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Heterosis contributes greatly to crop production, but the genetic basis of heterosis is not fully understood. To identify heterotic loci (HLs) for grain yield, 12 yield traits were evaluated in four rice (Oryza sativa L.) mapping populations: one parental population of chromosome segment substitution lines derived from a cross between the japonica cultivar Nipponbare and indica cultivar 9311 and three connected test populations in either a homozygous 9311 genetic background or a heterozygous background. A total of 390 HLs were detected for the measured traits in two environments. The genetic bases of heterosis differed between the backcross and testcross populations. At least 10 HLs were confirmed in F1 hybrids between 9311 and near-isogenic lines, each of which carried a heterotic locus of interest in the same 9311 background. All 10 showed overdominant or dominant effects on grain yield and yield components. Among them, three were verified as being associated with yield heterosis and colocalized in the same regions as those containing previously reported heterosis-associated genes. Five HLs were identified to be promising candidate loci that could be used to achieve more than 15% yield heterosis in several commercial rice hybrids. These findings suggest the potential of indica or japonica introgression for increasing yield in hybrid rice breeding programs.