Genome-wide variant atlas of cucumber sex determination reveals line-specific molecular networks as a candidate resource for cucumber breeding

Abstract

Sex determination in cucumber ( Cucumis sativus L.) shapes yield, hybrid-seed production and breeding efficiency, yet most genomic studies have focused on single phenotypes or individual loci. A broader, integrative genomic comparison of cucumber lines representing contrasting sexual phenotypes is still lacking. We generated > 20 million 100-bp paired-end reads for each of five lines that represent a broad spectrum of contrasting cucumber sexual phenotypes - male (859), recessive gynoecious (2gg), dominant gynoecious (Gy3) and two independent hermaphrodites (2667, Hgy3) - and mapped them to the high-quality B10 reference genome. Variant calling with FreeBayes and functional annotation with VEP identified 0.09-0.38 million SNVs (SNPs) and 0.03-0.08 million short InDels per line, but only 1.3% of filtered variants were shared across all genotypes, underscoring their distinct breeding histories. Among the coding consequences, 5.4% were predicted to be high-impact; these defined a set of 270 genes carrying high-impact variants relative to B10 in all lines and > 500 genotype-restricted loci, including 279 genes unique to the male line 859 and 48 unique to the recessive gynoecious line 2gg. Functional enrichment revealed that line 859 is dominated by a brassinosteroid/gibberellin/jasmonate module and DNA-repair factors, whereas dominant gynoecy is associated with S-adenosyl-methionine cycling and LEAFY variants, and in the two hermaphroditic lines high-impact variants were associated with distinct functional modules - arginine/nitric-oxide and secondary-metabolism in Hgy3, and secondary metabolism in 2667 - representing candidate rather than established routes. Hormone-biosynthetic genes ( ACS1G/11, CPS1, BR6OX1 ) and SWI/SNF chromatin-remodelling subunits co-localise with the classical F, M and Gy loci, pinpointing tractable candidates for functional validation. This work provides the first genome-wide comparison of all five cucumber lines representing sex phenotypes within a single analytical framework. The resulting variant atlas provides a candidate resource for marker development and future population-level validation, supporting further multi-omics dissection of hormonal, transcriptional and epigenetic components associated with cucumber floral fate and breeding-relevant sex expression.