Coupling RNA and BSA‐Seq to Unveil the Genetic and Physiological Basis of <i>Fusarium Wilt</i> (FON‐0) Resistance in Watermelon

ABSTRACT Fusarium wilt , caused by the soil‐borne Fusarium oxysporum f.sp. niveum (FON), is a devastating disease constraining global watermelon production. While three physiological races (0, 1 and 2) are established, resistance mechanisms to the foundational race remain largely unexplored. This study first evaluated seedling resistance to FON race 0 across 41 diverse watermelon accessions revealing that wild germplasm ( Citrullus amarus ) possessed superior resistance with 24.4% classified as highly resistant, whereas cultivated accessions were predominantly susceptible. The resistant accession WM216 and susceptible G42 were selected for in‐depth analysis. Physiological assessment demonstrated that WM216 mounted a robust and systemic defence response, characterized by a significant post‐inoculation induction of ROS‐scavenging enzymes like catalase and peroxidase. Integrated transcriptome and BSA‐seq analysis identified a major resistance QTL on chromosome 8 (15–22 Mb). Cross‐referencing these datasets pinpointed a single key candidate gene, ClG42_08g0072500 , encoding a two‐component response regulator (ARR family) implicated in cytokinin signalling. Expression profiling suggested this gene may act as a negative regulator of resistance. Our findings underscore the invaluable resistance alleles present in wild watermelon germplasm, provide a foundational genetic map for FON‐0 resistance and deliver critical molecular resources for marker‐assisted breeding of durable Fusarium wilt ‐resistant cultivars.