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Relationships between Iraqi Rice Varieties at the Nuclear and Plastid Genome Levels

Due to the importance of the rice crop in Iraq, this study was conducted to determine the origin of the major varieties and understand the evolutionary relationships between Iraqi rice varieties and other Asian rice accessions that could be significant in the improvement of this crop. Five varieties...

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Autores principales: Badro, Hayba, Furtado, Agnelo, Henry, Robert
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6918272/
https://www.ncbi.nlm.nih.gov/pubmed/31703353
http://dx.doi.org/10.3390/plants8110481
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author Badro, Hayba
Furtado, Agnelo
Henry, Robert
author_facet Badro, Hayba
Furtado, Agnelo
Henry, Robert
author_sort Badro, Hayba
collection PubMed
description Due to the importance of the rice crop in Iraq, this study was conducted to determine the origin of the major varieties and understand the evolutionary relationships between Iraqi rice varieties and other Asian rice accessions that could be significant in the improvement of this crop. Five varieties of Oryza sativa were obtained from Baghdad/Iraq, and the whole genomic DNA was sequenced, among these varieties, Amber33, Furat, Yasmin, Buhooth1 and Amber al-Baraka. Raw sequence reads of 33 domesticated Asian rice accessions were obtained from the Sequence Read Archive (SRA-NCBI). The sequence of the whole chloroplast-genome was assembled while only the sequence of 916 concatenated nuclear-genes was assembled. The phylogenetic analysis of both chloroplast and nuclear genomes showed that two main clusters, Indica and Japonica, and further five sub-clusters based upon their ecotype, indica, aus, tropical-japonica, temperate-japonica and basmati were created; moreover, Amber33, Furat, Yasmin and Buhooth1 belonged to the basmati, indica and japonica ecotypes, respectively, where Amber33 was placed in the basmati group as a sister of cultivars from Pakistan and India. This confirms the traditional story that Amber was transferred by a group of people who had migrated from India and settled in southern Iraq a long time ago.
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spelling pubmed-69182722019-12-24 Relationships between Iraqi Rice Varieties at the Nuclear and Plastid Genome Levels Badro, Hayba Furtado, Agnelo Henry, Robert Plants (Basel) Article Due to the importance of the rice crop in Iraq, this study was conducted to determine the origin of the major varieties and understand the evolutionary relationships between Iraqi rice varieties and other Asian rice accessions that could be significant in the improvement of this crop. Five varieties of Oryza sativa were obtained from Baghdad/Iraq, and the whole genomic DNA was sequenced, among these varieties, Amber33, Furat, Yasmin, Buhooth1 and Amber al-Baraka. Raw sequence reads of 33 domesticated Asian rice accessions were obtained from the Sequence Read Archive (SRA-NCBI). The sequence of the whole chloroplast-genome was assembled while only the sequence of 916 concatenated nuclear-genes was assembled. The phylogenetic analysis of both chloroplast and nuclear genomes showed that two main clusters, Indica and Japonica, and further five sub-clusters based upon their ecotype, indica, aus, tropical-japonica, temperate-japonica and basmati were created; moreover, Amber33, Furat, Yasmin and Buhooth1 belonged to the basmati, indica and japonica ecotypes, respectively, where Amber33 was placed in the basmati group as a sister of cultivars from Pakistan and India. This confirms the traditional story that Amber was transferred by a group of people who had migrated from India and settled in southern Iraq a long time ago. MDPI 2019-11-07 /pmc/articles/PMC6918272/ /pubmed/31703353 http://dx.doi.org/10.3390/plants8110481 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Badro, Hayba
Furtado, Agnelo
Henry, Robert
Relationships between Iraqi Rice Varieties at the Nuclear and Plastid Genome Levels
title Relationships between Iraqi Rice Varieties at the Nuclear and Plastid Genome Levels
title_full Relationships between Iraqi Rice Varieties at the Nuclear and Plastid Genome Levels
title_fullStr Relationships between Iraqi Rice Varieties at the Nuclear and Plastid Genome Levels
title_full_unstemmed Relationships between Iraqi Rice Varieties at the Nuclear and Plastid Genome Levels
title_short Relationships between Iraqi Rice Varieties at the Nuclear and Plastid Genome Levels
title_sort relationships between iraqi rice varieties at the nuclear and plastid genome levels
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6918272/
https://www.ncbi.nlm.nih.gov/pubmed/31703353
http://dx.doi.org/10.3390/plants8110481
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