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Zucchini Yellow Mosaic Virus (ZYMV) is an aphid-transmitted potyvirus that causes severe yield losses in squash ( Cucurbita moschata ) production worldwide. Development of resistant cultivars using traditional breeding approaches relies on rigorous and resource-intensive phenotypic assays. QTL-seq, a whole genome re-sequencing based bulked segregant analysis, is a powerful tool for mapping quantitative trait loci (QTL) in crop plants. In the current study, the QTL-seq approach was used to identify genetic loci associated with ZYMV resistance in an F 2 population (n = 174) derived from a cross between Nigerian Local (resistant) and Butterbush (susceptible). Whole genome re-sequencing of the parents and bulks of resistant and susceptible F 2 progeny revealed a mapping rate between 94.04% and 98.76%, and a final effective mapping depth ranging from 81.77 to 101.73 across samples. QTL-seq analysis identified four QTLs significantly ( p &lt; 0.05) associated with ZYMV resistance on chromosome 2 ( QtlZYMV-C02 ), 4 ( QtlZYMV-C04 ), 8 ( QtlZYMV-C08 ) and 20 ( QtlZYMV-C20 ). Seven markers within the QTL intervals were tested for association with ZYMV resistance in the entire F 2 population. For QtlZYMV-C08 , one single nucleotide polymorphism (SNP) marker (KASP-6) was found to be significantly ( p &lt; 0.05) associated with ZYMV resistance, while two SNPs (KASP-1 and KASP-3) and an indel (Indel-2) marker were linked to resistance within QtlZYMV-C20 . KASP-3 and KASP-6 are non-synonymous SNPs leading to amino acid substitutions in candidate disease resistant gene homologs on chromosomes 20 ( CmoCh20G003040.1 ) and 8 ( CmoCh08G007140.1 ), respectively. Identification of QTL and SNP markers associated with ZYMV resistance will facilitate marker-assisted selection for ZYMV resistance in squash.

Genetic Loci Associated with Resistance to Zucchini Yellow Mosaic Virus in Squash