Genes & Genomics

, Volume 31, Issue 4, pp 283–292

Analysis of genetic diversity and population structure of rice cultivars from Korea, China and Japan using SSR markers

  • Weiguo Zhao
  • Jong-Wook Chung
  • Kyung-Ho Ma
  • Tae-San Kim
  • Seung-Min Kim
  • Dong-Il Shin
  • Chang-Ho Kim
  • Han-Mo Koo
  • Yong-Jin Park
Article

Abstract

A total of 29 simple sequence repeat (SSR) markers were used to analyze the genetic diversity of 150 accessions of cultivated rice (Oryza sativa L.) from Korea, China, and Japan. A total of 375 alleles were detected with an average of 12.9 per locus. The averaged values of gene diversity and polymorphism information content (PIC) for each SSR locus were 0.7001 and 0.6683, respectively. Alleles per locus in Korean rice were 8.8, whereas 8.1 and 7.2 alleles per locus were found in Chinese and Japanese rice, respectively. The mean gene diversity in Korean, Chinese, and Japanese rice was 0.6058, 0.6457, and 0.5174, respectively, whereas the mean PIC values for each SSR locus were 0.5759, 0.6138, and 0.4881, respectively. The genetic diversity of the Korean and Chinese cultivars was higher than that of the Japanese cultivars, and the genetic diversity ofjaponica was higher than that ofindica. The model-based structure analysis revealed the presence of three subpopulations, which was basically consistent with clustering based on genetic distance. An AMOVA analysis showed that the between-population component of genetic variance was less than 22% in contrast to 78% for the within-population component. The overallFST value was 0.2180, indicating a moderate differentiation among groups. The results could be used for designing effective breeding programs aimed at broadening the genetic bases of commercially grown varieties.

Key words

Oryza sativa genetic diversity population structure SSR 

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Copyright information

© The Genetics Society of Korea & Springer 2009

Authors and Affiliations

  • Weiguo Zhao
    • 1
    • 2
  • Jong-Wook Chung
    • 1
    • 3
  • Kyung-Ho Ma
    • 4
  • Tae-San Kim
    • 4
  • Seung-Min Kim
    • 3
  • Dong-Il Shin
    • 3
  • Chang-Ho Kim
    • 3
  • Han-Mo Koo
    • 3
  • Yong-Jin Park
    • 3
  1. 1.Department of Applied BioscienceKonkuk UniversitySeoulRepublic of Korea
  2. 2.iangsu University of Science and Technology, Sericultural Research Institute Chinese Academy of Agricultural SciencesZhenjiang JiangsuChina
  3. 3.Department of Plant Resources, College of Industrial ScienceKongju National UniversityYesanRepublic of Korea
  4. 4.Genetic Resources DivisionNational Institute of Agricultural BiotechnologySuwonRepublic of Korea

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