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Rice stripe disease, caused by Rice stripe virus (RSV) and transmitted by the small brown planthopper (Laodelphax striatellus Fallen), is one of the most serious viral diseases of rice in temperate East Asian production regions. Prior quantitative trait loci (QTL) mapping has established that Oryza sativa L. subsp. indica 'IR24' carries positive alleles at the three loci qSTV3, qSTV7, and qSTV11-i. Here, we report an advanced backcross analysis based on three selected chromosome segment substitution lines (CSSLs), each predicted to carry one of these three QTL. Three sets of BC(4)F(2:3) populations were bred from a cross between the critical CSSL and its recurrent parent Oryza sativa L. subsp. japonica 'Asominori'. Both qSTV3 and qSTV11-i were detected in their respective population, but qSTV7 was not. An allelic analysis based on a known carrier of the major RSV resistance gene Stvb-i, which is located on chromosome 11, showed that qSTV11-i was not allelic with Stvb-i. A large mapping population was used to delimit the location of qSTV11-i to a 73.6-kb region. The de novo markers developed for this purpose will be useful as marker-assisted selection tools in efforts to introduce qSTV11-i into breeding programmes aiming to improve the level of RSV resistance.