Fine Mapping and Candidate Gene Prediction for White Immature Fruit Skin in Cucumber (Cucumis sativus L.)

Abstract

In this study, a single recessive gene (designated w0) was identified to control the white immature fruit color. Genetic mapping with simple sequence repeats (SSR) markers located the w0 gene in the distal region of cucumber chromosome 3 (Chr.3). Fine mapping was then conducted using the method of draft genome scaffold-assisted chromosome walking with 7304 F2 individuals, which allowed for the assignment of the gene locus to a 100.3 kb genomic DNA region with two flanking markers, Q138 and Q193. Thirteen candidate genes were predicted in the 100.3 kb region. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the expression of the Csa3G904140 gene, which encodes a two-component response regulator-like protein, was much higher in the immature fruit skin of the green parental line (Q1) than in the white parental line (H4). A coding sequence analysis suggested that a single-base insertion occurred at the ninth exon, resulting in a frameshift mutation in Csa3G904140 of H4, and the mutation was consistent with the phenotype in 17 green/white germplasms. Therefore, Csa3G904140 was taken as the likely candidate gene controlling the immature fruit color of cultivated cucumber. This study will contribute to the cloning of candidate genes and the development of white cucumber cultivars using marker-assisted breeding.

Localization of quantitative trait loci for cucumber fruit shape by a population of chromosome segment substitution lines

“…The QTLs for FGC and FLC were observed in the distal region of chromosome 3 ( Supplementary Fig. S3; Supplementary Table S2), being consistent with the previous results reported by Liu et al 57,58 and Tang et al 59 . The w gene controlling white immature fruit color was localized in this region of chromosome 3, but no difference in coding sequence (CDS) of w was observed between RNS7 and CNS21.…”

Metabolome and transcriptome analyses reveal chlorophyll and anthocyanin metabolism pathway associated with cucumber fruit skin color

“…S 4 ). In addition, Csa3G904140 was detected different expressed in the Lv and Bai, and Csa3G904140 is control immature fruit color of cultivated cucumber [ 26 ].

Fig.

…”

Development of SNP Markers for White Immature Fruit Skin Color in Cucumber (Cucumis sativus L.) Using QTL-seq and Marker Analyses

“…Recent studies have shown that a single gene controls the external fruit color trait and white skin color is recessive over dark green skin color in cucumber [2,15,16]. A frameshift mutation, which leads to a premature stop codon in the w gene (aprr2) on chromosome 3, was reported to be a sole candidate gene responsible for white immature fruit color phenotype in cucumber and associated with chlorophyll biosynthesis [15].…”

“…A frameshift mutation, which leads to a premature stop codon in the w gene (aprr2) on chromosome 3, was reported to be a sole candidate gene responsible for white immature fruit color phenotype in cucumber and associated with chlorophyll biosynthesis [15]. Tang et al [16] studied the genetics of white immature fruit color in cucumber and mapped a single recessive gene (w 0 ) for white immature fruit color on chromosome 3 to approximately 100.3 kb between two flanking markers, Q138 and Q193 [16]. In spite of several studies, Tang et al [16] proposed that further study is necessary to understand the genetic basis of white immature fruit skin color in cucumber.…”

“…Tang et al [16] studied the genetics of white immature fruit color in cucumber and mapped a single recessive gene (w 0 ) for white immature fruit color on chromosome 3 to approximately 100.3 kb between two flanking markers, Q138 and Q193 [16]. In spite of several studies, Tang et al [16] proposed that further study is necessary to understand the genetic basis of white immature fruit skin color in cucumber.…”