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

Theoretical and Applied Genetics volume 117, pages 1141–1153 (2008)Cite this article

Abstract

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.

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Acknowledgments

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).

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Affiliations

  1. Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), 100081, Beijing, People’s Republic of China

    Ronghuan Wang, Yongtao Yu, Yunsu Shi, Yanchun Song, Tianyu Wang & Yu Li

  2. Maize Research Center, Beijing Academy of Agricultural and Forestry Sciences, 100097, Beijing, People’s Republic of China

    Jiuran Zhao

Authors
  1. Ronghuan Wang
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  2. Yongtao Yu
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  3. Jiuran Zhao
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  4. Yunsu Shi
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  5. Yanchun Song
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  6. Tianyu Wang
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  7. Yu Li
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Corresponding authors

Correspondence to Tianyu Wang or Yu Li.

Additional information

R. Wang and Y. Yu contributed equally to the work.

Communicated by J. Yu.

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Wang, R., Yu, Y., Zhao, J. et al. Population structure and linkage disequilibrium of a mini core set of maize inbred lines in China. Theor Appl Genet 117, 1141–1153 (2008). https://doi.org/10.1007/s00122-008-0852-x

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  • DOI: https://doi.org/10.1007/s00122-008-0852-x

Keywords

  • Linkage Disequilibrium
  • Inbred Line
  • Association Mapping
  • Polymorphism Information Content
  • Simple Sequence Repeat Locus