Molecular Characterization of Fusarium Wilt Resistance in Naturally Colored and Elite Upland Cotton Germplasm

Fusarium wilt, caused by Fusarium oxysporum f. sp. vasinfectum (FOV), is a major disease threatening global cotton production, particularly in Central Asia. Host-plant resistance remains the most effective and sustainable control strategy. This study aimed to evaluate Fusarium wilt resistance in diverse Gossypium hirsutum L. genotypes with naturally colored fiber and to validate the SSR marker JESPR220 for its utility in marker-assisted selection. Genotypes were screened under artificial inoculation with a virulent FOV race 4 isolate, and disease severity was assessed using a 0–5 scale. Significant variation in resistance was observed among genotypes. The 145 bp allele of the JESPR220 marker showed a strong association with reduced disease severity. Genotypes carrying this allele exhibited a significantly lower mean disease index (1.34) compared to those lacking it (4.26). The marker explained 84% of the phenotypic variance (r = −0.917). Principal component and cluster analyses further confirmed the clear separation between resistant and susceptible groups. These results demonstrate that the JESPR220 marker is a reliable tool for early selection of Fusarium wilt resistance. Integration of this marker into cotton breeding programs can accelerate the development of resistant cultivars, although validation under field conditions and pyramiding with additional resistance loci are recommended for durable resistance.