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Xu W, Fan H, Pei X, Hua X, Xu T, He Q. mRNA-Seq and miRNA-Seq Analyses Provide Insights into the Mechanism of Pinellia ternata Bulbil Initiation Induced by Phytohormones. Genes (Basel) 2023; 14:1727. [PMID: 37761867 PMCID: PMC10531394 DOI: 10.3390/genes14091727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Pinellia ternata (Thunb.) Breit (abbreviated as P. ternata) is a plant with an important medicinal value whose yield is restricted by many factors, such as low reproductive efficiency and continuous cropping obstacles. As an essential breeding material for P. ternata growth and production, the bulbils have significant advantages such as a high survival rate and short breeding cycles. However, the location effect, influencing factors, and molecular mechanism of bulbil occurrence and formation have not been fully explored. In this study, exogenously applied phytohormones were used to induce in vitro petiole of P. ternata to produce bulbil structure. Transcriptome sequencing of mRNA and miRNA were performed in the induced petiole (TCp) and the induced bulbil (TCb). Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed for the identification of key genes and pathways involved in bulbil development. A total of 58,019 differentially expressed genes (DEGs) were identified. The GO and KEGG analysis indicated that DEGs were mainly enriched in plant hormone signal transduction and the starch and sucrose metabolism pathway. The expression profiles of miR167a, miR171a, and miR156a during bulbil induction were verified by qRT-PCR, indicating that these three miRNAs and their target genes may be involved in the process of bulbil induction and play an important role. However, further molecular biological experiments are required to confirm the functions of the identified bulbil development-related miRNAs and targets.
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Affiliation(s)
- Wenxin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (W.X.); (H.F.); (X.P.); (X.H.)
| | - Haoyu Fan
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (W.X.); (H.F.); (X.P.); (X.H.)
| | - Xiaomin Pei
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (W.X.); (H.F.); (X.P.); (X.H.)
| | - Xuejun Hua
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (W.X.); (H.F.); (X.P.); (X.H.)
| | - Tao Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (W.X.); (H.F.); (X.P.); (X.H.)
| | - Qiuling He
- Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Hangzhou 310018, China
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Yousefi K, Abdullah SNA, Hatta MAM, Ling KL. Genomics and Transcriptomics Reveal Genetic Contribution to Population Diversity and Specific Traits in Coconut. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091913. [PMID: 37176970 PMCID: PMC10181077 DOI: 10.3390/plants12091913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023]
Abstract
Coconut is an economically important palm species with a long history of human use. It has applications in various food, nutraceuticals, and cosmetic products, and there has been renewed interest in coconut in recent years due to its unique nutritional and medicinal properties. Unfortunately, the sustainable growth of the coconut industry has been hampered due to a shortage of good quality seedlings. Genetic improvement through the traditional breeding approach faced considerable obstacles due to its perennial nature, protracted juvenile period, and high heterozygosity. Molecular biotechnological tools, including molecular markers and next-generation sequencing (NGS), could expedite genetic improvement efforts in coconut. Researchers have employed various molecular markers to reveal genetic diversity among coconut populations and for the construction of a genetic map for exploitation in coconut breeding programs worldwide. Whole genome sequencing and transcriptomics on the different varieties have generated a massive amount of publicly accessible sequence data, substantially improving the ability to analyze and understand molecular mechanisms affecting crop performance. The production of high-yielding and disease-resilient coconuts and the deciphering of the complex coconut genome's structure can profit tremendously from these technologies. This paper aims to provide a comprehensive review of the progress of coconut research, using genomics, transcriptomics, and molecular markers initiatives.
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Affiliation(s)
- Kobra Yousefi
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Siti Nor Akmar Abdullah
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Laboratory of Sustainable Agronomy and Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Muhammad Asyraf Md Hatta
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Kong Lih Ling
- Laboratory of Sustainable Agronomy and Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
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3
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Sabana AA, Antony G, Rajesh MK, Gangaraj KP, Niral V, Sudha R, Jerard BA. Development and characterization of non-coding RNA-derived simple sequence repeat markers in coconut (Cocos nucifera L.). Funct Integr Genomics 2022; 22:1243-1251. [DOI: 10.1007/s10142-022-00911-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/29/2022]
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Tregear JW, Richaud F, Collin M, Esbelin J, Parrinello H, Cochard B, Nodichao L, Morcillo F, Adam H, Jouannic S. Micro-RNA-Regulated SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Expression and Cytokinin Accumulation Distinguish Early-Developing Male and Female Inflorescences in Oil Palm (Elaeis guineensis). PLANTS 2022; 11:plants11050685. [PMID: 35270155 PMCID: PMC8912876 DOI: 10.3390/plants11050685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 11/16/2022]
Abstract
Sexual differentiation of inflorescences and flowers is important for reproduction and affects crop plant productivity. We report here on a molecular study of the process of sexual differentiation in the immature inflorescence of oil palm (Elaeis guineensis). This species is monoecious and exhibits gender diphasy, producing male and female inflorescences separately on the same plant in alternation. Three main approaches were used: small RNA-seq to characterise and study the expression of miRNA genes; RNA-seq to monitor mRNA accumulation patterns; hormone quantification to assess the role of cytokinins and auxins in inflorescence differentiation. Our study allowed the characterisation of 30 previously unreported palm MIRNA genes. In differential gene and miRNA expression studies, we identified a number of key developmental genes and miRNA-mRNA target modules previously described in relation to their developmental regulatory role in the cereal panicle, notably the miR156/529/535-SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) gene regulatory module. Gene enrichment analysis highlighted the importance of hormone-related genes, and this observation was corroborated by the detection of much higher levels of cytokinins in the female inflorescence. Our data illustrate the importance of branching regulation within the developmental window studied, during which the female inflorescence, unlike its male counterpart, produces flower clusters on new successive axes by sympodial growth.
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Affiliation(s)
- James W. Tregear
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
- Correspondence:
| | - Frédérique Richaud
- CIRAD, UMR AGAP, 34398 Montpellier, France;
- AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France
| | - Myriam Collin
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
| | - Jennifer Esbelin
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
| | - Hugues Parrinello
- MGX-Montpellier GenomiX, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France;
| | | | | | - Fabienne Morcillo
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
- CIRAD, UMR DIADE, 34394 Montpellier, France
| | - Hélène Adam
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
| | - Stefan Jouannic
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
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Kalaipandian S, Mu Z, Kong EYY, Biddle J, Cave R, Bazrafshan A, Wijayabandara K, Beveridge FC, Nguyen Q, Adkins SW. Cloning Coconut via Somatic Embryogenesis: A Review of the Current Status and Future Prospects. PLANTS (BASEL, SWITZERLAND) 2021; 10:2050. [PMID: 34685859 PMCID: PMC8538321 DOI: 10.3390/plants10102050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 11/30/2022]
Abstract
Coconut [Cocos nucifera L.] is often called "the tree of life" because of its many uses in the food, beverage, medicinal, and cosmetic industries. Currently, more than 50% of the palms grown throughout the world are senile and need to be replanted immediately to ensure production levels meet the present and increasing demand for coconut products. Mass replanting will not be possible using traditional propagation methods from seed. Recent studies have indicated that in vitro cloning via somatic embryogenesis is the most promising alternative for the large-scale production of new coconut palms. This paper provides a review on the status and prospects for the application of somatic embryogenesis to mass clonal propagation of coconut.
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Affiliation(s)
- Sundaravelpandian Kalaipandian
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
| | - Zhihua Mu
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
| | - Eveline Yee Yan Kong
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
| | - Julianne Biddle
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
- Australian Centre for International Agricultural Research, Canberra, ACT 2617, Australia
| | - Robyn Cave
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
| | - Amirhossein Bazrafshan
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
| | - Kusinara Wijayabandara
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
| | - Fernanda Caro Beveridge
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
| | - Quang Nguyen
- Applied Biotechnology for Crop Development Research Unit, The International University, Ho Chi Minh City 700000, Vietnam;
| | - Steve W. Adkins
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
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Qin Z, Li J, Zhang Y, Xiao Y, Zhang X, Zhong L, Liu H, Chen B. Genome-wide identification of microRNAs involved in the somatic embryogenesis of Eucalyptus. G3-GENES GENOMES GENETICS 2021; 11:6163290. [PMID: 33693674 PMCID: PMC8049409 DOI: 10.1093/g3journal/jkab070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/24/2021] [Accepted: 02/27/2021] [Indexed: 11/13/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs (18-24 nt) and function in many biological processes in plants. Although Eucalyptus trees are widely planted across the world, our understanding of the miRNA regulation in the somatic embryogenesis (SE) of Eucalyptus is still poor. Here we reported, for the first time, the miRNA profiles of differentiated and dedifferentiated tissues of two Eucalyptus species and identified miRNAs involved in SE of Eucalyptus. Stem and tissue culture-induced callus were obtained from the subculture seedlings of E. camaldulensis and E. grandis x urophylla and were used as differentiated and dedifferentiated samples, respectively. Small RNA sequencing generated 304.2 million clean reads for the Eucalyptus samples (n = 3) and identified 888 miRNA precursors (197 known and 691 novel) for Eucalyptus. These miRNAs were mainly distributed in chromosomes Chr03, Chr05, and Chr08 and can produce 46 miRNA clusters. Then, we identified 327 and 343 differentially expressed miRNAs (DEmiRs) in the dedifferentiation process of E. camaldulensis and E. grandis x urophylla, respectively. DEmiRs shared by the two Eucalyptus species might be involved in the development of embryonic callus, such as MIR156, MIR159, MIR160, MIR164, MIR166, MIR169, MIR171, MIR399, and MIR482. Notably, we identified 81 upregulated and 67 downregulated miRNAs specific to E. camaldulensis, which might be associated with the high embryogenic potential. Target prediction and functional analysis showed that they might be involved in longevity regulating and plant hormone signal transduction pathways. Further, using the gene expression profiles, we observed the negative regulation of miRNA-target pairs, such as MIR160~ARF18, MIR396~GRF6, MIR166~ATHB15/HD-ZIP, and MIR156/MIR157~SPL1. Interestingly, transcription factors such as WRKY, MYB, GAMYB, TCP4, and PIL1 were found to be regulated by the DEmiRs. The genes encoding PIL1 and RPS21C, regulated by upregulated miRNAs (e.g., egd-N-miR63-5p, egd-N-miR63-5p, and MIR169,) were downregulated exclusively in the dedifferentiation of E. camaldulensis. This is the first time to study the miRNA regulation in the dedifferentiation process of Eucalyptus and it will provide a valuable resource for future studies. More importantly, it will improve our understanding of miRNA regulation during the somatic embryogenesis of Eucalyptus and benefit the Eucalyptus breeding program.
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Affiliation(s)
- Zihai Qin
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Junji Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Ye Zhang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Yufei Xiao
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Xiaoning Zhang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Lianxiang Zhong
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Hailong Liu
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Bowen Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
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Cao H, Zhang X, Ruan Y, Zhang L, Cui Z, Li X, Jia B. miRNA expression profiling and zeatin dynamic changes in a new model system of in vivo indirect regeneration of tomato. PLoS One 2020; 15:e0237690. [PMID: 33332392 PMCID: PMC7745965 DOI: 10.1371/journal.pone.0237690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/27/2020] [Indexed: 01/15/2023] Open
Abstract
Callus formation and adventitious shoot differentiation could be observed on the cut surface of completely decapitated tomato plants. We propose that this process can be used as a model system to investigate the mechanisms that regulate indirect regeneration of higher plants without the addition of exogenous hormones. This study analyzed the patterns of trans-zeatin and miRNA expression during in vivo regeneration of tomato. Analysis of trans-zeatin revealed that the hormone cytokinin played an important role in in vivo regeneration of tomato. Among 183 miRNAs and 1168 predicted target genes sequences identified, 93 miRNAs and 505 potential targets were selected based on differential expression levels for further characterization. Expression patterns of six miRNAs, including sly-miR166, sly-miR167, sly-miR396, sly-miR397, novel 156, and novel 128, were further validated by qRT-PCR. We speculate that sly-miR156, sly-miR160, sly-miR166, and sly-miR397 play major roles in callus formation of tomato during in vivo regeneration by regulating cytokinin, IAA, and laccase levels. Overall, our microRNA sequence and target analyses of callus formation during in vivo regeneration of tomato provide novel insights into the regulation of regeneration in higher plants.
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Affiliation(s)
- Huiying Cao
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
| | - Xinyue Zhang
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
| | - Yanye Ruan
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
- * E-mail: (YR); (LZ)
| | - Lijun Zhang
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
- * E-mail: (YR); (LZ)
| | - Zhenhai Cui
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
| | - Xuxiao Li
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
| | - Bing Jia
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, China
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miRNAs as key regulators via targeting the phytohormone signaling pathways during somatic embryogenesis of plants. 3 Biotech 2020; 10:495. [PMID: 33150121 DOI: 10.1007/s13205-020-02487-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/13/2020] [Indexed: 01/12/2023] Open
Abstract
Somatic embryogenesis is the regeneration of embryos from the somatic cell via dedifferentiation and redifferentiation without the occurrence of fertilization. A complex network of genes regulates the somatic embryogenesis process. Especially, microRNAs (miRNAs) have emerged as key regulators by affecting phytohormone biosynthesis, transport and signal transduction pathways. miRNAs are small, non-coding small RNA regulatory molecules involved in various developmental processes including somatic embryogenesis. Several types of miRNAs such as miR156, miR157, miR 159, miR 160, miR165, miR166, miR167, miR390, miR393 and miR396 have been reported to intricate in regulating somatic embryogenesis via targeting the phytohormone signaling pathways. Here we review current research progress on the miRNA-mediated regulation involved in somatic embryogenesis via regulating auxin, ethylene, abscisic acid and cytokinin signaling pathways. Further, we also discussed the possible role of other phytohormone signaling pathways such as gibberellins, jasmonates, nitric oxide, polyamines and brassinosteroids. Finally, we conclude by discussing the expression of miRNAs and their targets involved in somatic embryogenesis and possible regulatory mechanisms cross talk with phytohormones during somatic embryogenesis.
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Wójcik AM. Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis. Int J Mol Sci 2020; 21:E4969. [PMID: 32674459 PMCID: PMC7420248 DOI: 10.3390/ijms21144969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
During early plant embryogenesis, some of the most fundamental decisions on fate and identity are taken making it a fascinating process to study. It is no surprise that higher plant embryogenesis was intensively analysed during the last century, while somatic embryogenesis is probably the most studied regeneration model. Encoded by the MIRNA, short, single-stranded, non-coding miRNAs, are commonly present in all Eukaryotic genomes and are involved in the regulation of the gene expression during the essential developmental processes such as plant morphogenesis, hormone signaling, and developmental phase transition. During the last few years dedicated to miRNAs, analytical methods and tools have been developed, which have afforded new opportunities in functional analyses of plant miRNAs, including (i) databases for in silico analysis; (ii) miRNAs detection and expression approaches; (iii) reporter and sensor lines for a spatio-temporal analysis of the miRNA-target interactions; (iv) in situ hybridisation protocols; (v) artificial miRNAs; (vi) MIM and STTM lines to inhibit miRNA activity, and (vii) the target genes resistant to miRNA. Here, we attempted to summarise the toolbox for functional analysis of miRNAs during plant embryogenesis. In addition to characterising the described tools/methods, examples of the applications have been presented.
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Affiliation(s)
- Anna Maria Wójcik
- University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
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