Identification and characterization of a novel regulator of root development from natural genetic variation among isogenized Arabidopsis accessions

Roots are essential for plant anchorage and nutrient uptake. Although root system architecture is genetically determined, its high level of plasticity allows rapid as well as long term adaptation to the plants' environment. To confer such adaptability, favorable alleles have been selected within species to endow them with an optimized root system. The identification of such favorable alleles is therefore a central component of research in plant breeding.In an attempt to isolate novel factors that modulate root development, we exploited natural genetic variation in the model plant Arabidopsis thaliana. Tissue culture analysis of 44 accessions led to the identification of a line, Uk-1 (Umkirch-1), whose root system differs significantly from average accessions. A short primary root and an increased number of lateral and adventitious roots are typical for the Uk-1 root system, while the average Arabidopsis root system consists of a predominant primary root and few lateral roots. The major locus responsible for the Uk-1 phenotype, BREVIS RADIX (BRX), was successfully isolated by map-based cloning. Quantitative trait locus (QTL) analysis revealed that BRX is responsible for ca. 80% of the variance of the observed primary root length difference as compared to an average control accession.BRX controls the extent of cell proliferation and elongation in the growth zone of the root tip and is a member of a novel, small family of proteins that contain three distinct and highly conserved domains of unknown function. BRX is a low abundant, nuclear protein, which is expressed in the phloem and the pericycle at the phloem poles. BRX is also expressed in the columella. Since BRX is not expressed in the root meristem, it must affect root growth in a secondary manner, likely by modulating responses to the plant hormone auxin.Transcriptional profiling in root tissues revealed that BRX does so by maintaining optimal expression of the brassinosteroid biosynthesis gene CPD, and thereby optimal endogenous levels of the plant hormone brassinosteroid. Further analysis identified BRX as a central component of the interdependency of brassinosteroid signaling and auxin signaling