Development of KASP marker associated with gynoecious trait using BSA-seq in Cucumis sativus L

Gynoecy is a crucial trait for enhancing yield in cucumber. Phenotypic evaluation of F₂ and backcross populations derived from the Gy-14 × CMVR-1 cross over two growing seasons revealed that gynoecy is governed by an incomplete dominant gene influenced by modifiers or minor gene(s). To map the genomic region associated with this trait, whole genome resequencing based BSA-seq was performed on two extreme bulks (gynoecious and monoecious) along with parental lines derived from 250 F_2:3 individuals of the Gy-14 × CMVR-1 cross. Downstream analysis via QTLseqr and QTLseq identified a major QTL, qCu_gy6.1 spanning 24-28 Mb on chromosome 6 using the Cucumber_9930_V3 reference genome. Within this region, 27 SNPs were converted into high-throughput KASP markers, nine of which exhibited polymorphism. A linkage map was created using phenotypic and genotypic data from F_2:3 individuals using QTL IciMapping, that validated and fine mapped the qCu_gy6.1 region to 192 kb interval flanked by markers Cgy26200616 (0.4 cM) and Cgy26392478 (11.75 cM). The QTL qCu_gy6.1 demonstrated a LOD score of 13.27, accounting for 80.85% of the phenotypic variance, with additive effects of 0.5 and dominant effects of 0.02. This study represents the first report on developing KASP markers for the gynoecious trait in cucumber. Notably, closely linked marker Cgy26200616 (0.4 cM from qCu_gy6.1) showed non-synonym substitution resulting in asparagine to serine conversion in the coding exonic region of AP2-like ethylene transcription factor gene. This finding highlights significant potential for marker assisted selection (MAS) to introgress gynoecy trait into desirable cucumber genotypes.

The online version contains supplementary material available at 10.1007/s12298-025-01658-3.