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Ma Q, Niu C, Wang C, Chen C, Li Y, Wei M. Effects of differentially expressed microRNAs induced by rootstocks and silicon on improving chilling tolerance of cucumber seedlings (Cucumis sativus L.). BMC Genomics 2023; 24:250. [PMID: 37165319 PMCID: PMC10173649 DOI: 10.1186/s12864-023-09337-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/26/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Rootstocks can improve the chilling tolerance of grafted cucumbers, but their effectiveness varies. Rootstocks with strong de-blooming capacity may result in lower chilling tolerance of grafted cucumbers compared to those with weak de-blooming capacity, while also reducing the silicon absorption. However, it remains unclear whether this reduction in chilling tolerance is due to differences in rootstock genotypes or the reduction in silicon absorption. RESULTS The chilling tolerance of cucumber seedlings was improved by using rootstocks and silicon nutrition. Rootstocks had a more significant effect than silicon nutrition, and the weak de-blooming rootstock 'Yunnan figleaf gourd' was superior to the strong de-blooming rootstock 'Huangchenggen No. 2'. Compared to self-rooted cucumber, twelve miRNAs were regulated by two rootstocks, including seven identical miRNAs (novel-mir23, novel-mir26, novel-mir30, novel-mir37, novel-mir46, miR395a and miR398a-3p) and five different miRNAs (novel-mir32, novel-mir38, novel-mir65, novel-mir78 and miR397a). Notably, four of these miRNAs (novel-mir38, novel-mir65, novel-mir78 and miR397a) were only identified in 'Yunnan figleaf gourd'-grafted cucumbers. Furthermore, six miRNAs (miR168a-5p, miR390a-5p, novel-mir26, novel-mir55, novel-mir67 and novel-mir70) were found to be responsive to exogenous silicon. Target gene prediction for 20 miRNAs resulted in 520 genes. Functional analysis of these target genes showed that 'Yunnan figleaf gourd' improves the chilling tolerance of cucumber by regulating laccase synthesis and sulfate metabolism, while 'Huangchenggen No. 2' and exogenous silicon reduced chilling stress damage to cucumber by regulating ROS scavenging and protein protection, respectively. CONCLUSION Among the identified miRNAs, novel-mir46 and miR398a-3p were found in cucumbers in response to chilling stress and two types of rootstocks. However, no identical miRNAs were identified in response to chilling stress and silicon. In addition, the differential expression of novel-mir38, novel-mir65, novel-mir78 and miR397a may be one of the important reasons for the differences in chilling tolerance of grafted cucumbers caused by two types of rootstocks.
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Affiliation(s)
- Qiang Ma
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
| | - Chenxu Niu
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
| | - Chao Wang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
- Scientific Observing and Experimental Station of Environment Controlled Agricultural Engineering in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Taian, 271018, China
- State Key Laboratory of Crop Biology, Taian, 271018, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Taian, 271018, China
| | - Chunhua Chen
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
- State Key Laboratory of Crop Biology, Taian, 271018, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Taian, 271018, China
| | - Yan Li
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
- Scientific Observing and Experimental Station of Environment Controlled Agricultural Engineering in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Taian, 271018, China
- State Key Laboratory of Crop Biology, Taian, 271018, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Taian, 271018, China
| | - Min Wei
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China.
- Scientific Observing and Experimental Station of Environment Controlled Agricultural Engineering in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Taian, 271018, China.
- State Key Laboratory of Crop Biology, Taian, 271018, China.
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Taian, 271018, China.
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Lu L, Luo W, Yu W, Zhou J, Wang X, Sun Y. Identification and Characterization of Csa-miR395s Reveal Their Involvements in Fruit Expansion and Abiotic Stresses in Cucumber. FRONTIERS IN PLANT SCIENCE 2022; 13:907364. [PMID: 35783939 PMCID: PMC9240705 DOI: 10.3389/fpls.2022.907364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/13/2022] [Indexed: 05/06/2023]
Abstract
The miR395 plays an indispensable role in biochemical processes by regulating their target genes. However, little is known about the roles of miR395 in cucumber fruit expansion and response to abiotic stresses. Here, 4 Csa-miR395s and 8 corresponding target genes were identified in the cucumber genome. Csa-miR395s were all located on the same chromosome (Chr 5). Csa-miR395a/b/c and Csa-miR395d were distributed in different branches without a closer genetic relationship. Massive cis-acting elements, including light, phytohormone, and stress response elements, were detected in the promoter regions of Csa-MIR395s, indicating that Csa-miR395s might be involved in complex regulatory networks to control cucumber growth and development and stress response. In addition, Csa-miR395a/b/c shared the same target genes, and Csa-miR395d had its specific target genes. Tissue-specific expression analysis showed that Csa-miR395a/b/c were all expressed in the leaf, root, ovary, and expanded fruit of cucumber and highly expressed in the expanded fruits compared to the ovary, while Csa2G215520 and Csa1G502860 (target genes of Csa-miR395a/b/c) presented a downregulated trend in the expanded fruit compared to the ovary. Meanwhile, the protein co-expression network revealed that these target genes had interactions in sulfur metabolism. These results suggested that Csa-miR395a/b/c targeting Csa2G215520 and Csa1G502860 might promote cucumber fruit expansion by affecting sulfur metabolism. Additionally, Quantitative Real-time PCR analysis validated that Csa-miR395s could be regulated by NaCl stress, and Csa-miR395a/b/c could respond to PEG stress, which further confirmed the reliability of cis-acting elements data. Taken together, our results could be helpful for further exploration of the functions of miR395s in cucumber fruit expansion and response to abiotic stresses.
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Affiliation(s)
- Lin Lu
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Weirong Luo
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Wenjin Yu
- College of Agriculture, Guangxi University, Nanning, China
| | - Junguo Zhou
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Xinfa Wang
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Yongdong Sun
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
- *Correspondence: Yongdong Sun
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