Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting <i>Indica</i> Rice Cultivars under Reproductive-Stage Drought
Recurrent occurrence of drought stress in varying intensity has become a common phenomenon in the present era of global climate change, which not only causes severe yield losses but also challenges the cultivation of rice. This raises serious concerns for sustainable food production and global food...
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MDPI AG
2023-07-01
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| Series: | Genes |
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| author | Simardeep Kaur Karishma Seem Suresh Kumar Rakesh Kaundal Trilochan Mohapatra |
| author_facet | Simardeep Kaur Karishma Seem Suresh Kumar Rakesh Kaundal Trilochan Mohapatra |
| author_sort | Simardeep Kaur |
| collection | DOAJ |
| description | Recurrent occurrence of drought stress in varying intensity has become a common phenomenon in the present era of global climate change, which not only causes severe yield losses but also challenges the cultivation of rice. This raises serious concerns for sustainable food production and global food security. The root of a plant is primarily responsible to perceive drought stress and acquire sufficient water for the survival/optimal growth of the plant under extreme climatic conditions. Earlier studies reported the involvement/important roles of microRNAs (miRNAs) in plants’ responses to environmental/abiotic stresses. A number (738) of miRNAs is known to be expressed in different tissues under varying environmental conditions in rice, but our understanding of the role, mode of action, and target genes of the miRNAs are still elusive. Using contrasting rice [IR-64 (reproductive-stage drought sensitive) and N-22 (drought-tolerant)] cultivars, imposed with terminal (reproductive-stage) drought stress, we demonstrate differential expression of 270 known and 91 novel miRNAs in roots of the contrasting rice cultivars in response to the stress. Among the known miRNAs, osamiR812, osamiR166, osamiR156, osamiR167, and osamiR396 were the most differentially expressed miRNAs between the rice cultivars. In the root of N-22, 18 known and 12 novel miRNAs were observed to be exclusively expressed, while only two known (zero novels) miRNAs were exclusively expressed in the roots of IR-64. The majority of the target gene(s) of the miRNAs were drought-responsive transcription factors playing important roles in flower, grain development, auxin signaling, root development, and phytohormone-crosstalk. The novel miRNAs identified in this study may serve as good candidates for the genetic improvement of rice for terminal drought stress towards developing climate-smart rice for sustainable food production. |
| first_indexed | 2024-03-11T01:03:06Z |
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| language | English |
| last_indexed | 2024-03-11T01:03:06Z |
| publishDate | 2023-07-01 |
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| series | Genes |
| spelling | doaj.art-cb39246a7d334a8282609816d65fa4ad2023-11-18T19:29:45ZengMDPI AGGenes2073-44252023-07-01147139010.3390/genes14071390Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting <i>Indica</i> Rice Cultivars under Reproductive-Stage DroughtSimardeep Kaur0Karishma Seem1Suresh Kumar2Rakesh Kaundal3Trilochan Mohapatra4Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaDivision of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaDivision of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaDepartment of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USAIndian Council of Agricultural Research, New Delhi 110012, IndiaRecurrent occurrence of drought stress in varying intensity has become a common phenomenon in the present era of global climate change, which not only causes severe yield losses but also challenges the cultivation of rice. This raises serious concerns for sustainable food production and global food security. The root of a plant is primarily responsible to perceive drought stress and acquire sufficient water for the survival/optimal growth of the plant under extreme climatic conditions. Earlier studies reported the involvement/important roles of microRNAs (miRNAs) in plants’ responses to environmental/abiotic stresses. A number (738) of miRNAs is known to be expressed in different tissues under varying environmental conditions in rice, but our understanding of the role, mode of action, and target genes of the miRNAs are still elusive. Using contrasting rice [IR-64 (reproductive-stage drought sensitive) and N-22 (drought-tolerant)] cultivars, imposed with terminal (reproductive-stage) drought stress, we demonstrate differential expression of 270 known and 91 novel miRNAs in roots of the contrasting rice cultivars in response to the stress. Among the known miRNAs, osamiR812, osamiR166, osamiR156, osamiR167, and osamiR396 were the most differentially expressed miRNAs between the rice cultivars. In the root of N-22, 18 known and 12 novel miRNAs were observed to be exclusively expressed, while only two known (zero novels) miRNAs were exclusively expressed in the roots of IR-64. The majority of the target gene(s) of the miRNAs were drought-responsive transcription factors playing important roles in flower, grain development, auxin signaling, root development, and phytohormone-crosstalk. The novel miRNAs identified in this study may serve as good candidates for the genetic improvement of rice for terminal drought stress towards developing climate-smart rice for sustainable food production.https://www.mdpi.com/2073-4425/14/7/1390<i>Oryza sativa</i> L.abiotic stressterminal droughtmiRNome profilenovel miRNAstranscription factor |
| spellingShingle | Simardeep Kaur Karishma Seem Suresh Kumar Rakesh Kaundal Trilochan Mohapatra Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting <i>Indica</i> Rice Cultivars under Reproductive-Stage Drought Genes <i>Oryza sativa</i> L. abiotic stress terminal drought miRNome profile novel miRNAs transcription factor |
| title | Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting <i>Indica</i> Rice Cultivars under Reproductive-Stage Drought |
| title_full | Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting <i>Indica</i> Rice Cultivars under Reproductive-Stage Drought |
| title_fullStr | Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting <i>Indica</i> Rice Cultivars under Reproductive-Stage Drought |
| title_full_unstemmed | Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting <i>Indica</i> Rice Cultivars under Reproductive-Stage Drought |
| title_short | Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting <i>Indica</i> Rice Cultivars under Reproductive-Stage Drought |
| title_sort | comparative genome wide analysis of micrornas and their target genes in roots of contrasting i indica i rice cultivars under reproductive stage drought |
| topic | <i>Oryza sativa</i> L. abiotic stress terminal drought miRNome profile novel miRNAs transcription factor |
| url | https://www.mdpi.com/2073-4425/14/7/1390 |
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