Theoretical and Applied Genetics

, Volume 126, Issue 5, pp 1357–1366 | Cite as

QTL mapping and confirmation for tolerance of anaerobic conditions during germination derived from the rice landrace Ma-Zhan Red

  • Endang M. Septiningsih
  • John Carlos I. Ignacio
  • Pamella M. D. Sendon
  • Darlene L. Sanchez
  • Abdelbagi M. Ismail
  • David J. Mackill
Original Paper


Wide adoption of direct-seeded rice practices has been hindered by poorly leveled fields, heavy rainfall and poor drainage, which cause accumulation of water in the fields shortly after sowing, leading to poor crop establishment. This is due to the inability of most rice varieties to germinate and reach the water surface under complete submergence. Hence, tolerance of anaerobic conditions during germination is an essential trait for direct-seeded rice cultivation in both rainfed and irrigated ecosystems. A QTL study was conducted to unravel the genetic basis of tolerance of anaerobic conditions during germination using a population derived from a cross between IR42, a susceptible variety, and Ma-Zhan Red, a tolerant landrace from China. Phenotypic data was collected based on the survival rates of the seedlings at 21 days after sowing of dry seeds under 10 cm of water. QTL analysis of the mapping population consisting of 175 F2:3 families genotyped with 118 SSR markers identified six significant QTLs on chromosomes 2, 5, 6, and 7, and in all cases the tolerant alleles were contributed by Ma-Zhan Red. The largest QTL on chromosome 7, having a LOD score of 14.5 and an R2 of 31.7 %, was confirmed using a BC2F3 population. The QTLs detected in this study provide promising targets for further genetic characterization and for use in marker-assisted selection to rapidly develop varieties with improved tolerance to anaerobic condition during germination. Ultimately, this trait can be combined with other abiotic stress tolerance QTLs to provide resilient varieties for direct-seeded systems.

Supplementary material

122_2013_2057_MOESM1_ESM.pdf (171 kb)
Supplementary material 1 (PDF 171 kb)
122_2013_2057_MOESM2_ESM.pdf (173 kb)
Supplementary material 2 (PDF 172 kb)
122_2013_2057_MOESM3_ESM.pdf (207 kb)
Supplementary material 3 (PDF 207 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Endang M. Septiningsih
    • 1
  • John Carlos I. Ignacio
    • 1
  • Pamella M. D. Sendon
    • 1
  • Darlene L. Sanchez
    • 1
  • Abdelbagi M. Ismail
    • 1
  • David J. Mackill
    • 1
    • 2
  1. 1.International Rice Research InstituteMetro ManilaPhilippines
  2. 2.Department of Plant Science, MARS Food GlobalUniversity of CaliforniaDavisUSA

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