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Kaur S, Seem K, Duhan N, Kumar S, Kaundal R, Mohapatra T. Comparative miRNome and transcriptome analyses reveal the expression of novel miRNAs in the panicle of rice implicated in sustained agronomic performance under terminal drought stress. PLANTA 2024; 259:128. [PMID: 38639776 DOI: 10.1007/s00425-024-04399-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/27/2024] [Indexed: 04/20/2024]
Abstract
MAIN CONCLUSION Differential expression of 128 known and 111 novel miRNAs in the panicle of Nagina 22 under terminal drought stress targeting transcription factors, stress-associated genes, etc., enhances drought tolerance and helps sustain agronomic performance under terminal drought stress. Drought tolerance is a complex multigenic trait, wherein the genes are fine-tuned by coding and non-coding components in mitigating deleterious effects. MicroRNA (miRNA) controls gene expression at post-transcriptional level either by cleaving mRNA (transcript) or by suppressing its translation. miRNAs are known to control developmental processes and abiotic stress tolerance in plants. To identify terminal drought-responsive novel miRNA in contrasting rice cultivars, we constructed small RNA (sRNA) libraries from immature panicles of drought-tolerant rice [Nagina 22 (N 22)] and drought-sensitive (IR 64) cultivars grown under control and terminal drought stress. Our analysis of sRNA-seq data resulted in the identification of 169 known and 148 novel miRNAs in the rice cultivars. Among the novel miRNAs, 68 were up-regulated while 43 were down-regulated in the panicle of N 22 under stress. Interestingly, 31 novel miRNAs up-regulated in N 22 were down-regulated in IR 64, whereas 4 miRNAs down-regulated in N 22 were up-regulated in IR 64 under stress. To detect the effects of miRNA on mRNA expression level, transcriptome analysis was performed, while differential expression of miRNAs and their target genes was validated by RT-qPCR. Targets of the differentially expressed miRNAs include transcription factors and stress-associated genes involved in cellular/metabolic/developmental processes, response to abiotic stress, programmed cell death, photosynthesis, panicle/seed development, and grain yield. Differential expression of the miRNAs could be validated in an independent set of the samples. The findings might be useful in genetic improvement of drought-tolerant rice.
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Affiliation(s)
- Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
- ICAR-Research Complex for North Eastern Hill Region (NEH), Umiam, Meghalaya, 793103, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Naveen Duhan
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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2
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Szymonik K, Klimek-Chodacka M, Lukasiewicz A, Macko-Podgórni A, Grzebelus D, Baranski R. Comparative analysis of the carrot miRNAome in response to salt stress. Sci Rep 2023; 13:21506. [PMID: 38057586 PMCID: PMC10700493 DOI: 10.1038/s41598-023-48900-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
Soil salinity adversely affects the yield and quality of crops, including carrot. During salt stress, plant growth and development are impaired by restricted water uptake and ion cytotoxicity, leading to nutrient imbalance and oxidative burst. However, the molecular mechanisms of the carrot plant response to salt stress remain unclear. The occurrence and expression of miRNAs that are potentially involved in the regulation of carrot tolerance to salinity stress were investigated. The results of small RNA sequencing revealed that salt-sensitive (DH1) and salt-tolerant (DLBA) carrot varieties had different miRNA expression profiles. A total of 95 miRNAs were identified, including 71 novel miRNAs, of which 30 and 23 were unique to DH1 and DLBA, respectively. The comparison of NGS and qPCR results allowed identification of two conserved and five novel miRNA involved in carrot response to salt stress, and which differentiated the salt-tolerant and salt-sensitive varieties. Degradome analysis supported by in silico-based predictions and followed by expression analysis of exemplary target genes pointed at genes related to proline, glutathione, and glutamate metabolism pathways as potential miRNA targets involved in salt tolerance, and indicated that the regulation of osmoprotection and antioxidant protection, earlier identified as being more efficient in the tolerant variety, may be controlled by miRNAs. Furthermore, potential miRNA target genes involved in chloroplast protection, signal transduction and the synthesis and modification of cell wall components were indicated in plants growing in saline soil.
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Affiliation(s)
- Kamil Szymonik
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland.
| | - Magdalena Klimek-Chodacka
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland.
| | - Aneta Lukasiewicz
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland
| | - Alicja Macko-Podgórni
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland
| | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland
| | - Rafal Baranski
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland.
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3
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Wang Y, Liu K, Zhou Y, Chen Y, Jin C, Hu Y. Integrated Analysis of microRNA and RNA-Seq Reveals Phenolic Acid Secretion Metabolism in Continuous Cropping of Polygonatum odoratum. PLANTS (BASEL, SWITZERLAND) 2023; 12:943. [PMID: 36840290 PMCID: PMC9962977 DOI: 10.3390/plants12040943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Polygonatum odoratum (Mill.) Druce is an essential Chinese herb, but continuous cropping (CC) often results in a serious root rot disease, reducing the yield and quality. Phenolic acids, released through plant root exudation, are typical autotoxic substances that easily cause root rot in CC. To better understand the phenolic acid biosynthesis of P. odoratum roots in response to CC, this study performed a combined microRNA (miRNA)-seq and RNA-seq analysis. The phenolic acid contents of the first cropping (FC) soil and CC soil were determined by HPLC analysis. The results showed that CC soils contained significantly higher levels of p-coumaric acid, phenylacetate, and caffeic acid than FC soil, except for cinnamic acid and sinapic acid. Transcriptome identification and miRNA sequencing revealed 15,788 differentially expressed genes (DEGs) and 142 differentially expressed miRNAs (DEMs) in roots from FC and CC plants. Among them, 28 DEGs and eight DEMs were involved in phenolic acid biosynthesis. Meanwhile, comparative transcriptome and microRNA-seq analysis demonstrated that eight miRNAs corresponding to five target DEGs related to phenolic acid synthesis were screened. Among them, ath-miR172a, ath-miR172c, novel_130, sbi-miR172f, and tcc-miR172d contributed to phenylalanine synthesis. Osa-miR528-5p and mtr-miR2673a were key miRNAs that regulate syringyl lignin biosynthesis. Nta-miR156f was closely related to the shikimate pathway. These results indicated that the key DEGs and DEMs involved in phenolic acid anabolism might play vital roles in phenolic acid secretion from roots of P. odoratum under the CC system. As a result of the study, we may have a better understanding of phenolic acid biosynthesis during CC of roots of P. odoratum.
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Affiliation(s)
- Yan Wang
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha 410082, China
| | - Kaitai Liu
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Yunyun Zhou
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Yong Chen
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Chenzhong Jin
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Yihong Hu
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
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Lin B, Ma H, Zhang K, Cui J. Regulatory mechanisms and metabolic changes of miRNA during leaf color change in the bud mutation branches of Acer pictum subsp. mono. FRONTIERS IN PLANT SCIENCE 2023; 13:1047452. [PMID: 36714704 PMCID: PMC9879609 DOI: 10.3389/fpls.2022.1047452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Acer pictum subsp. mono is a colorful tree species with considerable ornamental and economic value. However, little is known about the metabolism and regulatory mechanism of leaf color change in A. p. subsp. mono. To reveal the molecular mechanism of leaf color change in A. p. subsp. mono, the present study examined the bud mutation branches and compared the metabolites of the red leaves (AR) of the bud mutation branches of A. p. subsp. mono with those of the green leaves (AG) of the wild-type branches. It was found that the chlorophyll and carotenoids content of the red leaves decreased significantly, while anthocyanins, and various antioxidant enzymes increased significantly compared with the green leaves. The glycosides cyanidin, pelargonidin, malvidin, petunidin, delphinidin, and peonidin were detected in AR by liquid chromatography-mass spectrometry. The cyanidin glycosides increased, and cyanidin 3-O-glycoside was significantly upregulated. We analyzed the transcriptome and small RNA of A. p. subsp. mono leaves and detected 4061 differentially expressed mRNAs and 116 differentially expressed miRNAs. Through miRNA-mRNA association analysis, five differentially expressed modules were found; one miRNA targeted three genes, and four miRNAs targeted a single gene. Among them, miR160b, miR6300, and miR396g were found to be the key miRNAs regulating stable anthocyanin accumulation in A. p. subsp. mono leaves. By revealing the physiological response of leaf color change and the molecular regulatory mechanism of the miRNA, this study provides new insight into the molecular regulatory mechanism of leaf color change, thereby offering a foundation for future studies.
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Affiliation(s)
- Baoli Lin
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - He Ma
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Kezhong Zhang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
- Laboratory of Urban and Rural Ecological Environment, Beijing University of Agriculture, Beijing, China
| | - Jinteng Cui
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
- Laboratory of Urban and Rural Ecological Environment, Beijing University of Agriculture, Beijing, China
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5
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Jeena GS, Singh N, Shukla RK. An insight into microRNA biogenesis and its regulatory role in plant secondary metabolism. PLANT CELL REPORTS 2022; 41:1651-1671. [PMID: 35579713 DOI: 10.1007/s00299-022-02877-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
The present review highlights the regulatory roles of microRNAs in plant secondary metabolism and focuses on different bioengineering strategies to modulate secondary metabolite content in plants. MicroRNAs (miRNAs) are the class of small endogenous, essential, non-coding RNAs that riboregulate the gene expression involved in various biological processes in most eukaryotes. MiRNAs has emerged as important regulators in plants that function by silencing target genes through cleavage or translational inhibition. These miRNAs plays an important role in a wide range of plant biological and metabolic processes, including plant development and various environmental response controls. Several important plant secondary metabolites like alkaloids, terpenoids, and phenolics are well studied for their function in plant defense against different types of pests and herbivores. Due to the presence of a wide range of biological and pharmaceutical properties of plant secondary metabolites, it is important to study the regulation of their biosynthetic pathways. The contribution of miRNAs in regulating plant secondary metabolism is not well explored. Recent advancements in molecular techniques have improved our knowledge in understanding the molecular function of genes, proteins, enzymes, and small RNAs involved in different steps of secondary metabolic pathways. In the present review, we have discussed the recent progress made on miRNA biogenesis, its regulation, and highlighted the current research developed in the field of identification, analysis, and characterizations of various miRNAs that regulate plant secondary metabolism. We have also discussed how different bioengineering strategies such as artificial miRNA (amiRNA), endogenous target mimicry, and CRISPR/Cas9 could be utilized to enhance the secondary metabolite production in plants.
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Affiliation(s)
- Gajendra Singh Jeena
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India
| | - Neeti Singh
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Rakesh Kumar Shukla
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
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6
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Begum Y. Regulatory role of microRNAs (miRNAs) in the recent development of abiotic stress tolerance of plants. Gene 2022; 821:146283. [PMID: 35143944 DOI: 10.1016/j.gene.2022.146283] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/12/2022] [Accepted: 02/03/2022] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are a distinct groups of single-stranded non-coding, tiny regulatory RNAs approximately 20-24 nucleotides in length. miRNAs negatively influence gene expression at the post-transcriptional level and have evolved considerably in the development of abiotic stress tolerance in a number of model plants and economically important crop species. The present review aims to deliver the information on miRNA-mediated regulation of the expression of major genes or Transcription Factors (TFs), as well as genetic and regulatory pathways. Also, the information on adaptive mechanisms involved in plant abiotic stress responses, prediction, and validation of targets, computational tools, and databases available for plant miRNAs, specifically focus on their exploration for engineering abiotic stress tolerance in plants. The regulatory function of miRNAs in plant growth, development, and abiotic stresses consider in this review, which uses high-throughput sequencing (HTS) technologies to generate large-scale libraries of small RNAs (sRNAs) for conventional screening of known and novel abiotic stress-responsive miRNAs adds complexity to regulatory networks in plants. The discoveries of miRNA-mediated tolerance to multiple abiotic stresses, including salinity, drought, cold, heat stress, nutritional deficiency, UV-radiation, oxidative stress, hypoxia, and heavy metal toxicity, are highlighted and discussed in this review.
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Affiliation(s)
- Yasmin Begum
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, APC Road, Kolkata 700009, West Bengal, India; Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, JD-2, Sector III, Salt Lake, Kolkata 700106, West Bengal, India.
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7
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Abbas A, Shah AN, Tanveer M, Ahmed W, Shah AA, Fiaz S, Waqas MM, Ullah S. MiRNA fine tuning for crop improvement: using advance computational models and biotechnological tools. Mol Biol Rep 2022; 49:5437-5450. [PMID: 35182321 DOI: 10.1007/s11033-022-07231-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/04/2022] [Indexed: 12/17/2022]
Abstract
MiRNAs modulate target genes expression at post-transcriptional levels, by reducing spatial abundance of mRNAs. MiRNAs regulats plant metabolism, and emerged as regulators of plant stress responses. Which make miRNAs promising candidates for fine tuning to affectively alter crop stress tolerance and other important traits. With recent advancements in the computational biology and biotechnology miRNAs structure and target prediction is possible resulting in pin point editing; miRNA modulation can be done by up or down regulating miRNAs using recently available biotechnological tools (CRISPR Cas9, TALENS and RNAi). In this review we have focused on miRNA biogenesis, miRNA roles in plant development, plant stress responses and roles in signaling pathways. Additionally we have discussed latest computational prediction models for miRNA to target gene interaction and biotechnological systems used recently for miRNA modulation. We have also highlighted setbacks and limitations in the way of miRNA modulation; providing entirely a new direction for improvement in plant genomics primarily focusing miRNAs.
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Affiliation(s)
- Asad Abbas
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan 64200, Punjab, Pakistan.
| | - Mohsin Tanveer
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
| | - Waseem Ahmed
- Department of Horticulture, The University of Haripur, Hatatr Road, Haripur, 22620, Pakistan
| | - Anis Ali Shah
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Muhammad Mohsin Waqas
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan 64200, Punjab, Pakistan
| | - Sami Ullah
- Department of Chemistry, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
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8
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Chen J, Luo Y, Cao J, Xie L. Fluoride exposure changed the expression of microRNAs in gills of male zebrafish (Danio rerio). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 233:105789. [PMID: 33667915 DOI: 10.1016/j.aquatox.2021.105789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
Fluoride has been found to cause detrimental effects on fish gills. Despite essential roles in various metabolism activities, whether and how miRNAs participate in the course of toxicity caused by fluoride in gills is still unclear. In this study, male zebrafish were exposed to 0, 20, 40 mg/L fluoride for 60 days to study the underlying osmotic regulatory mechanism by determining the influences of fluoride on the miRNAs and regulated genes in gills. mRNAs were isolated from the gills and the expression profiles were analyzed by using Illumina Hiseq 2500 platforms. Expressions of 7 differentially miRNAs and some related-genes in gills were validated by qRT-PCR. The results showed that miRNAs expressions were notably altered by fluoride. A total of 584 and 327 miRNAs were remarkably changed after 20 and 40 mg/L fluoride exposure, of which 322 were increased and 262 were decreased in 20 mg/L fluoride group, whereas 219 were elevated and 108 were reduced in 40 mg/L fluoride group. The differentially expressive miRNAs confirmed by qRT-PCR were consistent with micro-assay data. Cluster of Orthologous Groups of proteins (COG) function classification showed that the target genes of differentially expressive miRNAs are mainly related to signal transduction mechanisms, replication, transcription, inorganic ion transport and metabolism, repair and recombination, and energy formation and transformation. In addition, fluoride disturbed the expressions of target genes involved in the osmoregulation of the gill in the fluoride-exposed zebrafish, such as the increased expressions of OSTF1 and the decreased expressions of Na+-K+-ATPase, CFTR, and AQP-3, which provides a possibility that miRNAs regulation induced by fluoride has an effects on osmotic regulation, providing new hints to the osmotic regulatory mechanism of the toxicity caused by fluoride in zebrafish, and distinguishes new biomarkers of miRNAs for fluoride toxicity.
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Affiliation(s)
- Jianjie Chen
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Yongju Luo
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Science, Nanning, Guangxi, 530021, China
| | - Jinling Cao
- College of Food Science and Technology, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
| | - Lingtian Xie
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou, 510006, China.
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9
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Zhao X, Yang G, Liu X, Yu Z, Peng S. Integrated Analysis of Seed microRNA and mRNA Transcriptome Reveals Important Functional Genes and microRNA-Targets in the Process of Walnut ( Juglans regia) Seed Oil Accumulation. Int J Mol Sci 2020; 21:ijms21239093. [PMID: 33260456 PMCID: PMC7731449 DOI: 10.3390/ijms21239093] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/17/2020] [Accepted: 11/27/2020] [Indexed: 11/30/2022] Open
Abstract
Walnut (Juglans regia) is known as a promising woody oil crop with abundant polyunsaturated fatty acids in its kernel. However, the regulation mechanism of walnut oil accumulation and fatty acid metabolism is still poorly understood, which restricted the breeding and genetic improvement of high-quality oil-bearing walnuts. To reveal the molecular mechanism of walnut oil accumulation, considering the potential regulation of microRNA (miRNA) in seed development, in this study, the oil content of walnut kernel on the 80th, 100th and 120th day after flowering (DAF) was tested and the corresponding proportions are 11.51%, 40.40% and 53.20%. Between DAF of 80th~120th, the content of stearic acid and oleic acid tended to increase, but the proportion of other fatty acids tended to decrease. Meanwhile, comparative transcriptome and sRNA-seq analysis on three stages (80th, 100th and 120th DAF), found 204 conserved miRNAs and 554 novel miRNAs in walnut kernels, among which 104 key genes related to walnut oil accumulation were screened. The phospholipid:diacylglycerol acyltransferase metabolic pathway may contribute more to oil accumulation in walnut. 16 miRNA-mRNA regulatory modules related to walnut oil accumulation and fatty acid synthesis were constructed. 8 known miRNAs and 9 novel miRNAs regulate 28 genes involved in fatty acid (FA) metabolism and lipid synthesis. Among them, jre-miRn105, jre-miRn434, jre-miR477d and jre-miR156a.2 are key miRNAs that regulate walnut FA synthesis. Jre-miRn411 and jre-miR399a.1 are closely related to oil accumulation. These data provide new insights and lay the foundation for subsequent studies on walnut FA synthesis and oil accumulation.
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Affiliation(s)
- Xinchi Zhao
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling 712100, Shaanxi, China; (X.Z.); (G.Y.); (Z.Y.)
| | - Guiyan Yang
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling 712100, Shaanxi, China; (X.Z.); (G.Y.); (Z.Y.)
| | - Xiaoqiang Liu
- Department of Foreign Languages, Northwest A & F University, Yangling 712100, Shaanxi, China;
| | - Zhongdong Yu
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling 712100, Shaanxi, China; (X.Z.); (G.Y.); (Z.Y.)
| | - Shaobing Peng
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling 712100, Shaanxi, China; (X.Z.); (G.Y.); (Z.Y.)
- Correspondence: ; Tel.: +86-135-7293-1369
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10
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Asefpour Vakilian K. Gold nanoparticles-based biosensor can detect drought stress in tomato by ultrasensitive and specific determination of miRNAs. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 145:195-204. [PMID: 31706222 DOI: 10.1016/j.plaphy.2019.10.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 05/16/2023]
Abstract
Drought stress can significantly affect the yield and quality of tomato production. However, the development of a sensitive and specific method for the determination of drought stress is somehow challenging since plant common morpho-physiological and biochemical characteristic are not generally specific to biotic and abiotic stresses. As a solution, the concentration of miRNAs in plant tissues can be a selective and specific indicator of plant stress. In this study, an optical biosensor based on gold nanoparticles is introduced to determine miRNA-1886 in tomato plant roots. Results showed that irrigation levels from 100% to 60% of field capacity increased the concentration of miRNA-1886 in a range from ca. 100 to 6800 fM (fM) causing a linear change in the biosensor response (R2 = 0.97). Results also revealed that in contrast with plant conventional morpho-physiological and biochemical characteristic, miRNA-1886 concentration was not significantly affected (P < 0.01) by other stresses, i.e., salinity and temperature during the growth period. The biosensor introduced in this study is a reliable method to study stress-related functions of miRNAs in plants and their application in specific plant stress determination.
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Affiliation(s)
- Keyvan Asefpour Vakilian
- Department of Agrotechnology, College of Abouraihan, University of Tehran, Tehran, Iran; Private Laboratory of Biosensor Applications, Hamadan, Iran.
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