Genomics Approach Links ROS-Scavenging to Enhanced Lateral Root Development Under Salt Stress in Tomato

Salinity, projected to impact over 50% of arable land by 2050, threatens tomato—a crop of major agronomic and nutritional value. While salt stress effects on tomato shoot and fruit traits are well studied, the genetic basis of root development under salinity remains underexplored. Roots are the primary sensors of salt stress, making them central to plant adaptation. To uncover the genetic regulators of root system architecture (RSA) under salt, we analyzed a natural diversity panel consisting of 220 wild- and 25 cultivated-tomato varieties. We identified distinct RSA strategies, favouring either lateral root elongation or emergence. An F1 hybrid with superior root architecture under salt stress was used to generate an F2 population for Bulk Segregant Analysis (BSA), and a parallel GWAS was performed across the diversity panel. Integrating BSA and GWAS results yielded 22 candidate genes. RNA-seq analysis of contrasting accessions prioritised four candidates, including an l-ascorbate peroxidase involved in ROS homoeostasis. Further functional analysis revealed genotype-specific H₂O₂ dynamics, and exogenous ascorbate improved K⁺ retention under salt. Together, these results uncover a genetic link between lateral root development, ROS signalling, and ion homoeostasis under salinity, offering new targets for engineering salt-resilient tomato.