In this study, we combined QTL-seq  of an F2 segregating population with GWAS to identify a major QTL CsFS1 for fruit skin color in cucumber. The main advantage of QTL-seq is that there is no need to develop DNA markers and marker genotyping. The SNP available between parental strains is such a marker, reducing cost and time. In addition, the use of SNP-index allows accurate assessment of the frequency of parental alleles. These advantages make QTL-seq an attractive method to quickly identify genomic regions containing major QTLs.
Fruit skin color is an essential agronomic trait in cucumber that affects exterior quality and consumer preferences. In this study, we detected the major QTL CsFS1 on chromosome 3 between 39,531,980 and 39,626,163 bp. Previously, the w locus controlling the white fruit skin trait was also mapped to chromosome 3 (Liu et al. 2016), residing 281 kb upstream of the CsFS1 locus. In the w locus, Csa3G904140 (APRR2) harbors a single-nucleotide insertion that causes a frameshift mutation and a truncated protein in the white cucumber. Here, we found no sequence differences in APRR2 between the two parents, G35 and Q51. Therefore, CsFS1 is a novel QTL that controls green fruit skin in cucumber.
Through classical genetic mapping, CsFS1 was narrowed to a 94-kb physical interval that contains 15 predicted protein-coding genes. The Csa3G912920 gene encodes a GATA-type transcription factor, and its expression differed significantly between near isogenic lines with light- and dark-green fruit skins. Previous studies have shown that the GATA transcription factor families are highly conserved in Arabidopsis, rice, and other plants . The GATA transcription factors are evolutionarily conserved transcriptional regulators that recognize promoter elements with a G-A-T-A core sequence . The paralogous LLM-domain B-GATA transcription factors GNC and GNL contribute to chlorophyll biosynthesis and chloroplast formation in light-grown Arabidopsis seedlings [21, 26, 27]. Together, GNC and GNL control germination, greening, flowering time, and senescence downstream of auxin, cytokinin, gibberellin, and light signaling . Studies have confirmed that some GATA genes are preferentially expressed in the leaf . Leaves are the main organs for photosynthesis and light stress response in plants. High expression of a GATA transcription factor in leaves is consistent with its influence on chlorophyll synthesis. Therefore, it is reasonable to suggest that Csa3G912920 is the candidate gene for fruit skin color in cucumber. Nonetheless, additional experiments are required to provide evidence for Csa3G912920 gene function and robustly evaluate this hypothesis.
In conclusion, we identified a novel QTL, CsFS1, that controls green fruit skin color in cucumber and proposed a candidate gene, Csa3G912920, that may be responsible for the green color phenotype. Our results provide insight into the biological and molecular mechanisms of fruit skin color formation and can promote the development of attractive cucumber varieties with enhanced nutrients in the future.