Root angle modifications by the <i>DRO1</i> homolog improve rice yields in saline paddy fields.

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 <i>qSOR1</i> (<i>quantitative trait locus for SOIL SURFACE ROOTING 1</i>), that a shallower root growth angle (RGA) could enhance rice yields in saline paddies. <i>qSOR1</i> is negatively regulated by auxin, predominantly expressed in root columella cells, and involved in the gravitropic responses of roots. <i>qSOR1</i> was found to be a homolog of <i>DRO1</i> (<i>DEEPER ROOTING 1</i>), which is known to control RGA. CRISPR-Cas9 assays revealed that other <i>DRO1</i> homologs were also involved in RGA. Introgression lines with combinations of gain-of-function and loss-of-function alleles in <i>qSOR1</i> and <i>DRO1</i> demonstrated four different RSAs (ultra-shallow, shallow, intermediate, and deep rooting), suggesting that natural alleles of the <i>DRO1</i> homologs could be utilized to control RSA variations in rice. In saline paddies, near-isogenic lines carrying the <i>qSOR1</i> 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 <i>DRO1</i> homologs are valuable targets for RSA breeding and could lead to improved rice production in environments characterized by abiotic stress.