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Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop
Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of...
Autores principales: | , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Pub. Group
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667612/ https://www.ncbi.nlm.nih.gov/pubmed/26549859 http://dx.doi.org/10.1038/ncomms9824 |
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author | Hazzouri, Khaled M. Flowers, Jonathan M. Visser, Hendrik J. Khierallah, Hussam S. M. Rosas, Ulises Pham, Gina M. Meyer, Rachel S. Johansen, Caryn K. Fresquez, Zoë A. Masmoudi, Khaled Haider, Nadia El Kadri, Nabila Idaghdour, Youssef Malek, Joel A. Thirkhill, Deborah Markhand, Ghulam S. Krueger, Robert R. Zaid, Abdelouahhab Purugganan, Michael D. |
author_facet | Hazzouri, Khaled M. Flowers, Jonathan M. Visser, Hendrik J. Khierallah, Hussam S. M. Rosas, Ulises Pham, Gina M. Meyer, Rachel S. Johansen, Caryn K. Fresquez, Zoë A. Masmoudi, Khaled Haider, Nadia El Kadri, Nabila Idaghdour, Youssef Malek, Joel A. Thirkhill, Deborah Markhand, Ghulam S. Krueger, Robert R. Zaid, Abdelouahhab Purugganan, Michael D. |
author_sort | Hazzouri, Khaled M. |
collection | PubMed |
description | Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop. |
format | Online Article Text |
id | pubmed-4667612 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Nature Pub. Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-46676122015-12-10 Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop Hazzouri, Khaled M. Flowers, Jonathan M. Visser, Hendrik J. Khierallah, Hussam S. M. Rosas, Ulises Pham, Gina M. Meyer, Rachel S. Johansen, Caryn K. Fresquez, Zoë A. Masmoudi, Khaled Haider, Nadia El Kadri, Nabila Idaghdour, Youssef Malek, Joel A. Thirkhill, Deborah Markhand, Ghulam S. Krueger, Robert R. Zaid, Abdelouahhab Purugganan, Michael D. Nat Commun Article Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop. Nature Pub. Group 2015-11-09 /pmc/articles/PMC4667612/ /pubmed/26549859 http://dx.doi.org/10.1038/ncomms9824 Text en Copyright © 2015, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Hazzouri, Khaled M. Flowers, Jonathan M. Visser, Hendrik J. Khierallah, Hussam S. M. Rosas, Ulises Pham, Gina M. Meyer, Rachel S. Johansen, Caryn K. Fresquez, Zoë A. Masmoudi, Khaled Haider, Nadia El Kadri, Nabila Idaghdour, Youssef Malek, Joel A. Thirkhill, Deborah Markhand, Ghulam S. Krueger, Robert R. Zaid, Abdelouahhab Purugganan, Michael D. Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop |
title | Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop |
title_full | Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop |
title_fullStr | Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop |
title_full_unstemmed | Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop |
title_short | Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop |
title_sort | whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667612/ https://www.ncbi.nlm.nih.gov/pubmed/26549859 http://dx.doi.org/10.1038/ncomms9824 |
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