Coupling RNA and BSA‐Seq to Unveil the Genetic and Physiological Basis of Fusarium Wilt (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, ClG42₀8g0072500, 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.