Dominance and epistasis are the main contributors to heterosis for plant height in rice.

The genetic basis of heterosis has been debated for over 100 years regarding whether dominance or overdominance plays a more important role and the answer is still unclear. The major limitation to assess the contribution of a single locus has been the genetic background noise due to genome-wide segregation of multiple loci. To dissect the genetic basis of heterosis at a single locus for plant height, we developed a set of 202 chromosome segment substitution lines (CSSLs) of an elite hybrid, Shanyou 63, the best hybrid rice in China in the 1990s. Fifteen CSSLs had varied plant heights within lines. A total of 15 partial dominance QTLs for plant height were detected in these 15 CSSL-F2 populations. All hybrids between the 15 CSSLs and the recurrent parent, Zhenshan 97, were shorter than the corresponding CSSLs, but taller than Zhenshan 97. These indicated that these 15 QTLs were also heterosis loci (HLs) contributed to heterosis acted in dominance. Each HL contributed from -7.4 to 14.4% of midparent heterosis. Additive by additive (AA) and additive by dominance (AD) interactions were detected in the Tetra-F2 population segregating at the four major QTLs with the largest effects on plant height. Substantial negative AA effects were detected between two major QTLs QPH7.2 and QPH7.3, which increased heterosis in the study. Thus we concluded that dominance and epistasis are the major genetic basis of plant height heterosis, which could explain the better parent heterosis in Shanyou 63.