Development and characterization of a co-dominant molecular marker via sequence analysis of a genomic region containing the Female (F) locus in cucumber (Cucumis sativus L.)

Cucumber is a typical monoecious having separate male and female flowers on the same plant, and sex expression in cucumber is mainly determined by three major genes: F/f, M/m and A/a. Gynoecy plays an important role in cucumber hybrid breeding, and the use of gynoecious lines as maternal parents ensures high productivity. This study aimed to identify a co-dominant marker linked to Female (F) locus to distinguish homozygous and heterozygous gynoecious lines for efficient selection of gynoecy in cucumber breeding. Firstly, we analyzed a 50-kb genomic sequence of five gynoecious and five monoecious inbred lines to detect the polymorphism linked to F locus. A pair of specific primers, Cs-BCAT-F/Cs-BCAT-R, based on an In/Del polymorphism at 3′-UTR of branched-chain amino acid transaminase (BCAT) gene was designed to examine the polymorphism in gynoecious and monoecious parents, their F₁ hybrids and two F₂ segregating populations. The PCR fragments amplified with Cs-BCAT-F/Cs-BCAT-R co-segregated with sexual phenotypes in the F₂ populations, behaving as a co-dominant marker with two alleles: F (gynoecious) and f (monoecious). When we further verified the consistency of the co-dominant marker using additional 55 diverse inbred lines, it can explain ~90 % of accessions. Linkage analysis also showed that the gene which enhances the number of female flowers co-segregated with the co-dominant marker on the long arm of chromosome 6. This is the first report for the development of F locus-specific co-dominant marker which can distinguish perfectly homozygous and heterozygous gynoecious, and it could be used in marker-assisted selection in cucumber breeding.