Genetic analysis and candidate gene mining of flowering time in cucumber under low-light stress

Low-light stress significantly impacts the growth and yield of cucumber (<italic>Cucumis sativus</italic> L.), making it essential to comprehensively understand the genetic mechanisms governing flowering time adaptation. In this study, the genetic characteristics were analyzed using a mixed model encompassing major genes and polygenes and quantitative trait loci (QTL) mapping was performed via specific length amplified fragment sequencing (SLAF-seq), followed by precise QTL mapping with SSR markers. For the first female flowering time (<italic>FFT</italic>), the optimal model, E-1 (MX2-ADI-AD), includes two pairs of additive dominant epistatic major genes plus addictive-dominant polygenes, with an additive × dominant interaction (j_ab) of 4.16 and a major gene heritability (h²_mg) of 59.52%. For the first male flowering time (<italic>FMT</italic>), the optimal model was E-5 (MX2-ADE-AD), controlled by two pairs of completely dominant major genes and additive-dominant polygenes, with h²_mg and polygene heritability (h²_pg) of 28.48% and 58.33%, respectively. QTL analysis identified <italic>QFFT1.1</italic> on chromosome 1 (Chr.1) for <italic>FFT</italic>, explaining 11.77% of phenotypic variation (Max LOD = 3.825, additive effect (ADD) = 9.087, dominant effect (DOM) = −4.383) and comprising 52 candidate genes. For <italic>FMT</italic>, <italic>QFMT6.1</italic> on Chr.6 accounted for 6.89% of phenotypic variation (LOD = 3.320, additive effect = −2.123, dominance effect = −2.036), covering 479 kb and including 42 candidate genes. A total of two FFT-related genes and two FMT-related genes were identified, respectively through GO functional annotation and allelic diversity analysis. These findings provide a theoretical basis for further research into cucumber genes conferring low light.