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Identification of recombination events in outbred species with next-generation sequencing data

BACKGROUND: Meiotic recombination events include crossovers and non-crossovers or gene conversions. Although the rate of crossovers is often used for genetic mapping, the gene conversion events are not well studied especially in outbred species, which could produce distorted markers and thus affect...

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Autores principales: Tao, Shentong, Wu, Jiyan, Yao, Dan, Chen, Yuhua, Yang, Wenguo, Tong, Chunfa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5970487/
https://www.ncbi.nlm.nih.gov/pubmed/29801431
http://dx.doi.org/10.1186/s12864-018-4791-x
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author Tao, Shentong
Wu, Jiyan
Yao, Dan
Chen, Yuhua
Yang, Wenguo
Tong, Chunfa
author_facet Tao, Shentong
Wu, Jiyan
Yao, Dan
Chen, Yuhua
Yang, Wenguo
Tong, Chunfa
author_sort Tao, Shentong
collection PubMed
description BACKGROUND: Meiotic recombination events include crossovers and non-crossovers or gene conversions. Although the rate of crossovers is often used for genetic mapping, the gene conversion events are not well studied especially in outbred species, which could produce distorted markers and thus affect the precision of genetic maps. RESULTS: We proposed a strategy for identifying gene conversion events in Populus with the next-generation sequencing (NGS) data from the two parents and their progeny in an F(1) hybrid population. The strategy first involved phasing the heterozygous SNPs of the parents to obtain the parental haplotype blocks by NGS analytical tools, permitting to identify the parental gene conversion events with progeny genotypes. By incorporating available genetic linkage maps, longer haplotype blocks each corresponding to a chromosome can be created, not only allowing to detect crossover events but also possibly to locate a crossover in a small region. Our analysis revealed that gene conversions are more abundant than crossovers in Populus, with a higher probability to generate distorted markers in the regions involved than in the other regions on genome. The analytical procedures were implemented with Perl scripts as a freely available package, findGCO at https://github.com/tongchf/findGCO. CONCLUSIONS: The novel strategy and the new developed Perl package permit to identify gene conversion events with the next-generation sequencing technology in a hybrid population of outbred species. The new method revealed that in a genetic mapping population some distorted genetic markers are possibly due to the gene conversion events. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4791-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-59704872018-05-30 Identification of recombination events in outbred species with next-generation sequencing data Tao, Shentong Wu, Jiyan Yao, Dan Chen, Yuhua Yang, Wenguo Tong, Chunfa BMC Genomics Research Article BACKGROUND: Meiotic recombination events include crossovers and non-crossovers or gene conversions. Although the rate of crossovers is often used for genetic mapping, the gene conversion events are not well studied especially in outbred species, which could produce distorted markers and thus affect the precision of genetic maps. RESULTS: We proposed a strategy for identifying gene conversion events in Populus with the next-generation sequencing (NGS) data from the two parents and their progeny in an F(1) hybrid population. The strategy first involved phasing the heterozygous SNPs of the parents to obtain the parental haplotype blocks by NGS analytical tools, permitting to identify the parental gene conversion events with progeny genotypes. By incorporating available genetic linkage maps, longer haplotype blocks each corresponding to a chromosome can be created, not only allowing to detect crossover events but also possibly to locate a crossover in a small region. Our analysis revealed that gene conversions are more abundant than crossovers in Populus, with a higher probability to generate distorted markers in the regions involved than in the other regions on genome. The analytical procedures were implemented with Perl scripts as a freely available package, findGCO at https://github.com/tongchf/findGCO. CONCLUSIONS: The novel strategy and the new developed Perl package permit to identify gene conversion events with the next-generation sequencing technology in a hybrid population of outbred species. The new method revealed that in a genetic mapping population some distorted genetic markers are possibly due to the gene conversion events. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4791-x) contains supplementary material, which is available to authorized users. BioMed Central 2018-05-25 /pmc/articles/PMC5970487/ /pubmed/29801431 http://dx.doi.org/10.1186/s12864-018-4791-x Text en © The Author(s). 2018 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
Tao, Shentong
Wu, Jiyan
Yao, Dan
Chen, Yuhua
Yang, Wenguo
Tong, Chunfa
Identification of recombination events in outbred species with next-generation sequencing data
title Identification of recombination events in outbred species with next-generation sequencing data
title_full Identification of recombination events in outbred species with next-generation sequencing data
title_fullStr Identification of recombination events in outbred species with next-generation sequencing data
title_full_unstemmed Identification of recombination events in outbred species with next-generation sequencing data
title_short Identification of recombination events in outbred species with next-generation sequencing data
title_sort identification of recombination events in outbred species with next-generation sequencing data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5970487/
https://www.ncbi.nlm.nih.gov/pubmed/29801431
http://dx.doi.org/10.1186/s12864-018-4791-x
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