Genomics-Assisted Improvement on Blast Resistance and Low Cadmium Accumulation in An Elite Rice Variety ‘Xiangwanxian 13’

Xiangwanxian 13 (XWX13), a fragrant indica rice variety with high yield and good grain quality, is generally welcomed by farmers in China. However, the fact that XWX13 is highly susceptible to rice blast and its high grain cadmium (Cd) accumulation in Cd polluted paddy fields has been limiting its commercial utilization. Therefore, a genomics-assisted selection approach was employed to improve its blast resistance and lower grain Cd accumulation. In this study, four major genes, namely Pi1, Pi2, OsHMA3 and OsNramp5, were precisely introduced into XWX13 with the KASP marker-assisted selection followed by evaluation of genomic background with the genome-wide RICE 1K SNP array. Two preferable improved lines iXWX13-1 (stacking Pi1+Pi2+OsHMA3) and iXWX13-2 (stacking Pi1+Pi2+OsNramp5) were obtained with a genomic background recovery rates of 94.44% and 94.63%, respectively. Resistance spectrum assay showed that the two improved lines at the seedling stage exhibited high-level resistance to 39 Magnaporthe oryzae isolates, with more than 97.44% blast resistance frequency. Also, an enhanced resistance was observed for leaf and panicle neck blast in the two improved lines than that of the original XWX13 in natural blast nurseries. For grain Cd content, a multi-site field trial showed that a trace amount of grain Cd accumulation (0.009 to 0.077 mg/kg) was detected in the iXWX13-2, 90.98%-98.87% lower than that of XWX13. Moreover, the high similarity was observed in the yield, main agronomic traits and grain quality when comparing the improved lines to the original XWX13. This work was the first successful practice to apply molecular marker assisted backcrossing with genomics-based background selection to improve the blast resistance and lower grain Cd accumulation of XWX13 without penalty of the yield, main agronomic traits and grain quality. This proposed strategy would pave the way to integration of multiple desirable genes into the elite varieties in crop genetic improvement.