Genetic control of root plasticity in response to salt stress in maize

Key message GWAS identified 559 significant SNPs associated with the remodelling of the root architecture in response to salt, and 168 candidate genes were prioritized by integrating RNA-seq, DEG and WGCNA data. Salinity is a major environmental factor limiting crop growth and productivity. The root is the first plant organ to encounter salt stress, yet the effects of salinity on maize root development remain unclear. In this study, the natural variations in 14 root and 4 shoot traits were evaluated in 319 maize inbred lines under control and saline conditions. Considerable phenotypic variations were observed for all traits, with high salt concentrations decreasing the root length, but increasing the root diameter. A genome-wide association study was conducted to analyse these traits and their plasticity (relative variation). We detected 559 significant single nucleotide polymorphisms, of which 125, 181 and 253 were associated with the control condition, stress condition and trait plasticity, respectively. A total of 168 of 587 candidate genes identified by genome-wide association study were supported by the differentially expressed genes or co-expression networks. Two candidate genes ZmIAA1 and ZmGRAS43 were validated by resequencing. Among these genes, 130 were detected under stress condition or trait plasticity that involved in diverse biological processes including plant hormone signal transduction, phenylpropanoid biosynthesis and fatty acid biosynthesis. Our findings clarify the root remodelling to salinity, and the identified loci and candidate genes may be important for the genetic improvement of root traits and salt tolerance in maize.