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Research Progress and Application Prospects of Microsatellites

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (10 November 2020) | Viewed by 17813

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Special Issue Editors

Dr. Angela Cicatelli

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Guest Editor

Dept. Chemistry and Biology “Adolfo Zambelli”, University of Salerno, Fisciano (Salerno), Italy
Interests: biodiversity; molecular markers; epigenetic; bio-phytoremediation; microbiome

Dr. Francesco Guarino

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Department of Chemistry and Biology “A. Zambelli”, University of Salerno, 84084 Fisciano, Italy
Interests: biomonitoring; phytoremediation; biodiversity; environmental pollution
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Dear Colleagues,

In recent years, microsatellites—also known as simple sequence repeats (SSRs)—have gained considerable relevance for a large variety of biotechnological applications, including studies on diversity and evaluation of genetic relationships among individuals, germplasm management and fingerprinting, evolutionary studies, mapping of useful genes, construction of linkage maps, mapping of loci involved in quantitative traits, marker-assisted selections and backcrosses, population genetics, and phylogenetic studies. Numerous publications, aimed at SSR marker development and/or reporting their continuous application, confirm the current relevance of these molecular markers. The increasing importance and use of SSRs is due to many desirable genetic features, including the ease of PCR amplification, high level of polymorphism, their transferability among closely related species and genera, multiallelic nature, codominant inheritance, experimental reproducibility, relative abundance, extensive genome coverage including organellar genomes, chromosome specific location, and good amenability to high-throughput genotyping and automation. This Special Issue in ‘Research Progress and Application Prospects of Microsatellites’ will provide an overview of recent developments and the automatization of technology related to SSR, as well as on the various potential applications of these markers in specific biomolecular research fields.

Dr. Angela Cicatelli
Dr. Francesco Guarino
Guest Editors

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Keywords

Microsatellites
Fingerprinting
Population genetics
Genotyping
Linkage map

Published Papers (5 papers)

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Research

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18 pages, 3752 KiB

Open AccessArticle

Short Tandem Repeats (STRs) as Biomarkers for the Quantitative Follow-Up of Chimerism after Stem Cell Transplantation: Methodological Considerations and Clinical Application

by Almudena Navarro-Bailón, Diego Carbonell, Asunción Escudero, María Chicano, Paula Muñiz, Julia Suárez-González, Rebeca Bailén, Gillen Oarbeascoa, Mi Kwon, José Luis Díez-Martín, Carolina Martínez-Laperche and Ismael Buño

Genes 2020, 11(9), 993; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11090993 - 25 Aug 2020

Cited by 19 | Viewed by 3657

Abstract

Chimerism refers to the relative proportion of donor and recipient DNA after hematopoietic stem cell transplantation (HSCT) and its quantitative follow-up is of great clinical utility in this setting. PCR of short tandem repeats (STR-PCR) constitutes the gold standard method for chimerism quantification, although more sensitive PCR techniques (such as qPCR) have recently arisen. We compared the sensitivity and the quantification capacity of both techniques in patient samples and artificial mixtures and demonstrated adequate performance of both methods, with higher sensitivity of qPCR and better quantification skills of STR-PCR. By qPCR, we then prospectively followed up 57 patients that were in complete chimerism (CC) by STR-PCR. Twenty-seven patients (59%) showed 0.1–1% recipient DNA in the bone marrow. Only 4 patients presented 0.1–1% recipient DNA in peripheral blood (PB), and one of them relapsed. Finally, by qPCR, we retrospectively studied the last sample that showed CC by STR-PCR prior to relapse in 8 relapsed patients. At a median of 59 days prior to relapse, six patients presented mixed chimerism by qPCR in PB. Since both approaches have complementary characteristics, we conclude that different techniques should be applied in different clinical settings and therefore propose a methodological algorithm for chimerism follow-up after HSCT. Full article

(This article belongs to the Special Issue Research Progress and Application Prospects of Microsatellites)

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15 pages, 1431 KiB

Open AccessArticle

Genetic Diversity of Historical and Modern Populations of Russian Cattle Breeds Revealed by Microsatellite Analysis

by Alexandra S. Abdelmanova, Veronika R. Kharzinova, Valeria V. Volkova, Arina I. Mishina, Arsen V. Dotsev, Alexander A. Sermyagin, Oxana I. Boronetskaya, Lidia V. Petrikeeva, Roman Yu Chinarov, Gottfried Brem and Natalia A. Zinovieva

Genes 2020, 11(8), 940; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11080940 - 14 Aug 2020

Cited by 15 | Viewed by 4024

Abstract

Analysis of ancient and historical DNA has great potential to trace the genetic diversity of local cattle populations during their centuries-long development. Forty-nine specimens representing five cattle breeds (Kholmogor, Yaroslavl, Great Russian, Novgorod, and Holland), dated from the end of the 19th century to the first half of the 20th century, were genotyped for nine polymorphic microsatellite loci. Using a multiple-tube approach, we determined the consensus genotypes of all samples/loci analysed. Amplification errors, including allelic drop-out (ADO) and false alleles (FA), occurred with an average frequency of 2.35% and 0.79%, respectively. A significant effect of allelic length on ADO rate (r² = 0.620, p = 0.05) was shown. We did not observe significant differences in genetic diversity among historical samples and modern representatives of Kholmogor and Yaroslavl breeds. The unbiased expected heterozygosity values were 0.726–0.774 and 0.708–0.739; the allelic richness values were 2.716–2.893 and 2.661–2.758 for the historical and modern samples, respectively. Analyses of F_ST and Jost’s D genetic distances, and the results of STRUCTURE clustering, showed the maintenance of a part of historical components in the modern populations of Kholmogor and Yaroslavl cattle. Our study contributes to the conservation of biodiversity in the local Russian genetic resources of cattle. Full article

(This article belongs to the Special Issue Research Progress and Application Prospects of Microsatellites)

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18 pages, 3342 KiB

Open AccessArticle

Analyses of Hybrid Viability across a Hybrid Zone between Two Alnus Species Using Microsatellites and cpDNA Markers

by Jan Šmíd, Jan Douda, Karol Krak and Bohumil Mandák

Genes 2020, 11(7), 770; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11070770 - 09 Jul 2020

Cited by 9 | Viewed by 2470

Abstract

Diploid Alnus glutinosa s. str. and autotetraploid A. rohlenae form a narrow hybrid zone in a study area in southern Serbia, which results in triploid hybrid formation. The vast majority of previous studies have been focused on studies of maternal plants, but the offspring resulting from their crossing have not been much studied. Here, we use the variability of microsatellites and chloroplast DNA between these species and their putative hybrids to create an overall picture of the development of the hybrid zone and its predicted type. To elucidate the gene transfer within both species, the origins of individual ploidies and especially the role of triploid hybrids, a germination experiment was carried out linked with a flow cytometry study of the resulting seedlings. The tension zone model seems to offer the most adequate explanation of our observations, with selection against triploid hybrids and the spatial positioning of the hybrid zone. Despite selection against them, the triploid hybrids play an important role in the exchange of genes between the two species and therefore serve as a bridge for introgression. The presence of fertile triploids is essential for enriching the haplotype diversity between these species and for the development of new genetic lineages. Full article

(This article belongs to the Special Issue Research Progress and Application Prospects of Microsatellites)

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15 pages, 2644 KiB

Open AccessArticle

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

by Bin Jiang, Yikun Zhao, Hongmei Yi, Yongxue Huo, Haotian Wu, Jie Ren, Jianrong Ge, Jiuran Zhao and Fengge Wang

Genes 2020, 11(4), 373; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11040373 - 30 Mar 2020

Cited by 7 | Viewed by 3725

Abstract

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. Full article

(This article belongs to the Special Issue Research Progress and Application Prospects of Microsatellites)

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Review

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12 pages, 1098 KiB

Open AccessReview

Applications of Microsatellite Markers for the Characterization of Olive Genetic Resources of Tunisia

by Olfa Saddoud Debbabi, Sameh Rahmani Mnasri, Fathi Ben Amar, M’barek Ben Naceur, Cinzia Montemurro and Monica Marilena Miazzi

Genes 2021, 12(2), 286; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12020286 - 18 Feb 2021

Cited by 11 | Viewed by 3268

Abstract

Among the countries of the Mediterranean Basin, Tunisia is located at the crossroad for the immigration of several civilizations over the last two millennia, becoming a strategic place for gene flow, and a secondary center of diversity for olive species. Olive is one of the principal crop species in Tunisia and now it strongly characterizes the rural landscape of the country. In recent years, collecting missions on farm and in situ were carried out by various institutes, with special emphasis given to ex situ collections serving as a reference for the identification of olive germplasm. Simple Sequence Repeats (SSRs) represent the easiest and cheapest markers for olive genetic fingerprinting and have been the tool of choice for studying the genetic diversity of this crop in Tunisia, to resolve cases of homonymy and synonymy among the commercialized varieties, to identify rare cultivars, to improve knowledge about the genetic variability of this crop, to identify a hot spot of olive biodiversity in the Tunisian oasis of Degache, and to enrich the national reference collection of olive varieties. The present review describes the state of the art of the genetic characterization of the Tunisian olive germplasm and illustrate the progress obtained through the SSR markers, in individuating interesting genotypes that could be used for facing incoming problems determined by climate changes. Full article

(This article belongs to the Special Issue Research Progress and Application Prospects of Microsatellites)

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