Genetic diversity and population structure analysis of Triticum aestivum L. Landrace panel from Afghanistan
Landraces are a potential source of genetic diversity and provide useful genetic resources to cope with the current and future challenges in crop breeding. Afghanistan is located close to the centre of origin of hexaploid wheat. Therefore, understanding the population structure and genetic diversity of Afghan wheat landraces is of enormous importance in breeding programmes for the development of high‐yielding cultivars as well as broadening the genetic base of bread wheat. Here, a panel of 363 bread wheat landraces collected from seven north and north‐eastern provinces of Afghanistan were evaluated for population structure and genetic diversity using single nucleotide polymorphic markers (SNPs). The genotyping‐by‐sequencing of studied landraces after quality control provided 4897 high‐quality SNPs distributed across the genomes A (33.75%), B (38.73%), and D (27.50%). The population structure analysis was carried out by two methods using modelbased STRUCTURE analysis and cluster‐based discriminant analysis of principal components (DAPC). The analysis of molecular variance showed a higher proportion of variation within the sub‐populations compared with the variation observed as a whole between sub‐populations. STRUCTURE and DAPC analysis grouped the majority of the landraces from Badakhshan and Takhar together in one cluster and the landraces from Baghlan and Kunduz in a second cluster, which is in accordance with the micro‐climatic conditions prevalent within the north‐eastern agroecological zone. Genetic distance analysis was also studied to identify differences among the Afghan regions; the strongest correlation was observed for the Badakhshan and Takhar (0.003), whereas Samangan and Konarha (0.399) showed the highest genetic distance. The population structure and genetic diversity analysis highlighted the complex genetic variation present in the landraces which were highly correlated to the geographic origin and micro‐climatic conditions within the agro‐climatic zones of the landraces. The higher proportions of admixture could be attributed to historical unsupervised exchanges of seeds between the farmers of the central and north‐eastern provinces of Afghanistan. The results of this study will provide useful information for genetic improvement in wheat and is essential for association mapping and genomic prediction studies to identify novel sources for resistance to abiotic and biotic stresses.
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2021
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Subjects: | AGRICULTURAL SCIENCES AND BIOTECHNOLOGY, Afghan Wheat Landraces, WHEAT, LAND RACES, GENETIC DIVERSITY, POPULATION STRUCTURE, |
Online Access: | https://hdl.handle.net/10883/21329 |
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dig-cimmyt-10883-213292022-11-09T17:43:41Z Genetic diversity and population structure analysis of Triticum aestivum L. Landrace panel from Afghanistan Tehseen, M.M. Istipliler, D. Kehel, Z. Sansaloni, C.P. Lopes, M.S. Kurtulus, E. Muazzam, S. Nazari, K. AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Afghan Wheat Landraces WHEAT LAND RACES GENETIC DIVERSITY POPULATION STRUCTURE Landraces are a potential source of genetic diversity and provide useful genetic resources to cope with the current and future challenges in crop breeding. Afghanistan is located close to the centre of origin of hexaploid wheat. Therefore, understanding the population structure and genetic diversity of Afghan wheat landraces is of enormous importance in breeding programmes for the development of high‐yielding cultivars as well as broadening the genetic base of bread wheat. Here, a panel of 363 bread wheat landraces collected from seven north and north‐eastern provinces of Afghanistan were evaluated for population structure and genetic diversity using single nucleotide polymorphic markers (SNPs). The genotyping‐by‐sequencing of studied landraces after quality control provided 4897 high‐quality SNPs distributed across the genomes A (33.75%), B (38.73%), and D (27.50%). The population structure analysis was carried out by two methods using modelbased STRUCTURE analysis and cluster‐based discriminant analysis of principal components (DAPC). The analysis of molecular variance showed a higher proportion of variation within the sub‐populations compared with the variation observed as a whole between sub‐populations. STRUCTURE and DAPC analysis grouped the majority of the landraces from Badakhshan and Takhar together in one cluster and the landraces from Baghlan and Kunduz in a second cluster, which is in accordance with the micro‐climatic conditions prevalent within the north‐eastern agroecological zone. Genetic distance analysis was also studied to identify differences among the Afghan regions; the strongest correlation was observed for the Badakhshan and Takhar (0.003), whereas Samangan and Konarha (0.399) showed the highest genetic distance. The population structure and genetic diversity analysis highlighted the complex genetic variation present in the landraces which were highly correlated to the geographic origin and micro‐climatic conditions within the agro‐climatic zones of the landraces. The higher proportions of admixture could be attributed to historical unsupervised exchanges of seeds between the farmers of the central and north‐eastern provinces of Afghanistan. The results of this study will provide useful information for genetic improvement in wheat and is essential for association mapping and genomic prediction studies to identify novel sources for resistance to abiotic and biotic stresses. 2021-03-30T00:10:14Z 2021-03-30T00:10:14Z 2021 Article Published Version https://hdl.handle.net/10883/21329 10.3390/genes12030340 English https://www.mdpi.com/2073-4425/12/3/340#supplementary CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose Open Access Basel (Switzerland) MDPI 3 12 2073-4425 Genes 340 |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Afghan Wheat Landraces WHEAT LAND RACES GENETIC DIVERSITY POPULATION STRUCTURE AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Afghan Wheat Landraces WHEAT LAND RACES GENETIC DIVERSITY POPULATION STRUCTURE |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Afghan Wheat Landraces WHEAT LAND RACES GENETIC DIVERSITY POPULATION STRUCTURE AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Afghan Wheat Landraces WHEAT LAND RACES GENETIC DIVERSITY POPULATION STRUCTURE Tehseen, M.M. Istipliler, D. Kehel, Z. Sansaloni, C.P. Lopes, M.S. Kurtulus, E. Muazzam, S. Nazari, K. Genetic diversity and population structure analysis of Triticum aestivum L. Landrace panel from Afghanistan |
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Landraces are a potential source of genetic diversity and provide useful genetic resources to cope with the current and future challenges in crop breeding. Afghanistan is located close to the centre of origin of hexaploid wheat. Therefore, understanding the population structure and genetic diversity of Afghan wheat landraces is of enormous importance in breeding programmes for the development of high‐yielding cultivars as well as broadening the genetic base of bread wheat. Here, a panel of 363 bread wheat landraces collected from seven north and north‐eastern provinces of Afghanistan were evaluated for population structure and genetic diversity using single nucleotide polymorphic markers (SNPs). The genotyping‐by‐sequencing of studied landraces after quality control provided 4897 high‐quality SNPs distributed across the genomes A (33.75%), B (38.73%), and D (27.50%). The population structure analysis was carried out by two methods using modelbased STRUCTURE analysis and cluster‐based discriminant analysis of principal components (DAPC). The analysis of molecular variance showed a higher proportion of variation within the sub‐populations compared with the variation observed as a whole between sub‐populations. STRUCTURE and DAPC analysis grouped the majority of the landraces from Badakhshan and Takhar together in one cluster and the landraces from Baghlan and Kunduz in a second cluster, which is in accordance with the micro‐climatic conditions prevalent within the north‐eastern agroecological zone. Genetic distance analysis was also studied to identify differences among the Afghan regions; the strongest correlation was observed for the Badakhshan and Takhar (0.003), whereas Samangan and Konarha (0.399) showed the highest genetic distance. The population structure and genetic diversity analysis highlighted the complex genetic variation present in the landraces which were highly correlated to the geographic origin and micro‐climatic conditions within the agro‐climatic zones of the landraces. The higher proportions of admixture could be attributed to historical unsupervised exchanges of seeds between the farmers of the central and north‐eastern provinces of Afghanistan. The results of this study will provide useful information for genetic improvement in wheat and is essential for association mapping and genomic prediction studies to identify novel sources for resistance to abiotic and biotic stresses. |
format |
Article |
topic_facet |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Afghan Wheat Landraces WHEAT LAND RACES GENETIC DIVERSITY POPULATION STRUCTURE |
author |
Tehseen, M.M. Istipliler, D. Kehel, Z. Sansaloni, C.P. Lopes, M.S. Kurtulus, E. Muazzam, S. Nazari, K. |
author_facet |
Tehseen, M.M. Istipliler, D. Kehel, Z. Sansaloni, C.P. Lopes, M.S. Kurtulus, E. Muazzam, S. Nazari, K. |
author_sort |
Tehseen, M.M. |
title |
Genetic diversity and population structure analysis of Triticum aestivum L. Landrace panel from Afghanistan |
title_short |
Genetic diversity and population structure analysis of Triticum aestivum L. Landrace panel from Afghanistan |
title_full |
Genetic diversity and population structure analysis of Triticum aestivum L. Landrace panel from Afghanistan |
title_fullStr |
Genetic diversity and population structure analysis of Triticum aestivum L. Landrace panel from Afghanistan |
title_full_unstemmed |
Genetic diversity and population structure analysis of Triticum aestivum L. Landrace panel from Afghanistan |
title_sort |
genetic diversity and population structure analysis of triticum aestivum l. landrace panel from afghanistan |
publisher |
MDPI |
publishDate |
2021 |
url |
https://hdl.handle.net/10883/21329 |
work_keys_str_mv |
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1756086970731200512 |