Molecular and General Genetics MGG

, Volume 255, Issue 1, pp 1–8

Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping

  • S. Nandi
  • P. K. Subudhi
  • D. Senadhira
  • N. L. Manigbas
  • S. Sen-Mandi
  • N. Huang
ORIGINAL PAPER

DOI: 10.1007/s004380050468

Cite this article as:
Nandi, S., Subudhi, P., Senadhira, D. et al. Mol Gen Genet (1997) 255: 1. doi:10.1007/s004380050468

Abstract

By combining the amplified fragment length polymorphism (AFLP) technique with selective genotyping, we constructed a linkage map for rice and assigned each linkage group to a corresponding chromosome. The AFLP map, consisting of 202 AFLP markers, was generated from 74 recombinant inbred lines (RIL) which were selected from both extremes of the population (250 lines) with respect to the response to complete submergence. Map length was 1756 cM, with an average interval size of 8.5 cM. To assign linkage groups to chromosomes, we used 50 previously mapped AFLP markers as anchor markers distributed over the 12 chromosomes. Other AFLP markers were then assigned to specific chromosomes based on their linkage to anchor markers. This AFLP map is equivalent to the RFLP/AFLP map constructed previously as the anchors were in the same order in both maps. Furthermore, tests with two restriction fragment length polymorphism (RFLP) markers and two sequence-tagged site (STS) markers showed that they mapped in the expected positions. Using this AFLP map, a major gene for submergence tolerance was localized on chromosome 9. Quantitative trait loci (QTL) associated with submergence tolerance were detected on chromosomes 6, 7, 11, and 12. We conclude that the combination of AFLP mapping and selective genotyping provides a much faster and easier approach to QTL identification than the use of RFLP markers.

KeywordsOryza sativa L.  AFLP markers  Selective genotyping  Submergence tolerance  QTL analysis

Copyright information

© Springer-Verlag Berlin Heidelberg 1997

Authors and Affiliations

  • S. Nandi
    • 1
  • P. K. Subudhi
    • 1
  • D. Senadhira
    • 1
  • N. L. Manigbas
    • 1
  • S. Sen-Mandi
    • 2
  • N. Huang
    • 1
  1. 1.Division of Plant Breeding, Genetics and Biochemistry, International Rice Research Institute, PO Box 933, 1099 Manila, Philippines
  2. 2.Department of Botany, Bose Institute, Calcutta: 700 009, IndiaIN