Genomic architecture of heterosis for yield traits in rice

Increasing grain yield is a long-term goal in crop breeding to meet the demand for global food security. Heterosis, when a hybrid shows higher performance for a trait than both parents, offers an important strategy for crop breeding. To examine the genetic basis of heterosis for yield in rice, here we generate, sequence and record the phenotypes of 10,074 F 2 lines from 17 representative hybrid rice crosses. We classify modern hybrid rice varieties into three groups, representing different hybrid breeding systems. Although we do not find any heterosis-associated loci shared across all lines, within each group, a small number of genomic loci from female parents explain a large proportion of the yield advantage of hybrids over their male parents. For some of these loci, we find support for partial dominance of heterozygous locus for yield-related traits and better-parent heterosis for overall performance when all of the grain-yield traits are considered together. These results inform on the genomic architecture of heterosis and rice hybrid breeding. Insights into the genomic architecture of heterosis for grain yield in rice are presented, and further mapping of grain yield loci resolves candidate genes that could be useful for breeding. The genetics of high yield in rice The genetic basis of heterosis—the hybrid vigour in which hybrid plants show improved phenotypic qualities compared to those of both parents—has proved elusive despite the phenomenon having been known for more than a century and commonly used in plant breeding. Here Bin Han and colleagues generate, sequence and phenotype a collection of more than 10,000 lines from 17 representative elite hybrid rice crosses, which they classify into three major types representing different breeding systems. They map genomic loci associated with grain yield traits and analyse their heterotic effects and contributions to heterotic advantage. Although they do not identify heterosis loci shared across all varieties, for hybrids within the same group they identify a few loci from female parents that explain a large proportion of yield advantage of hybrids over their male parents. These insights into the genomic architecture of heterosis for grain yield in rice, along with further mapping to resolve candidate genes, will be useful for the development of new rice hybrids with desirable properties.