Root angle modifications by the DRO1 homolog improve rice yields in saline paddy fields

Significance

Genetically improving the root system architectures of plants is an effective strategy for developing climate-resilient crops. In this study, we revealed that a cloned rice quantitative trait locus associated with root growth angle, qSOR1, is a DRO1 homolog involved in root gravitropic responses. The loss-of-function allele qsor1 resulted in roots that developed on the soil surface and enabled plants to avoid the reducing stress found in saline paddy soils and, consequently, increased yields. We show that the DRO1 homologs could be useful for the controlled breeding of root system architectures that are adapted to the abiotic stress conditions caused by global climate change.

Abstract

The root system architecture (RSA) of crops can affect their production, particularly in abiotic stress conditions, such as with drought, waterlogging, and salinity. Salinity is a growing problem worldwide that negatively impacts on crop productivity, and it is believed that yields could be improved if RSAs that enabled plants to avoid saline conditions were identified. Here, we have demonstrated, through the cloning and characterization of qSOR1 ( quantitative trait locus for SOIL SURFACE ROOTING 1), that a shallower root growth angle (RGA) could enhance rice yields in saline paddies. qSOR1 is negatively regulated by auxin, predominantly expressed in root columella cells, and involved in the gravitropic responses of roots. qSOR1 was found to be a homolog of DRO1 ( DEEPER ROOTING 1), which is known to control RGA. CRISPR-Cas9 assays revealed that other DRO1 homologs were also involved in RGA. Introgression lines with combinations of gain-of-function and loss-of-function alleles in qSOR1 and DRO1 demonstrated four different RSAs (ultra-shallow, shallow, intermediate, and deep rooting), suggesting that natural alleles of the DRO1 homologs could be utilized to control RSA variations in rice. In saline paddies, near-isogenic lines carrying the qSOR1 loss-of-function allele had soil-surface roots (SOR) that enabled rice to avoid the reducing stresses of saline soils, resulting in increased yields compared to the parental cultivars without SOR. Our findings suggest that DRO1 homologs are valuable targets for RSA breeding and could lead to improved rice production in environments characterized by abiotic stress.