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

Abstract Fruit skin color is a crucial external trait that affects consumer preference in cucumber. In this study, an F2 population was constructed from a cross between the inbred lines G35 (with light-green fruit skin) and Q51 (with dark-green fruit skin) and used to investigate the inheritance patterns of fruit skin color in cucumber. Genetic analysis showed that dark-green fruit skin was dominant to light-green skin. A major QTL, Fruit skin 1 (CsFS1), was identified between 36.62 Mb and 39.77 Mb on chromosome 3 by BSA-seq and GWAS. We further narrowed down the CsFS1 locus to a 94-kb interval containing 15 candidate genes in three F2 recombinant individuals with light-green skin color and one BC4F2 recombinant individual with dark-green skin color. 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 novel allele for the improvement of fruit skin color in cucumber breeding.