Transcriptomic and genome-wide association study reveal long noncoding RNAs responding to nitrogen deficiency in maize

Ma, Ping; Zhang, Xiao; Luo, Bowen; Chen, Zhen; He, Xuan; Zhang, Haiying; Li, Binyang; Liu, Dan; Wu, Long‐Fei; Gao, Shuang; Gao, Duojiang; Zhang, Suzhi

doi:10.1186/s12870-021-02847-4

Cited by 21 publications

(13 citation statements)

References 65 publications

(76 reference statements)

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“…A large number of LN‐responsive candidate genes were identified using a GWAS, which combined high‐density SNPs (56,110 SNPs) from an association mapping panel with 17 variable seedling phenotypes under contrasting N concentrations (Ma et al . 2021). To investigate the regulatory roles of circRNAs–parent genes in maize seedlings under LN stress, we combined the candidate genes screened with LN‐responsive GWAS.…”

Section: Resultsmentioning

confidence: 99%

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Identification and characterization of circRNAs in maize seedlings under deficient nitrogen

Zhang

et al. 2021

Plant Biol J

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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.

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Section: Resultsmentioning

confidence: 99%

“…The transcriptome and small RNA data were collected from our previous study (Ma et al . 2021), including 24 samples from HN and LN conditions. The dataset can be downloaded from NCBI under the accession numbers PRJNA661965 and PRJNA662035.…”

Section: Methodsmentioning

confidence: 99%

Identification and characterization of circRNAs in maize seedlings under deficient nitrogen

Zhang

et al. 2021

Plant Biol J

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“…Numerous studies have demonstrated the changes in the expression level of different miRNA families in N limitation conditions in various plant species such as Arabidopsis [ 51 , 52 ], maize [ 53 , 54 ], sorghum [ 55 ], rice [ 32 ], and soybean [ 33 ]. The altered expression pattern of these miRNAs has been shown to play crucial roles in plant adaptive responses to N limitation via the mediation of the expression of their target genes involved in N uptake and remobilization [ 56 ].…”

Section: Biological Functions Of Micrornas In N Metabolismmentioning

confidence: 99%

miRNAomic Approach to Plant Nitrogen Starvation

Yousuf¹,

Shabir²,

Hakeem

2021

International Journal of Genomics

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Nitrogen (N) is one of the indispensable nutrients required by plants for their growth, development, and survival. Being a limited nutrient, it is mostly supplied exogenously to the plants, to maintain quality and productivity. The increased use of N fertilizers is associated with high-cost inputs and negative environmental consequences, which necessitates the development of nitrogen-use-efficient plants for sustainable agriculture. Understanding the regulatory mechanisms underlying N metabolism in plants under low N is one of the prerequisites for the development of nitrogen-use-efficient plants. One of the important and recently discovered groups of regulatory molecules acting at the posttranscriptional and translational levels are microRNAs (miRNAs). miRNAs are known to play critical roles in the regulation of gene expression in plants under different stress conditions including N stress. Several classes of miRNAs associated with N metabolism have been identified so far. These nitrogen-responsive miRNAs may provide a platform for a better understanding of the regulation of N metabolism and pave a way for the development of genotypes for better N utilization. The current review presents a brief outline of miRNAs and their regulatory role in N metabolism.

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“…There were 1229 differently expressed heat-responsive lncRNAs in Chinese cabbage [ 18 ]. In the maize root, a total of 40 distinct expressed lncRNAs implicated in nitrogen uptake were discovered [ 19 ]. The competitive endogenous (ce) RNA hypothesis has gained traction as a putative stress-resistance regulation mechanism in plants.…”

Section: Introductionmentioning

confidence: 99%

Integrated analysis of the lncRNA/circRNA-miRNA-mRNA expression profiles reveals novel insights into potential mechanisms in response to root-knot nematodes in peanut

Wang

et al. 2022

BMC Genomics

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Background Peanut is the most essential oil and food crop globally due to its high oil and protein content. Root-knot nematode infects peanut roots, causing poor development and severely limiting peanut yields worldwide. The discovery of peanut genome identified a considerable number of genetic loci controlling the peanut root-knot nematode; however, the molecular mechanism of root-knot nematode remains unknown. Results The heterogeneous response to root-knot nematode stress in peanut roots was identified using whole-transcriptome RNA-seq. A total of 430 mRNAs, 111 miRNAs, 4453 lncRNAs, and 123 circRNAs were found to have differential expression between infected and non-infected peanuts. The expression profiles of the lncRNA/circRNA-miRNA-mRNA network were developed to understand the potential pathways that lead to root-knot nematodes in peanut roots. During root-knot nematodes stress, a total of 10 lncRNAs, 4 circRNAs, 5 miRNAs, and 13 mRNAs can create competing endogenous RNA and participate in the oxidation–reduction process as well as other biological metabolism processes in peanuts. The findings will highlight the role of peanut ceRNAs in response to root-knot nematodes. Conclusion The GO classification and KEGG pathway enrichment study of core regulatory networks revealed that ceRNAs are involved in oxidation–reduction, peroxidase activity, lignin synthesis in the xylem, and flavonoid synthesis. Overall, these findings may help researchers better understand the role of non-coding RNAs in response to root-knot nematodes.

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Transcriptomic and genome-wide association study reveal long noncoding RNAs responding to nitrogen deficiency in maize

Cited by 21 publications

References 65 publications

Identification and characterization of circRNAs in maize seedlings under deficient nitrogen

Identification and characterization of circRNAs in maize seedlings under deficient nitrogen

miRNAomic Approach to Plant Nitrogen Starvation

Integrated analysis of the lncRNA/circRNA-miRNA-mRNA expression profiles reveals novel insights into potential mechanisms in response to root-knot nematodes in peanut

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