PDR 2013, 35(5) 537-546 DOI:   10.7677/ynzwyj201312151  ISSN: 2095-0845 CN: 53-1217/Q

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Nuclear gene
Oryza granulata
Single nucleotide polymorphisms
Genetic variation
Population genetic structure
TUN Chun-Yan-1、2
GAO Li-Zhi-1
Article by Tun, C. Y. 1、2
Article by Gao, L. Z. 1

SNP Analysis of Six Nuclear Gene Fragments for Studying Population Genetics of Oryza granulata from China

 WU  Chun-Yan-1、2, GAO  Li-Zhi-1

1 Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute
of Botany, Chinese Academy of Sciences, Kunming 650201, China; 2 University of Chinese
Academy of Sciences, Beijing 100049, China


A total of six rice genes of functional importance, including Osgstf3, OsNAC6, BADH, XCP2, EMF2 and ERCC4, were selected to assess suitable SNPs for use in an analysis of population genetic structure of Oryza granulata, a precious wild relative of Asian cultivated rice. An initial survey of 12 representative samples of O.granulata from Yunnan and Hainan, China, resolved few SNPs in Osgstf3, OsNAC6, BADH and XCP2, while low levels of variation were recorded within introns of EMF2 and ERCC4. A subsequent SNP survey was conducted within the EMF2 and ERCC4 fragments across a sample of 52 plants collected from three and two natural populations in Yunnan and Hainan, respectively. This survey showed that O.granulata exhibits fairly high genetic divergence between populations despite low levels of nucleotide diversity. Genetic divergence between populations was evident both between and within geographical regions. These findings imply that recent habitat fragmentation in tropical and subtropical forests led to severe restrictions to gene flow, which enhanced divergence among populations.

Keywords Nuclear gene   Oryza granulata   Single nucleotide polymorphisms   Genetic variation   Population genetic structure  
Received 2012-11-15 Revised  Online: 2013-01-05 
DOI: 10.7677/ynzwyj201312151
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