Population Genetic Studies Research Articles

Популяційно-генетичний аналіз населення Запорізької області за даними прізвищ

The genetic structure of a population determines its adaptability, which is reflected in the population’s health, cultural, and intellectual potential. This study aimed to determine the indicators that characterize the genetic structure of populations in the Zaporizhzhia oblast. Throughout its centuries, the Zaporizhzhia oblast has been a crossroads of cultures, making it one of the most ethnically and genetically diverse areas. Surname-based indicators were obtained to characterise populations of the Zaporizhzhia oblast at various hierarchical levels to deepen the understanding of the state of the Ukrainian gene pool. The method used was the description of the genetic structure of the population through surnames, as proposed by I. Barrai. The study used a list of surnames of residents of the Zaporizhzhia oblast from 2001 to 2005. Twenty separate district populations, the city of Zaporizhzhia, and the overall regional population were analysed. The results indicate a significant range of variation in the structural organization of district populations. The main indicator, the isonymy index (I), ranges from 3.6 to 19.0 (×10-4). The inbreeding coefficient (FST) varies from 8.9 to 47.6 (×10-5), the migration rate (v) ranges from 213.0 to 1168.6 (10-4), the diversity index (a) ranges from 5.5 to 28.8 (×102), and the entropy index (H) is between 10.1 and 12.9. The surname redundancy (R) also fluctuates significantly from 17.2 to 27.4. In some settlements, individuals with the same surname are clustered, which the founder effect can explain. The indicators of isonymy, inbreeding, and migration in district populations significantly exceed those of the regional population, indicating the specific genetic structure at the local level. The lowest levels of isonymy are observed in districts with high tourist and transit activity, which may indicate the influence of external factors on genetic diversity. This data provides valuable insights for further studies in population genetics and can be used to develop strategies for preserving genetic and cultural diversity in the country.

The Molecular Dialogue Between Zymoseptoria tritici and Wheat.

Zymoseptoria tritici is a highly damaging pathogen that causes high wheat yield losses in temperate climates. Z. tritici emerged during the domestication of wheat in the Fertile Crescent and has been extensively used as a model system for population genetic and genomic studies. New genetic tools and resources have provided a better understanding of the molecular components involved in the wheat-Z. tritici interaction, which is highlighted by the cloning of three wheat resistance genes and four Z. tritici avirulence genes. Despite the considerable progress made in the last few years, the mechanisms that mediate Z. tritici colonization remain largely unknown. In this review, we summarize the latest advances in understanding the molecular components mediating wheat-Z. tritici interactions, and we discuss future research lines to close current knowledge gaps. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

HapNetworkView: a tool for haplotype network exploration and visualization

BackgroundHaplotype networks are useful for investigating the genealogical relationships among haplotypes and have been extensively used in molecular evolution and population genetic studies. However, existing tools for visualizing haplotype networks lack comprehensive functionalities for data exploration and layout adjustments. Therefore, there is a need for a useful tool capable of constructing and visualizing haplotype networks, facilitating the exploration of data, particularly with datasets with large sample sizes.ResultsWe present HapNetworkView, a user-friendly tool that facilitates the construction and interactive visualization of haplotype networks, enabling users to explore haplotypes and mutation information effectively. HapNetworkView offers both automatic optimization and manual adjustment for haplotype network layouts. Additionally, HapNetworkView supports various input and output formats, as well as color customization.ConclusionsThese comprehensive functionalities collectively satisfy various needs of users in haplotype network analysis, making HapNetworkView a valuable tool.

Research Note: A low-density SNP genotyping panel for Chinese native chickens

The efficiency of molecular breeding largely depends on the cost of genotyping, which plays an important role in breeding and population genetic studies. Compared to pig, cattle, and sheep, poultry has a small size genome, and lower individual value. Developing a relatively low-density genotyping panel is needed to decrease the genotyping cost for poultries. In the present study, we developed a chicken 11 K single nucleotide polymorphism (SNP) genotyping panel for breeding and genetic analysis using genotyping by targeted sequencing (GBTS). The panel design was based on whole genome sequencing data from 7 local breeds and a commercial breed. In total 11,200 SNPs were included in the final chip. Population analyses of the eight breeds showed high SNP call rates and minor allele frequencies (MAF), enabling clear differentiation between populations. The families within population can also be identified. Additionally, the 11K panel was applied to a genomic prediction of Wenshang Barred chickens, the predictive ability and prediction accuracy between the WGS and chip dataset non-significantly differed. Therefore, the newly developed chicken low-density SNP is efficient, cost-effective, and well-suited for application in local Chinese chickens, which can accelerate chicken breeding improvements and enhance conservation efforts.

Landscape and conservation genetics of western black crested gibbons (Nomascus concolor) in China.

Despite decades of field study, very little is known about the molecular ecology of gibbons, particularly as it relates to their ability to disperse across degraded and fragmentary landscapes. The critically endangered western black crested gibbon (Nomascus concolor) has been reduced to a small, fragmented population with about 1300 individuals. In the largest population genetic study of free-ranging gibbons to date, we sampled 47 of these gibbons from 13 sites in China and generated 15 polymorphic autosomal microsatellite markers. We identify three population clusters of N. concolor in Yunnan centered in 1) the Wuliang and Ailao Mountains, 2) the Yongde Daxueshan Mountains, and 3) an isolated remnant near the border with Vietnam. Within the Wuliang Mountains, we identified four subclusters, three of which are bounded by high-altitude rhododendron forest, and one that is isolated from the main population by ~2 km of degraded forest and pasture. Least-cost path analysis and isolation by resistance modeling demonstrates that the population genetic distances among gibbons in Wuliangshan National Nature Reserve are significantly correlated with geographic paths that avoid use of high-altitude rhododendron forest in favor of evergreen broadleaf forest. Although these gibbons have likely undergone reductions in heterozygosity from recent consanguineous mating, we suggest that their active avoidance of inbreeding on the population level maintains higher than expected levels of genetic diversity. This research provides new insights into how gibbons interact with heterogeneous environments and expands our understanding of their molecular ecology and conservation genetics.

Phenotypic and molecular characterization of the largest worldwide cluster of hereditary angioedema type 1.

Hereditary angioedema type 1 (HAE1) is a rare, genetically heterogeneous, and autosomal dominant disease. It is a highly variable, insidious, and potentially life-threatening condition, characterized by sudden local, often asymmetric, and episodic subcutaneous and submucosal swelling, caused by pathogenic molecular variants in the SERPING1 gene, which codes for C1-Inhibitor protein. This study performed the phenotypic and molecular characterization of a HAE1 cluster that includes the largest number of affected worldwide. A geographically HAE1 cluster was found in the northeast Colombian department of Boyaca, which accounts for four unrelated families, with 79 suspected to be affected members. Next-Generation Sequencing (NGS) was performed in 2 out of 4 families (Family 1 and Family 4), identifying the variants c.1420C>T and c.1238T>G, respectively. The latter corresponds to a novel mutation. For Families 2 and 3, the c.1417G>A variant was confirmed by Sanger sequencing. This variant had been previously reported to the patient prior to the beginning of this study. Using deep-learning methods, the structure of the C1-Inhibitor protein, p.Gln474* and p.Met413Arg was predicted, and we propose the molecular mechanism related to the etiology of the disease. Using Sanger sequencing, family segregation analysis was performed on 44 individuals belonging to the families analyzed. The identification of this cluster and its molecular analysis will allow the timely identification of new cases and the establishment of adequate treatment strategies. Our results establish the importance of performing population genetic studies in a multi-cluster region for genetic diseases.

Genetic variability and association studies in F2 populations of Groundnut (Arachis hypogaea L.)

Groundnut is an extensively self-pollinating crop with a narrow genetic base; therefore, it relies on the F2 generation for optimal segregation and recombination. The genetic variability resulting from segregation and re- combination is essential for effective selection in crop improvement pro- grammes. F2 populations derived from the crosses BSR 2 × GPBD 4 and BSR 2 × TMV 2 were assessed for examining genetic variation, and correla- tion coefficients along path coefficients. Twenty-four yield-attributing, physiological, as well as biochemical characteristics were covered in the research, in the Kharif season of 2024. The assessment of the PCV along with GCV revealed that a majority of yield-related traits, including the number of pods, kernels, and pod yield, demonstrated high PCV along with GCV in both crosses, indicating substantial genetic variation. Regarding yield-related characteristics, high GAM along with high heritability in a broad sense were noted for both the crosses, suggesting that a breeding approach based on simple selection can be successful in increasing groundnut yield. Correla- tion and path coefficients indicated that the number of mature kernels and pod yield calculated for each plant possessed a high positive direct effect on kernel yield. Transgressive segregants were identified over twice the stand- ard deviation of the better parent mean for various traits. These findings can serve as a foundation for future breeding programmes aimed at enhancing the yield and oil content.

BIOLOGICAL NOMENCLATURE (TAXONOMY) AND CLASSIFICATION OF HONEY BEE. CURRENT STATE AND PROBLEMS

The chronology of scientific research achievements in the process of determining the biological nomenclature and classification of honey bees and the implementation of the results obtained for use in the practice of beekeeping in the selection and preservation of aboriginal breeds (races) of bees in modern environmental conditions is highlighted. An attempt is made to focus this study in the field of analysis of the chronology of methods used in the historical aspect of determining the taxonomy of insects, in particular bees. At the same time, the problems and prospects of scientific research in modern economic and natural and climatic conditions of the development of the industry are reflected. It is shown that initially only morphometry was used worldwide to identify bee breeds. However, morphometric features are not always informative in identifying subspecies, since they are subject to variability under the influence of environmental conditions. Later, biochemical methods for identifying bee subspecies based on polymorphism of allozyme loci were developed. It is shown that at the same time, methods for identifying bee subspecies based on polymorphism of mitochondrial DNA (mtDNA) loci were developed. This polymorphism was successfully used in phylogenetic and phylogeographic studies of honey bees. The disadvantage of mtDNA markers is the exclusively maternal type of inheritance. At the same time, methods for identifying bee subspecies were developed taking into account polymorphism of nuclear DNA (nDNA) loci. Recently, methods for identifying bee subspecies based on SNP analysis have been developed. These markers have become widely used in population, evolutionary and phylogenetic studies of bees due to the development of next-generation sequencing methods NGS (Next Generation Sequencing) Illumina. SNP markers are characterized by high resolution due to their number and stable inheritance over several generations, which can be successfully used in genetic mapping, population and evolutionary studies, selection of lines for economically useful traits and disease resistance, identification of taxonomic affiliation of bee families.

The Complete Mitochondrial Genome of the Luciocyprinus langsoni (Cypriniformes: Cyprinidae): Characterization, Phylogeny, and Genetic Diversity Analysis.

Background: Luciocyprinus langsoni is a species belonging to the Cyprinidae family. The objective of this study is to gain a comprehensive understanding of its evolutionary history and genetic characteristics. Methods: The complete mitochondrial genome of L. langsoni was determined using overlapping PCR. A phylogenetic analysis was conducted based on 13 protein-coding genes from 48 species. A population genetic diversity analysis using the COI gene and a selection analysis of 13 protein-coding genes were also performed. Results: The mitogenome is 16,586 base pairs long and consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and two control regions. It has a high adenine-thymine (A + T) content. The phylogenetic analysis confirms the placement of L. langsoni within the subfamily Cyprininae. The population genetic diversity analysis reveals low variability in the Hechi Longjiang population. The selection analysis shows that all 13 protein-coding genes have evolved under purifying selection with Ka/Ks ratios below 1. Conclusions: These results enhance our understanding of L. langsoni's evolutionary history and lay a genetic foundation for future studies in population genetics and phylogenetics.

Importance of anthropological genetics research in Honduras, Central America

With its unique geographic location at the northern end of the Central American isthmus, Honduras straddles the boundaries of two distinct cultural regions—the Mesoamerican and the Istmo-Colombian. In this context, we briefly discuss the progress of population genetics studies conducted within Honduras. The text underscores the importance of conducting fieldwork to improve our understanding of the genetic history, population dynamics, and emergence of diseases among the Indigenous communities of this country. Among the seven distinct Indigenous populations currently under genetic investigation, we highlight the case of the Garifuna people. We explore their origins, patterns of migration, genetic differentiation, and the prevalence of Hypertrophic Cardiomyopathy (HCM), which may be linked to founder effects. Our research endeavors in Honduras emphasize the value of an interdisciplinary approach in the study of local human populations that have been instrumental in shaping our evolving comprehension of the genetic landscapes within this unique geographical and cultural setting.

Full-length transcriptome-referenced analysis reveals developmental and olfactory regulatory genes in Dermestes frischii.

Dermestes frischii Kugelann, 1792 is a storage pest worldwide, and is important for estimating the postmortem interval in forensic entomology. However, because of the lack of transcriptome and genome resources, population genetics and biological control studies on D. frischii have been hindered. Here, single-molecule real-time sequencing and next-generation sequencing were combined to generate the full-length transcriptome of the five developmental stages of D. frischii, namely egg, young larva, mature larva, pupa and adult. A total of 41,665 full-length non-chimeric sequences and 59,385 non-redundant transcripts were generated, of which 42,756 were annotated in public databases. Using the weighted gene co-expression network analysis, gene co-expression modules related to the five developmental stages were constructed and screened, and the genes in these modules were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The expression patterns of the differentially expressed genes (DEGs) related to olfaction and insect hormone biosynthesis were also explored. Transcription of most odorant binding proteins was up-regulated in the adult stage, suggesting they are important for foraging in adults. Many genes encoding for the ecdysone-inducible protein were up-regulated in the pupal stage, may be mainly responsible for the tissue remodelling of metamorphosis. The results of the quantitative real-time polymerase chain reaction (qRT-PCR) were consistent with the RNA-seq results. This is the first full-length transcriptome sequencing of dermestids, and the data obtained here are vital for understanding the stage-specific development and olfactory system of D. frischii, providing valuable resources for storage pest and forensic research.

Looking out for the little guy: species distribution modeling and conservation implications of the elfin skimmer Nannothemis bella (Odonata: Libellulidae)

Nannothemis bella Uhler, 1857 (Odonata: Libellulidae), the smallest dragonfly in North America, inhabit bogs and sedge fens across their distribution, spanning from Quebec (Canada) south to Florida and west to Minnesota and Louisiana (USA). While common in the northern part of their range, N. bella is of conservation concern in the southern populations where they are disjunct and rare. Little work has been done on the ecology and geographic conservation of this species. To fill this knowledge gap, we constructed species distribution models (SDMs) to analyze the spatial distribution and climatic niche of N. bella, define factors in habitat suitability and estimate potential niche shifts under climate change and inform conservation efforts. Our present-day SDMs indicate the dominant environmental elements determining habitat suitability include the proportion of silt in soil, temperature seasonality, percentage of clay and coarse components in soil, and soil class. Our paleodistribution models show a southern distribution within the last glacial maximum, with a shift northward 8,326 to 4,200 years ago. Our projected SDMs for 2050 under RCP 2.6 and RCP 8.5 predict a significant decrease in habitat suitability throughout the entire range of N. bella. As such, N. bella is a species of conservation concern and conservation measures are imperative for its continued existence as a much-needed bioindicator for these freshwater ecosystems. Additionally, this ecological knowledge provides the foundation for identifying population sites from which to collect N. bella for future population genetic studies.

Development of a microhaplotype panel for steelhead/rainbow trout (Oncorhynchus mykiss) and application for phylogenetic analysis in California

AbstractAdvances in high-throughput sequencing and bioinformatic data processing have prompted a transition in wildlife and fisheries genetics from the use of allozymes, mtDNA, or microsatellites towards markers that are more amenable to genotyping by sequencing, increasing the amount of data obtained for a lower cost with less time-consuming techniques. Microhaplotypes are novel multi-allelic genetic markers that utilize a high-throughput genomic amplicon sequencing approach to genotype large numbers of individuals for parentage and kinship analysis and population genetic studies, including applications in monitoring and fisheries management. We describe the development of a panel of microhaplotypes for Oncorhynchus mykiss, a species of high cultural and economic importance throughout its native range and globally through introductions for aquaculture and due to its reputation as a prized sport fish among recreational fishers. The panel includes 124 loci presumed to be neutral, a marker for the sex determination locus (SdY), and 10 loci targeting previously identified adaptive genomic variants associated with important life-history traits in this species. We demonstrate that this panel provides high resolution for phylogeographic and other genetic analysis and on initial standardized reference population genetic baseline of California O. mykiss.

The genetic origins of species boundaries at subtropical and temperate ecoregions in the North American racers (Coluber constrictor).

Phylogeographically structured lineages are a common outcome of range-wide population genetic studies. In the southeastern United States, disconnection between populations found at the intersection of the southeastern coastal plains of peninsular Florida and the southeastern plains of the adjacent continent is readily apparent among many plants and animals. However, the timing and maintenance of species boundaries between these distinctly different subtropical and temperate regions remains unknown for all organisms studied there. Using genome-scale data, we examine the timing of origins, gene flow, and the movement of genes under selection in unique ecoregions within the North American racers (Coluber constrictor). Isolation-migration models along with tests of genome-wide selection, locus-environment associations, and spatial and genomic clines demonstrate that two unrecognized species are present and are in contact at the boundary of these two ecoregions. We show that selection at several loci associated with unique environments have maintained species boundaries despite constant levels of gene flow between these lineages over thousands of generations. This research provides a new avenue of research to examine speciation processes in poorly studied biodiversity hotspots.

Differentiation and Taxonomic Identification of Roburoid Oaks in the Caucasian and Crimean Regions Using Nuclear Microsatellite Markers

The inter- and intra-specific structure of genetic variability was studied using 18 microsatellite loci (nSSRs) in closely related roburoid oaks in the Crimean-Caucasian region.The seven most widespread Quercus taxa in the region were studied in 29 morphologically pure populations from different parts of the North Caucasus, Transcaucasia, Crimea and northeastern Europe. Most taxa were studied using nSSR markers for the first time. Among the 492 trees studied, Bayesian clustering method implemented in STRUCTURE identified clusters corresponding to the pedunculate oak Quercus robur, the Hartwiss oak Q. hartwissiana, the Caucasian oak Q. macranthera, the downy oak Q. pubescens and three subspecies of sessile oak: Q. petraea ssp. petraea, Q. petraea ssp. iberica, Q. petraea ssp. medwediewii. Geographic structure was identified within Q. robur, Q. pubescens and Q. p. ssp. petraea. The 18 nSSR loci used are efficient in the taxonomic assignment of individuals, and identifying hybrids. The close relationship between the “long-pedunculate” roburoid oaks (Q. robur and Q. hartwissiana) is shown, with a greater difference from other species. For one of the subspecies of sessile oak, widespread in the North Caucasus and Crimea Q. petraea ssp. medwediewii (syn. Q. calcarea), or limestone oak, significant differences from other taxa were found, reaching the species level. The assumption of a possible hybrid origin of this taxon as a result of hybridization of Q. petraea and Q. pubescens is not confirmed by genetic analysis. The other two subspecies of Q. petraea (Q. p. ssp. petraea and Georgian oak Q. p. ssp. iberica) are differentiated to a lesser extent and are related to each other, which confirms the legitimacy of distinguishing two geographically isolated taxa at the rank of subspecies. The highest variability was observed in Q. pubescens (He = 0.777). In Q. p. ssp. medwediewii variability was lower than in other widespread taxa (He = 0.652), and was approximately at the level of variability of Q. hartwissiana (He = 0.633) and Q. macranthera (He = 0.659). Clear differentiation of taxa by nuclear markers shows the limited introgression in closely related oak species in the Caucasus and Crimea. The identified genetic clusters can be used as reference groups for further population genetic studies of oaks in the Crimean-Caucasian region.

Cross-amplification of microsatellite markers on the endangered tree species Castanopsis argentea from other Castanopsis species: a valuable tool for genetic diversity analysis

Castanopsis argentea is an endangered tree naturally distributed in Java and Sumatera Island and considered a keystone species in the submontane forest ecosystem. A laboratory study was conducted to test the cross-amplification potential of seven pairs of Castanopsis cuspidata var. sieboldii microsatellite markers to be used for Castanopsis argentea. The rate of cross-amplification success, average number of alleles per locus (NA ), observed heterozygosity (HO ), expected heterozygosity (HE ), and fixation index (FIS ) were determined, and cross-amplification potential was investigated. The rate of amplification success was 85.71% (6 out of 7 markers were successful amplified), NA was 7.67, HO ranged from 0.467 to 0.923, HE ranged from 0.441 to 0.745, and the fixation index (FIS ) ranged from −0.413 to 0.278. Results indicate the high transferability of C. cuspidata var. sieboldii microsatellite markers to C. argentea. Six markers were suitable for genetic diversity and population genetic studies on C. argentea.

Genetic Polymorphism of Y-Chromosome in Turkmen Population from Turkmenistan.

This study investigates the Y-chromosome genetic diversity of the Turkmen population in Turkmenistan, analyzing 23 Y-STR loci for the first time in a sample of 100 individuals. Combined with comparative data from Turkmen populations in Afghanistan, Iran, Iraq, Russia, and Uzbekistan, this analysis offers insights into the genetic structure and relationships among Turkmen populations across regions across Central Asia and the Near East. High haplotype diversity in the Turkmen of Turkmenistan is shaped by founder effects (lineage expansions) from distinct haplogroups, with haplogroups Q and R1a predominating. Subhaplogroups Q1a and Q1b identified in Turkmenistan trace back to ancient Y-chromosome lineages from the Bronze Age. Comparative analyses, including genetic distance (RST), median-joining network, and multidimensional scaling (MDS), highlight the genetic proximity of the Turkmen in Turkmenistan to those in Afghanistan and Iran, while Iraqi Turkmen display unique characteristics, aligning with Near Eastern populations. This study underscores the Central Asian genetic affinity across most Turkmen populations. It demonstrates the value of deep-sequencing Y-chromosome data in tracing the patrilineal history of Central Asia for future studies. These findings contribute to a more comprehensive understanding of Turkmen genetic ancestry and add new data to the ongoing study of Central Asian population genetics.

Comparative Chloroplast Genome Study of Zingiber in China Sheds Light on Plastome Characterization and Phylogenetic Relationships.

Zingiber Mill., a morphologically diverse herbaceous perennial genus of Zingiberaceae, is distributed mainly in tropical to warm-temperate Asia. In China, species of Zingiber have crucial medicinal, edible, and horticultural values; however, their phylogenetic relationships remain unclear. To address this issue, the complete plastomes of the 29 Zingiber accessions were assembled and characterized. Comparative plastome analysis and phylogenetic analysis were conducted to develop genomic resources and elucidate the intraspecific phylogeny of Zingiber. The newly reported plastomes ranged from 161,495 to 163,880 bp in length with highly conserved structure. Results of comparative analysis suggested that IR expansions/contractions and changes of repeats were the main reasons that influenced the genome size of the Zingiber plastome. A large number of SSRs and six highly variable regions (rpl20, clpP, ycf1, petA-psbJ, rbcL-accD, and rpl32-trnL) have been identified, which could serve as potential DNA markers for future population genetics or phylogeographic studies on this genus. The well-resolved plastome phylogeny suggested that Zingiber could be divided into three clades, corresponding to sect. Pleuranthesis (sect. Zingiber + sect. Dymczewiczia) and sect. Cryptanthium. Overall, this study provided a robust phylogeny of Zingiber plants in China, and the newly reported plastome data and plastome-derived markers will be of great significance for the accurate identification, protection, and agricultural management of Zingiber resources in the future.

The Genomic SSR Millets Database (GSMDB): enhancing genetic resources for sustainable agriculture.

The global population surge demands increased food production and nutrient-rich options to combat rising food insecurity. Climate-resilient crops are vital, with millets emerging as superfoods due to nutritional richness and stress tolerance. Given limited genomic information, a comprehensive genetic resource is crucial to advance millet research. Whole-genome sequencing provides an unprecedented opportunity, and molecular genetic methodologies, particularly simple sequence repeats (SSRs), play a pivotal role in DNA fingerprinting, constructing linkage maps, and conducting population genetic studies. SSRs are composed of repetitive DNA sequences where one to six nucleotides are repeated in tandem and distributed throughout the genome. Different millet species exhibit genomic variations attributed to the presence of SSRs. While SSRs have been identified in a few millet species, the existing information only covers some of the sequenced genomes. Moreover, there is an absence of complete gene annotation and visualization features for SSRs. Addressing this disparity and leveraging the de-novo millet genome assembly available from the NCBI, we have developed the Genomic SSR Millets Database (GSMDB; https://bioinfo.icgeb.res.in/gsmdb/). This open-access repository provides a web-based tool offering search functionalities and comprehensive details on 6.747645 million SSRs mined from the genomic sequences of seven millet species. The database, featuring unrestricted public access and JBrowse visualization, is a pioneering resource for the research community dedicated to advancing millet cultivars and related species. GSMDB holds immense potential to support myriad studies, including genetic diversity assessments, genetic mapping, marker-assisted selection, and comparative population investigations aiming to facilitate the millet breeding programs geared toward ensuring global food security. Database URL: https://bioinfo.icgeb.res.in/gsmdb/.

What are microsatellites and how to choose the best tool: a user-friendly review of SSR and 74 SSR mining tools.

Microsatellites, also known as SSR or STR, are essential molecular markers in genomic research, playing crucial roles in genetic mapping, population genetics, and evolutionary studies. Their applications range from plant breeding to forensics, highlighting their diverse utility across disciplines. Despite their widespread use, traditional methods for SSR analysis are often laborious and time-consuming, requiring significant resources and expertise. To address these challenges, a variety of computational tools for SSR analysis have been developed, offering faster and more efficient alternatives to traditional methods. However, selecting the most appropriate tool can be daunting due to rapid technological advancements and the sheer number of options available. This study presents a comprehensive review and analysis of 74 SSR tools, aiming to provide researchers with a valuable resource for SSR analysis tool selection. The methodology employed includes thorough literature reviews, detailed tool comparisons, and in-depth analyses of tool functionality. By compiling and analyzing these tools, this study not only advances the field of genomic research but also contributes to the broader scientific community by facilitating informed decision-making in the selection of SSR analysis tools. Researchers seeking to understand SSRs and select the most appropriate tools for their projects will benefit from this comprehensive guide. Overall, this study enhances our understanding of SSR analysis tools, paving the way for more efficient and effective SSR research in various fields of study.