Identification of quantitative trait loci governing subgynoecy in cucumber

Key message QTL-seq analysis identified three major QTLs conferring subgynoecy in cucumbers. Furthermore, sequence and expression analyses predicted candidate genes controlling subgynoecy. The cucumber ( Cucumis sativus L.) is a typical monoecious having individual male and female flowers, and sex differentiation is an important developmental process that directly affects its fruit yield. Subgynoecy represents a sex form with a high degree of femaleness and would have alternative use as gynoecy under limited resource conditions. Recently, many studies have been reported that QTL-seq, which integrates the advantages of bulked segregant analysis and high-throughput whole-genome resequencing, can be a rapid and cost-effective way of mapping QTLs. Segregation analysis in the F 2 and BC 1 populations derived from a cross between subgynoecious LOSUAS and monoecious BMB suggested the quantitative nature of subgynoecy in cucumbers. Both genome-wide SNP profiling of subgynoecious and monoecious bulks constructed from F 2 and BC 1 plants consistently identified three significant genomic regions, one on chromosome 3 ( sg3.1 ) and another two on short and long arms of chromosome 1 ( sg1.1 and sg1.2 ). Classical QTL analysis using the F 2 confirmed sg3.1 ( R 2 = 42%), sg1.1 ( R 2 = 29%) and sg1.2 ( R 2 = 18%) as major QTLs. These results revealed the unique genetic inheritance of subgynoecious line LOSUAS through two distinct major QTLs, sg3.1 and sg1.1 , which mainly increase degree of femaleness, while another QTL, sg1.2 , contributes to decrease it. This study demonstrated that QTL-seq allows rapid and powerful detection of QTLs using preliminary generation mapping populations such as F 2 or BC 1 population and further that the identified QTLs could be useful for molecular breeding of cucumber lines with high yield potential.