Ipomoea batatas Raw sequence reads
Sweet potato is a globally important root and tuber crop. However, Fusarium root rot threatens its growth, affecting yield, quality, harvest, and storage. A deeper understanding of Fusarium pathogenicity and sweet potato defense is urgently needed. Here, seven Fusarium strains were isolated and purified from diseased plants. We identified FfRlpA2, a conserved Fusarium effector, as a protease inhibitor targeting sweet potato E3 ubiquitin ligase IbCHYR1, inhibiting its degradation. GWAS and haplotype analysis showed two SNPs within the IbCHYR1 promoter region were linked to root rot resistance. Overexpression of IbCHYR1 led to susceptibility to root rot and Fusarium wilt. IbCHYR1 interacts with a CCCH-type zinc-finger protein IbZnFR, promoting its degradation. IbZnFR conferred resistance to root rot and Fusarium wilt through pattern-triggered immunity (PTI) and also enhanced yield by more than 10%. Fusarium FfRlpA2 hijacks IbCHYR1 to degrade IbZnFR, inhibiting multiple defense pathways. These findings improve our understanding of Fusarium pathogenicity and provide strategies and candidate genes for developing broad-spectrum resistance to Fusarium in root and tuber crops without reducing yield.