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

Abstract

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.

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Acknowledgements

Technical assistance from J. Mendoza, E. Suiton, N. Ramos, Evangelina Ella, and G. Perez is gratefully acknowledged. The authors thank Drs. K. K. Jena and Parminder Virk for comments on the manuscript, and Dr. Matthias Frisch for helpful suggestions. The work reported here was supported in part by a grant from the German Federal Ministry for Economic Cooperation and Development (BMZ).

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Correspondence to D. J. Mackill.

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Communicated by S. J. Knapp.

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Neeraja, C.N., Maghirang-Rodriguez, R., Pamplona, A. et al. A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor Appl Genet 115, 767–776 (2007). https://doi.org/10.1007/s00122-007-0607-0

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Keywords

  • Bacterial Artificial Chromosome Clone
  • Flank Marker
  • Cleave Amplify Polymorphic Sequence Marker
  • Background Selection
  • Marker Assisted Backcross