Theoretical and Applied Genetics

, Volume 108, Issue 1, pp 131–140 | Cite as

Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program

  • S. B. Yu
  • W. J. Xu
  • C. H. M. Vijayakumar
  • J. Ali
  • B. Y. Fu
  • J. L. Xu
  • Y. Z. Jiang
  • R. Marghirang
  • J. Domingo
  • C. Aquino
  • S. S. Virmani
  • Z. K. Li

Abstract

One hundred and ninety three parental lines obtained from 26 countries for an international rice molecular breeding program were evaluated using 101 well-distributed simple sequence repeat (SSR) markers. An overall genetic diversity of 0.68 and an average of 6.3 alleles per locus were revealed, indicating a high level of genetic variation in these lines. Cluster analysis of the 193 accessions showed three major groups and nine subgroups. Group I corresponded to the classical indica subspecies, whereas groups II and III belong to the japonica subspecies. Indica and japonica differentiation accounted for only 6.5% of the total variation in the entire sample and 93.5% was due to within-subspecies diversity. Differentiation among eco-geographic regions accounted for 24% of the diversity within the subspecies. Larger amounts of the eco-geographical differentiation were resolved within japonica than within indica. The largest indica-japonica differentiation based on the single locus level was detected by markers on chromosomes 9 and 12, while the smallest differentiation was detected by markers on chromosomes 4 and 8. Furthermore, genetic differences at the single-locus and two-locus levels, as well as components due to allelic and gametic differentiation, were revealed between indica and japonica and among the main geographic regions. The multilocus analysis in genetic diversity showed a higher proportion of variation caused by predominant non-random associations of different loci within and among the classified subspecies and geographic subdivisions. The results suggest that selection for eco-geographical adaptation on multilocus associations was largely responsible for the maintenance of the extensive variation in the primary gene pool of rice.

Keywords

Microsatellite variation Genetic diversity Linkage disequilibrium Multilocus structure Rice (Oryza sativa L.) 

Notes

Acknowledgements

We are grateful to valuable comments from Dr. Q. F. Zhang and two anonymous reviewers on the early version of this paper. We thank Dr. McCouch from Cornell University for the primer information on the SSR markers used in the study. We also thank B. Hardy for the editorial help. Financial support from the Rockefeller Foundation, BMZ of the German government, and the National Natural Science Foundation of China is greatly appreciated.

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Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  • S. B. Yu
    • 1
    • 4
  • W. J. Xu
    • 1
  • C. H. M. Vijayakumar
    • 1
    • 2
  • J. Ali
    • 1
  • B. Y. Fu
    • 1
    • 3
  • J. L. Xu
    • 1
    • 3
  • Y. Z. Jiang
    • 1
    • 3
  • R. Marghirang
    • 1
  • J. Domingo
    • 1
  • C. Aquino
    • 1
  • S. S. Virmani
    • 1
  • Z. K. Li
    • 1
    • 3
  1. 1.Plant Breeding, Genetics, and Biochemistry DivisionInternational Rice Research InstituteMetro ManilaThe Philippines
  2. 2.The Directorate of Rice ResearchHyderabadIndia
  3. 3.Chinese Academy of Agricultural SciencesBeijingChina
  4. 4.National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina

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