Identification of introgressed alien chromosome segments associated with grain quality in Oryza rufipogon x MR219 advanced breeding lines using SSR markers

Genet Mol Res. 2012 Sep 26;11(3):3534-46. doi: 10.4238/2012.September.26.10.


A limited backcross procedure was utilized to introgress genes associated with grain quality traits from Oryza rufipogon (Accession No. IRGC 105491), a wild rice from Malaysia, to the cultivated rice O. sativa cv. MR219, a popular high yielding Malaysian rice cultivar. A set of 10 BC(2)F(7) progenies were selected based on the field performance and phenotypic appearance in BC(2)F(5) and BC(2)F(6) generations, which initially started with 266 progenies in the BC(2)F(2) generation. These 10 advanced breeding lines are similar to each other but differ in several important grain quality traits, which can be traced to O. rufipogon introgressions. Phenotyping and genotyping of BC(2)F(7) variants were considered for QTL analysis. The introgressed lines did not show any significant changes compared to the recurrent parent MR219 for the traits grain density and milled rice percentage. All 10 progenies showed significantly higher head rice percentages (70-88%) than the recurrent parent MR219. Variants G13 and G15 had higher amylose contents than MR219. All variants were analyzed using polymorphic SSR markers. Of the 34 SSR markers, only 18 showed introgression from O. rufipogon for chromosomes 1, 2, 3, 5, 6, 8, 10, and 11. Graphical genotypes were prepared for each variant, and association between the introgression regions and the traits that increased grain quality was visualized. Based on marker trait association, some of the QTLs are stable across environments and genetic backgrounds and could be used universally.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosomes, Plant / genetics*
  • Crosses, Genetic*
  • Genetic Markers
  • Genotype
  • Inbreeding*
  • Microsatellite Repeats / genetics*
  • Oryza / genetics*
  • Polymorphism, Genetic
  • Seeds / genetics*


  • Genetic Markers