The development of near-isogenic lines (NILs) is an important fundamental step in the cloning of quantitative trait loci (QTL) and molecular marker assisted breeding. In the present study, NILs for two major QTLs of basal root thickness (BRT) and 1000-grain-weight (TGW) were obtained by molecular marker-assisted selection (MAS) through foreground selection for target QTL and background selection in three backcross generations (BC1F1, BC2F1 and BC3F1). After phenotypic evaluation in the BC3F2 generation, nine BRT QTL-NILs with BRT ranges of 1.07–1.16 mm (6.11–15.18% greater than the recurrent parent) and an average recovery ratio of genetic background (RRGB) of 97.22%, and 11 TGW QTL-NILs with ranges of 21.25–26.25 g (7.05–32.16% greater than the recurrent parent) and 95.97% of RRGB, were selected.
