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Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids
BACKGROUND: Genetic and epigenetic alterations can be invoked by plant tissue culture, which may result in heritable changes in phenotypes, a phenomenon collectively termed somaclonal variation. Although extensive studies have been conducted on the molecular nature and spectrum of tissue culture-ind...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648424/ https://www.ncbi.nlm.nih.gov/pubmed/23642214 http://dx.doi.org/10.1186/1471-2229-13-77 |
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author | Wang, Xiaoran Wu, Rui Lin, Xiuyun Bai, Yan Song, Congdi Yu, Xiaoming Xu, Chunming Zhao, Na Dong, Yuzhu Liu, Bao |
author_facet | Wang, Xiaoran Wu, Rui Lin, Xiuyun Bai, Yan Song, Congdi Yu, Xiaoming Xu, Chunming Zhao, Na Dong, Yuzhu Liu, Bao |
author_sort | Wang, Xiaoran |
collection | PubMed |
description | BACKGROUND: Genetic and epigenetic alterations can be invoked by plant tissue culture, which may result in heritable changes in phenotypes, a phenomenon collectively termed somaclonal variation. Although extensive studies have been conducted on the molecular nature and spectrum of tissue culture-induced genomic alterations, the issue of whether and to what extent distinct plant genotypes, e.g., pure-lines, hybrids and polyploids, may respond differentially to the tissue culture condition remains poorly understood. RESULTS: We investigated tissue culture-induced genetic and epigenetic alterations in a set of rice genotypes including two pure-lines (different subspecies), a pair of reciprocal F1 hybrids parented by the two pure-lines, and a pair of reciprocal tetraploids resulted from the hybrids. Using two molecular markers, amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP), both genetic and DNA methylation alterations were detected in calli and regenerants from all six genotypes, but genetic alteration is more prominent than epigenetic alteration. While significant genotypic difference was observed in frequencies of both types of alterations, only genetic alteration showed distinctive features among the three types of genomes, with one hybrid (N/9) being exceptionally labile. Surprisingly, difference in genetic alteration frequencies between the pair of reciprocal F1 hybrids is much greater than that between the two pure-line subspecies. Difference also exists in the pair of reciprocal tetraploids, but is to a less extent than that between the hybrids. The steady-state transcript abundance of genes involved in DNA repair and DNA methylation was significantly altered in both calli and regenerants, and some of which were correlated with the genetic and/or epigenetic alterations. CONCLUSIONS: Our results, based on molecular marker analysis of ca. 1,000 genomic loci, document that genetic alteration is the major cause of somaclonal variation in rice, which is concomitant with epigenetic alterations. Perturbed expression by tissue culture of a set of 41 genes encoding for enzymes involved in DNA repair and DNA methylation is associated with both genetic and epigenetic alterations. There exist fundamental differences among distinct genotypes, pure-lines, hybrids and tetraploids, in propensities of generating both genetic and epigenetic alterations under the tissue culture condition. Parent-of-origin has a conspicuous effect on the alteration frequencies. |
format | Online Article Text |
id | pubmed-3648424 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-36484242013-05-09 Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids Wang, Xiaoran Wu, Rui Lin, Xiuyun Bai, Yan Song, Congdi Yu, Xiaoming Xu, Chunming Zhao, Na Dong, Yuzhu Liu, Bao BMC Plant Biol Research Article BACKGROUND: Genetic and epigenetic alterations can be invoked by plant tissue culture, which may result in heritable changes in phenotypes, a phenomenon collectively termed somaclonal variation. Although extensive studies have been conducted on the molecular nature and spectrum of tissue culture-induced genomic alterations, the issue of whether and to what extent distinct plant genotypes, e.g., pure-lines, hybrids and polyploids, may respond differentially to the tissue culture condition remains poorly understood. RESULTS: We investigated tissue culture-induced genetic and epigenetic alterations in a set of rice genotypes including two pure-lines (different subspecies), a pair of reciprocal F1 hybrids parented by the two pure-lines, and a pair of reciprocal tetraploids resulted from the hybrids. Using two molecular markers, amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP), both genetic and DNA methylation alterations were detected in calli and regenerants from all six genotypes, but genetic alteration is more prominent than epigenetic alteration. While significant genotypic difference was observed in frequencies of both types of alterations, only genetic alteration showed distinctive features among the three types of genomes, with one hybrid (N/9) being exceptionally labile. Surprisingly, difference in genetic alteration frequencies between the pair of reciprocal F1 hybrids is much greater than that between the two pure-line subspecies. Difference also exists in the pair of reciprocal tetraploids, but is to a less extent than that between the hybrids. The steady-state transcript abundance of genes involved in DNA repair and DNA methylation was significantly altered in both calli and regenerants, and some of which were correlated with the genetic and/or epigenetic alterations. CONCLUSIONS: Our results, based on molecular marker analysis of ca. 1,000 genomic loci, document that genetic alteration is the major cause of somaclonal variation in rice, which is concomitant with epigenetic alterations. Perturbed expression by tissue culture of a set of 41 genes encoding for enzymes involved in DNA repair and DNA methylation is associated with both genetic and epigenetic alterations. There exist fundamental differences among distinct genotypes, pure-lines, hybrids and tetraploids, in propensities of generating both genetic and epigenetic alterations under the tissue culture condition. Parent-of-origin has a conspicuous effect on the alteration frequencies. BioMed Central 2013-05-05 /pmc/articles/PMC3648424/ /pubmed/23642214 http://dx.doi.org/10.1186/1471-2229-13-77 Text en Copyright © 2013 Wang et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Wang, Xiaoran Wu, Rui Lin, Xiuyun Bai, Yan Song, Congdi Yu, Xiaoming Xu, Chunming Zhao, Na Dong, Yuzhu Liu, Bao Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids |
title | Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids |
title_full | Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids |
title_fullStr | Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids |
title_full_unstemmed | Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids |
title_short | Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids |
title_sort | tissue culture-induced genetic and epigenetic alterations in rice pure-lines, f1 hybrids and polyploids |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648424/ https://www.ncbi.nlm.nih.gov/pubmed/23642214 http://dx.doi.org/10.1186/1471-2229-13-77 |
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