Identification and characterization of circRNAs involved in the regulation of low nitrogen-promoted root growth in hexaploid wheat

Abstract

Background: CircRNAs are widespread in plants and play important roles in response to abiotic stresses. Low nitrogen (LN) promotes the growth of plant root system, allowing it to explore more nitrogen. However, whether circRNAs involved in the response to LN stress and the regulation of LN-promoted root growth in wheat remains unclear.

Methods: Two wheat varieties (LH9 and XN979) with contrasting root phenotypes to LN stress were used as materials to identify circRNAs under control and LN conditions by using high-throughput sequencing technology.

Results: Six differentially expressed circRNAs (DECs) involved in the common response to LN stress and 23 DECs involved in the regulation of LN-promoted root growth were successfully identified. GO analysis of the DEC-host genes involved in the regulation of LN-promoted root growth showed that GO terms related to biological regulation, responses to stimuli and signalling were significantly enriched. Moreover, seven DECs were predicted to have miRNA binding sites and may serve as miRNA sponges to capture miRNAs from their target genes.

Conclusions: LN stress altered the expression profiles of circRNAs in wheat. This is the first report of LN stress responsive circRNAs in plants. Our results provided new clues for investigating the functions of circRNAs in response to LN stress and in the regulation of LN-promoted wheat root growth.

Keywords: CircRNAs; Low nitrogen; Root; Triticum aestivum L..

Fig. 1

The response of the roots of XN979 and LH9 to low nitrogen (LN) stress. The maximum root length (a), root dry weight (b) and root morphology (c) of XN979 and LH9 under CK (2.0 mM NO₃⁻) and LN (0.1 mM NO₃⁻) conditions. Bar = 5 cm

Fig. 2

Statistical analysis of circRNAs and differentially expressed circRNAs (DECs) in the roots of LH9 and XN979 under control (CK) and low nitrogen (LN) conditions. a The number of exonic circRNAs, intergenic circRNAs, and intronic circRNAs in each sequenced sample. b Venn diagram analysis of DECs in the LH9_LN-LH9_CK and XN979_LN-XN979_CK comparisons

Fig. 3

Relative expression analysis of circRNAs under control (CK) and low nitrogen (LN) conditions. a, b The results of relative expression analysis of LH9 under CK and LN conditions by using real-time PCR (a) and RNA-sequence (b) technologies, respectively. c, d The results of relative expression analysis of XN979 under CK and LN conditions by using real-time PCR (c) and RNA-sequence (d) technologies, respectively; Each bar shows the mean ± standard errors (SE) of three replicates. (*P < 0.05, Duncan’s multiple range test)

Fig. 4

Relative expression analysis of circRNA-host genes in the roots of LH9 and XN979 under control (CK) and low nitrogen (LN) conditions. CircRNA347-H, circRNA998-H, circRNA866-H, circRNA414-H and circRNA782-H represent the host genes of circRNA347, circRNA998, circRNA866, circRNA414 and circRNA782, respectively. Significant difference at < 0.05 is indicated by different letters above the columns

Fig. 5

Gene Ontology analysis of the host genes of the differentially expressed circRNAs (DECs) that specifically identified in LH9. Columns in blue color represent GO terms belonging to the biological process category; Columns in red color represents GO terms belonging to the cellular component category; Columns in green color represents GO terms belonging to the molecular function category