Fine mapping of a yield-enhancing QTL cluster associated with transgressive variation in an Oryza sativa x O. rufipogon cross

A high-resolution physical map targeting a cluster of yield-related QTLs on the long arm of rice chromosome 9 has been constructed across a 37.4 kb region containing seven predicted genes. Using a series of BC3F4 nearly isogenic lines (NILs) derived from a cross between the Korean japonica cultivar Hwaseongbyeo and Oryza rufipogon (IRGC 105491), a total of seven QTLs for 1,000-grain weight, spikelets per panicle, grains per panicle, panicle length, spikelet density, heading date and plant height were identified in the cluster (P ≤ 0.0001). All seven QTLs were additive, and alleles from the low-yielding O. rufipogon parent were beneficial in the Hwaseongbyeo background. Yield trials with BC3F4 NILs showed that lines containing a homozygous O. rufipogon introgression in the target region out-yielded sibling NILs containing Hwaseongbyeo DNA by 14.2–17.7%, and out-yielded the Hwaseongbyeo parent by 16.2–23.7%. While higher yielding plants containing the O. rufipogon introgression were also taller and later than controls, the fact that all seven of the QTLs were co-localized in the same 37.4 kb interval suggests the possibility that a single, pleiotropic gene acting as a major regulator of plant development may control this suite of agronomically important plant phenotypes.