Fine Mapping of Short Hypocotyl Locus in Semi-Wild Xishuangbanna Cucumber

In cucumber (Cucumis sativus L), hypocotyl length is a useful trait in establishing strong seedlings before transplanting or grafting. The semi-wild Xishuangbanna cucumber (C. sativus var. xishuangbannanesis Qi et Yuan) (XIS) exhibits very short hypocotyl as compared with most cultivated cucumbers. In this study, we investigated the inheritance of short hypocotyl with 124 recombinant inbred lines (RILs) derived from a cross between a cultivated cucumber inbred line with normal hypocotyl length and the XIS cucumber SWCC8. We confirmed that a single recessive gene, sh, controlled the short hypocotyl. Initial framework mapping with microsatellite markers located sh locus in cucumber chromosome 3. Fine mapping was conducted with draft genome scaffold-assisted chromosome walking and stepwise increase of mapping population sizes, which allowed delimiting the sh locus to a 63 kb genomic DNA region in a mapping population of 664 F₂ plants. Annotation of this region identified four putative genes including a Arabidopsis thaliana RAD5 DNA repair gene. Sequence alignment of the RAD5 homologs between the two parents revealed a single nucleotide polymorphism (SNP) in the sixth exon of this candidate gene. A dCAPS maker based on this SNP was co-segregating with the hypocotyl length in both RIL and F₂ populations. This RAD5 gene seems to be the best candidate gene for the sh locus conditioning the short hypocotyl of the XIS cucumber.