Theoretical and Applied Genetics

, Volume 117, Issue 7, pp 1141–1153 | Cite as

Population structure and linkage disequilibrium of a mini core set of maize inbred lines in China

  • Ronghuan Wang
  • Yongtao Yu
  • Jiuran Zhao
  • Yunsu Shi
  • Yanchun Song
  • Tianyu WangEmail author
  • Yu LiEmail author
Original Paper


Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations are of great importance and the prerequisite for association mapping. In the present study, 145 genome-wide SSR markers were used to assess the genetic diversity, population structure, and LD of a set of 95 maize inbred lines which represented the Chinese maize inbred lines. Results showed that the population included a diverse genetic variation. A model-based population structure analysis subdivided the inbred lines into four subgroups that correspond to the four major empirical germplasm origins in China, i.e., Lancaster, Reid, Tangsipingtou and P. Among all of the inbred lines, 65.3% were assigned into the corresponding subgroups; others were assigned into a “mixed” subgroup. LD was significant at a 0.01 level between 63.89% of the SSR pairs in the entire sample and with a range of 18.75–40.28% in the subgroups. Among factors influencing LD, linkage was the major cause for LD of SSR loci. The results suggested that the population may be used in the detection of genome-wide SSR marker–phenotype association.


Linkage Disequilibrium Inbred Line Association Mapping Polymorphism Information Content Simple Sequence Repeat Locus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors thank Dr. Chenyang Hao for technical support, Prof. Jizeng Jia and Xueyong Zhang for advice. We are also grateful to Zhizhai Liu and Ronghua Guo for their kind assistance and suggestions. The research was partly supported by the projects of the Ministry of Science and Technology (2006CB101700), the National Natural Science Foundation (30571133), the Ministry of Agriculture (nb07-070401) and the Beijing Agricultural Innovative Platform - Beijing Natural Science Fund Program (Yzpt02-06).

Supplementary material

122_2008_852_MOESM1_ESM.xls (192 kb)
Supplementary material (XLS 191 kb)


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  1. 1.Institute of Crop ScienceChinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)BeijingPeople’s Republic of China
  2. 2.Maize Research CenterBeijing Academy of Agricultural and Forestry SciencesBeijingPeople’s Republic of China

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