Characteristics of microRNAs and Target Genes in Maize Root under Drought Stress
Maize (<i>Zea mays</i>) is an important multi-functional crop. The growth and yield of maize are severely affected by drought stress. Previous studies have shown that microRNAs (miRNAs) in maize play important roles in response to abiotic stress; however, their roles in response to droug...
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MDPI AG
2022-04-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/9/4968 |
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| author | Qi Tang Haozhe Lv Qimeng Li Xiaoyue Zhang Le Li Jie Xu Fengkai Wu Qingjun Wang Xuanjun Feng Yanli Lu |
| author_facet | Qi Tang Haozhe Lv Qimeng Li Xiaoyue Zhang Le Li Jie Xu Fengkai Wu Qingjun Wang Xuanjun Feng Yanli Lu |
| author_sort | Qi Tang |
| collection | DOAJ |
| description | Maize (<i>Zea mays</i>) is an important multi-functional crop. The growth and yield of maize are severely affected by drought stress. Previous studies have shown that microRNAs (miRNAs) in maize play important roles in response to abiotic stress; however, their roles in response to drought stress in maize roots is unclear. In our study, we found 375 miRNAs in the roots of 16 inbred lines. Of the 16 lines, zma-MIR168, zma-MIR156, and zma-MIR166 were highly expressed, whereas zma-MIR399, zma-MIR2218, and zma-MIR2275 exhibited low expression levels. The expression patterns of miRNA in parental lines and their derived RILs are different. Over 50% of miRNAs exhibited a lower expression in recombinant inbred lines than in parents. The expression of 50 miRNAs was significantly altered under water stress (WS) in at least three inbred lines, and the expression of miRNAs in drought-tolerant lines changed markedly. To better understand the reasons for miRNA response to drought, the degree of histone modifications for miRNA genes was estimated. The methylation level of H3K4 and H3K9 in miRNA precursor regions changed more noticeably after WS, but no such phenomenon was seen for DNA methylation and m6A modification. After the prediction of miRNA targets using psRNATarget and psRobot, we used correlation analysis and qRT-PCR to further investigate the relationship between miRNAs and target genes. We found that 87 miRNA–target pairs were significantly negatively correlated. In addition, a weighted gene co-expression network analysis using miRNAs, as well as their predicted targets, was conducted to reveal that miR159, miR394, and miR319 may be related to maize root growth. The results demonstrated that miRNAs might play essential roles in the response to drought stress. |
| first_indexed | 2024-03-10T04:05:18Z |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T04:05:18Z |
| publishDate | 2022-04-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-599b7cb737a7410e99779661cb97e8352023-11-23T08:24:58ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-04-01239496810.3390/ijms23094968Characteristics of microRNAs and Target Genes in Maize Root under Drought StressQi Tang0Haozhe Lv1Qimeng Li2Xiaoyue Zhang3Le Li4Jie Xu5Fengkai Wu6Qingjun Wang7Xuanjun Feng8Yanli Lu9State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, ChinaState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, ChinaState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, ChinaState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, ChinaState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, ChinaState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, ChinaState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, ChinaState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, ChinaState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, ChinaState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, ChinaMaize (<i>Zea mays</i>) is an important multi-functional crop. The growth and yield of maize are severely affected by drought stress. Previous studies have shown that microRNAs (miRNAs) in maize play important roles in response to abiotic stress; however, their roles in response to drought stress in maize roots is unclear. In our study, we found 375 miRNAs in the roots of 16 inbred lines. Of the 16 lines, zma-MIR168, zma-MIR156, and zma-MIR166 were highly expressed, whereas zma-MIR399, zma-MIR2218, and zma-MIR2275 exhibited low expression levels. The expression patterns of miRNA in parental lines and their derived RILs are different. Over 50% of miRNAs exhibited a lower expression in recombinant inbred lines than in parents. The expression of 50 miRNAs was significantly altered under water stress (WS) in at least three inbred lines, and the expression of miRNAs in drought-tolerant lines changed markedly. To better understand the reasons for miRNA response to drought, the degree of histone modifications for miRNA genes was estimated. The methylation level of H3K4 and H3K9 in miRNA precursor regions changed more noticeably after WS, but no such phenomenon was seen for DNA methylation and m6A modification. After the prediction of miRNA targets using psRNATarget and psRobot, we used correlation analysis and qRT-PCR to further investigate the relationship between miRNAs and target genes. We found that 87 miRNA–target pairs were significantly negatively correlated. In addition, a weighted gene co-expression network analysis using miRNAs, as well as their predicted targets, was conducted to reveal that miR159, miR394, and miR319 may be related to maize root growth. The results demonstrated that miRNAs might play essential roles in the response to drought stress.https://www.mdpi.com/1422-0067/23/9/4968miRNAdrought stressmaizeroottarget genes |
| spellingShingle | Qi Tang Haozhe Lv Qimeng Li Xiaoyue Zhang Le Li Jie Xu Fengkai Wu Qingjun Wang Xuanjun Feng Yanli Lu Characteristics of microRNAs and Target Genes in Maize Root under Drought Stress International Journal of Molecular Sciences miRNA drought stress maize root target genes |
| title | Characteristics of microRNAs and Target Genes in Maize Root under Drought Stress |
| title_full | Characteristics of microRNAs and Target Genes in Maize Root under Drought Stress |
| title_fullStr | Characteristics of microRNAs and Target Genes in Maize Root under Drought Stress |
| title_full_unstemmed | Characteristics of microRNAs and Target Genes in Maize Root under Drought Stress |
| title_short | Characteristics of microRNAs and Target Genes in Maize Root under Drought Stress |
| title_sort | characteristics of micrornas and target genes in maize root under drought stress |
| topic | miRNA drought stress maize root target genes |
| url | https://www.mdpi.com/1422-0067/23/9/4968 |
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