Natural allelic variations in IbJAZ10 ‐ IbNF ‐ YA3 complex regulate Rhizopus soft rot resistance in sweet potato

Summary 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.