Identification of a gene causing yellow endocarp in Cucumis sativus through high-throughput sequencing

Abstract

Cucumber (Cucumis sativus) is a globally valued and widely cultivated vegetable crop. However, most commercially available cucumbers contain white or green fruit flesh color, which has very low ß-carotene and other carotenoids. Conversely, orange or yellow-fleshed cucumbers are rich in carotenoids and offer significant dietary and nutritional benefits. To generate cucumber varieties with carotenoid-enriched fruit flesh, we conducted high-throughput sequencing of a yellow-fleshed cucumber PI200815 (CS-C) and white-fleshed cucumbers JEF, and KWSA, to identify the genomic region responsible for yellow-fleshed fruit. Building on the previous report by Lu et al. (2015), we identified seven unique DNA variations in five genes specific to the CS-C line using HiSeq2000 and genomic mapping to 'Chinese-Long v3′. Further, based on the Sanger gene sequencing, among the five candidate genes, we found the CsaV3_7G029170 (encodes for an ATP-binding cassette (ABC) transporter C family member 4 [CsaYf]) gene with a single nucleotide polymorphism (SNP) variation in the third exon resulted in a missense mutation caused an amino acid change from Aspartic acid (Asp) to Aspargine (Asn) in the CS-C line. Accordingly, the gene segregation analysis based on the SNP variation revealed that the CsaYf gene confers the yellow endocarp trait in the CS-C line through recessive Mendelian single-gene inheritance. Notably, we observed a negative correlation between the downregulation of CsaYf gene expression and the accumulation of ß-carotene in meso and endo carp tissues in the CS-C line, suggesting a further investigation into the underlying molecular mechanism. This finding provides a novel genetic basis for breeding cucumbers with enriched carotenoid content to enhance their nutritional value.