feb 27;20(1):87.
doi: 10.1186/s12870-020-2296-7.

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

Gege Hou  1 , Chenyang Du  1 , Honghuan Gao  1 , Sujun Liu  1 , Wan Sun  1 , Hongfang Lu  1 , Juan Kang  1 , Yingxin Xie  1 , Dongyun Ma  2   3 , Chenyang Wang  4   5
Affiliations

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

Gege Hou et al. BMC Plant Biol. .

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.

Keywords: Differentially expressed miRNAs; Grain development; Nitrogen application level; Wheat.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Length distribution of miRNAs in developing wheat grain of plants grown under two nitrogen application levels and sampled at 7, 17, and 27 DAA. HN-7, HN-17 and HN-27 represent grain at 7, 17, and 27 DAA under high nitrogen application levels, respectively. LN-7, LN-17 and LN-27 represent grain at 7, 17, and 27 DAA under low nitrogen application levels, respectively
Fig. 2
Fig. 2
Venn diagram of differentially expressed miRNAs in different libraries at three grain developmental stages under high (HN) and low (LN) nitrogen treatment. HN-7, HN-17 and HN-27 represent grain at 7, 17, and 27 days after anthesis under high nitrogen application levels, respectively. LN-7, LN-17 and LN-27 represent grain at 7, 17, and 27 days after anthesis under low nitrogen application levels, respectively. The number outside (inside) the brackets represents the number of total (novel) differentially expressed miRNAs
Fig. 3
Fig. 3
The major GO categories of “cellular component”, “biological process”, and “molecular function” for the predicted genes of all the differentially expressed miRNAs during grain development
Fig. 4
Fig. 4
Relationships within a miRNA-gene-GO network for cell differentiation, seed development and response to heat stress as determined by Cytoscape. The red, green, and yellow colors indicate miRNAs, target gene functions and GO terms, respectively
Fig. 5
Fig. 5
Model for miRNAs and their target genes associated with grain development and the response to N levels. The black letters in green circles indicate miRNAs, and the red letters in black boxes indicate the target gene function. The black arrows represent the direction of regulation. TF, transcription factor; CRF, cytokinin response factor; SCF, Skp-cullin-F-box; GLU, glucosyltransferase; BRI, brassinosteroid insensitive; ASR, alternative splicing regulator; LRR-RPK, leucine-rich-repeat receptor-like protein kinase; K1P-PSS1, kinesin-1-like protein PSS1; ARF, auxin response factor; HNT, high-affinity nitrate transport; Redox, reduction-oxidation; HSP, heat-shock protein; POD, peroxidase
Fig. 6
Fig. 6
Verification of the expression patterns of nine miRNAs present in developing wheat grain. The different lowercase letters above the columns indicate significant differences (P < 0.05)
Fig. 7
Fig. 7
Verification of the expression patterns of miRNA target genes in developing wheat grain. The different lowercase letters above the columns indicate significant differences (P < 0.05)
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