Asian rice (Oryza sativa) was domesticated fromO. rufipogon, and reduced seed-shattering behaviour was selected to increase yields. Two seed-shattering loci,qSH3andsh4, are involved in reducing seed shattering in bothjaponicaandindicarice cultivars, whileqSH1andqCSS3are likely specific tojaponicacultivars. Inindicacultivars,qSH3andsh4fail to explain the degree of seed shattering, as an introgression line (IL) ofO. rufipogonW630 carrying domesticated alleles atqSH3andsh4still showed seed shattering. Here we analysed differences in seed-shattering degree between the IL and theindicacultivar IR36. The values for grain detachment in the segregating population between the IL and IR36 were continuous. Based on QTL-seq analysis using the BC1F2population between the IL and IR36, we detected two novel loci,qCSS2andqCSS7(QTLs for the Control of Seed Shattering in rice on chromosomes 2 and 7), which contributed to the reduced seed shattering in IR36. We further investigated the genetic interaction ofqCSS2andqCSS7under the presence ofqSH3andsh4mutations inO. rufipogonW630 and found that IL carrying IR36 chromosomal segments covering all four loci are required to explain seed-shattering degree in IR36. SinceqCSS2andqCSS7were not detected in previous studies on seed shattering injaponica, their control may be specific toindicacultivars. Therefore, they are important to understanding the history of rice domestication as well as to adjusting the seed-shattering degree ofindicacultivars to maximise their yield.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00438-023-02027-z.