Validating Single Nucleotide Polymorphism Markers for Fusarium Basal Rot Resistance in Short-Day Onion Cultivars through Kompetitive Allele-Specific PCR

Fusarium Basal Rot (FBR) caused by Fusarium oxysporum f. sp. cepae is a detrimental disease affecting onions and leading to significant bulb yield losses. Understanding the genetic mechanisms underlying FBR resistance is crucial for developing FBR-resistant cultivars. This study investigated whether the favorable alleles associated with FBR resistance have been fixed in the onion cultivar populations selected for FBR resistance, utilizing eight single nucleotide polymorphism (SNP) markers. DNA was extracted from cultivar populations including susceptible and partially-resistant check cultivars and subjected to Kompetitive allele-specific PCR (KASP) genotyping. Allelic frequencies were calculated for each marker across all cultivar populations. Among the eight SNP markers, Isotig_33746_1093 exhibited a clear allelic discrimination for check cultivars and presented a negative correlation with FBR incidence (%), suggesting its potential association with FBR resistance. Another marker Isotig_44683_192 presented near fixation of the favorable allele in the most advanced selections, including the partially-resistant check, suggesting a strong link to the loci on chromosome 4A for FBR resistance. Additionally, Isotig_33439_640 predominantly featured the desired allele in the most advanced selections, indicating a potential connection with FBR resistance. Moreover, Isotig_30594_1021 exhibited an abundance of the desirable allele in the most advanced selections, proposing its possible link to the genomic region on chromosome 8 for FBR resistance. However, the small sample size warrants caution, and future studies with larger sample sizes are required to validate the association of other potential SNP markers with FBR resistance.