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Chromosome single segment substitution lines (CSSSLs) are useful for the precise mapping of quantitative trait loci (QTLs) and dissection of the genetic basis of complex traits.In this study, two whole-genome sequenced rice cultivars, the japonica Nipponbare and indica 9311 were used as recipient and donor, respectively.We developed a set of novel CSSL population through crossing andback-crossing assisted by molecular markers.