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Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection

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Abstract

A rice mini-core collection consisting of 217 accessions has been developed to represent the USDA core and whole collections that include 1,794 and 18,709 accessions, respectively. To improve the efficiency of mining valuable genes and broadening the genetic diversity in breeding, genetic structure and diversity were analyzed using both genotypic (128 molecular markers) and phenotypic (14 numerical traits) data. This mini-core had 13.5 alleles per locus, which is the most among the reported germplasm collections of rice. Similarly, polymorphic information content (PIC) value was 0.71 in the mini-core which is the highest with one exception. The high genetic diversity in the mini-core suggests there is a good possibility of mining genes of interest and selecting parents which will improve food production and quality. A model-based clustering analysis resulted in lowland rice including three groups, aus (39 accessions), indica (71) and their admixtures (5), upland rice including temperate japonica (32), tropical japonica (40), aromatic (6) and their admixtures (12) and wild rice (12) including glaberrima and four other species of Oryza. Group differentiation was analyzed using both genotypic distance Fst from 128 molecular markers and phenotypic (Mahalanobis) distance D2 from 14 traits. Both dendrograms built by Fst and D2 reached similar-differentiative relationship among these genetic groups, and the correlation coefficient showed high value 0.85 between Fst matrix and D2 matrix. The information of genetic and phenotypic differentiation could be helpful for the association mapping of genes of interest. Analysis of genotypic and phenotypic diversity based on genetic structure would facilitate parent selection for broadening genetic base of modern rice cultivars via breeding effort.

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Acknowledgments

The authors thank Ellen McWhirter for critical review, Tiffany Sookaserm, Tony Beaty, Yao Zhou, LaDuska Simpson, Curtis Kerns and Sarah Hendrix for technical assistance.

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Authors and Affiliations

  1. College of Life Sciences, Zhejiang University, Hangzhou, China

    Xiaobai Li

  2. State Key Lab of Rice Biology, IAEA Collaborating Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China

    Limeng Jia & Dianxing Wu

  3. University of Arkansas, Rice Research and Extension Center, Stuttgart, AR, USA

    Xiaobai Li, Hesham Agrama, Limeng Jia & Karen Moldenhauer

  4. USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, AR, USA

    Xiaobai Li, Wengui Yan, Limeng Jia, Melissa Jia, Aaron Jackson & Anna McClung

  5. Rice Research Insititute, Jiangxi Academy of Agricultural Sciences, Nanchang, China

    Biaolin Hu

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  1. Xiaobai Li
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Correspondence to Wengui Yan or Dianxing Wu.

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Li, X., Yan, W., Agrama, H. et al. Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection. Genetica 138, 1221–1230 (2010). https://doi.org/10.1007/s10709-010-9521-5

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