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Identification of miRNAs and Their Target Genes Involved in Cucumber Fruit Expansion Using Small RNA and Degradome Sequencing. Biomolecules 2019; 9:biom9090483. [PMID: 31547414 PMCID: PMC6769560 DOI: 10.3390/biom9090483] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 11/17/2022] Open
Abstract
Fruit expansion is an essential and very complex biological process. Regulatory roles of microRNAs (miRNAs) and miRNA-mRNA modules in the cucumber fruit expansion are not yet to be investigated. In this work, 1253 known and 1269 novel miRNAs were identified from nine cucumber fruit small RNA (sRNA) libraries through high-throughput sequencing. A total of 105 highly differentially expressed miRNAs were recognized in the fruit on five days post anthesis with pollination (EXP_5d) sRNA library. Further, expression patterns of 11 differentially expressed miRNAs were validated by quantitative real-time PCR (qRT-PCR). The expression patterns were similar to sRNAs sequencing data. Transcripts of 1155 sequences were predicted as target genes of differentially expressed miRNAs by degradome sequencing. Gene Ontology (GO) enrichment showed that these target genes were involved in 24 biological processes, 15 cell components and nine molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that these target genes were significantly enriched in 19 pathways and the enriched KEGG pathways were associated with environmental adaptation, signal transduction and translation. Based on the functional prediction of miRNAs and target genes, our findings suggest that miRNAs have a potential regulatory role in cucumber fruit expansion by targeting their target genes, which provide important data for understanding the miRNA-mediated regulatory networks controlling fruit expansion in cucumber. Specific miRNAs could be selected for further functional research and molecular breeding in cucumber.
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Jiu S, Leng X, Haider MS, Dong T, Guan L, Xie Z, Li X, Shangguan L, Fang J. Identification of copper (Cu) stress-responsive grapevine microRNAs and their target genes by high-throughput sequencing. ROYAL SOCIETY OPEN SCIENCE 2019; 6:180735. [PMID: 30800341 PMCID: PMC6366190 DOI: 10.1098/rsos.180735] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/24/2018] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) are a class of single-stranded non-coding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play important roles in plant growth, development and stress responses. With more copper (Cu) and copper containing compounds used as bactericides and fungicides in plants, Cu stress has become one of the serious environmental problems that affect plant growth and development. In order to uncover the hidden response mechanisms of Cu stress, two small RNA libraries were constructed from Cu-treated and water-treated (Control) leaves of 'Summer Black' grapevine. Following high-throughput sequencing and filtering, a total of 158 known and 98 putative novel miRNAs were identified in the two libraries. Among these, 100 known and 47 novel miRNAs were identified as differentially expressed under Cu stress. Subsequently, the expression patterns of nine Cu-responsive miRNAs were validated by quantitative real-time PCR (qRT-PCR). There existed some consistency in expression levels of Cu-responsive miRNAs between high throughput sequencing and qRT-PCR assays. The targets prediction of miRNAs indicates that miRNA may regulate some transcription factors, including AP2, SBP, NAC, MYB and ARF during Cu stress. The target genes for two known and two novel miRNAs showed specific cleavage sites at the 10th and/or 11th nucleotide from the 5'-end of the miRNA corresponding to their miRNA complementary sequences. The findings will lay the foundation for exploring the role of the regulation of miRNAs in response to Cu stress and provide valuable gene information for breeding some Cu-tolerant grapevine cultivars.
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Affiliation(s)
- Songtao Jiu
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xiangpeng Leng
- College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Muhammad Salman Haider
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
| | - Tianyu Dong
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
| | - Le Guan
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
| | - Zhenqiang Xie
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
| | - Xiaopeng Li
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
| | - Lingfei Shangguan
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
| | - Jinggui Fang
- Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
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Zeng X, Xu Y, Jiang J, Zhang F, Ma L, Wu D, Wang Y, Sun W. Identification of cold stress responsive microRNAs in two winter turnip rape (Brassica rapa L.) by high throughput sequencing. BMC PLANT BIOLOGY 2018; 18:52. [PMID: 29587648 PMCID: PMC5870505 DOI: 10.1186/s12870-018-1242-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/17/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Low temperature is a major abiotic stress affecting the production of rapeseed in China by impeding plant growth and development. A comprehensive knowledge of small-RNA expression pattern in Brassica rapa under cold stress could improve our knowledge of microRNA-mediated stress responses. RESULTS A total of 353 cold-responsive miRNAs, 84 putative novel and 269 conserved miRNAs, were identified from the leaves and roots of two winter turnip rape varieties 'Longyou 7' (cold-tolerant) and 'Tianyou 4' (cold-sensitive), which were stressed under - 4 °C for 8 h. Eight conserved (miR166h-3p-1, miR398b-3p, miR398b-3p-1, miR408d, miR156a-5p, miR396h, miR845a-1, miR166u) and two novel miRNAs (Bra-novel-miR3153-5p and Bra-novel-miR3172-5p) were differentially expressed in leaves of 'Longyou 7' under cold stress. Bra-novel-miR3936-5p was up-regulated in roots of 'Longyou 7' under cold stress. Four and five conserved miRNAs were differentially expressed in leaves and roots of 'Tianyou 4' after cold stress. Besides, we found two conserved miRNAs (miR319e and miR166m-2) were down-regulated in non-stressed roots of 'Longyou 7' compared with 'Tianyou 4'. After cold stress, we found two and eight miRNAs were differentially expressed in leaves and roots of 'Longyou 7' compared with 'Tianyou 4'. The differentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR166 and miR319 families. A total of 211 target genes for 15 known miRNAs and two novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Five differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR, and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR166e, miR319, and Bra-novel-miR3936-5p) may play important roles in plant response to cold stress. CONCLUSIONS Our work indicates that miRNA and putative target genes mediated metabolic processes and stress responses are significant to cold tolerance in B. rapa.
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Affiliation(s)
- Xiucun Zeng
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
| | - Yaozhao Xu
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
| | - Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Fenqin Zhang
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
| | - Li Ma
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
| | - Dewei Wu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Wancang Sun
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
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Ma C, Yang J, Cheng Q, Mao A, Zhang J, Wang S, Weng Y, Wen C. Comparative analysis of miRNA and mRNA abundance in determinate cucumber by high-throughput sequencing. PLoS One 2018; 13:e0190691. [PMID: 29304061 PMCID: PMC5755913 DOI: 10.1371/journal.pone.0190691] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 12/19/2017] [Indexed: 12/31/2022] Open
Abstract
Determinate cucumber is a type of short vines, fewer nodes, and terminal flowers, it is suitable for high-density planting and available harvesting in field cultivation, whereas the indeterminate cucumber is preferred to cultivate in greenhouses. However, many biotic or abiotic stresses could lead indeterminate cucumber to be determinate in greenhouse cultivation, which may decrease yield and fruit quality. Therefore, it is urgent and essential to investigate the key factors forming determinate and terminal flowering in cucumber. In this study, two close background inbred lines were selected and conducted the miRNA and mRNA high throughput sequencing. Interestingly, ethylene-associated miRNAs and mRNAs were intensively obtained, indicating that the plant hormone ethylene is a key factor impacting determinate and terminal flowering in cucumber. The ethylene metabolites analysis showed that significant higher ethylene was observed in determinate line than that in the indeterminate line. The RT-qPCR validation of ethylene related miRNAs Cas-miR172, Cas-miR396, and Cas-miR414 and their target mRNAs showed a significant negative correlation. These data suggested that ethylene-associated miRNAs might affect determinate and terminal flower phenotypes by regulating their target genes expression. This study not only provides a potential molecular mechanism for determinate formation in cucumber but also establishes a method to demonstrate important physiological processes through the comprehensive association of miRNA and mRNA high-throughput sequencing.
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Affiliation(s)
- Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
| | - Qing Cheng
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- College of Horticulture, China Agricultural University, Beijing, China
| | - Aijun Mao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
| | - Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Institute of Agro-food Science and Technology, Key Laboratory of Agro-products Processing Technology of Shandong, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison WI, United States of America
- USDA-ARS Vegetable Crops Research Unit, Madison, WI, United States of America
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- * E-mail:
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Pawełkowicz M, Zieliński K, Zielińska D, Pląder W, Yagi K, Wojcieszek M, Siedlecka E, Bartoszewski G, Skarzyńska A, Przybecki Z. Next generation sequencing and omics in cucumber (Cucumis sativus L.) breeding directed research. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:77-88. [PMID: 26566826 DOI: 10.1016/j.plantsci.2015.07.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/29/2015] [Accepted: 07/28/2015] [Indexed: 05/10/2023]
Abstract
In the post-genomic era the availability of genomic tools and resources is leading us to novel generation methods in plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. In this study we have mainly concentrated on the Cucumis sativus and (but much less) Cucurbitaceae family several important vegetable crops. There are many reports on research conducted in Cucurbitaceae plant breeding programs on the ripening process, phloem transport, disease resistance, cold tolerance and fruit quality traits. This paper presents the role played by new omic technologies in the creation of knowledge on the mechanisms of the formation of the breeding features. The analysis of NGS (NGS-next generation sequencing) data allows the discovery of new genes and regulatory sequences, their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Firstly a high density map should be created for the reference genome, then each re-sequencing data could be mapped and new markers brought out into breeding populations. The paper also presents methods that could be used in the future for the creation of variability and genomic modification of the species in question. It has been shown also the state and usefulness in breeding the chloroplastomic and mitochondriomic study.
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Affiliation(s)
- Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Konrad Zieliński
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Dorota Zielińska
- Department of Food Gastronomy and Food Hygiene, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Kouhei Yagi
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Michał Wojcieszek
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Ewa Siedlecka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Grzegorz Bartoszewski
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Agnieszka Skarzyńska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Zbigniew Przybecki
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
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