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AFLP and PCR-based markers linked to Rf3, a fertility restorer gene for S cytoplasmic male sterility in maize


The Rf3 gene restores the pollen fertility disturbed by S male sterile cytoplasm. In order to develop molecular markers tightly linked to Rf3, we used amplified fragment length polymorphism (AFLP) technique with near isogenic lines (NILs) and bulk segregant analysis (BSA). A BC1F1 population from a pair of NILs with different Rf3 locus was constructed and 528 primer combinations was screened. A linkage map was constructed around the Rf3 locus, which was mapped on the distal region of chromosome 2 long arm with the help of SSR marker UMC2184. The closest marker E7P6 was 0.9 cM away from Rf3. Marker E3P1, 2.4 cM from Rf3, and E12M7, 1.8 cM from Rf3, were converted into a codominant CAPS and a dominant SCAR marker, and designated as CAPSE3P1 and SCARE12M7, respectively. These markers are useful for marker-assisted selection and map-based cloning of the Rf3 gene.

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Amplified fragment length polymorphism


Fertile DNA bulks


Sterile DNA bulks


Bulk segregant analysis


Cleaved amplified polymorphic sequence


Cytoplasmic male sterility

E/M :


P/M :


P/E :



Marker-assisted selection


Near isogenic lines


Open reading frames


Primer combinations


Pentatricopeptide repeat


Random amplified polymorphic DNA


Restriction fragment length polymorphism


Sequence characterized amplified regions


Singe nucleotide polymorphism


Simple sequence repeat, microsatellite


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The authors thank Prof. Neil Forsberg for critical review of this manuscript. This research was supported by the National High Technique Foundation of China “863” (2004AA222160), “948” Fund in Ministry of Agronomy of China (201010), the State Key Basic Research and Development Plan of China “973” (2001CB1088).

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Correspondence to Y. L. Zheng.

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Communicated by R. Hagemann

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Zhang, Z.F., Wang, Y. & Zheng, Y.L. AFLP and PCR-based markers linked to Rf3, a fertility restorer gene for S cytoplasmic male sterility in maize. Mol Genet Genomics 276, 162–169 (2006).

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  • Maize
  • Fertility restorer
  • Near isogenic lines
  • Bulk segregant analysis
  • AFLP
  • PCR-based markers
  • Marker-assisted selection
  • Map-based cloning