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

Liu, Peng; Zhu, Yuxiao; Líu, Hao; Liang, Zhenjuan; Zhang, Minyan; Zou, Chaoying; Gao, Suping; Pan, Guangtang; Shen, Yaou; Ma, Langlang

doi:10.3390/ijms23179755

Cited by 15 publications

(12 citation statements)

References 86 publications

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“…MiRNA plays a crucial role in responding to different stress conditions by regulating target genes [ 40 ]. miRNA was found to be involved in the response to salt stress in sorghum, sweet potato, maize, and rice [ 41 , 42 , 43 , 44 ]. The involvement of MiRNA has also been reported in the regulation of salt stress in wheat in recent studies.…”

Section: Discussionmentioning

confidence: 99%

Comparative Analysis of miRNA Expression Profiles under Salt Stress in Wheat

Qiao

Jiao

Wang

et al. 2023

Genes

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Salt stress is one of the important environmental factors that inhibit the normal growth and development of plants. Plants have evolved various mechanisms, including signal transduction regulation, physiological regulation, and gene transcription regulation, to adapt to environmental stress. MicroRNAs (miRNAs) play a role in regulating mRNA expression. Nevertheless, miRNAs related to salt stress are rarely reported in bread wheat (Triticum aestivum L.). In this study, using high−throughput sequencing, we analyzed the miRNA expression profile of wheat under salt stress. We identified 360 conserved and 859 novel miRNAs, of which 49 showed considerable changes in transcription levels after salt treatment. Among them, 25 were dramatically upregulated and 24 were downregulated. Using real−time quantitative PCR, we detected significant changes in the relative expression of miRNAs, and the results showed the same trend as the sequencing data. In the salt−treated group, miR109 had a higher expression level, while miR60 and miR202 had lower expression levels. Furthermore, 21 miRNAs with significant changes were selected from the differentially expressed miRNAs, and 1023 candidate target genes were obtained through the prediction of the website psRNATarget. Gene ontology (GO) analysis of the candidate target genes showed that the expressed miRNA may be involved in the response to biological processes, molecular functions, and cellular components. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis confirmed their important functions in RNA degradation, metabolic pathways, synthesis pathways, peroxisome, environmental adaptation, global and overview maps, and stress adaptation and the MAPK signal pathway. These findings provide a basis for further exploring the function of miRNA in wheat salt tolerance.

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Section: Discussionmentioning

confidence: 99%

Comparative Analysis of miRNA Expression Profiles under Salt Stress in Wheat

Qiao

Jiao

Wang

et al. 2023

Genes

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“…Moreover, in maize, glycine betaine [ 34 , 35 ], trehalose [ 36 ], ascorbate–proline–glutathione [ 37 ], and phosphate [ 28 ], are applied to counter salt stress, which is favorable for the maintenance of Na + /K + balance and improvements in antioxidant defense. Recently, single or combined analyses of genomes [ 38 ], transcriptomes [ 34 , 39 ], proteomes [ 40 , 41 , 42 , 43 ], and metabolomes [ 44 , 45 ] and a genome-wide association study (GWAS) revealed differential expression genes, small RNAs, and regulatory networks in plants under salt stress [ 46 , 47 , 48 ], which provided valuable information to understand the mechanism of salt response.…”

Section: Introductionmentioning

confidence: 99%

Reshifting Na+ from Shoots into Long Roots Is Associated with Salt Tolerance in Two Contrasting Inbred Maize (Zea mays L.) Lines

Zhao

Zheng

Wang

et al. 2023

Plants

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Maize, as a glycophyte, is hypersensitive to salinity, but the salt response mechanism of maize remains unclear. In this study, the physiological, biochemical, and molecular responses of two contrasting inbred lines, the salt-tolerant QXH0121 and salt-sensitive QXN233 lines, were investigated in response to salt stress. Under salt stress, the tolerant QXH0121 line exhibited good performance, while in the sensitive QXN233 line, there were negative effects on the growth of the leaves and roots. The most important finding was that QXH0121 could reshift Na+ from shoots into long roots, migrate excess Na+ in shoots to alleviate salt damage to shoots, and also improve K+ retention in shoots, which were closely associated with the enhanced expression levels of ZmHAK1 and ZmNHX1 in QXH0121 compared to those in QXN233 under salt stress. Additionally, QXH0121 leaves accumulated more proline, soluble protein, and sugar contents and had higher SOD activity levels than those observed in QXN233, which correlated with the upregulation of ZmP5CR, ZmBADH, ZmTPS1, and ZmSOD4 in QXH0121 leaves. These were the main causes of the higher salt tolerance of QXH0121 in contrast to QXN233. These results broaden our knowledge about the underlying mechanism of salt tolerance in different maize varieties, providing novel insights into breeding maize with a high level of salt resistance.

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“…Recently, it was shown that circular RNAs are involved in reprogramming the genomic function during adaptation to salt stress in maize [ 12 ]. It was also revealed that salt stress causes several epigenetic changes [ 13 ] including histone modifications [ 14 ], alterations of DNA methylation processes, and causes other epigenetic changes [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

Effect of Salt Stress on the Activity, Expression, and Promoter Methylation of Succinate Dehydrogenase and Succinic Semialdehyde Dehydrogenase in Maize (Zea mays L.) Leaves

Федорин

Епринцев

Caro

et al. 2022

Plants

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The effect of salt stress on the expression of genes, the methylation of their promoters, and the enzymatic activity of succinate dehydrogenase (SDH) and succinic semialdehyde dehydrogenase (SSADH) was investigated in maize (Zea mays L.). The incubation of maize seedlings in a 150 mM NaCl solution for 24 h led to a several-fold increase in the activity of SSADH that peaked at 6 h of NaCl treatment, which was preceded by an increase in the Ssadh1 gene expression and a decrease in its promoter methylation observed at 3 h of salt stress. The increase in SDH activity and succinate oxidation by mitochondria was slower, developing by 24 h of NaCl treatment, which corresponded to the increase in expression of the genes Sdh1-2 and Sdh2-3 encoding SDH catalytic subunits and of the gene Sdh3-1 encoding the anchoring SDH subunit. The increase in the Sdh2-3 expression was accompanied by the decrease in promoter methylation. It is concluded that salt stress results in the rapid increase in succinate production via SSADH operating in the GABA shunt, which leads to the activation of SDH, the process partially regulated via epigenetic mechanisms. The role of succinate metabolism under the conditions of salt stress is discussed.

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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

Cited by 15 publications

References 86 publications

Comparative Analysis of miRNA Expression Profiles under Salt Stress in Wheat

Comparative Analysis of miRNA Expression Profiles under Salt Stress in Wheat

Reshifting Na+ from Shoots into Long Roots Is Associated with Salt Tolerance in Two Contrasting Inbred Maize (Zea mays L.) Lines

Effect of Salt Stress on the Activity, Expression, and Promoter Methylation of Succinate Dehydrogenase and Succinic Semialdehyde Dehydrogenase in Maize (Zea mays L.) Leaves

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