Genomics-Assisted Improvement in Blast Resistance and Low Cadmium Accumulation in an Elite Rice Variety

Xiangwanxian 13 (XWX13), an elite fragrant indica rice, is highly susceptible to rice blast and accumulates cadmium (Cd) in grain above the food safety limit in Cd-contaminated paddies, severely constraining its commercial use. Despite these shortcomings, the variety is widely grown for its high yield and superior grain quality. To overcome these limitations, we conducted marker-assisted backcrossing (MABC) complemented by genome-wide background selection. Four major genes, namely Pi1, Pi2, OsHMA3, and OsNramp5, were precisely introduced into XWX13. Two preferable BC3MF5 improved lines iXWX13-1 (stacking Pi1 + Pi2 + OsHMA3) and iXWX13-2 (stacking Pi1 + Pi2 + OsNramp5) were obtained with genomic background recovery rates of 94.44% and 94.63%, evaluated by using the RICE 1K SNP array, respectively. Seedling resistance spectrum assays demonstrated more than a 97% blast resistance rate against 39 Magnaporthe oryzae isolates, and both lines showed enhanced leaf and panicle neck blast resistance in natural nurseries. Multi-site field trials revealed grain Cd concentrations of 0.009–0.077 mg kg−1 in iXWX13-2, 90.98–98.87% lower than those in XWX13. Importantly, yield, major agronomic traits, and grain quality remained indistinguishable from the original variety. This study provides the first demonstration that MABC coupled with SNP array background selection can simultaneously enhance blast resistance and reduce grain Cd in XWX13 without yield or quality penalties, offering a robust strategy for pyramiding multiple desirable genes into elite cultivars.