QTL pyramiding reveals a crucial role of DEEPER ROOTING 1 on root system architecture adapted to drought stress in rice

Abstract

Drought limits water availability and negatively impacts rice growth. One of the strategies to overcome drought stress is the genetic improvement of root traits by marker-assisted selection (MAS). Using the MAS strategy, pyramiding quantitative trait loci (QTLs) efficiently stacks multiple QTLs. To elucidate the effects of pyramiding root QTLs on shoot production under drought, we used near-isogenic lines (NILs) and pyramided lines (PYLs), introducing single or multiple QTLs derived from Kinandang Patong (upland rice) into IR64 (lowland rice). We selected one QTL from each root morphological trait: root growth angle (DRO1), root thickness (Sta1), root length (qRL6.1), and root volume (qFSR4). We evaluated the effects of pyramiding root QTLs on root system architecture (RSA). In the basket method and 3D imaging by X-ray computed tomography, all NIL and PYLs with DRO1 showed robustly steeper root growth angle. In a hydroponic culture assay, root length QTL qRL6.1 increased maximum root length. In a lysimeter experiment, root volume QTL qFSR4 increased root volume per stem. Next, we examined the NILs and PYLs for shoot biomass production under drought conditions in lysimeter and field experiments. Two lines (DRO1-NIL and Sta1+DRO1-PYL) had a higher shoot biomass production under drought than IR64. DRO1-NIL exhibited deeper RSAs and increased water uptake compared to IR64. Sta1+DRO1-PYL was not as deep as DRO1-NIL but had a higher normalized difference vegetation index, lower canopy temperature, and higher shoot biomass in the field experiment. In summary, DRO1 plays a critical role in RSA, and pyramiding Sta1 with DRO1 increases shoot biomass during drought. This suggests the pyramiding of root QTLs could improve RSA and enhance biomass production under drought stress.