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Identification of QTLs for Drought-Related Traits in Alien Introgression Lines Derived from Crosses of Rice (Oryza sativa cv. IR64) × O. glaberrima under Lowland Moisture Stress


Drought is a major abiotic stress that limits rice productivity in rain-fed and upland ecosystems. African rice, Oryza glaberrima, has low yields but is tolerant to drought and other stresses. We evaluated 513 BC2F3 progenies from alien introgression lines (AILs) that were derived from crosses of Oryza sativa (IR64) × O. glaberrima. They were assessed for yield and other traits when grown under drought at two locations. Such conditions reduced grain production by 59% compared with the recurrent parent (IR64). However, 33 AILs had higher yields, thus demonstrating their potential as genetic material for transferring drought-related traits from O. glaberrima to O. sativa. A set of 200 AILs was selectively genotyped with 173 simple sequence repeat and sequenced tagged site markers. Molecular analysis showed that a mean of 4.5% of the O. glaberrima genome was introgressed in BC2F3 AILs. Our analysis revealed 33 quantitative trait loci (QTLs; including 10 novel) for different traits. O. glaberrima contributed 50% of the alleles to those newly identified QTLs, with one for grain yield per plant (ypp9.1) being new. A QTL at RM208 on chromosome 2 positively affected yield under stress, accounting for 22% of the genetic variation. Our identification of drought-related QTLs for yield and yield components will be useful to future research efforts in marker-assisted selection.

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Alien introgression line




International Rice Research Institute




Likelihood ratio statistics


Quantitative trait locus


Simple sequence repeat


Sequenced tagged site


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This research, part of a Ph.D. study by I.K. Bimpong, was made possible thanks to funding from the Rockefeller Foundation (IRRI Ref. No.: DPPC2004-76) through the International Rice Research Institute. The authors are also grateful to Ms. Socorro Carrandang, Ms. Eloisa Suiton, Mr. Rolly Torres, and the Wide Hybridization group at IRRI for their technical assistance with both field and laboratory aspects.

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Correspondence to Isaac Kofi Bimpong.

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Supplementary Table 1

Chi-square (χ 2) values for markers showing segregation distortion in the test cross progeny (DOC 94 kb)

Supplementary Figure 1

Segregation distortion detected on 12 rice chromosomes; χ 2 values for each marker are shown on y-axis; χ2 >12.5 corresponds to significance threshold at P = 0.00. (PPT 102 kb)

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Bimpong, I.K., Serraj, R., Chin, J.H. et al. Identification of QTLs for Drought-Related Traits in Alien Introgression Lines Derived from Crosses of Rice (Oryza sativa cv. IR64) × O. glaberrima under Lowland Moisture Stress. J. Plant Biol. 54, 237–250 (2011).

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  • AIL
  • Alien introgression line
  • Drought
  • Oryza glaberrima
  • O. sativa
  • QTL
  • SSR
  • STS