1
|
Tondepu SAG, Manova V, Vadivel D, Dondi D, Pagano A, Macovei A. MicroRNAs potentially targeting DDR-related genes are differentially expressed upon exposure to γ-rays during seed germination in wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108771. [PMID: 38820913 DOI: 10.1016/j.plaphy.2024.108771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 05/08/2024] [Accepted: 05/22/2024] [Indexed: 06/02/2024]
Abstract
DNA damage response (DDR), a complex network of cellular pathways that cooperate to sense and repair DNA lesions, is regulated by several mechanisms, including microRNAs. As small, single-stranded RNA molecules, miRNAs post-transcriptionally regulate their target genes by mRNA cleavage or translation inhibition. Knowledge regarding miRNAs influence on DDR-associated genes is still scanty in plants. In this work, an in silico analysis was performed to identify putative miRNAs that could target DDR sensors, signal transducers and effector genes in wheat. Selected putative miRNA-gene pairs were tested in an experimental system where seeds from two wheat mutant lines were irradiated with 50 Gy and 300 Gy gamma(γ)-rays. To evaluate the effect of the treatments on wheat germination, phenotypic and molecular (DNA damage, ROS accumulation, gene/miRNA expression profile) analyses have been carried out. The results showed that in dry seeds ROS accumulated immediately after irradiation and decayed soon after while the negative impact on seedling growth was supported by enhanced accumulation of DNA damage. When a qRT-PCR analysis was performed, the selected miRNAs and DDR-related genes were differentially modulated by the γ-rays treatments in a dose-, time- and genotype-dependent manner. A significant negative correlation was observed between the expression of tae-miR5086 and the RAD50 gene, involved in double-strand break sensing and homologous recombination repair, one of the main processes that repairs DNA breaks induced by γ-rays. The results hereby reported can be relevant for wheat breeding programs and screening of the radiation response and tolerance of novel wheat varieties.
Collapse
Affiliation(s)
- Sri Amarnadh Gupta Tondepu
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Adolfo Ferrata 9, 27100, Pavia, Italy
| | - Vasilissa Manova
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences "Acad. G. Bonchev", Street Bldg. 21, 1113, Sofia, Bulgaria.
| | - Dhanalakshmi Vadivel
- Department of Chemistry, University of Pavia, Via Torquato Taramelli 12, 27100, Pavia, Italy
| | - Daniele Dondi
- Department of Chemistry, University of Pavia, Via Torquato Taramelli 12, 27100, Pavia, Italy
| | - Andrea Pagano
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Adolfo Ferrata 9, 27100, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Adolfo Ferrata 9, 27100, Pavia, Italy.
| |
Collapse
|
2
|
Božić M, Ignjatović Micić D, Delić N, Nikolić A. Maize miRNAs and their putative target genes involved in chilling stress response in 5-day old seedlings. BMC Genomics 2024; 25:479. [PMID: 38750515 PMCID: PMC11094857 DOI: 10.1186/s12864-024-10403-1] [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: 01/22/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND In the context of early sowing of maize as a promising adaptation strategy that could significantly reduce the negative effects of climate change, an in-depth understanding of mechanisms underlying plant response to low-temperature stress is demanded. Although microRNAs (miRNAs) have been recognized as key regulators of plant stress response, research on their role in chilling tolerance of maize during early seedling stages is scarce. Therefore, it is of great significance to explore chilling-responsive miRNAs, reveal their expression patterns and associated target genes, as well as to examine the possible functions of the conserved and novel miRNAs. In this study, the role of miRNAs was examined in 5d-old maize seedlings of one tolerant and one sensitive inbred line exposed to chilling (10/8 °C) stress for 6 h and 24 h, by applying high throughput sequencing. RESULTS A total of 145 annotated known miRNAs belonging to 30 families and 876 potentially novel miRNAs were identified. Differential expression (DE) analysis between control and stress conditions identified 98 common miRNAs for both genotypes at one time point and eight miRNAs at both time points. Target prediction and enrichment analysis showed that the DE zma-miR396, zma-miR156, zma-miR319, and zma-miR159 miRNAs modulate growth and development. Furthermore, it was found that several other DE miRNAs were involved in abiotic stress response: antioxidative mechanisms (zma-miR398), signal transduction (zma-miR156, zma-miR167, zma-miR169) and regulation of water content (zma-miR164, zma-miR394, zma-miR396). The results underline the zma-miRNAs involvement in the modulation of their target genes expression as an important aspect of the plant's survival strategy and acclimation to chilling stress conditions. CONCLUSIONS To our understanding, this is the first study on miRNAs in 5-d old seedlings' response to chilling stress, providing data on the role of known and novel miRNAs post-transcriptional regulation of expressed genes and contributing a possible platform for further network and functional analysis.
Collapse
Affiliation(s)
- Manja Božić
- Laboratory for Molecular Genetics and Physiology, Research and Development Department, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Dragana Ignjatović Micić
- Laboratory for Molecular Genetics and Physiology, Research and Development Department, Maize Research Institute Zemun Polje, Belgrade, Serbia.
| | - Nenad Delić
- Laboratory for Molecular Genetics and Physiology, Research and Development Department, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Ana Nikolić
- Laboratory for Molecular Genetics and Physiology, Research and Development Department, Maize Research Institute Zemun Polje, Belgrade, Serbia
| |
Collapse
|
3
|
Zhang T, Wang X, Yuan Y, Zhu S, Liu C, Zhang Y, Gai S. PsmiR159b- PsMYB65 module functions in the resumption of bud growth after endodormancy by affecting the cell cycle in tree peony. HORTICULTURE RESEARCH 2024; 11:uhae052. [PMID: 38638681 PMCID: PMC11025381 DOI: 10.1093/hr/uhae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/16/2024] [Indexed: 04/20/2024]
Abstract
Bud endodormancy in perennial plants is a sophisticated system that adapts to seasonal climatic changes. Growth-promoting signals such as low temperature and gibberellins (GAs) are crucial for facilitating budbreak following endodormancy release (EDR). However, the regulatory mechanisms underlying GA-mediated budbreak in tree peony (Paeonia suffruticosa) remain unclear. In tree peony, the expression of PsmiR159b among three differentially expressed miR159 members was inhibited with the prolonged chilling, and overexpression of PsMIR159b delayed budbreak, whereas silencing PsmiR159b promoted budbreak after dormancy. PsMYB65, a downstream transcription factor in the GA pathway, was induced by prolonged chilling and exogenous GA3 treatments. PsMYB65 was identified as a target of PsmiR159b, and promoted budbreak in tree peony. RNA-seq of PsMYB65-slienced buds revealed significant enrichment in the GO terms regulation of 'cell cycle' and 'DNA replication' among differentially expressed genes. Yeast one-hybrid and electrophoretic mobility shift assays demonstrated that PsMYB65 directly bound to the promoter of the type-D cyclin gene PsCYCD3;1. Dual-luciferase reporter assay indicated that PsMYB65 positively regulate PsCYCD3;1 expression, suggesting that miR159b-PsMYB65 module contributes to budbreak by influencing the cell cycle. Our findings revealed that the PsmiR159b-PsMYB65 module functioned in budbreak after dormancy by regulating cell proliferation, providing valuable insights into the endodormancy release regulation mechanism.
Collapse
Affiliation(s)
- Tao Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
- University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xinyu Wang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
- University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China
| | - Yanchao Yuan
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
- University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China
| | - Shoujie Zhu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
- University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China
| | - Chunying Liu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
- University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China
| | - Yuxi Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
- University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China
| | - Shupeng Gai
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
- University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, 266109, China
| |
Collapse
|
4
|
Zeng F, Zheng C, Ge W, Gao Y, Pan X, Ye X, Wu X, Sun Y. Regulatory function of the endogenous hormone in the germination process of quinoa seeds. FRONTIERS IN PLANT SCIENCE 2024; 14:1322986. [PMID: 38259945 PMCID: PMC10801742 DOI: 10.3389/fpls.2023.1322986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/08/2023] [Indexed: 01/24/2024]
Abstract
The economic and health significance of quinoa is steadily growing on a global scale. Nevertheless, the primary obstacle to achieving high yields in quinoa cultivation is pre-harvest sprouting (PHS), which is intricately linked to seed dormancy. However, there exists a dearth of research concerning the regulatory mechanisms governing PHS. The regulation of seed germination by various plant hormones has been extensively studied. Consequently, understanding the mechanisms underlying the role of endogenous hormones in the germination process of quinoa seeds and developing strategies to mitigate PHS in quinoa cultivation are of significant research importance. This study employed the HPLC-ESI-MS/MS internal standard and ELISA method to quantify 8 endogenous hormones. The investigation of gene expression changes before and after germination was conducted using RNA-seq analysis, leading to the discovery of 280 differentially expressed genes associated with the regulatory pathway of endogenous hormones. Additionally, a correlation analysis of 99 genes with significant differences identified 14 potential genes that may act as crucial "transportation hubs" in hormonal interactions. Through the performance of an analysis on the modifications in hormone composition and the expression of associated regulatory genes, we posit a prediction that implies the presence of a negative feedback regulatory mechanism of endogenous hormones during the germination of quinoa seeds. This mechanism is potentially influenced by the unique structure of quinoa seeds. To shed light on the involvement of endogenous hormones in the process of quinoa seed germination, we have established a regulatory network. This study aims to offer innovative perspectives on the breeding of quinoa varieties that exhibit resistance to PHS, as well as strategies for preventing PHS.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Xiaoyong Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yanxia Sun
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, China
| |
Collapse
|
5
|
Yang W, Liu X, Yu S, Liu J, Jiang L, Lu X, Liu Y, Zhang J, Li X, Zhang S. The maize ATP-binding cassette (ABC) transporter ZmMRPA6 confers cold and salt stress tolerance in plants. PLANT CELL REPORTS 2023; 43:13. [PMID: 38135780 DOI: 10.1007/s00299-023-03094-7] [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: 08/03/2023] [Accepted: 11/10/2023] [Indexed: 12/24/2023]
Abstract
KEY MESSAGE ZmMRPA6 was cloned and characterized as the first ATP-binding cassette (ABC) transporter in maize to be proven to participate in cold and salt tolerance. Homologous genes AtABCC4 and AtABCC14 of ZmMRPA6 also responded to salt stress. ATP-binding cassette (ABC) proteins are major transmembrane transporters that play significant roles in plant development against various abiotic stresses. However, available information regarding stress-related ABC genes in maize is minimal. In this study, a maize ABC transporter gene, ZmMRPA6, was identified through genome-wide association analysis (GWAS) for cold tolerance in maize seeds germination and functionally characterized. During germination and seedling stages, the zmmrpa6 mutant exhibited enhanced resistance to cold or salt stress. Mutated of ZmMRPA6 did not affect the expression of downstream response genes related cold or salt response at the transcriptional level. Mass spectrometry analysis revealed that most of the differential proteins between zmmrpa6 and wild-type plants were involved in response to stress process including oxidative reduction, hydrolase activity, small molecule metabolism, and photosynthesis process. Meanwhile, the plants which lack the ZmMRPA6 homologous genes AtABCC4 or AtABCC14 were sensitive to salt stress in Arabidopsis. These results indicated that ZmMRPA6 and its homologous genes play a conserved role in cold and salt stress, and functional differentiation occurs in monocotyledonous and dicotyledonous plants. In summary, these findings dramatically improved our understanding of the function of ABC transporters resistance to abiotic stresses in plants.
Collapse
Affiliation(s)
- Wei Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiao Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Shaowei Yu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Jisheng Liu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, Shandong, China
| | - Lijun Jiang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, Shandong, China
| | - Yinggao Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Jiedao Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
| | - Shuxin Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
| |
Collapse
|
6
|
Raza A, Charagh S, Karikari B, Sharif R, Yadav V, Mubarik MS, Habib M, Zhuang Y, Zhang C, Chen H, Varshney RK, Zhuang W. miRNAs for crop improvement. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107857. [PMID: 37437345 DOI: 10.1016/j.plaphy.2023.107857] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.
Collapse
Affiliation(s)
- Ali Raza
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture and Landscape Architecture, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
| | - Vivek Yadav
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shanxi, 712100, China
| | | | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Rd., Islamabad 45500, Pakistan
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Hua Chen
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Rajeev K Varshney
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China; WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Weijian Zhuang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China.
| |
Collapse
|
7
|
Wu Q, Yang L, Liang H, Yin L, Chen D, Shen P. Integrated analyses reveal the response of peanut to phosphorus deficiency on phenotype, transcriptome and metabolome. BMC PLANT BIOLOGY 2022; 22:524. [PMID: 36372886 PMCID: PMC9661748 DOI: 10.1186/s12870-022-03867-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Phosphorus (P) is one of the most essential macronutrients for crops. The growth and yield of peanut (Arachis hypogaea L.) are always limited by P deficiency. However, the transcriptional and metabolic regulatory mechanisms were less studied. In this study, valuable phenotype, transcriptome and metabolome data were analyzed to illustrate the regulatory mechanisms of peanut under P deficiency stress. RESULT In present study, two treatments of P level in deficiency with no P application (-P) and in sufficiency with 0.6 mM P application (+ P) were used to investigate the response of peanut on morphology, physiology, transcriptome, microRNAs (miRNAs), and metabolome characterizations. The growth and development of plants were significantly inhibited under -P treatment. A total of 6088 differentially expressed genes (DEGs) were identified including several transcription factor family genes, phosphate transporter genes, hormone metabolism related genes and antioxidant enzyme related genes that highly related to P deficiency stress. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that 117 genes were annotated in the phenylpropanoid biosynthesis pathway under P deficiency stress. A total of 6 miRNAs have been identified significantly differential expression between + P and -P group by high-throughput sequencing of miRNAs, including two up-regulated miRNAs (ahy-miR160-5p and ahy-miR3518) and four down-regulated miRNAs (ahy-miR408-5p, ahy-miR408-3p, ahy-miR398, and ahy-miR3515). Further, the predicted 22 target genes for 6 miRNAs and cis-elements in 2000 bp promoter region of miRNA genes were analyzed. A total of 439 differentially accumulated metabolites (DAMs) showed obviously differences in two experimental conditions. CONCLUSIONS According to the result of transcripome and metabolome analyses, we can draw a conclusion that by increasing the content of lignin, amino acids, and levan combining with decreasing the content of LPC, cell reduced permeability, maintained stability, raised the antioxidant capacity, and increased the P uptake in struggling for survival under P deficiency stress.
Collapse
Affiliation(s)
- Qi Wu
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetics & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, 126 Wannianquan Road, Qingdao, 266100 China
| | - Liyu Yang
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetics & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, 126 Wannianquan Road, Qingdao, 266100 China
| | - Haiyan Liang
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetics & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, 126 Wannianquan Road, Qingdao, 266100 China
| | - Liang Yin
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetics & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, 126 Wannianquan Road, Qingdao, 266100 China
| | - Dianxu Chen
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetics & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, 126 Wannianquan Road, Qingdao, 266100 China
| | - Pu Shen
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetics & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, 126 Wannianquan Road, Qingdao, 266100 China
| |
Collapse
|
8
|
Li J, Wang C, Zhou T, Jin H, Liu X. Identification and characterization of miRNAome and target genes in Pseudostellaria heterophylla. PLoS One 2022; 17:e0275566. [PMID: 36197881 PMCID: PMC9534447 DOI: 10.1371/journal.pone.0275566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 09/19/2022] [Indexed: 11/30/2022] Open
Abstract
miRNAs play a crucial role in the development and growth of plants by inhibiting the function of targeted genes at the post-transcription level. However, no miRNAs in Pseudostellaria heterophylla have been reported and their function in the morphogenesis of organs is still unclear. In this study, a total of 159 conserved miRNAs (belonging to 64 families) and 303 level miRNAs were identified from P. heterophylla. Some of them showed specifically up or down-regulated expression in different tissues and numbers of unigenes involved in Plant-pathogen interaction and MAPK signaling pathway-plant were targeted. The significant negative correlation of expression profiles between 30 miRNAs and their target genes (37 unigenes) was observed, respectively. Further, a large number of genes involved with signal transduction of auxin, zeatin, abscisic acid and, jasmonic acid were targeted. Predicated targets of two miRNAs were validated by 5'RLM-RACE, respectively. A large number of mRNAs from four pathogens were targeted by miRNAs from P. heterophylla and some of them were targeted by miR414. In summary, we reported a population of miRNAs from four different vegetative tissues of P. heterophylla by high throughput sequencing, which was analyzed by combining with the constructed transcriptome. These results may help to explain the function of miRNAs in the morphogenesis of organs and defense of pathogens, and may provide theoretical basis for breeding and genetic improvement of P. heterophylla.
Collapse
Affiliation(s)
- Jun Li
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
- * E-mail:
| | - Chongmin Wang
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Tao Zhou
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Haijun Jin
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Xiaoqing Liu
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
| |
Collapse
|
9
|
Jing X, Zhang H, Huai X, An Q, Qiao Y. Identification and characterization of miRNAs and PHAS loci related to the early development of the embryo and endosperm in Fragaria × ananassa. BMC Genomics 2022; 23:638. [PMID: 36076187 PMCID: PMC9454143 DOI: 10.1186/s12864-022-08864-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The strawberry fleshy fruit is actually enlarged receptacle tissue, and the successful development of the embryo and endosperm is essential for receptacle fruit set. MicroRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs) play indispensable regulatory roles in plant growth and development. However, miRNAs and phasiRNAs participating in the regulation of strawberry embryo and endosperm development have yet to be explored. RESULTS Here, we performed genome-wide identification of miRNA and phasiRNA-producing loci (PHAS) in strawberry seeds with a focus on those involved in the development of the early embryo and endosperm. We found that embryos and endosperm have different levels of small RNAs. After bioinformatics analysis, the results showed that a total of 404 miRNAs (352 known and 52 novel) and 156 PHAS genes (81 21-nt and 75 24-nt genes) could be found in strawberry seed-related tissues, of which four and nine conserved miRNA families displayed conserved expression in the endosperm and embryo, respectively. Based on refined putative annotation of PHAS loci, some auxin signal-related genes, such as CM3, TAR2, AFB2, ASA1, NAC and TAS3, were found, which demonstrates that IAA biosynthesis is important for endosperm and embryo development during early fruit growth. Additionally, some auxin signal-related conserved (miR390-TAS3) and novel (miR156-ASA1) trigger-PHAS pairs were identified. CONCLUSIONS Taken together, these results expand our understanding of sRNAs in strawberry embryo and endosperm development and provide a genomic resource for early-stage fruit development.
Collapse
Affiliation(s)
- Xiaotong Jing
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Hong Zhang
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Xinjia Huai
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Qi An
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Yushan Qiao
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, People's Republic of China.
| |
Collapse
|
10
|
Identification and expression analysis of miRNAs in germination and seedling growth of Tibetan hulless barley. Genomics 2021; 113:3735-3749. [PMID: 34517091 DOI: 10.1016/j.ygeno.2021.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 01/30/2023]
Abstract
Germination and seedling growth are crucial for plant development and agricultural production. While, the regulatory mechanisms during these processes in Tibetan hulless barley (Hordeum vulgare L. var. nudum) are not well understood. Given the regulatory roles of microRNAs (miRNAs) in crop plants and the irreplaceability of barley in the highland area of China, we herein presented a genome-wide survey of miRNAs to reveal a potential regulatory network in the early developmental stages of two Tibetan hulless barleys, from which a total of 156 miRNAs was identified including 35 known and 121 novel ones. Six of the identified novel miRNAs were further experimentally validated. According to the evolutionary analysis, miR156, miR166, miR168, and miR171 were conserved across Tibetan hulless barleys and eight other seed plants. Expression profiles of ten known miRNAs showed that they were involved in phytohormone signaling, carbohydrate and lipid metabolism, as well as juvenile-adult transition during barley development. Moreover, a total of 1280 genes targeted by 101 miRNAs were predicted from both barley libraries. Three genes (PLN03212, MATE eukaryotic, and GRAS) were validated via the RNA ligase-mediated 5'-rapid amplification of cDNA ends (RLM-5' RACE) to be the targets of hvu-miR159a, hvu-miR166a, and hvu-miR171-3p, respectively. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of putative targets, the most abundant pathways were related to "metabolism". These results revealed that miRNA-target pairs participating in the regulation of multigene expression and the embryonic development of Tibetan hulless barleys were controlled by complex mechanisms involving the concordant expression of different miRNAs and feedback loops among miRNAs as well as their targets. The study provides insight into the regulatory network of barley miRNAs for better understanding of miRNA functions during germination and seedling growth.
Collapse
|