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Asymmetric somatic hybridization induces point mutations and indels in wheat

BACKGROUND: Allopolyploid genome needs wide structural variation to deal with genomic shock. The introgression line, generated via asymmetric somatic hybridization, is introgressed with a minimum of exogenous chromatin, which also leads to genomic shock to induce genetic variation. However, the exte...

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Autores principales: Wang, Mengcheng, Liu, Chun, Xing, Tian, Wang, Yanxia, Xia, Guangmin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609470/
https://www.ncbi.nlm.nih.gov/pubmed/26476565
http://dx.doi.org/10.1186/s12864-015-1974-6
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author Wang, Mengcheng
Liu, Chun
Xing, Tian
Wang, Yanxia
Xia, Guangmin
author_facet Wang, Mengcheng
Liu, Chun
Xing, Tian
Wang, Yanxia
Xia, Guangmin
author_sort Wang, Mengcheng
collection PubMed
description BACKGROUND: Allopolyploid genome needs wide structural variation to deal with genomic shock. The introgression line, generated via asymmetric somatic hybridization, is introgressed with a minimum of exogenous chromatin, which also leads to genomic shock to induce genetic variation. However, the extent of its genomic variation and its difference from allopolyploidies remains unknown. METHODS: Here, we explored this issue using the bread wheat cultivar SR3, a derivative of an asymmetric somatic hybrid between the cultivar JN177 and an accession of tall wheatgrass (Thinopyrum elongatum). The ESTs (expressed sequence taqs) were large-scale sequenced using the cDNA library constructed in each of SR3 and JN177. Point mutations and indels (insertions and deletions) of SR3 were calculated, and their difference from the genetic variation of bread wheat and its ancestors were compared, with aim to analyze the extent and pattern of sequence variation induced by somatic hybridization. RESULTS: Both point mutations and indels (insertions and deletions) were frequently induced by somatic hybridization in the coding sequences. While the genomic shock caused by allopolyploidization tends to favor deletion over insertion, there was no evidence for such a preference following asymmetric somatic hybridization. The GC content of sequence adjacent to indel sites was also distinct from what has been observed in allopolyploids. CONCLUSIONS: This study demonstrates that asymmetric somatic hybridization induces high frequency of genetic variation in a manner partially different from allopolipoidization. Asymmetric somatic hybridization provides appropriate material to comprehensively explore the nature of the genetic variation induced by genomic shock. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1974-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-46094702015-10-19 Asymmetric somatic hybridization induces point mutations and indels in wheat Wang, Mengcheng Liu, Chun Xing, Tian Wang, Yanxia Xia, Guangmin BMC Genomics Research Article BACKGROUND: Allopolyploid genome needs wide structural variation to deal with genomic shock. The introgression line, generated via asymmetric somatic hybridization, is introgressed with a minimum of exogenous chromatin, which also leads to genomic shock to induce genetic variation. However, the extent of its genomic variation and its difference from allopolyploidies remains unknown. METHODS: Here, we explored this issue using the bread wheat cultivar SR3, a derivative of an asymmetric somatic hybrid between the cultivar JN177 and an accession of tall wheatgrass (Thinopyrum elongatum). The ESTs (expressed sequence taqs) were large-scale sequenced using the cDNA library constructed in each of SR3 and JN177. Point mutations and indels (insertions and deletions) of SR3 were calculated, and their difference from the genetic variation of bread wheat and its ancestors were compared, with aim to analyze the extent and pattern of sequence variation induced by somatic hybridization. RESULTS: Both point mutations and indels (insertions and deletions) were frequently induced by somatic hybridization in the coding sequences. While the genomic shock caused by allopolyploidization tends to favor deletion over insertion, there was no evidence for such a preference following asymmetric somatic hybridization. The GC content of sequence adjacent to indel sites was also distinct from what has been observed in allopolyploids. CONCLUSIONS: This study demonstrates that asymmetric somatic hybridization induces high frequency of genetic variation in a manner partially different from allopolipoidization. Asymmetric somatic hybridization provides appropriate material to comprehensively explore the nature of the genetic variation induced by genomic shock. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1974-6) contains supplementary material, which is available to authorized users. BioMed Central 2015-10-17 /pmc/articles/PMC4609470/ /pubmed/26476565 http://dx.doi.org/10.1186/s12864-015-1974-6 Text en © Wang et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Wang, Mengcheng
Liu, Chun
Xing, Tian
Wang, Yanxia
Xia, Guangmin
Asymmetric somatic hybridization induces point mutations and indels in wheat
title Asymmetric somatic hybridization induces point mutations and indels in wheat
title_full Asymmetric somatic hybridization induces point mutations and indels in wheat
title_fullStr Asymmetric somatic hybridization induces point mutations and indels in wheat
title_full_unstemmed Asymmetric somatic hybridization induces point mutations and indels in wheat
title_short Asymmetric somatic hybridization induces point mutations and indels in wheat
title_sort asymmetric somatic hybridization induces point mutations and indels in wheat
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609470/
https://www.ncbi.nlm.nih.gov/pubmed/26476565
http://dx.doi.org/10.1186/s12864-015-1974-6
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