Fine linkage mapping enables dissection of closely linked quantitative trait loci for seed dormancy and heading in rice

Theor Appl Genet. 2003 Nov;107(7):1174-80. doi: 10.1007/s00122-003-1364-3. Epub 2003 Jul 26.


Two quantitative trait loci (QTLs) for seed dormancy (tentatively designated Sdr1) and heading date ( Hd8) have been mapped to approximately the same region on chromosome 3 by interval mapping of backcross inbred lines derived from crosses between the rice cultivars Nipponbare (japonica) and Kasalath (indica). To clarify whether Sdr1 and Hd8 could be dissected genetically, we carried out fine-scale mapping with an advanced backcross progeny. We selected a BC(4)F(1) plant, in which a small chromosomal region including Sdr1 and Hd8, on the short arm of chromosome 3, remained heterozygous, whereas all the other chromosomal regions were homozygous for Nipponbare. Days-to-heading and seed germination rate in the BC(4)F(2) plants showed continuous variation. Ten BC(4)F(2) plants with recombination in the vicinity of Sdr1 and Hd8 were selected on the basis of the genotypes of the restriction fragment length polymorphism (RFLP) markers flanking both QTLs. Genotypes of those plants for Sdr1 and Hd8 were determined by advanced progeny testing of BC(4)F(4) families. Sdr1 was mapped between the RFLP markers R10942 and C2045, and co-segregated with C1488. Hd8 was also mapped between C12534S and R10942. Six recombination events were detected between Sdr1 and Hd8. These results clearly demonstrate that Sdr1 and Hd8 were tightly linked. Nearly isogenic lines for Sdr1 and Hd8 were selected by marker-assisted selection.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping*
  • Chromosomes, Plant
  • Epistasis, Genetic*
  • Genes, Plant*
  • Genetic Markers
  • Genotype
  • Germination
  • Oryza / genetics*
  • Phenotype
  • Polymorphism, Restriction Fragment Length
  • Quantitative Trait Loci*
  • Recombination, Genetic
  • Seeds / genetics*


  • Genetic Markers