FINE MAPPING AND POSITIONAL CLONING OF A MAJOR ROOT SYSTEM ARCHITECTURE QTL IN MAIZE

The spatial configuration of roots is defined as root system architecture (RSA). Given its relevance, the manipulation of RSA is crucial in addressing the optimization of soil resource utilization. Hence, comprehensive understanding of the genetic and physiological processes underlying RSA regulation is critical in order to inform breeding programs aimed at improving resilience to abiotic stresses. In this study, we characterized and cloned qRoot-yield-1.06, a major QTL associated to maize RSA traits and yield stability over water regimes. qRoot-yield-1.06 was previously mapped on bin 1.06 in the cross between Lo964 and Lo1016, two inbred lines known to differ in their RSA. The QTL effect was confirmed by developing a pair of near-isogenic lines, NIL120 (-/-) and NIL129 (+/+), which solely differed in the allelic constitution of the target QTL, showing small and large root systems, respectively. QTL fine mapping and positional cloning were carried out exploiting a large nearly-isogenic recombinant population. Root phenotyping was based on shovelomics combined with softwareassisted root images analysis. A list of candidate genes was prioritized and the causative gene, a SOS-like gene, was identified using a combination of approaches including TILLING, qRT-PCR and transcriptomics. We showed that the (+) QTL allele from Lo1016 enhances the root system size by increasing in the number and length of lateral roots, in comparison with the (-) QTL allele from Lo964. Our findings indicated that native allele sequence variation at the SOS-like gene encoding for a sodium/H antiporter impacts RSA under non-saline conditions, suggesting a role of this gene in root development.