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

Yikun Zhao,Rui Wang,Bin Jiang,Fengge Wang,Hongli Tian,Haotian Wu,Yongxue Huo,Hongmei Yi,Jiuran Zhao

doi:10.3390/agriculture11111027

Yikun Zhao, Rui Wang + Show 7 more

Open Access

https://doi.org/10.3390/agriculture11111027

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Abstract

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.

Highlights

In 1984, Alec Jeffreys proposed applying DNA information to the field of human identity recognition and termed this process ‘DNA fingerprinting’, which has subsequently received considerable attention owing to its practical value and characteristics of high variability and stable heredity [1,2]
As a single nucleotide polymorphism (SNP) and InDel marker-based genotyping experimental system, we developed a plant SNP database management system (PSNPdms) for data management based on the Kompetitive Allele Specific PCR (KASP) and SNP array platforms
The PSNPdms system is based on the principle of “design before experiment” to provide a standardized pre-experiment design module to standardize the design method, such as standardized design of barcode number, set DNA extraction and PCR amplification plate information, and other processes and information

Summary

Introduction

In 1984, Alec Jeffreys proposed applying DNA information to the field of human identity recognition and termed this process ‘DNA fingerprinting’, which has subsequently received considerable attention owing to its practical value and characteristics of high variability and stable heredity [1,2]. DNA fingerprinting technology is an effective tool used in plant sciences, human genetics, and animal breeding-related fields [7,8,9,10,11,12,13,14,15]. Single-nucleotide polymorphisms (SNPs) have been successfully used to construct DNA fingerprints This has become the preferred approach for genotyping laboratories because the unique features of SNPs, such as multiple loci, high variability, and somatic stability, are irreplaceable [23,24,25]. The development of DNA fingerprinting using SNP markers has attracted substantial interest because of the practical potential [26,27,28], such as for marker-assisted selection (MAS), owing to accurate identification at the cultivar level. Applications include the improvement of crops, such as rice and onion (Allium cepa) [33,34]

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