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Development of Chloroplast Genomic Resources for Oryza Species Discrimination

Rice is the most important crop in the world as the staple food for over half of the population. The wild species of Oryza represent an enormous gene pool for genetic improvement of rice cultivars. Accurate and rapid identification of these species is critical for effective utilization of the wild r...

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Autores principales: Song, Yun, Chen, Yan, Lv, Jizhou, Xu, Jin, Zhu, Shuifang, Li, MingFu, Chen, Naizhong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5661024/
https://www.ncbi.nlm.nih.gov/pubmed/29118779
http://dx.doi.org/10.3389/fpls.2017.01854
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author Song, Yun
Chen, Yan
Lv, Jizhou
Xu, Jin
Zhu, Shuifang
Li, MingFu
Chen, Naizhong
author_facet Song, Yun
Chen, Yan
Lv, Jizhou
Xu, Jin
Zhu, Shuifang
Li, MingFu
Chen, Naizhong
author_sort Song, Yun
collection PubMed
description Rice is the most important crop in the world as the staple food for over half of the population. The wild species of Oryza represent an enormous gene pool for genetic improvement of rice cultivars. Accurate and rapid identification of these species is critical for effective utilization of the wild rice germplasm. In this study, we developed valuable chloroplast molecular markers by comparing the chloroplast genomes for species identification. Four chloroplast genomes of Oryza were newly sequenced on the Illumina HiSeq platform and other 14 Oryza species chloroplast genomes from Genbank were simultaneously taken into consideration for comparative analyses. Among 18 Oryza chloroplast genomes, five variable regions (rps16-trnQ, trnTEYD, psbE-petL, rpoC2 and rbcL-accD) were detected for DNA barcodes, in addition to differences in simple sequence repeats (SSR) and repeat sequences. The highest species resolution (72.22%) was provided by rpoC2 and rbcL-accD with distance-based methods. Three-marker combinations (rps16-trnQ + trnTEYD + rbcL-accD, rps16-trnQ + trnTEYD + rpoC2 and rpoC2 + trnTEYD + psbE-petL) showed the best species resolution (100%). Phylogenetic analysis based on the chloroplast genome provided the best resolution of Oryza. In the comparison of chloroplast genomes in this study, identification of the most variable regions and assessment of the focal regions of divergence were efficient in developing species-specific DNA barcodes. Based on evaluation of the chloroplast genomic resources, we conclude that chloroplast genome sequences are a reliable and valuable molecular marker for exploring the wild rice genetic resource in rice improvement.
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spelling pubmed-56610242017-11-08 Development of Chloroplast Genomic Resources for Oryza Species Discrimination Song, Yun Chen, Yan Lv, Jizhou Xu, Jin Zhu, Shuifang Li, MingFu Chen, Naizhong Front Plant Sci Plant Science Rice is the most important crop in the world as the staple food for over half of the population. The wild species of Oryza represent an enormous gene pool for genetic improvement of rice cultivars. Accurate and rapid identification of these species is critical for effective utilization of the wild rice germplasm. In this study, we developed valuable chloroplast molecular markers by comparing the chloroplast genomes for species identification. Four chloroplast genomes of Oryza were newly sequenced on the Illumina HiSeq platform and other 14 Oryza species chloroplast genomes from Genbank were simultaneously taken into consideration for comparative analyses. Among 18 Oryza chloroplast genomes, five variable regions (rps16-trnQ, trnTEYD, psbE-petL, rpoC2 and rbcL-accD) were detected for DNA barcodes, in addition to differences in simple sequence repeats (SSR) and repeat sequences. The highest species resolution (72.22%) was provided by rpoC2 and rbcL-accD with distance-based methods. Three-marker combinations (rps16-trnQ + trnTEYD + rbcL-accD, rps16-trnQ + trnTEYD + rpoC2 and rpoC2 + trnTEYD + psbE-petL) showed the best species resolution (100%). Phylogenetic analysis based on the chloroplast genome provided the best resolution of Oryza. In the comparison of chloroplast genomes in this study, identification of the most variable regions and assessment of the focal regions of divergence were efficient in developing species-specific DNA barcodes. Based on evaluation of the chloroplast genomic resources, we conclude that chloroplast genome sequences are a reliable and valuable molecular marker for exploring the wild rice genetic resource in rice improvement. Frontiers Media S.A. 2017-10-25 /pmc/articles/PMC5661024/ /pubmed/29118779 http://dx.doi.org/10.3389/fpls.2017.01854 Text en Copyright © 2017 Song, Chen, Lv, Xu, Zhu, Li and Chen. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Song, Yun
Chen, Yan
Lv, Jizhou
Xu, Jin
Zhu, Shuifang
Li, MingFu
Chen, Naizhong
Development of Chloroplast Genomic Resources for Oryza Species Discrimination
title Development of Chloroplast Genomic Resources for Oryza Species Discrimination
title_full Development of Chloroplast Genomic Resources for Oryza Species Discrimination
title_fullStr Development of Chloroplast Genomic Resources for Oryza Species Discrimination
title_full_unstemmed Development of Chloroplast Genomic Resources for Oryza Species Discrimination
title_short Development of Chloroplast Genomic Resources for Oryza Species Discrimination
title_sort development of chloroplast genomic resources for oryza species discrimination
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5661024/
https://www.ncbi.nlm.nih.gov/pubmed/29118779
http://dx.doi.org/10.3389/fpls.2017.01854
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