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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...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285734/ https://www.ncbi.nlm.nih.gov/pubmed/25610449 http://dx.doi.org/10.3389/fpls.2014.00768 |
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author | Xu, Xuewen Xu, Ruixue Zhu, Biyun Yu, Ting Qu, Wenqin Lu, Lu Xu, Qiang Qi, Xiaohua Chen, Xuehao |
author_facet | Xu, Xuewen Xu, Ruixue Zhu, Biyun Yu, Ting Qu, Wenqin Lu, Lu Xu, Qiang Qi, Xiaohua Chen, Xuehao |
author_sort | Xu, Xuewen |
collection | PubMed |
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 F(2) 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. |
format | Online Article Text |
id | pubmed-4285734 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
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 Front Plant Sci 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 F(2) 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. |
spellingShingle | Plant Science 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) |
title | 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_short | 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) |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285734/ https://www.ncbi.nlm.nih.gov/pubmed/25610449 http://dx.doi.org/10.3389/fpls.2014.00768 |
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