Estimates Of Diversity Research Articles

Nascent evolution of recombination rate differences as a consequence of chromosomal rearrangements.

Reshuffling of genetic variation occurs both by independent assortment of chromosomes and by homologous recombination. Such reshuffling can generate novel allele combinations and break linkage between advantageous and deleterious variants which increases both the potential and the efficacy of natural selection. Here we used high-density linkage maps to characterize global and regional recombination rate variation in two populations of the wood white butterfly (Leptidea sinapis) that differ considerably in their karyotype as a consequence of at least 27 chromosome fissions and fusions. The recombination data were compared to estimates of genetic diversity and measures of selection to assess the relationship between chromosomal rearrangements, crossing over, maintenance of genetic diversity and adaptation. Our data show that the recombination rate is influenced by both chromosome size and number, but that the difference in the number of crossovers between karyotypes is reduced as a consequence of a higher frequency of double crossovers in larger chromosomes. As expected from effects of selection on linked sites, we observed an overall positive association between recombination rate and genetic diversity in both populations. Our results also revealed a significant effect of chromosomal rearrangements on the rate of intergenic diversity change between populations, but limited effects on polymorphisms in coding sequence. We conclude that chromosomal rearrangements can have considerable effects on the recombination landscape and consequently influence both maintenance of genetic diversity and efficiency of selection in natural populations.

Occurrence of Some Freshwater Rotifers from Visapur Dam, Ahmednagar, Maharashtra, India

Rotifers from a reservoir (Vispaur Dam, Ahmednagar, Maharashtra) were studied for a period of seven months. Samples were collected using a 50-micron mesh size plankton net, preserved in 4% formalin and identified under a compound microscope using standard rotifer literature. Nineteen species belonging to 9 families were seen in the studied samples, with family Brachionidae being species rich with 9 species. The genus Brachionus was well represented with 5 species. The results are compared with studies done on rotifers from reservoirs all over Maharashtra state. Detailed studies in the future are required for more exact estimate of rotifer diversity. Detailed studies in future will add to the checklist of rotifers from the studied waterbody.

Strong purifying selection in haploid tissue-specific genes of Scots pine supports the masking theory.

The masking theory states that genes expressed in haploid stage will be under more efficient selection. In contrast, selection will be less efficient in genes expressed in diploid stage, where the fitness effects of recessive deleterious or beneficial mutations can be hidden from selection in heterozygous form. This difference can influence several evolutionary processes such as the maintenance of genetic variation, adaptation rate, and genetic load. Masking theory expectations have been confirmed in single-cell haploid and diploid organisms. However, in multicellular organisms, such as plants, the effects of haploid selection are not clear-cut. In plants, the great majority of studies indicating haploid selection have been carried out using male haploid tissues in angiosperms. Hence, evidence in these systems is confounded with the effects of sexual selection and intra-specific competition. Evidence from other plant groups is scarce and results show no support for the masking theory. Here we have used a gymnosperm Scots pine megagametophyte, a maternally-derived seed haploid tissue, and four diploid tissues to test the strength of purifying selection on a set of genes with tissue-specific expression. By using targeted resequencing data of those genes, we obtained estimates of genetic diversity, the site frequency spectrum of 0-fold and 4-fold sites, and inferred the distribution of fitness effects (DFE) of new mutations in haploid and diploid tissue-specific genes. Our results show that purifying selection is stronger for tissue-specific genes expressed in the haploid megagametophyte tissue, and that this signal of strong selection is not an artifact driven by high expression levels.

Implications of Qualitative Traits Diversity for Future Chickpea Improvement and Conservation

Morphological characterization and diversity estimation are essential in plant breeding. In this endeavor, the researcher performed a visual assessment of 18 phenotypic DUS listed traits of 32 Kabuli chickpea genotypes in rabi 2021-2022. Nine traits were monomorphic, four traits were dimorphic, while five traits were polymorphic. Shannon’s diversity indices were estimated using Microsoft excel. The index ranged from 0.00 to 1.06, with a mean value of 0.36. Seed size (g) obtained the highest value of the 32 genotpyes, few were unique as they could be distinguished based on a single trait, while the majority were very closely related. Cluster analysis revealed that the 32 genotypes were grouped into two major clusters—similar genotypes concerning different traits clustered in the same clusters and vice versa.

Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linkedand autosomal loci, and conduct sex assignment.

Identifying sex-linked markers in genomic datasets is important because their presence in supposedly neutral autosomal datasets can result in incorrect estimates of genetic diversity, population structure and parentage. However, detecting sex-linked loci can be challenging, and available scripts neglect some categories of sex-linked variation. Here, we present new R functions to (1) identify and separate sex-linked loci in ZW and XY sex determination systems and (2) infer the genetic sex of individuals based on these loci. We tested these functions on genomic data for two bird and one mammal species and compared the biological inferences made before and after removing sex-linked loci using our function. We found that our function identified autosomal loci with ≥98.8% accuracy and sex-linked loci with an average accuracy of 87.8%. We showed that standard filters, such as low read depth and call rate, failed to remove up to 54.7% of sex-linked loci. This led to (i) overestimation of population FIS by up to 24%, and the number of private alleles by up to 8%; (ii) wrongly inferring significant sex differences in heterozygosity; (iii) obscuring genetic population structure and (iv) inferring ~11% fewer correct parentages. We discuss how failure to remove sex-linked markers can lead to incorrect biological inferences (e.g. sex-biased dispersal and cryptic population structure) and misleading management recommendations. For reduced-representation datasets with at least 15 known-sex individuals of each sex, our functions offer convenient resources to remove sex-linked loci and to sex the remaining individuals (freely available at https://github.com/drobledoruiz/conservation_genomics).

VariantscanR: an R-package as a clinical tool for variant filtering of known phenotype-associated variants in domestic animals

BackgroundSince the introduction of next-generation sequencing (NGS) techniques, whole-exome sequencing (WES) and whole-genome sequencing (WGS) have not only revolutionized research, but also diagnostics. The gradual switch from single gene testing to WES and WGS required a different set of skills, given the amount and type of data generated, while the demand for standardization remained. However, most of the tools currently available are solely applicable for human analysis because they require access to specific databases and/or simply do not support other species. Additionally, a complicating factor in clinical genetics in animals is that genetic diversity is often dangerously low due to the breeding history. Combined, there is a clear need for an easy-to-use, flexible tool that allows standardized data processing and preferably, monitoring of genetic diversity as well. To fill these gaps, we developed the R-package variantscanR that allows an easy and straightforward identification and prioritization of known phenotype-associated variants identified in dogs and other domestic animals.ResultsThe R-package variantscanR enables the filtering of variant call format (VCF) files for the presence of known phenotype-associated variants and allows for the estimation of genetic diversity using multi-sample VCF files. Next to this, additional functions are available for the quality control and processing of user-defined input files to make the workflow as easy and straightforward as possible. This user-friendly approach enables the standardisation of complex data analysis in clinical settings.ConclusionWe developed an R-package for the identification of known phenotype-associated variants and calculation of genetic diversity.

Estimation of Species Diversity and Carbon Storage in 5-, 15- and 22-year-old Mango Agroforest (Cameroon)

Estimation of Species Diversity and Carbon Storage in 5-, 15- and 22-year-old Mango Agroforest (Cameroon)

Mayfly Larvae (Ephemeroptera) in Thailand: Diversity and Science Communication

Mayflies (Ephemeroptera) are one of the most common components of aquatic assemblages in freshwater environments and contribute to ecosystem services. Mayflies have been widely used as indicators of water quality and frequently play an important role in biomonitoring protocols. Mayflies exhibit a decrease in taxa richness with increases in stream or river pollution and degradation. A series of taxonomic studies on Thai mayflies reported 19 families, 73 genera, and approximately 176 species. The families Baetidae and Heptageniidae are the most diverse and widespread groups of Thai mayflies. Our understanding of the diversity of Thai mayflies has steadily increased in recent years. New genera are being described: Cymbalcloeon Suttinun, Gattolliat & Boonsoong, 2020; Elatosara Malzacher, 2020; Megabranchiella Phlai-ngam & Tungpairojwong, 2022; Mekongellina Malzacher, 2019; Sangpradubina Boonsoong & Sartori, 2016; and Thainis Malzacher, 2020. New species and new country records are constantly being discovered in Thailand. Nevertheless, the number of genera and species seems to be lower than the species diversity estimation, and several genera and species remain undescribed. Research on the systematics and ecology of mayflies has been increasing in recent years. DNA barcoding can provide a powerful supplement to the traditional morphological approach to species delimitation. The book entitled “Mayfly Larvae in Thailand” (Thai version) and the boardgame “Thai Mayflies” were developed for environmental science communication. Further efforts are required to assess the conservation status of mayfly species. Thus, data on mayfly diversity and ecological requirements could be used as tools to evaluate environmental impacts on water resources and to drive future research on biodiversity conservation management strategies.

Uncovering the hidden: Leveraging sub-pixel spectral diversity to estimate plant diversity from space

Remotely sensed spectral diversity has emerged as a promising proxy for plant diversity. However, spectral diversity approaches relate image spectra to plant community diversity by only incorporating variation among adjacent pixels, considering each pixel as a homogeneous entity composed of one class, and disregarding the within-pixel variability. Although such approaches might work for remotely-sensed data with fine spatial resolution, they might not be viable solutions to estimate plant diversity using coarse-resolution data from forthcoming spaceborne imagers. To address the limitations associated with spectral diversity approaches, we proposed a novel approach, known as endmember diversity, for remote estimation of plant diversity through quantifying spectral diversity at the sub-pixel level and taking into account the within-pixel variability. The approach consisted of deriving the number and abundance of distinct spectral entities within each pixel via spectral unmixing. In doing so, we considered the spectral signature of each pixel as a mixture of distinct spectral entities, commonly known as endmembers. We then used the per-pixel endmembers and their abundance to calculate different spectral diversity metrics for every pixel. We assessed the performance of the endmember diversity approach at estimating plant taxonomic and phylogenetic diversity based on two experiments using a simulated spectral dataset and a real-world spaceborne DESIS (DLR Earth Sensing Imaging Spectrometer) dataset. In both experiments, we found significant associations between endmember diversity and in situ plant diversity. Additionally, our method applied to DESIS data outperformed a conventional spectral diversity metric based on the coefficient of variation when applied to 1-m airborne imaging spectroscopy data. Collectively, our results demonstrate the capability of forthcoming spaceborne imagers to monitor local plant diversity.

Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra- and interspecific genetic diversity in Mediterranean invertebrates.

The ability to gather genetic information using DNA metabarcoding of bulk samples obtained directly from the environment is crucial to determine biodiversity baselines and understand population dynamics in the marine realm. While DNA metabarcoding is effective in evaluating biodiversity at community level, genetic patterns within species are often concealed in metabarcoding studies and overlooked for marine invertebrates. In the present study, we implement recently developed bioinformatics tools to investigate intraspecific genetic variability for invertebrate taxa in the Mediterranean Sea. Using metabarcoding samples from Autonomous Reef Monitoring Structures (ARMS) deployed in three locations, we present haplotypes and diversity estimates for 145 unique species. While overall genetic diversity was low, we identified several species with high diversity records and potential cryptic lineages. Further, we emphasize the spatial scale of genetic variability, which was observed from locations to individual sampling units (ARMS). We carried out a population genetic analysis of several important yet understudied species, which highlights the current knowledge gap concerning intraspecific genetic patterns for the target taxa in the Mediterranean basin. Our approach considerably enhances biodiversity monitoring of charismatic and understudied Mediterranean species, which can be incorporated into ARMS surveys.

Extensive intragenomic variation in the internal transcribed spacer region of fungi

Fungi are among the most biodiverse organisms in the world. Accurate species identification is imperative for studies on fungal ecology and evolution. The internal transcribed spacer (ITS) rDNA region has been widely accepted as the universal barcode for fungi. However, several recent studies have uncovered intragenomic sequence variation within the ITS in multiple fungal species. Here, we mined the genome of 2414 fungal species to determine the prevalence of intragenomic variation and found that the genomes of 641 species, about one-quarter of the 2414 species examined, contained multiple ITS copies. Of those 641 species, 419 (∼65%) contained variation among copies revealing that intragenomic variation is common in fungi. We proceeded to show how these copies could result in the erroneous description of hundreds of fungal species and skew studies evaluating environmental DNA (eDNA) especially when making diversity estimates. Additionally, many genomes were found to be contaminated, especially those of unculturable fungi.

Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum: Nematomorpha).

In recent years, parasite conservation has become a globally significant issue. Because of this, there is a need for standardized methods for inferring population status and possible cryptic diversity. However, given the lack of molecular data for some groups, it is challenging to establish procedures for genetic diversity estimation. Therefore, universal tools, such as double-digest restriction-site-associated DNA sequencing (ddRADseq), could be useful when conducting conservation genetic studies on rarely studied parasites. Here, we generated a ddRADseq dataset that includes all 3 described Taiwanese horsehair worms (Phylum: Nematomorpha), possibly one of the most understudied animal groups. Additionally, we produced data for a fragment of the cytochrome c oxidase subunit I (COXI) for the said species. We used the COXI dataset in combination with previously published sequences of the same locus for inferring the effective population size (Ne) trends and possible population genetic structure.We found that a larger and geographically broader sample size combined with more sequenced loci resulted in a better estimation of changes in Ne. We were able to detect demographic changes associated with Pleistocene events in all the species. Furthermore, the ddRADseq dataset for Chordodes formosanus did not reveal a genetic structure based on geography, implying a great dispersal ability, possibly due to its hosts. We showed that different molecular tools can be used to reveal genetic structure and demographic history at different historical times and geographical scales, which can help with conservation genetic studies in rarely studied parasites.

Assessing the environmental impact of diet – Influence of using different databases of foods' environmental footprints

Current food systems compromise many environmental impact boundaries, and a dietary transition towards sustainable dietary patterns is needed. The definition of policies to promote the dietary transition implies accurate knowledge of dietary choices' environmental impact. For its assessment, life cycle assessment (LCA) has been employed, but methodological heterogeneity and limited access to LCA data hinder comprehensive comparisons. Several publicly accessible standardized foods’ environmental impact databases have been developed to address these challenges. However, variations in indicators included and data sources raise questions about their impact on assessing dietary environmental footprints and the correlation amid various indicators within and between databases. This study aims to evaluate the effect of using different public-access food LCA databases on estimating the individual dietary environmental impact in a nationally representative survey through multiple indicators as well as the correlations between them.Food-specific environmental impact indicators data from three databases (Poore&Nemececk, SHARP-ID, SU-EATABLE LIFE) were merged with individual food consumption data from the Portuguese Food, Nutrition, and Physical Activity Survey (IAN-AF, 2015–2016) (n = 5811) to estimate the usual environmental impact of diet for each indicator. Food groups' percentual contribution (%) to the environmental footprints and the Pearson correlation between indicators were also estimated.Our results showed that different databases of foods’ environmental impacts led to diverse estimates for common indicators when linked to the same food consumption data (e.g., GHGE – P50(P25–P75) SHARP-ID: 4.42(3.44–5.64)kgCO2eq, Poore&Nemececk: 6.17(4.46–8.41)kgCO2eq, SU-EATABLE LIFE: 5.64(4.26–7.36)kgCO2eq). However, except for water footprints, most indicators from all databases were highly correlated with each other, with meat and other animal-based foods as the top contributors.In conclusion, the absolute differences observed can compromise the validity of the findings and their comparability with other countries' estimates when different LCA data are used. A standardized, consolidated database covering a judicious selection of indicators across Europe along with official guidelines for assessing dietary environmental impacts would facilitate its assessment benefiting the establishment of food sustainability policies and recommendations at national and pan-European levels.

Species diversity of forest floor biota in non‐native Douglas‐fir stands is similar to that of native stands

AbstractCultivation of non‐native tree species is a promising option to adapt managed forests to climate change. However, consequences of non‐native tree species on flora, fauna, and microorganisms that occur in forest ecosystems (forest associates) need to be considered when managing forests. We lack a solid understanding of how cultivating non‐native tree species in pure stands and in mixture with native tree species impacts abundance and species diversity of forest associates. We compared abundance, alpha‐, beta‐ and gamma‐diversity of eight forest‐floor‐associated taxa that are relevant for ecosystem functioning (including fungi, plants, arthropods, and small mammals) between different forest ecosystems. We addressed pure stands of non‐native coniferous Douglas‐fir (Pseudotsuga menziesii) and two native species, broad‐leaved European beech (Fagus sylvatica) and coniferous Norway spruce (Picea abies), as well as mixed stands of European beech with each conifer in two regions with differing site conditions in temperate Northwest Germany. Diversity indices revealed differences among species groups. Gamma‐diversity and alpha‐diversity of forest associates in Douglas‐fir and spruce stands were usually higher than in beech stands. Estimates of species diversity of mixed stands are intermediate between estimates for the respective pure stands. Differences in the diversity between the two study regions were highly taxon specific with no clear support for a general trend toward a higher or lower species diversity of forest associates depending on site quality. Abundance values show a pattern similar to our diversity estimates, but with a higher statistical uncertainty. Non‐native Douglas‐fir stands provided habitats to support associated species communities of equally high or higher diversity than stands of native beech or spruce. Mixed stands of non‐native and native tree species may be a management option to achieve different goals, that is, to provide habitats for species that are strictly associated with beech and to increase resilience to climate change. However, the overall diversity of forest‐floor‐associated biota is not improved by cultivating Douglas‐fir or spruce in mixture with beech.

Complete Chloroplast Genomes of Pterodon emarginatus Vogel and Pterodon pubescens Benth: Comparative and Phylogenetic Analyses.

The species Pterodon emarginatus and P. pubescens, popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity. Considering that the chloroplast genome exhibits a conserved structure and genes, the analysis of its sequences can contribute to the understanding of evolutionary, phylogenetic, and diversity issues. The chloroplast genomes of P. emarginatus and P. pubescens were sequenced on the Illumina MiSeq platform. The genomes were assembled based on the de novo strategy. We performed the annotation of the genes and the repetitive regions of the genomes. The nucleotide diversity and phylogenetic relationships were analyzed using the gene sequences of these species and others of the Leguminosae family, whose genomes are available in databases. The complete chloroplast genome of P. emarginatus is 159,877 bp, and that of P. pubescens is 159,873 bp. The genomes of both species have circular and quadripartite structures. A total of 127 genes were predicted in both species, including 110 single-copy genes and 17 duplicated genes in the inverted regions. 141 microsatellite regions were identified in P. emarginatus and 140 in P. pubescens. The nucleotide diversity estimates of the gene regions in twenty-one species of the Leguminosae family were 0.062 in LSC, 0.086 in SSC, and 0.036 in IR. The phylogenetic analysis demonstrated the proximity between the genera Pterodon and Dipteryx, both from the clade Dipterygeae. Ten pairs of primers with potential for the development of molecular markers were designed. The genetic information obtained on the chloroplast genomes of P. emarginatus and P. pubescens presented here reinforces the similarity and evolutionary proximity between these species, with a similarity percentage of 99.8%.

A novel approach to T-cell receptor beta chain (TCRB) repertoire encoding using lossless string compression.

T-cell receptor beta chain (TCRB) repertoires are crucial for understanding immune responses. However, their high diversity and complexity present significant challenges in representation and analysis. The main motivation of this study is to develop a unified and compact representation of a TCRB repertoire that can efficiently capture its inherent complexity and diversity and allow for direct inference. We introduce a novel approach to TCRB repertoire encoding and analysis, leveraging the Lempel-Ziv 76 algorithm. This approach allows us to create a graph-like model, identify-specific sequence features, and produce a new encoding approach for an individual's repertoire. The proposed representation enables various applications, including generation probability inference, informative feature vector derivation, sequence generation, a new measure for diversity estimation, and a new sequence centrality measure. The approach was applied to four large-scale public TCRB sequencing datasets, demonstrating its potential for a wide range of applications in big biological sequencing data. Python package for implementation is available https://github.com/MuteJester/LZGraphs.

An Experimental Study of Genetic Divergence in Fenugreek (Trigonella foenum-graecum L.)

A research work on genetic divergence, analysis was estimated in 75 genotypes of fenugreek (Trigonella foenum-graecum L.) grown in an Augmented Block Design during Rabi season of 2019-20 at Main Experiment Station of Department of Vegetable Science Acharya Narendra Deva University of Agriculture and Technology, Ayodhya. The objective of this study was to characterize morphological differences and yield related traits among 75 fenugreek accessions. Genetic diversity among 75 fenugreek genotypes (Trigonella foenum-graecum L.) was assessed. The estimation of genetic diversity among tested genotypes was highly significant, which got grouped into 8 clusters with cluster VI comprising maximum genotypes. Maximum intra-cluster distance (31.23) was observed in cluster V followed by cluster IV (15.51). Similarly maximum inter cluster distance was recorded between the cluster V and VIII (111.88) followed by cluster III and VIII (111.81) respectively. Although maximum cluster means for seed yield traits was recorded for cluster V and III respectively, suggesting a wide range of diversity for most of the economic traits that would enable breeder to identify the genotypes with suitable traits to be used in direct selection and also in improvement programme for broadening the genetic base. 75 accession showed distinguished variation in the dendrogram for all the studied parameters.

Genetic diversity of mtDNA in the grey wolf population of Belarus threatened by wolf-dog admixture

Hybridisation with domestic species is one of the prominent threats to conser-vation of numerous valuable species in Belarus, in particular the grey wolf (Canis lupus Linnaeus, 1758), the population of which has previously shown unusually divergent genotypes, indicating a possible admixture with free-ranging dogs (Canis lupus familiaris Linnaeus, 1758). Such admixture could threaten the future of the species already weakened by anthropogenic pressure. Reports of hybrids in Belarus based on morphological characteristics have been steadily increasing in frequency since 2010, which can be tied with a growing food availability for feral dogs and low population density of grey wolf facili-tating hybridisation. A limited number of genetic studies with sampling that partially covered Belarus did not detect any traces of hybridisation. Here we report our estimate of genetic diversity in the Belarusian population of grey wolf according to control region (D-loop) mtDNA sequence analysis. We ana-lysed tissue samples from 35 specimens harvested during legal hunts across 25 administrative districts from all 6 regions of Belarus between 2009 and 2022, with 9 of the specimens reported to have morphological characteristics of wolf–dog hybrids. We detected 6 haplotypes among those 35 specimens, 4 of which were found among the likely wolf–dog hybrids. Clade analysis of the obtained sequences with 100 confirmed sequences of wolves, dogs, and their hybrids from the NCBI Genbank database has shown the presence of possible wolf–dog hybrids in our sample. The Belarusian wolf population has shown a low nucleotide and a relatively high haplotype diversity. The discovered genet-ic diversity data of the Belarusian wolf population is mostly in line with studies of similar wolf populations across Europe. The persistence of large wolf meta-populations across Eastern Europe and Russia, combined with the high mobility of the animal, seems to be the probable cause of genetic diversity of wolf populations in Belarus, but some degree of wolf–dog hybridisation could also explain the observed genetic heterogeneity, which invites further research based on nuclear markers.

Attitude estimation in a modular plug-and-play satellite

Spacecraft modularity is a powerful design methodology for shortening satellite development cycles and reducing costs. The exploitation of standardized and reusable modules, universal interfaces and protocols, generic design, and a set of defined conventions, allows for rapidly integrating a flexible and cost-effective platform with ease of component modifications. Anyhow, the implementation of modularity poses several issues at any level of mission and spacecraft design, including subsystem design. This paper deals with the Attitude Determination and Control Subsystem (ADCS), with a particular accent on making the estimation software independent of any specific requirements dictated by the application in question. In this respect, a generic and reusable Murrell's Multiplicative Extended Kalman Filter (MMEKF) that can operate on different satellites, with diverse estimation requirements, working with changeable integrated ADCS boxes and sensor suites, but without changes either in the equations or in the interface with the rest of the system, has been proposed. The algorithm has been designed to maximize flexibility and ease of applicability to different missions without a priori-knowledge of the actual configuration. The execution of the algorithm is based on a plug-and-play logic in which middleware software enables the automatic discovery of the available sensors and the transmission of required data to the estimation algorithms. An adaptable and modular 3D simulator has been built to test and validate the performance of the generic MMEKF over multiple test cases with assigned configurations. The results of the simulations confirm the capability of the algorithm to meet estimation requirements for each simulated case, without ad-hoc, case-by-case, optimization, or customization.

DNA Fingerprinting of Crops and Its Significance in Crop Improvement

One of the improvements made possible by the era of genomics is DNA fingerprinting. DNA fingerprinting can be used to detect a variety of genetic changes. In breeding programmes fingerprinting is used to improve productivity and performance. Variety differentiation was relied on morphological characteristics prior to the introduction of genomics and proteomics approaches. Although morphological markers have been used for decades, protein-based markers like isozymes were discovered in the middle of the twentieth century and used for fingerprinting and crop genetic variety assessments. But nowadays, the emergence of genome sequencing has led to the widespread use of genetic markers for crop fingerprinting. The discovery of DNA-based genetic markers has improved genetic research. For genetic diversity estimation, crop evolution, gene mapping and phylogeny, diploid/haploid crop appraisal, heterosis analysis, varietal identification by using marker assisted selection (MAS), highly polymorphic DNA markers are generated. The use of DNA markers for crop fingerprinting started with RFLPs that did not involve PCR and subsequently advanced to PCR amplifiable markers such as AFLPs, RAPDs, SSRs, ISSRs, SNPs, and GBS.This review will provide an outlook on several types of markers and their significance in DNA fingerprinting of crops and possible applications, as well as suggestions for further research.