Heterosis of An Elite Rice Hybrid Is Greatly Achieved by Manipulating Major QTLs for Yield

Strong heterosis hybrids have been developed every year in rice, but no studies have attempted to assemble heterosis by direct selection. In this study, we try to answer how much hetreosis of an elite rice hybrid Shanyou 63 can be achieved by direct selection for major QTLs. We identified thirteen partial dominance QTLs for spikelets per panicle (SPP) using a set of 202 chromosome segment substitution lines (CSSLs) in the female parent Zhenshan 97 background. Of them, nine QTLs contribute to yield per plant. Without exception, all hybrids between nine CSSLs each harboring one yield QTL and Zhenshan 97 exhibited intermediate performance, indicating that these heterosis loci (HLs) contribute to heterosis in a dominance fashion. Four known yield-related genes of Ghd7, Ghd7.1, Hd1 and GS3 were harbored in their substitution segments of four CSSLs. Functional and non-functional alleles at these four genes were dispersing in both parents. Quantitative real-time PCR showed that functional alleles of these genes were expressed in partial dominance in Shanyou 63 and single segment hybrids. We assembled single segement heterosis (SSH) of 8 HLs into Zhenshan 97. The yield per plant and its middle parent heterosis of the hybrid pyramiding 8 HLs reached up to 87.3% and 75.4% of the original hybrid Shanyou 63, respectively. Five hybrids pyramiding 7 to 9 QTL regions in a mixture genome background by crossing two recombinant inbred lines showed similar yield performance to that of Shanyou 63. These results suggest that dominance contributed by parental functional complementation is the important contributor to grain yield heterosis, and heterosis assembly is greatly achieved by manipulating several major dominance HLs.