A High-Performance Database Management System for Managing and Analyzing Large-Scale SNP Data in Plant Genotyping and Breeding Applications

A DNA fingerprint database is an efficient, stable, and automated tool for plant molecular research that can provide comprehensive technical support for multiple fields of study, such as pan-genome analysis and crop breeding. However, constructing a DNA fingerprint database for plants requires signi...

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Autores principales:	Yikun Zhao, Bin Jiang, Yongxue Huo, Hongmei Yi, Hongli Tian, Haotian Wu, Rui Wang, Jiuran Zhao, Fengge Wang
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	SNP SNP array KASP database DNA fingerprint algorithms Agriculture (General) S1-972
Acceso en línea:	https://doaj.org/article/206423fb4b8a40dbab89be79188b144b
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spelling	oai:doaj.org-article:206423fb4b8a40dbab89be79188b144b2021-11-25T15:57:54ZA High-Performance Database Management System for Managing and Analyzing Large-Scale SNP Data in Plant Genotyping and Breeding Applications10.3390/agriculture111110272077-0472https://doaj.org/article/206423fb4b8a40dbab89be79188b144b2021-10-01T00:00:00Zhttps://www.mdpi.com/2077-0472/11/11/1027https://doaj.org/toc/2077-0472A DNA fingerprint database is an efficient, stable, and automated tool for plant molecular research that can provide comprehensive technical support for multiple fields of study, such as pan-genome analysis and crop breeding. However, constructing a DNA fingerprint database for plants requires significant resources for data output, storage, analysis, and quality control. Large amounts of heterogeneous data must be processed efficiently and accurately. Thus, we developed plant SNP database management system (PSNPdms) using an open-source web server and free software that is compatible with single nucleotide polymorphism (SNP), insertion–deletion (InDel) markers, Kompetitive Allele Specific PCR (KASP), SNP array platforms, and 23 species. It fully integrates with the KASP platform and allows for graphical presentation and modification of KASP data. The system has a simple, efficient, and versatile laboratory personnel management structure that adapts to complex and changing experimental needs with a simple workflow process. PSNPdms internally provides effective support for data quality control through multiple dimensions, such as the standardized experimental design, standard reference samples, fingerprint statistical selection algorithm, and raw data correlation queries. In addition, we developed a fingerprint-merging algorithm to solve the problem of merging fingerprints of mixed samples and single samples in plant detection, providing unique standard fingerprints of each plant species for construction of a standard DNA fingerprint database. Different laboratories can use the system to generate fingerprint packages for data interaction and sharing. In addition, we integrated genetic analysis into the system to enable drawing and downloading of dendrograms. PSNPdms has been widely used by 23 institutions and has proven to be a stable and effective system for sharing data and performing genetic analysis. Interested researchers are required to adapt and further develop the system.Yikun ZhaoBin JiangYongxue HuoHongmei YiHongli TianHaotian WuRui WangJiuran ZhaoFengge WangMDPI AGarticleSNPSNP arrayKASPdatabaseDNA fingerprintalgorithmsAgriculture (General)S1-972ENAgriculture, Vol 11, Iss 1027, p 1027 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	SNP SNP array KASP database DNA fingerprint algorithms Agriculture (General) S1-972
spellingShingle	SNP SNP array KASP database DNA fingerprint algorithms Agriculture (General) S1-972 Yikun Zhao Bin Jiang Yongxue Huo Hongmei Yi Hongli Tian Haotian Wu Rui Wang Jiuran Zhao Fengge Wang A High-Performance Database Management System for Managing and Analyzing Large-Scale SNP Data in Plant Genotyping and Breeding Applications
description	A DNA fingerprint database is an efficient, stable, and automated tool for plant molecular research that can provide comprehensive technical support for multiple fields of study, such as pan-genome analysis and crop breeding. However, constructing a DNA fingerprint database for plants requires significant resources for data output, storage, analysis, and quality control. Large amounts of heterogeneous data must be processed efficiently and accurately. Thus, we developed plant SNP database management system (PSNPdms) using an open-source web server and free software that is compatible with single nucleotide polymorphism (SNP), insertion–deletion (InDel) markers, Kompetitive Allele Specific PCR (KASP), SNP array platforms, and 23 species. It fully integrates with the KASP platform and allows for graphical presentation and modification of KASP data. The system has a simple, efficient, and versatile laboratory personnel management structure that adapts to complex and changing experimental needs with a simple workflow process. PSNPdms internally provides effective support for data quality control through multiple dimensions, such as the standardized experimental design, standard reference samples, fingerprint statistical selection algorithm, and raw data correlation queries. In addition, we developed a fingerprint-merging algorithm to solve the problem of merging fingerprints of mixed samples and single samples in plant detection, providing unique standard fingerprints of each plant species for construction of a standard DNA fingerprint database. Different laboratories can use the system to generate fingerprint packages for data interaction and sharing. In addition, we integrated genetic analysis into the system to enable drawing and downloading of dendrograms. PSNPdms has been widely used by 23 institutions and has proven to be a stable and effective system for sharing data and performing genetic analysis. Interested researchers are required to adapt and further develop the system.
format	article
author	Yikun Zhao Bin Jiang Yongxue Huo Hongmei Yi Hongli Tian Haotian Wu Rui Wang Jiuran Zhao Fengge Wang
author_facet	Yikun Zhao Bin Jiang Yongxue Huo Hongmei Yi Hongli Tian Haotian Wu Rui Wang Jiuran Zhao Fengge Wang
author_sort	Yikun Zhao
title	A High-Performance Database Management System for Managing and Analyzing Large-Scale SNP Data in Plant Genotyping and Breeding Applications
title_short	A High-Performance Database Management System for Managing and Analyzing Large-Scale SNP Data in Plant Genotyping and Breeding Applications
title_full	A High-Performance Database Management System for Managing and Analyzing Large-Scale SNP Data in Plant Genotyping and Breeding Applications
title_fullStr	A High-Performance Database Management System for Managing and Analyzing Large-Scale SNP Data in Plant Genotyping and Breeding Applications
title_full_unstemmed	A High-Performance Database Management System for Managing and Analyzing Large-Scale SNP Data in Plant Genotyping and Breeding Applications
title_sort	high-performance database management system for managing and analyzing large-scale snp data in plant genotyping and breeding applications
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/206423fb4b8a40dbab89be79188b144b
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A High-Performance Database Management System for Managing and Analyzing Large-Scale SNP Data in Plant Genotyping and Breeding Applications

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