Natural allelic variations in <scp>IbJAZ10</scp> ‐ <scp>IbNF</scp> ‐ <scp>YA3</scp> complex regulate <i>Rhizopus</i> soft rot resistance in sweet potato

Sweet potato is a globally important root and tuber crop. Soft rot severely threatens its postharvest quality and market value. However, research on the pathogenic mechanisms of soft rot remains limited. Here, we isolated a highly virulent fungal strain, Rhizopus stolonifer MY03, and identified one single nucleotide polymorphism within the promoter region of JASMONATE-ZIM domain protein 10 (IbJAZ10) linked to soft rot resistance. In susceptible varieties, the expression of IbJAZ10^Hap2 was significantly upregulated. Overexpression of IbJAZ10 enhanced susceptibility to soft rot. IbJAZ10 interacts with NUCLEAR FACTOR-Y protein 3 (IbNF-YA3). The high dosage Pro::IbNF-YA3^Hap1 allele led to a substantial increase in IbNF-YA3 expression, which conferred resistance to soft rot and improved yield by > 9.7%. Moreover, a MY03-specific effector RsSUN41 hijacks IbJAZ10 to degrade IbNF-YA3, thereby inhibiting multiple defense pathways. Our findings provide insights into Rhizopus pathogenicity and establish a genetic basis for soft rot research as well as the development of disease-resistant crops.