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Genetic diversity and population structure of a diverse set of rice germplasm for association mapping

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Abstract

Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25–50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker–trait association mapping. This new association population has the potential to identify quantitative trait loci (QTL) with small effects, which will aid in dissecting complex traits and in exploiting the rich diversity present in rice germplasm.

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Acknowledgments

The authors thank Yun Shen and Jian Chen for assistance in SSR marker genotyping. Financial support for this research was provided in part by the Program for New Century Excellent Talents in University (NCET-08-0484), National High Technology Development Project of China (2006AA10Z193), Zhejiang Provincial Natural Science Foundation of China (R3080016), Natural Science Foundation of China (30771327), and a Hong Kong Research Grants Council GRF award (7507/06M).

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Authors and Affiliations

  1. Institute of Nuclear Agricultural Sciences, Key Laboratory of Zhejiang Province and Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Zhejiang University, Hua Jiachi Campus, Hangzhou, 310029, People’s Republic of China

    Liang Jin, Yan Lu, Peng Xiao & Jinsong Bao

  2. School of Biological Sciences, The University of Hong Kong, Hong Kong, People’s Republic of China

    Mei Sun & Harold Corke

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  1. Liang Jin
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  2. Yan Lu
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  3. Peng Xiao
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  4. Mei Sun
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  5. Harold Corke
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  6. Jinsong Bao
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Correspondence to Harold Corke or Jinsong Bao.

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Communicated by T. Sasaki.

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Jin, L., Lu, Y., Xiao, P. et al. Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theor Appl Genet 121, 475–487 (2010). https://doi.org/10.1007/s00122-010-1324-7

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  • DOI: https://doi.org/10.1007/s00122-010-1324-7

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