*4.5. Marker Analysis*

Five gene-specific primers, Xa4F/4R, RM604F/604R, Xa7F/7-1R/7-2R, Xa13F/13R, and Xa21F/21R, tightly linked to the resistance genes *Xa4, xa5, Xa7, xa13* and *Xa21*, respectively, were used to confirm the presence of the R genes in each generation. All markers in this study were published in the previous report [10]. In addition, a total of 36 and 44 markers of known chromosomal positions were used for genotyping in BC1F1 and BC2F1, respectively. In BC2F2, 117 markers, including 57 SSRs, 9 STS, and 51 InDel, distributed evenly on the 12 chromosomes with an average marker interval of 12.76 cM, were used in a genome-wide survey to identify the chromosome segment substitution locations. These polymorphic markers were used for background selection in order to select plants having maximum recovery of the recurrent parent genome. The genotypes from polymorphic bands are recorded as A (IRBB66), B (TNG82) and H (IRBB66/TNG82). The Graphical Geno Types (GGT) Version 2.0 [46] software program was used for the assessment of the recurrent parent genome (%RPG) in the selected recombinants, based on marker data.
