Molecular mapping of flowering traits revealed a major QTL, qDFFF3.3.1 associated with early maturity in cucumber (Cucumis sativus L.)

Background Cucumber is an important cucurbitaceous vegetable with high demand in both domestic and international markets. It is primarily cultivated as a summer crop in tropical and subtropical regions. This study focused on flowering-related traits, such as early pistillate flowering and lower nodes for female flower initiation, which are desirable traits in breeding cucumber varieties and hybrids worldwide. Results A mapping population exhibiting considerable phenotypic variation was developed using two contrasting cucumber parental lines—DC-83 (early flowering) and DC-48 (late flowering)—selected for their differences in flowering time and shelf-life traits. Significant positive correlations were observed among flowering, shelf-life, and yield-related characteristics. Out of 1,200 SSR primers spanning all seven cucumber linkage groups, 106 polymorphic primers were selected based on a genome-wide polymorphism screening of the parental lines. These primers were then used for genotyping 125 individuals from the F₂ mapping population derived from DC-83 and DC-48. A comparative analysis of phenotypic and genotypic data led to the identification and mapping of four quantitative trait loci (QTLs) associated with days to first female flower (DFFF) and node to first female flower (NFFF). These QTLs were located on chromosome 2 (qNFFF2.1), chromosome 3 (qDFFF3.3.1 and qDFFF3.1), and chromosome 7 (qDFFF7.3.2). This study represents the first report of QTLs linked to DFFF and NFFF traits in cucumber genotypes of Indian origin, where a broad range of trait diversity is present. Notably, most of the identified QTLs exhibited higher phenotypic variance explained (PVE) percentages compared to earlier reports: qDFFF3.3.1 (35.14%), qDFFF3.1 (27.18%), qNFFF2.1 (6.95%), and qDFFF7.3.2 (4.7%). Conclusion Overall, the results from this study including phenotyping, SSR marker screening, QTL mapping, and flanking marker locations offer a strong scientific foundation to support cucumber improvement programs. These advancements include marker-assisted selection (MAS), genomic research, diversity analysis, DNA fingerprinting and genetic mapping for yield-related traits, facilitating the development of high-yielding cucumber varieties and hybrids.