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Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis

Green foxtail (Setaria viridis) is a new model plant for the genomic investigation of C(4) photosynthesis biology. As the ancestor of foxtail millet (Setaria italica), an ancient cereal of great importance in arid regions of the world, green foxtail is crucial for the study of domestication and evol...

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Autores principales: Jia, Guanqing, Shi, Shenkui, Wang, Chunfang, Niu, Zhengang, Chai, Yang, Zhi, Hui, Diao, Xianmin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3745726/
https://www.ncbi.nlm.nih.gov/pubmed/23956411
http://dx.doi.org/10.1093/jxb/ert198
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author Jia, Guanqing
Shi, Shenkui
Wang, Chunfang
Niu, Zhengang
Chai, Yang
Zhi, Hui
Diao, Xianmin
author_facet Jia, Guanqing
Shi, Shenkui
Wang, Chunfang
Niu, Zhengang
Chai, Yang
Zhi, Hui
Diao, Xianmin
author_sort Jia, Guanqing
collection PubMed
description Green foxtail (Setaria viridis) is a new model plant for the genomic investigation of C(4) photosynthesis biology. As the ancestor of foxtail millet (Setaria italica), an ancient cereal of great importance in arid regions of the world, green foxtail is crucial for the study of domestication and evolution of this ancient crop. In the present study, 288 green foxtail accessions, which were collected from all geographical regions of China, were analysed using 77 simple sequence repeats (SSRs) that cover the whole genome. A high degree of molecular diversity was detected in these accessions, with an average of 33.5 alleles per locus. Two clusters, which were inconsistent with the distribution of eco-geographical regions in China, were inferred from STRUCTURE, Neighbor–Joining, and principal component analysis, indicating a partially mixed distribution of Chinese green foxtails. The higher subpopulation diversity was from accessions mainly collected from North China. A low level of linkage disequilibrium was observed in the green foxtail genome. Furthermore, a combined analysis of green foxtail and foxtail millet landraces was conducted, and the origin and domestication of foxtail millet was inferred in North China.
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spelling pubmed-37457262013-08-19 Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis Jia, Guanqing Shi, Shenkui Wang, Chunfang Niu, Zhengang Chai, Yang Zhi, Hui Diao, Xianmin J Exp Bot Research Paper Green foxtail (Setaria viridis) is a new model plant for the genomic investigation of C(4) photosynthesis biology. As the ancestor of foxtail millet (Setaria italica), an ancient cereal of great importance in arid regions of the world, green foxtail is crucial for the study of domestication and evolution of this ancient crop. In the present study, 288 green foxtail accessions, which were collected from all geographical regions of China, were analysed using 77 simple sequence repeats (SSRs) that cover the whole genome. A high degree of molecular diversity was detected in these accessions, with an average of 33.5 alleles per locus. Two clusters, which were inconsistent with the distribution of eco-geographical regions in China, were inferred from STRUCTURE, Neighbor–Joining, and principal component analysis, indicating a partially mixed distribution of Chinese green foxtails. The higher subpopulation diversity was from accessions mainly collected from North China. A low level of linkage disequilibrium was observed in the green foxtail genome. Furthermore, a combined analysis of green foxtail and foxtail millet landraces was conducted, and the origin and domestication of foxtail millet was inferred in North China. Oxford University Press 2013-09 2013-08-14 /pmc/articles/PMC3745726/ /pubmed/23956411 http://dx.doi.org/10.1093/jxb/ert198 Text en © The Author [2013]. Published by Oxford University Press on behalf of the Society for Experimental Biology. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Research Paper
Jia, Guanqing
Shi, Shenkui
Wang, Chunfang
Niu, Zhengang
Chai, Yang
Zhi, Hui
Diao, Xianmin
Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis
title Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis
title_full Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis
title_fullStr Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis
title_full_unstemmed Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis
title_short Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis
title_sort molecular diversity and population structure of chinese green foxtail [setaria viridis (l.) beauv.] revealed by microsatellite analysis
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3745726/
https://www.ncbi.nlm.nih.gov/pubmed/23956411
http://dx.doi.org/10.1093/jxb/ert198
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