How rice defeats the floodwaters: Deepwater rice varieties grow taller when flooded, in a growth response driven by the plant hormones gibberellin and ethylene. This keeps the leaves above the water. Kuroha et al. identified the genes underlying this phenotype, which encode a component of the gibberellin biosynthetic pathway and its regulatory ethylene-responsive transcription factor. This genetic relay drives growth of the plant stem internodes in response to flooding. Modern cultivated deepwater rice, which has been domesticated for adaptation to the monsoon season of Bangladesh, emerged from the genetic variation found in wild rice strains over a broader geographic region. Science , this issue p. 181

Grain weight is an important crop yield component; however, its underlying regulatory mechanisms are largely unknown. Here, we identify a grain-weight quantitative trait locus (QTL) encoding a new-type GNAT-like protein that harbors intrinsic histone acetyltransferase activity (OsglHAT1). Our genetic and molecular evidences pinpointed the QTL-OsglHAT1’s allelic variations to a 1.2-kb region upstream of the gene body, which is consistent with its function as a positive regulator of the traits. Elevated OsglHAT1 expression enhances grain weight and yield by enlarging spikelet hulls via increasing cell number and accelerating grain filling, and increases global acetylation levels of histone H4. OsglHAT1 localizes to the nucleus, where it likely functions through the regulation of transcription. Despite its positive agronomical effects on grain weight, yield, and plant biomass, the rare allele elevating OsglHAT1 expression has so far escaped human selection. Our findings reveal the first example, to our knowledge, of a QTL for a yield component trait being due to a chromatin modifier that has the potential to improve crop high-yield breeding. Significance Grain weight is an important crop yield component; however, its underlying regulatory mechanisms are largely unknown. Here, we identify a grain-weight quantitative trait locus (QTL) in rice encoding a new-type GNAT-like protein that harbors intrinsic histone acetyltransferase activity (OsglHAT1). Elevated OsglHAT1 expression enhances grain weight and yield by enlarging spikelet hulls via increasing cell number and accelerating grain filling, and increases global acetylation levels of histone H4. Our findings reveal the first example, to our knowledge, of a QTL for a yield component trait being due to a chromatin modifier that has the potential to improve crop high-yield breeding.

Under flooded conditions, the leaves and internodes of deepwater rice can elongate above the water surface to capture oxygen and prevent drowning. Our previous studies showed that three major quantitative trait loci (QTL) regulate deepwater‐dependent internode elongation in deepwater rice. In this study, we investigated the age‐dependent internode elongation in deepwater rice. We also investigated the relationship between deepwater‐dependent internode elongation and the phytohormone gibberellin (GA) by physiological and genetic approach using a QTL pyramiding line (NIL‐1 + 3 + 12). Deepwater rice did not show internode elongation before the sixth leaf stage under deepwater condition. Additionally, deepwater‐dependent internode elongation occurred on the sixth and seventh internodes during the sixth leaf stage. These results indicate that deepwater rice could not start internode elongation until the sixth leaf stage. Ultra‐performance liquid chromatography tandem mass‐spectrometry (UPLC‐MS/MS) method for the phytohormone contents showed a deepwater‐dependent GA₁ and GA₄ accumulation in deepwater rice. Additionally, a GA inhibitor abolished deepwater‐dependent internode elongation in deepwater rice. On the contrary, GA feeding mimicked internode elongation under ordinary growth conditions. However, mutations in GA biosynthesis and signal transduction genes blocked deepwater‐dependent internode elongation. These data suggested that GA biosynthesis and signal transduction are essential for deepwater‐dependent internode elongation in deepwater rice.