Genome-wide Association Analysis Reveals a Novel QTL CsFS1 for Fruit Skin Color in Cucumber

Background: Cucumber is an important melon crop in the world, with different skin colors. However, the candidate genes and the underlying genetic mechanism for such an important trait in cucumber are unknown. In this study, a locus controlling fruit skin color was found on chromosome 3 of cucumber genome.Results: In this study, the light green inbred line G35 and the dark green inbred line Q51 were used as parents to construct an F2 population. On chromosome 3, we identified a major QTL CsFS1 (Fruit skin 1). We further narrowed down the CsFS1 locus to a 94-kb interval containing 15 candidate genes. Among these genes, Csa3G912920, which encodes a GATA transcription factor, was expressed at a higher level in the pericarp of the NIL-1334 line (with light-green fruit skin) than in that of the NIL-1325 line (with dark-green fruit skin). This study provides a new allele for the improvement of cucumber fruit skin color.Conclusion: A major QTL that controls fruit skin color in cucumber, CsFS1, was identified in a 94-kb region that harbors the strong candidate gene CsGATA1.