Identification and characterization of circRNAs in maize seedlings under deficient nitrogen

Abstract

Here, deep sequencing results of the maize transcriptome in leaves and roots were compared under high‐nitrogen (HN) and low‐nitrogen (LN) conditions to identify differentially expressed circRNAs (DECs). Circular RNAs (circRNAs) are covalently closed non‐coding RNA with widely regulatory potency that has been identified in animals and plants. However, the understanding of circRNAs involved in responsive nitrogen deficiency remains to be elucidated. A total of 24 and 22 DECs were obtained from the leaves and roots, respectively. Ten circRNAs were validated by divergent and convergent primers, and 6 DECs showed the same expression tendency validated by reverse transcriptase‐quantitative PCR. Integrating the identified differentially expressed miRNAs, 34 circRNAs could act as miRNA decoys, which might play important roles in multiple biological processes, including organonitrogen compound biosynthesis and regulation of the metabolic process. A total of 51 circRNA‐parent genes located in the genome‐wide association study identified loci were assessed between HN and LN conditions and were associated with root growth and development. In summary, our results provide valuable information regarding further study of maize circRNAs under nitrogen deficiency and provide new insights into screening of candidate genes as well as the improvement of maize regarding nitrogen deficiency resistance. CircRNA–miRNA–mRNA co‐expression networks were constructed to explore the circRNAs that participated in biological development and nitrogen metabolism.

Identification and Functional Prediction of Poplar Root circRNAs Involved in Treatment With Different Forms of Nitrogen

“…Moreover, miRNAs, as noncoding RNAs also play a key role in regulating poplar root responses to different N forms (Zhou and Wu, 2022a). CircRNAs, as another noncoding RNA, exist widely in different tissues of plants and play a key role in plant regulation of growth and development and resistance to abiotic stress (Zhang et al, 2020;Huang et al, 2021;Li et al, 2021;Ma et al, 2021). However, circRNAs in poplar root responses to different N forms have not been reported.…”

“…CircRNAs can act as miRNA sponges to affect the inhibition of miRNAs on target genes, thus achieving regulation (Hansen et al, 2013;Kulcheski et al, 2016). CircRNA responses to N in plants have also been reported (Liu et al, 2020;Ma et al, 2021). For example, 24 and 22 differentially expressed circRNAs (DECs) were shown to participate in the low N response of roots and leaves of maize (Zea mays L.; Ma et al, 2021).…”

“…CircRNA responses to N in plants have also been reported (Liu et al, 2020;Ma et al, 2021). For example, 24 and 22 differentially expressed circRNAs (DECs) were shown to participate in the low N response of roots and leaves of maize (Zea mays L.; Ma et al, 2021). In poplar (Populus × canescens) xylem, 163 DECs were found to participate in the low N response (Liu et al, 2020).…”

A Combination of a Genome-Wide Association Study and a Transcriptome Analysis Reveals circRNAs as New Regulators Involved in the Response to Salt Stress in Maize

“…For example, under a low-temperature treatment, 1759 circRNAs were induced in tomato leaves [ 52 ]. In maize, a total of 24 and 22 DECs obtained from the leaves and roots, respectively, were responsive to deficient nitrogen stress [ 53 ]. However, knowledge of the roles of circRNAs in response to salt stress are still limited in maize.…”

Identification, biogenesis, function, and mechanism of action of circular RNAs in plants

“… The numbers represent the total number of circRNAs identified in each study ( Bai et al., 2021 ; Bao et al., 2019 ; Bian et al., 2021 ; Chen et al., 2017 , 2022 ; Darbani et al., 2016 ; Dong et al., 2021 ; Eisenberg and Levanon, 2018 ; Fu et al., 2019 , 2020 ; Ghorbani et al., 2018 ; Han et al., 2021 ; He et al., 2020 ; Hong et al., 2020 ; Jiang et al., 2021 ; Li et al., 2020a , 2020b , 2021a ; Liang et al., 2019 ; Liu et al., 2017 , 2019c , 2020a , 2021a ; Luo et al., 2020 ; Lv et al., 2020 ; Ma et al., 2021a , 2021b ; Medina et al., 2021 ; Meng et al., 2018 ; Pan et al., 2018 ; Qin et al., 2018 ; Ren et al., 2018 ; Salih et al., 2021 ; Shi et al., 2021 , 2022 ; Shu et al., 2021 ; Sun et al., 2016 , 2020 , 2021 , Tang et al., 2018 ; Tong et al., 2018 ; Wang et al., 2017a , 2017b , 2018a , 2018b , 2019c , 2019e , 2020a , 2021a , 2021b , 2021c , 2022a , 2022b , Wu et al., 2020 ; ...…”