LAUSR

We previously identified a cluster of yield-related QTL including plant height and heading date in CR4379, a near-isogenic line from an interspecific cross between Oryza sativa spp. japonica cultivar 'Hwaseong' and the wild relative O. rufipogon. Map-based cloning and transgenic approaches revealed that APX9 (LOC_Os09g36750) which encodes an L-ascorbate peroxidase 4 is associated with this cluster. Sequence differences in the APX9 promoter and coding regions were observed including a 3-bp InDel leading to the addition of a valine in Hwaseong compared to O. rufipogon. CR4379 showed higher APX9 expression in various tissues than Hwaseong. We generated APX9 over-expression (OE) transgenics in the Hwaseong background. APX9-OE plants were taller and exhibited delayed heading compared to Hwaseong. Consistent with those results, APX9 T-DNA insertion mutants in the japonica cultivar Dongjin showed reduced plant height. These results confirm that APX9 is the causal gene for the QTL cluster. CR4379 had higher antioxidant ability and APX activity than Hwaseong, which may be responsible for the increased drought tolerance observed in seedlings with the APX9  OR allele. Sequence analysis of APX9 from 303 rice accessions revealed that the 3-bp InDel clearly differentiates japonica (APX9  HS) and O. rufipogon (APX9  OR) alleles. Indica shared both APX9  HS and APX9  ORalleles suggesting that APX9  HS was introgressed into indica followed by crossing. The finding that O. rufipogon accessions with different origins carry APX9  OR strongly suggests that the 3-bp insertion was specifically selected in japonica rice during its domestication. In this study, we demonstrated that a pleiotropic gene APX9 acts as a major regulator of plant development by controlling a valuable suite of agronomically important traits in rice.