QTL mapping of cucumber fruit flesh thickness by SLAF-seq

Cucumber is an agriculturally and economically important vegetable crop worldwide. Fruit flesh thickness is an important trait for cucumber and also a central determinant of yield, yet little is known about the underlying mechanism of this trait. In this study, bulked segregant analysis (BSA) combin...

Full description

Bibliographic Details
Main Authors:	Xu, Xuewen, Lu, Lu, Zhu, Biyun, Xu, Qiang, Qi, Xiaohua, Chen, Xuehao
Format:	Online
Language:	English
Published:	Nature Publishing Group 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4623748/

id	pubmed-4623748
recordtype	oai_dc
spelling	pubmed-46237482015-11-03 QTL mapping of cucumber fruit flesh thickness by SLAF-seq Xu, Xuewen Lu, Lu Zhu, Biyun Xu, Qiang Qi, Xiaohua Chen, Xuehao Article Cucumber is an agriculturally and economically important vegetable crop worldwide. Fruit flesh thickness is an important trait for cucumber and also a central determinant of yield, yet little is known about the underlying mechanism of this trait. In this study, bulked segregant analysis (BSA) combined with specific length amplified fragment sequencing (SLAF-seq) was applied to finely map the gene that underlies fruit flesh thickness in cucumber. A 0.19-Mb-long quantitative trait locus on chromosome 2 controlling fruit flesh thickness (QTL fft2.1) was identified and further confirmed by simple sequence repeat (SSR) marker-based classical QTL mapping in 138 F2 individuals. Gene prediction of this 0.19-Mb region identified 20 genes. Quantitative RT-PCR revealed higher expression levels of Csa2 M058670.1 (SET domain protein-lysine methyltransferase) in D8 (thick fruit flesh parent) compared with that in XUE1 (thin fruit flesh parent) during fruit development. Sequence alignment analysis of Csa2M058670.1 from thick and thin fruit flesh cucumber lines revealed a 4-bp deletion mutation in the promoter region of this candidate gene, which may result in the loss of Csa2M058670.1 activation in thin fruit flesh lines. The data presented herein suggest that Csa2M058670.1 is a possible candidate gene for controlling flesh thickness in cucumber. Nature Publishing Group 2015-10-28 /pmc/articles/PMC4623748/ /pubmed/26508560 http://dx.doi.org/10.1038/srep15829 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Xu, Xuewen Lu, Lu Zhu, Biyun Xu, Qiang Qi, Xiaohua Chen, Xuehao
spellingShingle	Xu, Xuewen Lu, Lu Zhu, Biyun Xu, Qiang Qi, Xiaohua Chen, Xuehao QTL mapping of cucumber fruit flesh thickness by SLAF-seq
author_facet	Xu, Xuewen Lu, Lu Zhu, Biyun Xu, Qiang Qi, Xiaohua Chen, Xuehao
author_sort	Xu, Xuewen
title	QTL mapping of cucumber fruit flesh thickness by SLAF-seq
title_short	QTL mapping of cucumber fruit flesh thickness by SLAF-seq
title_full	QTL mapping of cucumber fruit flesh thickness by SLAF-seq
title_fullStr	QTL mapping of cucumber fruit flesh thickness by SLAF-seq
title_full_unstemmed	QTL mapping of cucumber fruit flesh thickness by SLAF-seq
title_sort	qtl mapping of cucumber fruit flesh thickness by slaf-seq
description	Cucumber is an agriculturally and economically important vegetable crop worldwide. Fruit flesh thickness is an important trait for cucumber and also a central determinant of yield, yet little is known about the underlying mechanism of this trait. In this study, bulked segregant analysis (BSA) combined with specific length amplified fragment sequencing (SLAF-seq) was applied to finely map the gene that underlies fruit flesh thickness in cucumber. A 0.19-Mb-long quantitative trait locus on chromosome 2 controlling fruit flesh thickness (QTL fft2.1) was identified and further confirmed by simple sequence repeat (SSR) marker-based classical QTL mapping in 138 F2 individuals. Gene prediction of this 0.19-Mb region identified 20 genes. Quantitative RT-PCR revealed higher expression levels of Csa2 M058670.1 (SET domain protein-lysine methyltransferase) in D8 (thick fruit flesh parent) compared with that in XUE1 (thin fruit flesh parent) during fruit development. Sequence alignment analysis of Csa2M058670.1 from thick and thin fruit flesh cucumber lines revealed a 4-bp deletion mutation in the promoter region of this candidate gene, which may result in the loss of Csa2M058670.1 activation in thin fruit flesh lines. The data presented herein suggest that Csa2M058670.1 is a possible candidate gene for controlling flesh thickness in cucumber.
publisher	Nature Publishing Group
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4623748/
_version_	1613494079612518400

QTL mapping of cucumber fruit flesh thickness by SLAF-seq

Similar Items