Theoretical and Applied Genetics

, Volume 115, Issue 6, pp 767–776

A marker-assisted backcross approach for developing submergence-tolerant rice cultivars


  • C. N. Neeraja
    • International Rice Research Institute
    • Directorate of Rice Research
  • R. Maghirang-Rodriguez
    • International Rice Research Institute
    • Greenwood Genetic Center
  • A. Pamplona
    • International Rice Research Institute
  • S. Heuer
    • International Rice Research Institute
  • B. C. Y. Collard
    • International Rice Research Institute
    • Department of Primary Industries and FisheriesHermitage Research Station
  • E. M. Septiningsih
    • International Rice Research Institute
  • G. Vergara
    • International Rice Research Institute
  • D. Sanchez
    • International Rice Research Institute
  • K. Xu
    • Department of Viticulture and EnologyUniversity of California
  • A. M. Ismail
    • International Rice Research Institute
    • International Rice Research Institute
Original Paper

DOI: 10.1007/s00122-007-0607-0

Cite this article as:
Neeraja, C.N., Maghirang-Rodriguez, R., Pamplona, A. et al. Theor Appl Genet (2007) 115: 767. doi:10.1007/s00122-007-0607-0


Submergence stress regularly affects 15 million hectares or more of rainfed lowland rice areas in South and Southeast Asia. A major QTL on chromosome 9, Sub1, has provided the opportunity to apply marker assisted backcrossing (MAB) to develop submergence tolerant versions of rice cultivars that are widely grown in the region. In the present study, molecular markers that were tightly linked with Sub1, flanking Sub1, and unlinked to Sub1 were used to apply foreground, recombinant, and background selection, respectively, in backcrosses between a submergence-tolerant donor and the widely grown recurrent parent Swarna. By the BC2F2 generation a submergence tolerant plant was identified that possessed Swarna type simple sequence repeat (SSR) alleles on all fragments analyzed except the tip segment of rice chromosome 9 that possessed the Sub1 locus. A BC3F2 double recombinant plant was identified that was homozygous for all Swarna type alleles except for an approximately 2.3–3.4 Mb region surrounding the Sub1 locus. The results showed that the mega variety Swarna could be efficiently converted to a submergence tolerant variety in three backcross generations, involving a time of two to three years. Polymorphic markers for foreground and recombinant selection were identified for four other mega varieties to develop a wider range of submergence tolerant varieties to meet the needs of farmers in the flood-prone regions. This approach demonstrates the effective use of marker assisted selection for a major QTL in a molecular breeding program.

Supplementary material

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© Springer-Verlag 2007