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Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology

BACKGROUND: Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic lin...

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Autores principales: Zhigunov, Anatoly V., Ulianich, Pavel S., Lebedeva, Marina V., Chang, Peter L., Nuzhdin, Sergey V., Potokina, Elena K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5688504/
https://www.ncbi.nlm.nih.gov/pubmed/29143610
http://dx.doi.org/10.1186/s12870-017-1127-y
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author Zhigunov, Anatoly V.
Ulianich, Pavel S.
Lebedeva, Marina V.
Chang, Peter L.
Nuzhdin, Sergey V.
Potokina, Elena K.
author_facet Zhigunov, Anatoly V.
Ulianich, Pavel S.
Lebedeva, Marina V.
Chang, Peter L.
Nuzhdin, Sergey V.
Potokina, Elena K.
author_sort Zhigunov, Anatoly V.
collection PubMed
description BACKGROUND: Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe. RESULTS: We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits. We performed RADseq of 122 F1 progenies and two parents yielding 15,732 high-quality SNPs that were successfully identified using the reference genome of P. trichocarpa. 2055 SNPs were employed for the construction of maternal and paternal linkage maps. The maternal linkage map was assembled with 1000 SNPs, containing 19 linkage groups and spanning 3054.9 cM of the genome, with an average distance of 3.05 cM between adjacent markers. The paternal map consisted of 1055 SNPs and the same number of linkage groups with a total length of 3090.56 cM and average interval distance of 2.93 cM. The linkage maps were employed for QTL mapping of one-year-old seedlings height variation. The most significant QTL (LOD = 5.73) was localized to LG5 (96.94 cM) of the male linkage map, explaining 18% of the phenotypic variation. CONCLUSIONS: The set of 15,732 SNPs polymorphic in aspen and high-density genetic linkage maps constructed for the P. tremula intra-specific cross will provide a valuable source for QTL mapping and identification of candidate genes facilitating marker-assisted selection in European aspen. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-017-1127-y) contains supplementary material, which is available to authorized users.
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spelling pubmed-56885042017-11-22 Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology Zhigunov, Anatoly V. Ulianich, Pavel S. Lebedeva, Marina V. Chang, Peter L. Nuzhdin, Sergey V. Potokina, Elena K. BMC Plant Biol Research BACKGROUND: Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe. RESULTS: We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits. We performed RADseq of 122 F1 progenies and two parents yielding 15,732 high-quality SNPs that were successfully identified using the reference genome of P. trichocarpa. 2055 SNPs were employed for the construction of maternal and paternal linkage maps. The maternal linkage map was assembled with 1000 SNPs, containing 19 linkage groups and spanning 3054.9 cM of the genome, with an average distance of 3.05 cM between adjacent markers. The paternal map consisted of 1055 SNPs and the same number of linkage groups with a total length of 3090.56 cM and average interval distance of 2.93 cM. The linkage maps were employed for QTL mapping of one-year-old seedlings height variation. The most significant QTL (LOD = 5.73) was localized to LG5 (96.94 cM) of the male linkage map, explaining 18% of the phenotypic variation. CONCLUSIONS: The set of 15,732 SNPs polymorphic in aspen and high-density genetic linkage maps constructed for the P. tremula intra-specific cross will provide a valuable source for QTL mapping and identification of candidate genes facilitating marker-assisted selection in European aspen. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-017-1127-y) contains supplementary material, which is available to authorized users. BioMed Central 2017-11-14 /pmc/articles/PMC5688504/ /pubmed/29143610 http://dx.doi.org/10.1186/s12870-017-1127-y Text en © The Author(s). 2017 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
Zhigunov, Anatoly V.
Ulianich, Pavel S.
Lebedeva, Marina V.
Chang, Peter L.
Nuzhdin, Sergey V.
Potokina, Elena K.
Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology
title Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology
title_full Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology
title_fullStr Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology
title_full_unstemmed Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology
title_short Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology
title_sort development of f1 hybrid population and the high-density linkage map for european aspen (populus tremula l.) using radseq technology
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5688504/
https://www.ncbi.nlm.nih.gov/pubmed/29143610
http://dx.doi.org/10.1186/s12870-017-1127-y
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