Development of SNP Markers for White Immature Fruit Skin Color in Cucumber (<i>Cucumis sativus</i> L.) Using QTL-seq and Marker Analyses
Despite various efforts in identifying the genes governing the white immature fruit skin color in cucumber, the genetic basis of the white immature fruit skin color is not well known. In the present study, genetic analysis showed that a recessive gene confers the white immature fruit skin-color phen...
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MDPI AG
2021-10-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/10/11/2341 |
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| author | D. S. Kishor Hemasundar Alavilli Sang-Choon Lee Jeong-Gu Kim Kihwan Song |
| author_facet | D. S. Kishor Hemasundar Alavilli Sang-Choon Lee Jeong-Gu Kim Kihwan Song |
| author_sort | D. S. Kishor |
| collection | DOAJ |
| description | Despite various efforts in identifying the genes governing the white immature fruit skin color in cucumber, the genetic basis of the white immature fruit skin color is not well known. In the present study, genetic analysis showed that a recessive gene confers the white immature fruit skin-color phenotype over the light-green color of a Korean slicer cucumber. High-throughput QTL-seq combined with bulked segregation analysis of two pools with the extreme phenotypes (white and light-green fruit skin color) in an F<sub>2</sub> population identified two significant genomic regions harboring QTLs for white fruit skin color within the genomic region between 34.1 and 41.67 Mb on chromosome 3, and the genomic region between 12.2 and 12.7 Mb on chromosome 5. Further, nonsynonymous SNPs were identified with a significance of <i>p</i> < 0.05 within the QTL regions, resulting in eight homozygous variants within the QTL region on chromosome 3. SNP marker analysis uncovered the novel missense mutations in <i>Chr3CG52930</i> and <i>Chr3CG53640</i> genes and showed consistent results with the phenotype of light-green and white fruit skin-colored F<sub>2</sub> plants. These two genes were located 0.5 Mb apart on chromosome 3, which are considered strong candidate genes. Altogether, this study laid a solid foundation for understanding the genetic basis and marker-assisted breeding of immature fruit skin color in cucumber. |
| first_indexed | 2024-03-10T05:07:45Z |
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| id | doaj.art-6238a0b5a22647ffa1cba84fd524ddc8 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T05:07:45Z |
| publishDate | 2021-10-01 |
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| series | Plants |
| spelling | doaj.art-6238a0b5a22647ffa1cba84fd524ddc82023-11-23T01:04:04ZengMDPI AGPlants2223-77472021-10-011011234110.3390/plants10112341Development of SNP Markers for White Immature Fruit Skin Color in Cucumber (<i>Cucumis sativus</i> L.) Using QTL-seq and Marker AnalysesD. S. Kishor0Hemasundar Alavilli1Sang-Choon Lee2Jeong-Gu Kim3Kihwan Song4Department of Bioresources Engineering, Sejong University, Seoul 05006, KoreaDepartment of Bioresources Engineering, Sejong University, Seoul 05006, KoreaPHYZEN, Seongnam-si 13558, Gyeonggi-do, KoreaNational Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, KoreaDepartment of Bioresources Engineering, Sejong University, Seoul 05006, KoreaDespite various efforts in identifying the genes governing the white immature fruit skin color in cucumber, the genetic basis of the white immature fruit skin color is not well known. In the present study, genetic analysis showed that a recessive gene confers the white immature fruit skin-color phenotype over the light-green color of a Korean slicer cucumber. High-throughput QTL-seq combined with bulked segregation analysis of two pools with the extreme phenotypes (white and light-green fruit skin color) in an F<sub>2</sub> population identified two significant genomic regions harboring QTLs for white fruit skin color within the genomic region between 34.1 and 41.67 Mb on chromosome 3, and the genomic region between 12.2 and 12.7 Mb on chromosome 5. Further, nonsynonymous SNPs were identified with a significance of <i>p</i> < 0.05 within the QTL regions, resulting in eight homozygous variants within the QTL region on chromosome 3. SNP marker analysis uncovered the novel missense mutations in <i>Chr3CG52930</i> and <i>Chr3CG53640</i> genes and showed consistent results with the phenotype of light-green and white fruit skin-colored F<sub>2</sub> plants. These two genes were located 0.5 Mb apart on chromosome 3, which are considered strong candidate genes. Altogether, this study laid a solid foundation for understanding the genetic basis and marker-assisted breeding of immature fruit skin color in cucumber.https://www.mdpi.com/2223-7747/10/11/2341cucumberQTL-seqSNP markerswhite immature fruit skin color |
| spellingShingle | D. S. Kishor Hemasundar Alavilli Sang-Choon Lee Jeong-Gu Kim Kihwan Song Development of SNP Markers for White Immature Fruit Skin Color in Cucumber (<i>Cucumis sativus</i> L.) Using QTL-seq and Marker Analyses Plants cucumber QTL-seq SNP markers white immature fruit skin color |
| title | Development of SNP Markers for White Immature Fruit Skin Color in Cucumber (<i>Cucumis sativus</i> L.) Using QTL-seq and Marker Analyses |
| title_full | Development of SNP Markers for White Immature Fruit Skin Color in Cucumber (<i>Cucumis sativus</i> L.) Using QTL-seq and Marker Analyses |
| title_fullStr | Development of SNP Markers for White Immature Fruit Skin Color in Cucumber (<i>Cucumis sativus</i> L.) Using QTL-seq and Marker Analyses |
| title_full_unstemmed | Development of SNP Markers for White Immature Fruit Skin Color in Cucumber (<i>Cucumis sativus</i> L.) Using QTL-seq and Marker Analyses |
| title_short | Development of SNP Markers for White Immature Fruit Skin Color in Cucumber (<i>Cucumis sativus</i> L.) Using QTL-seq and Marker Analyses |
| title_sort | development of snp markers for white immature fruit skin color in cucumber i cucumis sativus i l using qtl seq and marker analyses |
| topic | cucumber QTL-seq SNP markers white immature fruit skin color |
| url | https://www.mdpi.com/2223-7747/10/11/2341 |
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