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

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.

Automated summary

This study identified the gene CsaYf responsible for the yellow flesh color in cucumbers through high-throughput sequencing and gene segregation analysis. The finding provides a genetic basis for breeding cucumbers with enriched carotenoid content and enhancing their nutritional value.