Two plants (P45-39-1 and P61-6-29) with more than 95% recipient alleles were selected and advanced to BC3F2. There were 2380 BC3F2 seeds produced and used for screening of salt tolerance. Previous research has shown that a sufficiently high proportion of the recurrent genome can be recovered after 2 or 3 generations of marker-based background selection [31]. It has also been indicated that background selection is more efficient in late BC generations than in early BC generations [32]. We therefore used the 151 polymorphic background SSR markers to finally genotype 80 ILs at BC3F3(Supplementary Table 2). The use of 24 markers on chromosome 1 which were outside the Saltol region was enough to provided adequate information to select introgression lines with minimal donor background. In a similar research, between 7 and 13 markers on chromosome 1 were successfully used to select introgression lines with minimal donor background [33] and [34]. When we consider map distances between markers as the basis for estimating the extent of allele’s introgressed from each of the parent in the ILs, it can be observed that the recurrent parent had the longest distance of 102.2 Mb, while the donor distance was 13.6 Mb (Fig. 3 and Supplementary Fig. 1). On average, 81% of the recurrent parent genome alleles were noted in the ILs, while the donor parent genome had 11.5. These results demonstrated the effectiveness of MAS to breed salt tolerant version of a popular cultivar in a short period.