In the current study, 52 S2, 22 S4 lines, and early generation hybrids were subjected to genetic variation analysis by SSR makers. The results showed that 61 allelic variations were detected in S2 by 20 pairs of core primers, while 39 in S4, with each pair of primer detecting 3.1 and 1.95 alleles, and 4.7 and 2.15 genotypes in S2 and S4, respectively. According to the UPGMA, 52 S2 lines were divided into 7 groups, among which A9 22 and A9 37 were grouped separately while the rest were within the similar resource of pedigree; 22 S4 lines were into 4 groups, which were consistent with their pedigree. The discrepant sites in S2 and S4 lines were 2 to 37 and 0 to 23, respectively, and the discrepant sites between the lines from the same pedigree were less than those from different pedigrees. It was proved at the molecular level that S2 went sharp separation generation, and with the generation increase, S4 tended to become stable and the population uniformity increased, so did their corresponding hybrid combinations. Thus, in the breeding practice it is beneficial to increase the amount of fine individuals from S2 lines and retain those of different pedigrees in S4 generation.
