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Sharma U, Sikdar A, Igamberdiev AU, Debnath SC. Exploring Genetic and Epigenetic Changes in Lingonberry Using Molecular Markers: Implications for Clonal Propagation. Curr Issues Mol Biol 2023; 45:6296-6310. [PMID: 37623216 PMCID: PMC10453208 DOI: 10.3390/cimb45080397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/20/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023] Open
Abstract
Lingonberry (Vaccinium vitis-idaea L.) is an important and valuable horticultural crop due to its high antioxidant properties. Plant tissue culture is an advanced propagation system employed in horticultural crops. However, the progeny derived using this technique may not be true-to-type. In order to obtain the maximum return of any agricultural enterprise, uniformity of planting materials is necessary, which sometimes is not achieved due to genetic and epigenetic instabilities under in vitro culture. Therefore, we analyzed morphological traits and genetic and epigenetic variations under tissue-culture and greenhouse conditions in lingonberry using molecular markers. Leaf length and leaf width under greenhouse conditions and shoot number per explant, shoot height and shoot vigor under in vitro conditions were higher in hybrid H1 compared to the cultivar Erntedank. Clonal fidelity study using one expressed sequence tag (EST)-polymerase chain reaction (PCR), five EST-simple sequence repeat (SSR) and six genomic (G)-SSR markers revealed monomorphic bands in micropropagated shoots and plants in lingonberry hybrid H1 and cultivar Erntedank conforming genetic integrity. Epigenetic variation was studied by quantifying cytosine methylation using a methylation-sensitive amplification polymorphism (MSAP) technique. DNA methylation ranged from 32% in greenhouse-grown hybrid H1 to 44% in cultivar Erntedank under a tissue culture system. Although total methylation was higher in in vitro grown shoots, fully methylated bands were observed more in the greenhouse-grown plants. On the contrary, hemimethylated DNA bands were more prominent in tissue culture conditions as compared to the greenhouse-grown plants. The study conclude that lingonberry maintains its genetic integrity but undergoes variable epigenetic changes during in vitro and ex vitro conditions.
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Affiliation(s)
- Umanath Sharma
- Department of Biology, Memorial University of Newfoundland, 45 Arctic Avenue, St. John’s, NL A1C 5S7, Canada; (U.S.); (A.S.); (A.U.I.)
- St. John’s Research and Development Centre, Agriculture and Agri-Food Canada, 204 Brookfield Road, St. John’s, NL A1E 0B2, Canada
| | - Arindam Sikdar
- Department of Biology, Memorial University of Newfoundland, 45 Arctic Avenue, St. John’s, NL A1C 5S7, Canada; (U.S.); (A.S.); (A.U.I.)
- St. John’s Research and Development Centre, Agriculture and Agri-Food Canada, 204 Brookfield Road, St. John’s, NL A1E 0B2, Canada
| | - Abir U. Igamberdiev
- Department of Biology, Memorial University of Newfoundland, 45 Arctic Avenue, St. John’s, NL A1C 5S7, Canada; (U.S.); (A.S.); (A.U.I.)
| | - Samir C. Debnath
- St. John’s Research and Development Centre, Agriculture and Agri-Food Canada, 204 Brookfield Road, St. John’s, NL A1E 0B2, Canada
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Sikdar A, Sharma U, Barua R, Igamberdiev AU, Debnath SC. Epigenomic insight of lingonberry and health-promoting traits during micropropagation. Sci Rep 2022; 12:12487. [PMID: 35864145 PMCID: PMC9304418 DOI: 10.1038/s41598-022-16530-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 07/12/2022] [Indexed: 11/09/2022] Open
Abstract
Epigenetic variation plays a role in developmental gene regulation and responses to the environment. An efficient interaction of zeatin-induced cytosine methylation and secondary compounds has been displayed for the first time in tissue-culture shoots/plants of lingonberry (Vaccinium vitis-idaea L.) cultivar Erntedank in vitro (NC1, in a liquid medium; NC2, on a semi-solid medium), ex vitro (NC3, node culture-derived plants; LC1, leaf culture-derived plants) and its cutting-propagated (ED) plants. Through methylation-sensitive amplification polymorphism (MSAP) assay, we observed highest methylated sites in leaf regenerants (LC1) from all primer combinations (108 bands), along with the highest secondary metabolites. The four types of tissue culture-derived shoots/plants (NC1, NC2, NC3, LC1) showed higher methylation bands than cutting propagated donor plants (ED) that exhibited 79 bands of methylation, which is comparatively low. Our study showed more methylation in micropropagated shoots/plants than those derived from ED plants. On the contrary, we observed higher secondary metabolites in ED plants but comparatively less in micropropagated shoots (NC1, NC2) and plants (NC3, LC1).
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Affiliation(s)
- Arindam Sikdar
- St. John's Research and Development Centre, Agriculture and Agri-Food Canada, St. John's, Newfoundland and Labrador, Canada.,Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Umanath Sharma
- St. John's Research and Development Centre, Agriculture and Agri-Food Canada, St. John's, Newfoundland and Labrador, Canada.,Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Rajesh Barua
- St. John's Research and Development Centre, Agriculture and Agri-Food Canada, St. John's, Newfoundland and Labrador, Canada.,Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Samir C Debnath
- St. John's Research and Development Centre, Agriculture and Agri-Food Canada, St. John's, Newfoundland and Labrador, Canada.
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Gao Y, Wang QM, An Q, Cui J, Zhou Y, Qi X, Zhang L, Li L. A novel micropropagation of Lycium ruthenicum and epigenetic fidelity assessment of three types of micropropagated plants in vitro and ex vitro. PLoS One 2021; 16:e0247666. [PMID: 33621255 PMCID: PMC7901770 DOI: 10.1371/journal.pone.0247666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/10/2021] [Indexed: 11/18/2022] Open
Abstract
Lycium ruthenicum is an excellent eco-economic shrub. Numerous researches have been conducted for the function of its fruits but scarcely focused on the somaclonal variation and DNA methylation. An efficient micropropagation protocol from leaves and stems of L. ruthenicum was developed in this study, in which not only the leaf explants but also the stem explants of L. ruthenicum were dedifferentiated and produced adventitious buds/multiple shoots on one type of medium. Notably, the efficient indirect organogenesis of stem explants was independent of exogenous auxin, which is contrary to the common conclusion that induction and proliferation of calli is dependent on exogenous auxin. We proposed that sucrose supply might be the crucial regulator of stem callus induction and proliferation of L. ruthenicum. Furthermore, results of methylation-sensitive amplified polymorphism (MSAP) showed that DNA methylation somaclonal variation (MSV) of CNG decreased but that of CG increased after acclimatization. Three types of micropropagated plants (from leaf calli, stem calli and axillary buds) were epigenetically diverged more from each other after acclimatization and the ex vitro micropropagated plants should be selected to determine the fidelity. In summary, plants micropropagated from axillary buds and leaves of L. ruthenicum was more fidelity and might be suitable for preservation and propagation of elite germplasm. Also, leaf explants should be used in transformation. Meanwhile, plants from stem calli showed the highest MSV and might be used in somaclonal variation breeding. Moreover, one MSV hotspot was found based on biological replicates. The study not only provided foundations for molecular breeding, somaclonal variation breeding, preservation and propagation of elite germplasm, but also offered clues for further revealing novel mechanisms of both stem-explant dedifferentiation and MSV of L. ruthenicum.
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Affiliation(s)
- Yue Gao
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Qin-Mei Wang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Qinxia An
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Jianguo Cui
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yongbin Zhou
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xinyu Qi
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Lijie Zhang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Lujia Li
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
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