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Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing

Markers linked to agronomic traits are of the prerequisite for molecular breeding. Genotyping-by-sequencing (GBS) data enables to detect small polymorphisms including single nucleotide polymorphisms (SNPs) and short insertions or deletions (InDels) that can be used, for instance, for marker-assisted...

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Autores principales: Keilwagen, Jens, Lehnert, Heike, Berner, Thomas, Beier, Sebastian, Scholz, Uwe, Himmelbach, Axel, Stein, Nils, Badaeva, Ekaterina D., Lang, Daniel, Kilian, Benjamin, Hackauf, Bernd, Perovic, Dragan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6771380/
https://www.ncbi.nlm.nih.gov/pubmed/31608087
http://dx.doi.org/10.3389/fpls.2019.01133
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author Keilwagen, Jens
Lehnert, Heike
Berner, Thomas
Beier, Sebastian
Scholz, Uwe
Himmelbach, Axel
Stein, Nils
Badaeva, Ekaterina D.
Lang, Daniel
Kilian, Benjamin
Hackauf, Bernd
Perovic, Dragan
author_facet Keilwagen, Jens
Lehnert, Heike
Berner, Thomas
Beier, Sebastian
Scholz, Uwe
Himmelbach, Axel
Stein, Nils
Badaeva, Ekaterina D.
Lang, Daniel
Kilian, Benjamin
Hackauf, Bernd
Perovic, Dragan
author_sort Keilwagen, Jens
collection PubMed
description Markers linked to agronomic traits are of the prerequisite for molecular breeding. Genotyping-by-sequencing (GBS) data enables to detect small polymorphisms including single nucleotide polymorphisms (SNPs) and short insertions or deletions (InDels) that can be used, for instance, for marker-assisted selection, population genetics, and genome-wide association studies (GWAS). Here, we aim at detecting large chromosomal modifications in barley and wheat based on GBS data. These modifications could be duplications, deletions, substitutions including introgressions as well as alterations of DNA methylation. We demonstrate that GBS coverage analysis is capable to detect Hordeum vulgare/Hordeum bulbosum introgression lines. Furthermore, we identify large chromosomal modifications in barley and wheat collections. Hence, large chromosomal modifications, including introgressions and copy number variations (CNV), can be detected easily and can be used as markers in research and breeding without additional wet-lab experiments.
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spelling pubmed-67713802019-10-11 Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing Keilwagen, Jens Lehnert, Heike Berner, Thomas Beier, Sebastian Scholz, Uwe Himmelbach, Axel Stein, Nils Badaeva, Ekaterina D. Lang, Daniel Kilian, Benjamin Hackauf, Bernd Perovic, Dragan Front Plant Sci Plant Science Markers linked to agronomic traits are of the prerequisite for molecular breeding. Genotyping-by-sequencing (GBS) data enables to detect small polymorphisms including single nucleotide polymorphisms (SNPs) and short insertions or deletions (InDels) that can be used, for instance, for marker-assisted selection, population genetics, and genome-wide association studies (GWAS). Here, we aim at detecting large chromosomal modifications in barley and wheat based on GBS data. These modifications could be duplications, deletions, substitutions including introgressions as well as alterations of DNA methylation. We demonstrate that GBS coverage analysis is capable to detect Hordeum vulgare/Hordeum bulbosum introgression lines. Furthermore, we identify large chromosomal modifications in barley and wheat collections. Hence, large chromosomal modifications, including introgressions and copy number variations (CNV), can be detected easily and can be used as markers in research and breeding without additional wet-lab experiments. Frontiers Media S.A. 2019-09-24 /pmc/articles/PMC6771380/ /pubmed/31608087 http://dx.doi.org/10.3389/fpls.2019.01133 Text en Copyright © 2019 Keilwagen, Lehnert, Berner, Beier, Scholz, Himmelbach, Stein, Badaeva, Lang, Kilian, Hackauf and Perovic http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Keilwagen, Jens
Lehnert, Heike
Berner, Thomas
Beier, Sebastian
Scholz, Uwe
Himmelbach, Axel
Stein, Nils
Badaeva, Ekaterina D.
Lang, Daniel
Kilian, Benjamin
Hackauf, Bernd
Perovic, Dragan
Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing
title Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing
title_full Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing
title_fullStr Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing
title_full_unstemmed Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing
title_short Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing
title_sort detecting large chromosomal modifications using short read data from genotyping-by-sequencing
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6771380/
https://www.ncbi.nlm.nih.gov/pubmed/31608087
http://dx.doi.org/10.3389/fpls.2019.01133
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