Selection Of Genetic Markers Research Articles

First transcriptomic insight into the working muscles of racing pigeons during a competition flight

BackgroundThe currently known homing pigeon is a result of a sharp one-sided selection for flight characteristics focused on speed, endurance, and spatial orientation. This has led to extremely well-adapted athletic phenotypes in racing birds.MethodsHere, we identify genes and pathways contributing to exercise adaptation in sport pigeons by applying next-generation transcriptome sequencing of m.pectoralis muscle samples, collected before and after a 300 km competition flight.ResultsThe analysis of differentially expressed genes pictured the central role of pathways involved in fuel selection and muscle maintenance during flight, with a set of genes, in which variations may therefore be exploited for genetic improvement of the racing pigeon population towards specific categories of competition flights.ConclusionsThe presented results are a background to understanding the genetic processes in the muscles of birds during flight and also are the starting point of further selection of genetic markers associated with racing performance in carrier pigeons.

Mitochondrial and ribosomal markers in the identification of nematodes of clinical and veterinary importance

BackgroundNematodes of the Ascarididae, Ancylostomatidae and Onchocercidae families are parasites of human and veterinary importance causing infections with high prevalence worldwide. Molecular tools have significantly improved the diagnosis of these helminthiases, but the selection of genetic markers for PCR or metabarcoding purposes is often challenging because of the resolution these may show.MethodsNuclear 18S rRNA, internal transcribed spacers 1 (ITS-1) and 2 (ITS-2), mitochondrial gene cytochrome oxidase 1 (cox1) and mitochondrial rRNA genes 12S and 16S loci were studied for 30 species of the mentioned families. Accordingly, their phylogenetic interspecies resolution, pairwise nucleotide p-distances and sequence availability in GenBank were analyzed.ResultsThe 18S rRNA showed the least interspecies resolution since separate species of the Ascaris, Mansonella, Toxocara or Ancylostoma genus were intermixed in phylogenetic trees as opposed to the ITS-1, ITS-2, cox1, 12S and 16S loci. Moreover, pairwise nucleotide p-distances were significantly different in the 18S compared to the other loci, with an average of 99.1 ± 0.1%, 99.8 ± 0.1% and 98.8 ± 0.9% for the Ascarididae, Ancylostomatidae and Onchocercidae families, respectively. However, ITS-1 and ITS-2 average pairwise nucleotide p-distances in the three families ranged from 72.7% to 87.3%, and the cox1, 12S and 16S ranged from 86.4% to 90.4%. Additionally, 2491 cox1 sequences were retrieved from the 30 analyzed species in GenBank, whereas 212, 1082, 994, 428 and 143 sequences could be obtained from the 18S, ITS-1, ITS-2, 12S and 16S markers, respectively.ConclusionsThe use of the cox1 gene is recommended because of the high interspecies resolution and the large number of sequences available in databases. Importantly, confirmation of the identity of an unknown specimen should always be complemented with the careful morphological examination of worms and the analysis of other markers used for specific parasitic groups.Graphical

Improved computations for relationship inference using low-coverage sequencing data

Pedigree inference, for example determining whether two persons are second cousins or unrelated, can be done by comparing their genotypes at a selection of genetic markers. When the data for one or more of the persons is from low-coverage next generation sequencing (lcNGS), currently available computational methods either ignore genetic linkage or do not take advantage of the probabilistic nature of lcNGS data, relying instead on first estimating the genotype. We provide a method and software (see familias.name/lcNGS) bridging the above gap. Simulations indicate how our results are considerably more accurate compared to some previously available alternatives. Our method, utilizing a version of the Lander-Green algorithm, uses a group of symmetries to speed up calculations. This group may be of further interest in other calculations involving linked loci.

Experimental validation of taxon-specific mini-barcode primers for metabarcoding of zooplankton.

Metabarcoding to determine the species composition and diversity of marine zooplankton communities is a fast-developing field in which the standardization of methods is yet to be fully achieved. The selection of genetic markers and primer choice are particularly important because they substantially influence species detection rates and accuracy. Validation is therefore an important step in the design of metabarcoding protocols. We developed taxon-specific mini-barcode primers for the cytochrome c oxidase subunit I (COI) gene region and used an experimental approach to test species detection rates and primer accuracy of the newly designed primers for prawns, shrimps and crabs and published primers for marine lobsters and fish. Artificially assembled mock communities (with known species ratios) and unsorted coastal tow-net zooplankton samples were sequenced and the detected species were compared with those seeded in mock communities to test detection rates. Taxon-specific primers increased detection rates of target taxa compared with a universal primer set. Primer cocktails (multiple primer sets) significantly increased species detection rates compared with single primer pairs and could detect up to 100% of underrepresented target taxa in mock communities. Taxon-specific primers recovered fewer false-positive or false-negative results than the universal primer. The methods used to design taxon-specific mini-barcodes and the experimental mock community validation protocols shown here can easily be applied to studies on other groups and will allow for a level of standardization among studies undertaken in different ecosystems or geographic locations.

Defining what constitutes a reliable dataset to test for hybridization and introgression in marine zooplankton: Comment on Choquet et al. 2020 “No evidence for hybridization between Calanus finmarchicus and C. glacialis in a subarctic area of sympatry”

AbstractThe article ‘No evidence for hybridization between Calanus finmarchicus and C. glacialis in a subarctic area of sympatry’ (Choquet et al. 2020) concludes that “no evidence supports a potential for hybridization between C. finmarchicus and C. glacialis”. We argue that the InDel markers used by Choquet et al. (2020) may have limited capacity to detect admixed genotypes between C. finmarchicus and C. glacialis due to an inappropriate choice of reference sample for each species during the marker development. We first review terms and concepts used in genetic classification using reference samples and describe problems associated with the selection of genetic markers in the context of possible hybridization. We reanalyze InDel genotypes provided with Choquet et al. (2017) and identified an admixed individual. We then contrast methods used by Choquet et al. (2017) and Parent et al. (2012) and explain how Parent et al. (2012) developed microsatellite markers capable of discriminating admixed genotypes from parental species. In this comment, we have identified a major issue that must be considered when selecting reference samples in the context of testing for possible hybridization.

A Review on Environmental DNA (eDNA) Metabarcoding Markers for Wildlife Monitoring Research

Environmental DNA or eDNA utilizes traceable genetic materials in the environment for monitoring the presence of organisms in a given area and it is now gaining popularity as an alternative for traditional monitoring methods. Thus, the selection of genetic markers is crucial for identification of species in wildlife monitoring. This paper aims to review several DNA markers which are appropriate and reliable for detection of organisms from the environmental samples. We performed systematic literature search from SCOPUS database to review all molecular markers of eDNA. This study focuses on the importance of markers selection which can be utilized by next-generation sequencing (NGS) for biodiversity monitoring. Cytochrome C oxidase Subunit I (COI) are noted as the most widely used marker in metabarcoding research for detection of targeted species.

Laparoscopic Ovum Pick-Up Followed by In Vitro Embryo Production and Transfer in Assisted Breeding Programs for Ruminants.

Simple SummaryIn vitro embryo production from oocytes collected by laparoscopy has the potential of producing more offspring from genetically superior females of ruminant species (e.g., sheep, goats, cervids) or ages (e.g., prepubertal cattle and buffalo) that are too small to be eligible for oocyte collection by the transvaginal ultrasound-guided method used in cows. This article reviews the multiple applications of the technology, how it is done, the pros and cons, the limitations to widespread use, and the envisioned improvements that are expected in the years to come. In small ruminants, where conventional embryo recovery is most commonly done by surgery, the technology offers a less invasive approach, i.e., more animal welfare-friendly and with minimum risks of surgical sequels. Thereby, it enables repeating the procedure in the same animals exponentially more times, resulting in the potential for an increased number of offspring born from elite donors. Furthermore, the emerging most attractive application is for the in vitro production of embryos from prepubertal animals at very young ages, which allows having progeny born from genetically superior donors before they reach the age and weight to be bred for the first time.The potential of laparoscopic ovum pick-up (LOPU) followed by in vitro embryo production (IVEP) as a tool for accelerated genetic programs in ruminants is reviewed in this article. In sheep and goats, the LOPU-IVEP platform offers the possibility of producing more offspring from elite females, as the procedure is minimally invasive and can be repeated more times and more frequently in the same animals compared with conventional surgical embryo recovery. On average, ~10 and ~14 viable oocytes are recovered by LOPU from sheep and goats, respectively, which results in 3–5 transferable embryos and >50% pregnancy rate after transfer. LOPU-IVEP has also been applied to prepubertal ruminants of 2–6 months of age, including bovine and buffalo calves. In dairy cattle, the technology has gained momentum in the past few years stemming from the development of genetic marker selection that has allowed predicting the production phenotype of dairy females from shortly after birth. In Holstein calves, we obtained an average of ~22 viable oocytes and ~20% transferable blastocyst rate, followed by >50% pregnancy rate after transfer, declaring the platform ready for commercial application. The present and future of this technology are discussed with a focus on improvements and research needed.

New approaches to the selection of genetic markers associated with multifactorial phenotypic traits

Modern approaches to searching for associations between the studied phenotype and structural variations of the human genome are analyzed. Most complex phenotypic traits, including diseases, do not follow the laws of Mendelian inheritance, but have a multi-factor nature, that is, a significant contribution to their development is made by the genetic component in combination with the influence of environmental factors. In General, there are several approaches to the design of a limited set of polymorphic markers for point genotyping. Selection of individual molecular genetic markers is carried out based on either their statistically significant Association with the studied multivariate feature, or their functional significance for the implementation of this feature. The candidate gene approach allows you to focus on one or more polymorphic variants in the region of a gene (allelic variant), the product of which is likely involved in the development of a disease or trait. The cheaper procedure for full-genome screening using ultra-high-density microchips has made available another approach for searching for genetic predispositions - full - genome Association search. We believe that the unification of both approaches into a single algorithm for the choice of molecular genetic markers to conduct point genotyping will allow for both markers selected based on a priori assumptions about the functional significance of candidate genes, and Association with the studied trait on the basis of genome-wide associations search. This approach will optimize the diagnostic efficiency of the created test suite.

Selection of nuclear microsatellite loci for specific identification of Larix gmélinii Rupr. and comparison of genetic profiles of Larix to solve agricultural problems

Preservation and study of forest plant species diversity is one of the fundamental challenges of modern botany, genetics, and dendrology. Genetic structure determines variability and controls adaptation mechanisms, letting every population adapt to environmental conditions. The most topical issue is genetic study of valuable forest species to ensure their integrity, specific identification, and control over wood origin. One of such environmentally and economically important coniferous species in our country is larch (Larix). Currently, there is a problem to use azonal larch species for reforestation in Russia, particularly in the Russian Far East. In this regard, selection of genetic markers that let us detect differences between Larix gmélinii Rupr. and Larix sibírica Ledeb. and their subspecies is a crucial and relevant task.

Sparse Representation-Based Patient-Specific Diagnosis and Treatment for Esophageal Squamous Cell Carcinoma.

Precision medicine and personalized treatment have attracted attention in recent years. However, most genetic medicines mainly target one genetic site, while complex diseases like esophageal squamous cell carcinoma (ESCC) usually present heterogeneity that involves variations of many genetic markers. Here, we seek an approach to leverage genetic data and ESCC knowledge data to forward personalized diagnosis and treatment for ESCC. First, 851 ESCC-related gene markers and their druggability were studied through a comprehensive literature analysis. Then, a sparse representation-based variable selection (SRVS) was employed for patient-specific genetic marker selection using gene expression datasets. Results showed that the SRVS method could identify a unique gene vector for each patient group, leading to significantly higher classification accuracies compared to randomly selected genes (100, 97.17, 100, 100%; permutation p values: 0.0032, 0.0008, 0.0004, and 0.0008). The SRVS also outperformed an ANOVA-based gene selection method in terms of the classification ratio. The patient-specific gene markers are targets of ESCC effective drugs, providing specific guidance for medicine selection. Our results suggest the effectiveness of integrating previous database utilizing SRVS in assisting personalized medicine selection and treatment for ESCC.

Characterization of Colistin-Resistant Escherichia coli Isolated from Diseased Pigs in France.

We studied a collection of 79 colistin-resistant Escherichia coli isolates isolated from diseased pigs in France between 2009 and 2013. We determined a number of phenotypic and genetic characters using broth microdilution to characterize their antimicrobial susceptibility. We performed pulse field gel electrophoresis (PFGE) to assess their genetic diversity and assign them to phylogroups. High-throughput real-time PCR micro-array was used to screen for a selection of genetic markers of virulence, and PCR and sequencing of the main recognized resistance genes allowed us to investigate the mechanisms of colistin resistance. Results showed that isolates belonged to several phylogroups and most had a unique PFGE profile. More than 50% of the isolates were also resistant to sulfonamides, trimethoprim, tetracycline, ampicillin or chloramphenicol. The mcr-1 gene was detected in 70 out of 79 isolates and was transferred by conjugation in 33 of them, sometimes together with resistance to sulfonamides, trimethoprim, tetracycline, ampicillin, chloramphenicol, cefotaxime, or gentamicin. Mutations in the amino-acid sequences of proteins MgrB, PhoP, PhoQ, PmrB, but not PmrA, were detected in isolates with or without the mcr-1 gene. More than one-third of the isolates harbored the F18, F4, astA, hlyA, estI, estII, elt, stx2e, iha, orfA, orfB, paa, terE, ecs1763, or ureD virulence markers. In conclusion, although most isolates had a unique PFGE profile, a few particular combinations of phylogenetic groups, virulence genes and mutations in the sequenced genes involved in colistin resistance were identified on a number of occasions, suggesting the persistence of certain isolates over several years.

Microsatellites mapping for non-model species with chromosomal rearrangement: a case study in the frog Quasipaa boulengeri (Anura: Dicroglossidae).

Gene mapping is an important resource for understanding the evolution of genes and cytogenetics. Model species with a known genetic map or genome sequence allow for the selection of genetic markers on a desired chromosome, while it is hard to locate these markers on chromosomes of non-model species without such references. A frog species, Quasipaa boulengeri, shows chromosomal rearrangement polymorphisms, making itself a fascinating model for chromosomal speciation mediated by suppressed recombination. However, no markers have been located on its rearranged chromosomes. We present a complete protocol to map microsatellites based on mechanical microdissection and chromosome amplification techniques. Following this protocol, we mapped 71 microsatellites of Q. boulengeri at the chromosome level. In total, eight loci were assigned to rearranged chromosomes, and the other 63 loci might attach to other chromosomes. These microsatellites could be used to compare the gene flow and verify the chromosomal suppressed recombination hypothesis in Q. boulengeri. This integrated protocol could be effectively used to map genes to chromosomes for non-model species.

Selection of Genetic Markers to Determine Diversity in Theileria annulata Populations after Recombination.

Selecting polymorphic mini- and microsatellite markers to determine genetic diversity and chromosomal regions exhibiting elevated rates of recombination in Theileria annulata populations after recombination. The Unipro UGENE software was used to select markers. A score at which 10 times more tandem repeats (TRs) were identified in the real DNA sequence than those in the scrambled sequences of T. annulata was used as the cutoff. TRs containing minimum three nucleotides in length for microsatellite and six nucleotides for minisatellite regions and having a repeat motif identity between 96%-100% with the unit size repeated minimum three times were screened through the whole genome using the suffix array algorithm. A total of 359 minisatellites and 8973 microsatellites were identified. TRs were screened one by one through the whole genome; mini- and microsatellites representing a single region and having suitable regions for primer design were selected based on their localization on T. annulata chromosomes, their repeat motif identity (>96%), and their repeat length (<1500 bp). The primers used to amplify selected candidates were designed, and each primer was used to check 27 different isolates of T. annulata. In the present study, a total of 13 polymorphic mini- and microsatellite markers located on the different chromosomes were selected to determine the population diversity of T. annulata.

Biclustering strategies for genetic marker selection in gynecologic tumor cell lines.

Over the past few decades great interest has been focused on cell lines derived from tumors, because of their usability as models to understand the biology of cancer. At the same time, advanced technologies such as DNA-microarrays have been broadly used to study the expression level of thousands of genes in primary tumors or cancer cell lines in a single experiment. Results from microarray analysis approaches have provided valuable insights into the underlying biology and proven useful for tumor classification, prognostication and prediction. Our approach utilizes biclustering methods for the discovery of genes with coherent expression across a subset of conditions (cell lines of a tumor type). More specifically, we present a novel modification on Cheng & Church's algorithm that searches for differences across the studied conditions, but also enforces consistent intensity characteristics of each cluster within each condition. The application of this approach on a gynecologic panel of cell lines succeeds to derive discriminant groups of compact bi-clusters across four types of tumor cell lines. In this form, the proposed approach is proven efficient for the derivation of tumor-specific markers.

Критерии отбора генетических маркеров для анализа предрасположенности к многофакторным фенотипическим особенностям

Критерии отбора генетических маркеров для анализа предрасположенности к многофакторным фенотипическим особенностям

A practical toolbox for design and analysis of landscape genetics studies

Landscape genetics integrates theory and analytical methods of population genetics and landscape ecology. Research in this area has increased in recent decades, creating a plethora of options for study design and analysis. Here we present a practical toolbox for the design and analysis of landscape genetics studies following a seven-step framework: (1) define the study objectives, (2) consider the spatial and temporal scale of the study, (3) design a sampling regime, (4) select a genetic marker, (5) generate genetic input data, (6) generate spatial input data, and (7) choose an analytical method that integrates genetic and spatial data. Study design considerations discussed include choices of spatial and temporal scale, sample size and spatial distribution, and genetic marker selection. We present analytical methods suitable for achieving different study objectives. As emerging technologies generate genetic and spatial data sets of increasing size, complexity, and resolution, landscape geneticists are challenged to execute hypothesis-driven research that combines empirical data and simulation modeling. The landscape genetics framework presented here can accommodate new design considerations and analyses, and facilitate integration of genetic and spatial data by guiding new landscape geneticists through study design, implementation, and analysis.

Jumping on the Train of Personalized Medicine: A Primer for Non-Geneticist Clinicians: Part 2. Fundamental Concepts in Genetic Epidemiology

With the decrease in sequencing costs, personalized genome sequencing will eventually become common in medical practice. We therefore write this series of three reviews to help non-geneticist clinicians to jump into the fast-moving field of personalized medicine. In the first article of this series, we reviewed the fundamental concepts in molecular genetics. In this second article, we cover the key concepts and methods in genetic epidemiology including the classification of genetic disorders, study designs and their implementation, genetic marker selection, genotyping and sequencing technologies, gene identification strategies, data analyses and data interpretation. This review will help the reader critically appraise a genetic association study. In the next article, we will discuss the clinical applications of genetic epidemiology in the personalized medicine area.

Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency.

The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index (FST) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu’s inbred populations. Inbreeding values (FIS) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity (HE) or FST, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, FST and D-scores were used. Only 6 to 8 markers ranking HE, FST or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, FST and allelic number of close lineage populations.

The Economic Value of Improvements in Beef Tenderness by Genetic Marker Selection

A genetic simulation model is combined with an economic model of the U.S. beef industry to determine how consumer demand shifts, resulting from bull and heifer selection strategies that improve steak tenderness, affect economic profitability at four points in the beef supply chain. The results indicate that a selection strategy in which bulls in the upper 30% of genetic merit are selected each year would result in increased profitability of $9.60/head for feeder cattle and $1.23/head for fed cattle in 20 years. The net present value of the genetic improvement program is estimated to produce economic benefits of $7.6 billion.

P238 Identification of Beijing strain of Mycobacterium tuberculosis super family in pulmonary tuberculosis patients with culture positive specimens with multiplex PCR

A selection of genetic markers was used to study the evolution of Mycobacterium tuberculosis Beijing family strains in northwestern Russia. A total of 221 of 434 epidemiologically unlinked isolates studied in 1996–2001 belonged to the Beijing family as determined by standard spoligotyping (signals 35–43). Ninety-six percent of these Beijing isolates (“typical”) were closely related in IS6110-RFLP (D > 0.85) while 9 remaining isolates (2 different profiles, “atypical”) were more distant from the rest (D = 0.6–0.7). Further analysis was performed on a selection of 12 typical and both atypical Beijing strains with different IS6110-RFLP profiles (2 isolates each). All 28 Beijing isolates studied had the KatG 463Leu allele, an intact mtp40 fragment of the mpcA gene, and an identical structure of the DR locus (15 DVRs) with an upstream IS6110 copy in opposite orientation. The IS6110-RFLP based neighbor-joining (distance) and quartet-puzzling (maximum-likelihood) trees showed that the branch lengths were considerably longer for atypical Beijing strains. Typical Beijing strains had the 1.02 kb Rv3135 PPE-family gene and two IS1547 copies (iplA and iplB), one of them (iplB) disrupted by IS6110 insertion. Atypical Beijing strains had the 1.97 kb Rv3135 gene and a single intact IS1547/iplA copy. We suggest that the M. tuberculosis Beijing family strains currently circulating in the northwest of Russia are relatively ancient and thus appear to be endemic in this region since evolutionarily distant time. The prevalent typical Beijing strains (96%) are likely to be of monophyletic origin and their ongoing dissemination has started recently: these strains differ in rapidly evolving IS6110-RFLP but have identical structure of other polymorphic genome regions studied. The atypical Beijing strains (4%) are evolutionary older; they probably had a common (unknown) ancestor with typical Beijing strains.