Under the IRRI-Japan Collaborative Research Project, The International Rice Research Institute (IRRI) and the Japan International Research Center for Agricultural Sciences (JIRCAS) have developed four universal differential variety sets, which comprise monogenic lines (MLs) with the Japonica-type variety Lijian-xintuan-heigu (LTH) genetic background, and near isogenic lines (NILs) with LTH, Indica-type variety CO39, and universal susceptible line US-2 genetic backgrounds. These target 24 resistance genes: Pia, Pib, Pii, Pik, Pik-h, Pik-m, Pik-p, Pik-s, Pish, Pita(Pi4), Pita-2, Pit, Piz, Piz-5(Pi-2), Piz-t, Pi1, Pi3(t), Pi5(t), Pi7(t), Pi9, Pi11(t), Pi12(t), Pi19(t) and Pi20(t), and the MLs have been distributed to more than 15 countries. To characterize these chromosome components and confirm the introgression of chromosome segments harboring resistance genes, graphical genotypes were investigated using 162 simple sequence repeat (SSR) markers distributed across all 12 rice chromosomes. The chromosome components of the three sets of NILs were more　uniform than those of MLs when compared to the corresponding recurrent parent. Several introgression segments, which corresponded to the locations of blast resistance genes, were also confirmed. Almost all the MLs were developed by backcrossing one or two times, while some lines were backcrossed three to　five times with the recurrent parent, LTH. The restoration rate of genomic chromosomes of 31 MLs relative to LTH ranged from 50 to 90.0%, averaging 77.3%. All LTH, CO39, and US-2 NILs were developed by backcrossing six times with each recurrent parent. The genome restoration rate relative to the parent in 34 LTH NILs ranged from 75.6% to 96.9%, averaging 90.6%; lower than the theoretical value of 99%. The 31 CO39 NILs showed a genome restoration rate greater than 90% relative to the recurrent parent, averaging 97.3%. The 16 US-2 NILs were highly similar to those of the recurrent parent: these genome restoration rates ranged from 88.9% to 98.8%, averaging 94.6%. Genetic characterizations of four universal differential sets of varieties were carried out using DNA markers. This DNA marker data combined with resistance genes is potentially very useful for marker-assisted selection (MAS) in breeding programs since the　differential varieties can be applied as gene sources.