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Genetic diversity, linkage disequilibrium, and population structure of tetraploid wheat landraces originating from Europe and Asia

BACKGROUND: Durum wheat is one of the most important crops, especially in the Mediterranean region. Insight into the genetic diversity of germplasm can improve the breeding program management in various traits. This study was done using single nucleotide polymorphisms (SNP) markers to characterize t...

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Autores principales: Rabieyan, Ehsan, Darvishzadeh, Reza, Mohammadi, Reza, Gul, Alvina, Rasheed, Awais, Akhar, Fatemeh Keykha, Abdi, Hossein, Alipour, Hadi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10644499/
https://www.ncbi.nlm.nih.gov/pubmed/37964224
http://dx.doi.org/10.1186/s12864-023-09768-6
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author Rabieyan, Ehsan
Darvishzadeh, Reza
Mohammadi, Reza
Gul, Alvina
Rasheed, Awais
Akhar, Fatemeh Keykha
Abdi, Hossein
Alipour, Hadi
author_facet Rabieyan, Ehsan
Darvishzadeh, Reza
Mohammadi, Reza
Gul, Alvina
Rasheed, Awais
Akhar, Fatemeh Keykha
Abdi, Hossein
Alipour, Hadi
author_sort Rabieyan, Ehsan
collection PubMed
description BACKGROUND: Durum wheat is one of the most important crops, especially in the Mediterranean region. Insight into the genetic diversity of germplasm can improve the breeding program management in various traits. This study was done using single nucleotide polymorphisms (SNP) markers to characterize the genetic distinctiveness and differentiation of tetraploid wheat landraces collected from nine European and Asian countries. A sum of 23,334 polymorphic SNPs was detected in 126 tetraploid wheat landraces in relation to the reference genome. RESULTS: The number of identified SNPs was 11,613 and 11,721 in A and B genomes, respectively. The highest and lowest diversity was on 6B and 6 A chromosomes, respectively. Structure analysis classified the landraces into two distinct subpopulations (K = 2). Evaluating the principal coordinate analysis (PCoA) and weighted pair-group method using arithmetic averages (WPGMA) clustering results demonstrated that landraces (99.2%) are categorized into one of the two chief subpopulations. Therefore, the grouping pattern did not clearly show the presence of a clear pattern of relationships between genetic diversity and their geographical derivation. Part of this result could be due to the historical exchange between different germplasms. Although the result did not separate landraces based on their region of origin, the landraces collected from Iran were classified into the same group and cluster. Analysis of molecular variance (AMOVA) also confirmed the results of population structure. Finally, Durum wheat landraces in some countries, including Turkey, Russia, Ukraine, and Afghanistan, were highly diverse, while others, including Iran and China, were low-diversity. CONCLUSION: The recent study concluded that the 126 tetraploid wheat genotypes and their GBS-SNP markers are very appropriate for quantitative trait loci (QTLs) mapping and genome-wide association studies (GWAS). The core collection comprises two distinct subpopulations. Subpopulation II genotypes are the most diverse genotypes, and if they possess desired traits, they may be used in future breeding programs. The degree of diversity in the landraces of countries can provide the ground for the improvement of new cultivars with international cooperation. linkage disequilibrium (LD) hotspot distribution across the genome was investigated, which provides useful information about the genomic regions that contain intriguing genes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09768-6.
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spelling pubmed-106444992023-11-14 Genetic diversity, linkage disequilibrium, and population structure of tetraploid wheat landraces originating from Europe and Asia Rabieyan, Ehsan Darvishzadeh, Reza Mohammadi, Reza Gul, Alvina Rasheed, Awais Akhar, Fatemeh Keykha Abdi, Hossein Alipour, Hadi BMC Genomics Research BACKGROUND: Durum wheat is one of the most important crops, especially in the Mediterranean region. Insight into the genetic diversity of germplasm can improve the breeding program management in various traits. This study was done using single nucleotide polymorphisms (SNP) markers to characterize the genetic distinctiveness and differentiation of tetraploid wheat landraces collected from nine European and Asian countries. A sum of 23,334 polymorphic SNPs was detected in 126 tetraploid wheat landraces in relation to the reference genome. RESULTS: The number of identified SNPs was 11,613 and 11,721 in A and B genomes, respectively. The highest and lowest diversity was on 6B and 6 A chromosomes, respectively. Structure analysis classified the landraces into two distinct subpopulations (K = 2). Evaluating the principal coordinate analysis (PCoA) and weighted pair-group method using arithmetic averages (WPGMA) clustering results demonstrated that landraces (99.2%) are categorized into one of the two chief subpopulations. Therefore, the grouping pattern did not clearly show the presence of a clear pattern of relationships between genetic diversity and their geographical derivation. Part of this result could be due to the historical exchange between different germplasms. Although the result did not separate landraces based on their region of origin, the landraces collected from Iran were classified into the same group and cluster. Analysis of molecular variance (AMOVA) also confirmed the results of population structure. Finally, Durum wheat landraces in some countries, including Turkey, Russia, Ukraine, and Afghanistan, were highly diverse, while others, including Iran and China, were low-diversity. CONCLUSION: The recent study concluded that the 126 tetraploid wheat genotypes and their GBS-SNP markers are very appropriate for quantitative trait loci (QTLs) mapping and genome-wide association studies (GWAS). The core collection comprises two distinct subpopulations. Subpopulation II genotypes are the most diverse genotypes, and if they possess desired traits, they may be used in future breeding programs. The degree of diversity in the landraces of countries can provide the ground for the improvement of new cultivars with international cooperation. linkage disequilibrium (LD) hotspot distribution across the genome was investigated, which provides useful information about the genomic regions that contain intriguing genes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09768-6. BioMed Central 2023-11-14 /pmc/articles/PMC10644499/ /pubmed/37964224 http://dx.doi.org/10.1186/s12864-023-09768-6 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Rabieyan, Ehsan
Darvishzadeh, Reza
Mohammadi, Reza
Gul, Alvina
Rasheed, Awais
Akhar, Fatemeh Keykha
Abdi, Hossein
Alipour, Hadi
Genetic diversity, linkage disequilibrium, and population structure of tetraploid wheat landraces originating from Europe and Asia
title Genetic diversity, linkage disequilibrium, and population structure of tetraploid wheat landraces originating from Europe and Asia
title_full Genetic diversity, linkage disequilibrium, and population structure of tetraploid wheat landraces originating from Europe and Asia
title_fullStr Genetic diversity, linkage disequilibrium, and population structure of tetraploid wheat landraces originating from Europe and Asia
title_full_unstemmed Genetic diversity, linkage disequilibrium, and population structure of tetraploid wheat landraces originating from Europe and Asia
title_short Genetic diversity, linkage disequilibrium, and population structure of tetraploid wheat landraces originating from Europe and Asia
title_sort genetic diversity, linkage disequilibrium, and population structure of tetraploid wheat landraces originating from europe and asia
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10644499/
https://www.ncbi.nlm.nih.gov/pubmed/37964224
http://dx.doi.org/10.1186/s12864-023-09768-6
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