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Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species

Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplific...

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Autores principales: Sorkheh, Karim, Dehkordi, Mehrana Koohi, Ercisli, Sezai, Hegedus, Attila, Halász, Júlia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5519738/
https://www.ncbi.nlm.nih.gov/pubmed/28729554
http://dx.doi.org/10.1038/s41598-017-06084-4
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author Sorkheh, Karim
Dehkordi, Mehrana Koohi
Ercisli, Sezai
Hegedus, Attila
Halász, Júlia
author_facet Sorkheh, Karim
Dehkordi, Mehrana Koohi
Ercisli, Sezai
Hegedus, Attila
Halász, Júlia
author_sort Sorkheh, Karim
collection PubMed
description Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity.
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spelling pubmed-55197382017-07-26 Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species Sorkheh, Karim Dehkordi, Mehrana Koohi Ercisli, Sezai Hegedus, Attila Halász, Júlia Sci Rep Article Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity. Nature Publishing Group UK 2017-07-20 /pmc/articles/PMC5519738/ /pubmed/28729554 http://dx.doi.org/10.1038/s41598-017-06084-4 Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Sorkheh, Karim
Dehkordi, Mehrana Koohi
Ercisli, Sezai
Hegedus, Attila
Halász, Júlia
Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
title Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
title_full Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
title_fullStr Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
title_full_unstemmed Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
title_short Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
title_sort comparison of traditional and new generation dna markers declares high genetic diversity and differentiated population structure of wild almond species
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5519738/
https://www.ncbi.nlm.nih.gov/pubmed/28729554
http://dx.doi.org/10.1038/s41598-017-06084-4
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