The establishment of a DNA fingerprinting database for 73 varieties of Lactuca sativa capitate L. using SSR molecular markers

Zhou, Haijun; Zhang, Penghang; Luo, Jianxun; Liu, Xueying; Su, Fan; Liu, Chaojie; Han, Yingyan

doi:10.1007/s13580-018-0102-3

Cited by 8 publications

(15 citation statements)

References 31 publications

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“…In order to solve the problems of low identification rates of the single marker, some researchers tried to use the method of combined markers [35,36]. The number of markers have a big impact on the ability of the marker combinations identification, and some markers with sufficient informativeness remarkably enhance the identification rates of the marker combinations [30].…”

Section: Discussionmentioning

confidence: 99%

Efficient Fingerprinting of the Tetraploid Salix psammophila Using SSR Markers

Lian

Zhai

Zhang

et al. 2020

Forests

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Salix psammophila C. Wang et Ch. Y. Yang is an important desert shrub that is mainly distributed in northwest China, including the Mu Us sandland and Kubuqi desert. It plays a crucial role in vegetation rehabilitation and as a forestation plant. The traditional identification of its accessions based on phenotypic traits is usually unreliable. SSR (Simple Sequence Repeat) has the advantages of repeatability and codominant inheritance, and most species have had specific SSR primers developed for them already. Currently, there is no simple and rapid method used for identifying the tetraploid Salix psammophila with SSR markers. In this study, we construct fingerprints among 261 accessions of S. psammophila by screening of marker combinations. We identified a nine-marker combination which could completely distinguish each of the 261 accessions to their unique fingerprinting profiles. For this marker combination (G+I+J+N+O+Q+S+T+U), identification rate of combined markers (MC2) and total Polymorphism Information Content (PIC) were the highest, at 100% and 6.05, respectively. We used fingerprinting profiles with the nine-marker combination to produce two-dimensional barcodes, which could be screened rapidly and conveniently using a barcode scanned by a computer. The results of this study can provide an efficient genetic toolkit for identification, traceability management and protection of intellectual property rights of particular accessions of tetraploid S. psammophila.

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Section: Discussionmentioning

confidence: 99%

Efficient Fingerprinting of the Tetraploid Salix psammophila Using SSR Markers

Lian

Zhai

Zhang

et al. 2020

Forests

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“…The high variability and somatic stability of DNA fingerprints can be used to identify individuals, which is of great value in determining kinship among individuals and in forensics to identify criminals [3][4][5][6]. In other applications, DNA fingerprints can provide accurate identification at the varieties level [7][8][9], and play important roles in plant breeding [10][11][12]. DNA fingerprints are also commonly used in research on animal evolutionary trends and animal varieties identification [8,13].…”

Section: Introductionmentioning

confidence: 99%

“…Simple sequence repeats (SSRs) are molecular markers that have the advantages of simplicity, rapidity, high repeatability, and abundant polymorphisms [14][15][16]. SSRs have been used successfully to construct DNA fingerprints that are used widely in plant genetic studies and crop breeding [9,11]. The identification of varieties relies heavily on accurate plant genotype indicators to ensure the genetic and physiological consistency of improved crop varieties [17].…”

Section: Introductionmentioning

confidence: 99%

“…For example, plant DNA fingerprint databases can have two sampling methods, mixed and individual samples, which is unlike a human DNA fingerprint database, which will have only individual samples [1,3,4,9]. Therefore, a management system of plant DNA fingerprint data must be able to merge the fingerprints of multiple individual samples, individual and mixed samples, and mixed samples [9,10,30]. Second, plant varieties tend to have poor consistency between individual samples [9,10].…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, a management system of plant DNA fingerprint data must be able to merge the fingerprints of multiple individual samples, individual and mixed samples, and mixed samples [9,10,30]. Second, plant varieties tend to have poor consistency between individual samples [9,10]. When collecting DNA fingerprints of mixed samples, it is difficult to describe high and low peaks, and three or multiple peaks quantitatively because of the low consistency of samples.…”

Section: Introductionmentioning

confidence: 99%

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PIDS: A User-Friendly Plant DNA Fingerprint Database Management System

Jiang

Zhao

et al. 2020

Genes

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The high variability and somatic stability of DNA fingerprints can be used to identify individuals, which is of great value in plant breeding. DNA fingerprint databases are essential and important tools for plant molecular research because they provide powerful technical and information support for crop breeding, variety quality control, variety right protection, and molecular marker-assisted breeding. Building a DNA fingerprint database involves the production of large amounts of heterogeneous data for which storage, analysis, and retrieval are time and resource consuming. To process the large amounts of data generated by laboratories and conduct quality control, a database management system is urgently needed to track samples and analyze data. We developed the plant international DNA-fingerprinting system (PIDS) using an open source web server and free software that has automatic collection, storage, and efficient management functions based on merging and comparison algorithms to handle massive microsatellite DNA fingerprint data. PIDS also can perform genetic analyses. This system can match a corresponding capillary electrophoresis image on each primer locus as fingerprint data to upload to the server. PIDS provides free customization and extension of back-end functions to meet the requirements of different laboratories. This system can be a significant tool for plant breeders and can be applied in forensic science for human fingerprint identification, as well as in virus and microorganism research.

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Transcriptome-derived SSR markers for DNA fingerprinting and inter-populations genetic diversity assessment of Atractylodes chinensis

Zhao²,

Su³

et al. 2022

Nucleus

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Atractylodes chinensis (fam. Asteraceae) is an important medicinal plant due to its unique pharmacological activity. The species is widely distributed in most areas of northern China. It is difficult to identify different populations of A. chinensis due to their similarity in characteristics. This study was the first investigation to date that assessed the genetic diversity of A. chinensis from different geographical counties of northern China using simple sequence repeat (SSR) markers. Of the 106 SSR primers in the clusters classified in the sesquiterpenoid biosynthesis pathway in the transcriptomic database of A. chinensis, ten with high polymorphism were used to analyze the inter-populations genetic diversity and construct DNA fingerprinting of 19 A. chinensis populations. A total of 78 alleles were detected, with an average number of 6.5 alleles per primer. The PIC value ranged from 0.4748 to 0.8918 with a mean of 0.6265. The neighbor-joining tree was used to classify 19 populations of A. chinensis into three clusters. DNA fingerprinting was performed according to these ten SSR markers. The results revealed that geographic origin is not exactly related to genetic diversity, as populations belonging to different provinces are grouped in the same cluster. The results of this study confirm that SSR markers are effective for genetic diversity analysis. The inter-populations genetic diversity and fingerprinting of A. chinensis in this study could provide a scientific basis for species identification and selective breeding.

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The establishment of a DNA fingerprinting database for 73 varieties of Lactuca sativa capitate L. using SSR molecular markers

Cited by 8 publications

References 31 publications

Efficient Fingerprinting of the Tetraploid Salix psammophila Using SSR Markers

Efficient Fingerprinting of the Tetraploid Salix psammophila Using SSR Markers

PIDS: A User-Friendly Plant DNA Fingerprint Database Management System

Transcriptome-derived SSR markers for DNA fingerprinting and inter-populations genetic diversity assessment of Atractylodes chinensis

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