A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq)

A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq)

High-density genetic map provides an essential framework for accurate and efficient genome assembly and QTL fine mapping. Construction of high-density genetic maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of...

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Main Authors: Xu, Xuewen, Xu, Ruixue, Zhu, Biyun, Yu, Ting, Qu, Wenqin, Lu, Lu, Xu, Qiang, Qi, Xiaohua, Chen, Xuehao
Format: Online
Language:English
Published: Frontiers Media S.A. 2015
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285734/
id pubmed-4285734
recordtype oai_dc
spelling pubmed-42857342015-01-21 A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq) Xu, Xuewen Xu, Ruixue Zhu, Biyun Yu, Ting Qu, Wenqin Lu, Lu Xu, Qiang Qi, Xiaohua Chen, Xuehao Plant Science High-density genetic map provides an essential framework for accurate and efficient genome assembly and QTL fine mapping. Construction of high-density genetic maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. In this research, a high-density genetic map of cucumber (Cucumis sativus L.) was successfully constructed across an F2 population by a recently developed Specific Length Amplified Fragment sequencing (SLAF-seq) method. In total, 18.69 GB of data containing 93,460,000 paired-end reads were obtained after preprocessing. The average sequencing depth was 44.92 in the D8 (female parent), 42.16 in the Jin5-508 (male parent), and 5.01 in each progeny. 79,092 high-quality SLAFs were detected, of which 6784 SLAFs were polymorphic, and 1892 of the polymorphic markers met the requirements for constructing genetic map. The genetic map spanned 845.87 cm with an average genetic distance of 0.45 cm. It is a reliable linkage map for fine mapping and molecular breeding of cucumber for its high marker density and well-ordered markers. Frontiers Media S.A. 2015-01-07 /pmc/articles/PMC4285734/ /pubmed/25610449 http://dx.doi.org/10.3389/fpls.2014.00768 Text en Copyright © 2015 Xu, Xu, Zhu, Yu, Qu, Lu, Xu, Qi and Chen. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
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
Xu, Ruixue
Zhu, Biyun
Yu, Ting
Qu, Wenqin
Lu, Lu
Xu, Qiang
Qi, Xiaohua
Chen, Xuehao
spellingShingle Xu, Xuewen
Xu, Ruixue
Zhu, Biyun
Yu, Ting
Qu, Wenqin
Lu, Lu
Xu, Qiang
Qi, Xiaohua
Chen, Xuehao
A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq)
author_facet Xu, Xuewen
Xu, Ruixue
Zhu, Biyun
Yu, Ting
Qu, Wenqin
Lu, Lu
Xu, Qiang
Qi, Xiaohua
Chen, Xuehao
author_sort Xu, Xuewen
title A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq)
title_short A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq)
title_full A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq)
title_fullStr A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq)
title_full_unstemmed A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq)
title_sort high-density genetic map of cucumber derived from specific length amplified fragment sequencing (slaf-seq)
description High-density genetic map provides an essential framework for accurate and efficient genome assembly and QTL fine mapping. Construction of high-density genetic maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. In this research, a high-density genetic map of cucumber (Cucumis sativus L.) was successfully constructed across an F2 population by a recently developed Specific Length Amplified Fragment sequencing (SLAF-seq) method. In total, 18.69 GB of data containing 93,460,000 paired-end reads were obtained after preprocessing. The average sequencing depth was 44.92 in the D8 (female parent), 42.16 in the Jin5-508 (male parent), and 5.01 in each progeny. 79,092 high-quality SLAFs were detected, of which 6784 SLAFs were polymorphic, and 1892 of the polymorphic markers met the requirements for constructing genetic map. The genetic map spanned 845.87 cm with an average genetic distance of 0.45 cm. It is a reliable linkage map for fine mapping and molecular breeding of cucumber for its high marker density and well-ordered markers.
publisher Frontiers Media S.A.
publishDate 2015
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285734/
_version_ 1613173820429959168

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