FINE MAPPING AND POSITIONAL CLONING OF A MAJOR QTL LINKING MAIZE ROOT ARCHITECTURE, YIELD STABILITY, AND ION HOMEOSTASIS

Understanding the genetic and physiological mechanisms controlling root system architecture (RSA) in maize is crucial for optimizing breeding strategies for resilience to abiotic stresses. Modifying RSA can enhance maize's uptake of water and nutrients from the soil, mitigating yield losses under limiting growth conditions. Utilizing a large nearly-isogenic recombinant population and a root phenotyping pipeline based on shovelomics combined with software-assisted root image analysis, a major QTL influencing both maize RSA and yield stability, designated qRootyield- 1.06, was identified and cloned. This QTL, initially mapped to bin 1.06 in a Lo964 x Lo1016 cross, was confirmed using near-isogenic lines NIL120 (-/-) and NIL129 (+/+). These lines differ solely at this locus and exhibiting contrasting root systems; the (+) QTL allele from Lo1016 enhances root system size by increasing the number and length of lateral roots compared to the (-) QTL allele from Lo964. The causative gene, a SOS-like gene, was identified using a combination of approaches including TILLING, qRT-PCR, and transcriptomics. Considering the SOS pathway's established role in Na+ homeostasis and salt tolerance, and its potential to disrupt the uptake of other essential nutrients like K, Ca, and Mg, the concentrations of these elements were quantified in the shoot and root tissues of the two NILs under both control (0 mM NaCl) and salt stress (90 mM NaCl) conditions using ICP-OES. While no significant differences in ion content were observed in shoots of the two NILs under control or salt stress, NIL120 roots exhibited an impaired accumulation of ion compared to NIL129. Notably, a positive correlation between dry weight biomass and Na accumulation was observed, suggesting a possible growth-promoting effect of Na. Our findings suggest that allele variation in a SOS-like gene influences RSA and specific root ion accumulation even under non-saline conditions, pointing to its crucial role in root development.