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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Autores principales:	D. S. Kishor, Hemasundar Alavilli, Sang-Choon Lee, Jeong-Gu Kim, Kihwan Song
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	cucumber QTL-seq SNP markers white immature fruit skin color Botany QK1-989
Acceso en línea:	https://doaj.org/article/6238a0b5a22647ffa1cba84fd524ddc8
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spelling	oai:doaj.org-article:6238a0b5a22647ffa1cba84fd524ddc82021-11-25T18:45:35ZDevelopment of SNP Markers for White Immature Fruit Skin Color in Cucumber (<i>Cucumis sativus</i> L.) Using QTL-seq and Marker Analyses10.3390/plants101123412223-7747https://doaj.org/article/6238a0b5a22647ffa1cba84fd524ddc82021-10-01T00:00:00Zhttps://www.mdpi.com/2223-7747/10/11/2341https://doaj.org/toc/2223-7747Despite 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.D. S. KishorHemasundar AlavilliSang-Choon LeeJeong-Gu KimKihwan SongMDPI AGarticlecucumberQTL-seqSNP markerswhite immature fruit skin colorBotanyQK1-989ENPlants, Vol 10, Iss 2341, p 2341 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	cucumber QTL-seq SNP markers white immature fruit skin color Botany QK1-989
spellingShingle	cucumber QTL-seq SNP markers white immature fruit skin color Botany QK1-989 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
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.
format	article
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
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_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_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_sort	development of snp markers for white immature fruit skin color in cucumber (<i>cucumis sativus</i> l.) using qtl-seq and marker analyses
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/6238a0b5a22647ffa1cba84fd524ddc8
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Development of SNP Markers for White Immature Fruit Skin Color in Cucumber (<i>Cucumis sativus</i> L.) Using QTL-seq and Marker Analyses

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