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Ruan Q, Bai X, Wang Y, Zhang X, Wang B, Zhao Y, Zhu X, Wei X. Regulation of endogenous hormone and miRNA in leaves of alfalfa (Medicago sativa L.) seedlings under drought stress by endogenous nitric oxide. BMC Genomics 2024; 25:229. [PMID: 38429670 PMCID: PMC10908014 DOI: 10.1186/s12864-024-10024-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 01/17/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Alfalfa (Medicago sativa. L) is one of the best leguminous herbage in China and even in the world, with high nutritional and ecological value. However, one of the drawbacks of alfalfa is its sensitivity to dry conditions, which is a global agricultural problem. The objective of this study was to investigate the regulatory effects of endogenous nitric oxide (NO) on endogenous hormones and related miRNAs in alfalfa seedling leaves under drought stress. The effects of endogenous NO on endogenous hormones such as ABA, GA3, SA, and IAA in alfalfa leaves under drought stress were studied. In addition, high-throughput sequencing technology was used to identify drought-related miRNAs and endogenous NO-responsive miRNAs in alfalfa seedling leaves under drought stress. RESULT By measuring the contents of four endogenous hormones in alfalfa leaves, it was found that endogenous NO could regulate plant growth and stress resistance by inducing the metabolism levels of IAA, ABA, GA3, and SA in alfalfa, especially ABA and SA in alfalfa. In addition, small RNA sequencing technology and bioinformatics methods were used to analyze endogenous NO-responsive miRNAs under drought stress. It was found that most miRNAs were enriched in biological pathways and molecular functions related to hormones (ABA, ETH, and JA), phenylpropane metabolism, and plant stress tolerance. CONCLUSION In this study, the analysis of endogenous hormone signals and miRNAs in alfalfa leaves under PEG and PEG + cPTIO conditions provided an important basis for endogenous NO to improve the drought resistance of alfalfa at the physiological and molecular levels. It has important scientific value and practical significance for endogenous NO to improve plant drought resistance.
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Affiliation(s)
- Qian Ruan
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Pratacultural College, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Xiaoming Bai
- Pratacultural College, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Yizhen Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- College of agronomy, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Xiaofang Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Baoqiang Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Ying Zhao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Xiaolin Zhu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- College of agronomy, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China
| | - Xiaohong Wei
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China.
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou, Gansu, 730070, China.
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou, Gansu, 730070, China.
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Zhang Z, Wang L, Chen W, Fu Z, Zhao S, E Y, Zhang H, Zhang B, Sun M, Han P, Chang Y, Tang K, Gao Y, Zhang H, Li X, Zheng W. Integration of mRNA and miRNA analysis reveals the molecular mechanisms of sugar beet (Beta vulgaris L.) response to salt stress. Sci Rep 2023; 13:22074. [PMID: 38086906 PMCID: PMC10716384 DOI: 10.1038/s41598-023-49641-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/10/2023] [Indexed: 12/18/2023] Open
Abstract
The continuous increase of saline-alkali areas worldwide has led to the emergence of saline-alkali conditions, which are the primary abiotic stress or hindering the growth of plants. Beet is among the main sources of sugar, and its yield and sugar content are notably affected by saline-alkali stress. Despite sugar beet being known as a salt-tolerant crop, there are few studies on the mechanisms underlying its salt tolerance, and previous studies have mainly delineated the crop's response to stress induced by NaCl. Recently, advancements in miRNA-mRNA network analysis have led to an increased understanding of how plants, including sugar beet, respond to stress. In this study, seedlings of beet variety "N98122" were grown in the laboratory using hydroponics culture and were exposed to salt stress at 40 days of growth. According to the phenotypic adaptation of the seedlings' leaves from a state of turgidity to wilting and then back to turgidity before and after exposure, 18 different time points were selected to collect samples for analysis. Subsequently, based on the data of real-time quantitative PCR (qRT-PCR) of salt-responsive genes, the samples collected at the 0, 2.5, 7.5, and 16 h time points were subjected to further analysis with experimental materials. Next, mRNA-seq data led to the identification of 8455 differentially expressed mRNAs (DEMs) under exposure to salt stress. In addition, miRNA-seq based investigation retrieved 3558 miRNAs under exposure to salt stress, encompassing 887 known miRNAs belonging to 783 families and 2,671 novel miRNAs. With the integrated analysis of miRNA-mRNA network, 57 miRNA-target gene pairs were obtained, consisting of 55 DEMIs and 57 DEMs. Afterwards, we determined the pivotal involvement of aldh2b7, thic, and δ-oat genes in the response of sugar beet to the effect of salt stress. Subsequently, we identified the miRNAs novel-m035-5p and novel-m0365-5p regulating the aldh gene and miRNA novel-m0979-3p regulating the thic gene. The findings of miRNA and mRNA expression were validated by qRT-PCR.
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Affiliation(s)
- Ziqiang Zhang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Liang Wang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Wenjin Chen
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Zengjuan Fu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Shangmin Zhao
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Yuanyuan E
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Hui Zhang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Bizhou Zhang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Mengyuan Sun
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Pingan Han
- Inner Mongolia Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Yue Chang
- Inner Mongolia Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Kuangang Tang
- Inner Mongolia Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Yanyan Gao
- Linxi County Agriculture and Animal Husbandry Bureau, Chifeng, 025250, China
| | - Huizhong Zhang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Xiaodong Li
- Inner Mongolia Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China.
| | - Wenzhe Zheng
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China.
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Yu J, Bennett D, Dardick C, Zhebentyayeva T, Abbott AG, Liu Z, Staton ME. Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach. Front Mol Biosci 2021; 8:612881. [PMID: 33968979 PMCID: PMC8098804 DOI: 10.3389/fmolb.2021.612881] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/15/2021] [Indexed: 11/15/2022] Open
Abstract
Bud dormancy is under the regulation of complex mechanisms including genetic and epigenetic factors. To study the function of regulatory non-coding RNAs in winter dormancy release, we analyzed the small RNA and long non-coding RNA (lncRNA) expression from peach (Prunus persica) floral buds in endodormancy, ecodormancy and bud break stages. Small RNAs underwent a major shift in expression primarily between dormancy and flowering with specific pairs of microRNAs and their mRNA target genes undergoing coordinated differential expression. From endodormancy to ecodormancy, ppe-miR6285 was significantly upregulated while its target gene, an ASPARAGINE-RICH PROTEIN involved in the regulation of abscisic acid signaling, was downregulated. At ecodormancy, ppe-miR2275, a homolog of meiosis-specific miR2275 across angiosperms, was significantly upregulated, supporting microsporogenesis in anthers at a late stage of dormancy. The expression of 785 lncRNAs, unlike the overall expression pattern in the small RNAs, demonstrated distinctive expression signatures across all dormancy and flowering stages. We predicted that a subset of lncRNAs were targets of microRNAs and found 18 lncRNA/microRNA target pairs with both differentially expressed across time points. The genome-wide differential expression and network analysis of non-coding RNAs and mRNAs from the same tissues provide new candidate loci for dormancy regulation and suggest complex noncoding RNA interactions control transcriptional regulation across these key developmental time points.
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Affiliation(s)
- Jiali Yu
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States
| | - Dennis Bennett
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Christopher Dardick
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Tetyana Zhebentyayeva
- Department of Ecosystem Science and Management, Schatz Center for Tree Molecular Genetics, The Pennsylvania State University, University Park, PA, United States
| | - Albert G Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY, United States
| | - Zongrang Liu
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Margaret E Staton
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States.,Department of Entomology and Plant Pathology, Institute of Agriculture, University of Tennessee, Knoxville, TN, United States
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Liu D, Chen L, Chen C, An X, Zhang Y, Wang Y, Li Q. Full-length transcriptome analysis of Phytolacca americana and its congener P. icosandra and gene expression normalization in three Phytolaccaceae species. BMC PLANT BIOLOGY 2020; 20:396. [PMID: 32854620 PMCID: PMC7450566 DOI: 10.1186/s12870-020-02608-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Phytolaccaceae species in China are not only ornamental plants but also perennial herbs that are closely related to human health. However, both large-scale full-length cDNA sequencing and reference gene validation of Phytolaccaceae members are still lacking. Therefore, single-molecule real-time sequencing technology was employed to generate full-length transcriptome in invasive Phytolacca americana and non-invasive exotic P. icosandra. Based on the transcriptome data, RT-qPCR was employed to evaluate the gene expression stability in the two plant species and another indigenous congener P. acinosa. RESULTS Total of 19.96 Gb and 19.75 Gb clean reads of P. americana and P. icosandra were generated, including 200,857 and 208,865 full length non-chimeric (FLNC) reads, respectively. Transcript clustering analysis of FLNC reads identified 89,082 and 98,448 consensus isoforms, including 86,989 and 96,764 high-quality ones. After removing redundant reads, 46,369 and 50,220 transcripts were obtained. Based on structure analysis, total 1675 and 1908 alternative splicing variants, 25,641 and 31,800 simple sequence repeats (SSR) as well as 34,971 and 36,841 complete coding sequences were detected separately. Furthermore, 3574 and 3833 lncRNA were predicted and 41,676 and 45,050 transcripts were annotated respectively. Subsequently, seven reference genes in the two plant species and a native species P. acinosa were selected and evaluated by RT-qPCR for gene expression analysis. When tested in different tissues (leaves, stems, roots and flowers), 18S rRNA showed the highest stability in P. americana, whether infested by Spodoptera litura or not. EF2 had the most stable expression in P. icosandra, while EF1-α was the most appropriate one when attacked by S. litura. EF1-α showed the highest stability in P.acinosa, whereas GAPDH was recommended when infested by S. litura. Moreover, EF1-α was the most stable one among the three plant species whenever germinating seeds or flowers only were considered. CONCLUSION Full-length transcriptome of P. americana and P. icosandra were produced individually. Based on the transcriptome data, the expression stability of seven candidate reference genes under different experimental conditions was evaluated. These results would facilitate further exploration of functional and comparative genomic studies in Phytolaccaceae and provide insights into invasion success of P. americana.
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Affiliation(s)
- Danfeng Liu
- Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, Yunnan University, Kunming, 650504, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650504, China
| | - Li Chen
- Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, Yunnan University, Kunming, 650504, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650504, China
| | - Chao Chen
- Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, Yunnan University, Kunming, 650504, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650504, China
| | - Xingkui An
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100191, China
| | - Yongjun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100191, China
| | - Yi Wang
- Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, Yunnan University, Kunming, 650504, China.
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650504, China.
| | - Qingjun Li
- Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, Yunnan University, Kunming, 650504, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650504, China
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Neller KCM, Klenov A, Hudak KA. Prediction and Characterization of miRNA/Target Pairs in Non-Model Plants Using RNA-seq. ACTA ACUST UNITED AC 2019; 4:e20090. [PMID: 31083771 PMCID: PMC9285518 DOI: 10.1002/cppb.20090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Plant microRNAs (miRNAs) are ∼20- to 24-nucleotide small RNAs that post-transcriptionally regulate gene expression of mRNA targets. Here, we present a workflow to characterize the miRNA transcriptome of a non-model plant, focusing on miRNAs and targets that are differentially expressed under one experimental treatment. We cover RNA-seq experimental design to create paired small RNA and mRNA libraries and perform quality control of raw data, de novo mRNA transcriptome assembly and annotation, miRNA prediction, differential expression, target identification, and functional enrichment analysis. Additionally, we include validation of differential expression and miRNA-induced target cleavage using qRT-PCR and modified RNA ligase-mediated 5' rapid amplification of cDNA ends, respectively. Our procedure relies on freely available software and web resources. It is intended for users that lack programming skills but can navigate a command-line interface. To enable an understanding of formatting requirements and anticipated results, we provide sample RNA-seq data and key input/output files for each stage. © 2019 The Authors. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
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Affiliation(s)
- Kira C M Neller
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Alexander Klenov
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Katalin A Hudak
- Department of Biology, York University, Toronto, Ontario, Canada
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