Dataset Information

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 w?) was identified to control the white immature fruit color. Genetic mapping with simple sequence repeats (SSR) markers located the w? 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 F? 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.

SUBMITTER: Tang HY

PROVIDER: S-EPMC5983590 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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

Tang Hong-Yu HY Dong Xu X Wang Jian-Ke JK Xia Jun-Hui JH Xie Fei F Zhang Yu Y Yao Xuan X Xu Yue-Jin YJ Wang Zheng-Jie ZJ

International journal of molecular sciences 20180517 5

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, ...[more]

PMID: 29772757

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Project description:Parthenocarpy is an excellent agronomic trait that enables crops to set fruit in the absence of pollination and fertilization, and therefore to produce seedless fruit. Although parthenocarpy is widely recognized as a hormone-dependent process, hormone-insensitive parthenocarpy can also be observed in cucumber; however, its mechanism is poorly understood. To improve the global understanding of parthenocarpy and address the hormone-insensitive parthenocarpy shown in cucumber, we conducted a physiological and proteomic analysis of differently developed fruits.Physiological analysis indicated that the natural hormone-insensitive parthenocarpy of 'EC1' has broad hormone-inhibitor resistance, and the endogenous hormones in the natural parthenocarpy (NP) fruits were stable and relatively lower than those of the non-parthenocarpic cultivar '8419 s-1.' Based on the iTRAQ technique, 683 fruit developmental proteins were identified from NP, cytokinin-induced parthenocarpic (CP), pollinated and unpollinated fruits. Gene Ontology (GO) analysis showed that proteins detected from both set and aborted fruits were involved in similar biological processes, such as cell growth, the cell cycle, cell death and communication. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that 'protein synthesis' was the major biological process that differed between fruit set and fruit abortion. Clustering analysis revealed that different protein expression patterns were involved in CP and NP fruits. Forty-one parthenocarpy-specialized DEPs (differentially expressed proteins) were screened and divided into two distinctive groups: NP-specialized proteins and CP-specialized proteins. Furthermore, qRT-PCR and western blot analysis indicated that NP-specialized proteins showed hormone- or hormone-inhibitor insensitive expression patterns in both ovaries and seedlings.In this study, the global molecular regulation of fruit development in cucumber was revealed at the protein level. Physiological and proteomic comparisons indicated the presence of hormone-independent parthenocarpy and suppression of fruit abortion in cucumber. The proteomic analysis suggested that hormone-independent parthenocarpy is regulated by hormone-insensitive proteins such as the NP-specialized proteins. Moreover, the regulation of fruit abortion suppression may be closely related to protein synthesis pathways.

Dataset Information

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

Publications

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

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