Near-isogenic lines of IR64 (<i>Oryza sativa</i> subsp. <i>indica</i> cv.) introgressed with <i>DEEPER ROOTING 1</i> and <i>STELE TRANSVERSAL AREA 1</i> improve rice yield formation over the background parent across three water management regimes

<p>Three near-isogenic lines (NILs) of <i>Oryza sativa</i> subsp. <i>indica</i> cv. IR64 (Dro1-NIL, Sta1-NIL, Dro1+Sta1-NIL) with <i>DEEPER ROOTING 1</i> (<i>DRO1</i>), a novel gene for steeper root growth angle, and/or with <i>Stele Transversal Area 1</i> (<i>Sta1</i>), a QTL for wider stele area, were tested under flooded lowland (FL), alternate wetting and drying lowland (AWD), and rainfed upland (UP) conditions in 2013 and 2014 to compare the effects of <i>DRO1</i> and <i>Sta1</i> on yield across different water management regimes. Genotypic variation and water management effects were significant for grain yield, aboveground biomass, and harvest index, as well as their interactions with year, but no significant genotype × water interaction was detected. Dro1-NIL had 14% higher yield than that of IR64 across the three water conditions due to higher harvest index, aboveground biomass, leaf area index, and number of grains. <i>Sta1</i> tended to reduce the carbon isotope composition (δ<sup>13</sup>C), leading to a higher harvest index of Sta1-NIL than that of IR64, but grain yield was not increased. Dro1+Sta1-NIL had the highest fraction of intercepted radiation, cumulative radiation interception, and panicle number, with a small but insignificant yield improvement over IR64, but the combination of <i>DRO1</i> and <i>Sta1</i> did not surpass the increment from the effects of <i>DRO1</i> alone. AWD in the more rainy year 2014 attained both higher water productivity and higher biomass, with significant water by year interaction for water productivity. Genotypic variation in water productivity was related with higher leaf area index and fraction interception, with Dro1-NIL larger than in IR64 and Sta1-NIL.</p>