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Population Genetic Considerations for Using Biobanks As International
Carress et al. BMC Genomics (2021) 22:351 https://doi.org/10.1186/s12864-021-07618-x REVIEW Open Access Population genetic considerations for using biobanks as international resources in the pandemic era and beyond Hannah Carress1, Daniel John Lawson2 and Eran Elhaik1,3* Abstract The past years have seen the rise of genomic biobanks and mega-scale meta-analysis of genomic data, which promises to reveal the genetic underpinnings of health and disease. However, the over-representation of Europeans in genomic studies not only limits the global understanding of disease risk but also inhibits viable research into the genomic differences between carriers and patients. Whilst the community has agreed that more diverse samples are required, it is not enough to blindly increase diversity; the diversity must be quantified, compared and annotated to lead to insight. Genetic annotations from separate biobanks need to be comparable and computable and to operate without access to raw data due to privacy concerns. Comparability is key both for regular research and to allow international comparison in response to pandemics. Here, we evaluate the appropriateness of the most common genomic tools used to depict population structure in a standardized and comparable manner. The end goal is to reduce the effects of confounding and learn from genuine variation in genetic effects on phenotypes across populations, which will improve the value of biobanks (locally and internationally), increase the accuracy of association analyses and inform developmental efforts. Keywords: Bioinformatics, Population structure, Population stratification bias, Genomic medicine, Biobanks Background individuals, families, communities and populations, ne- Association studies aim to detect whether genetic vari- cessitated genomic biobanks. -
Horizontal Gene Transfer
Genetic Variation: The genetic substrate for natural selection Horizontal Gene Transfer Dr. Carol E. Lee, University of Wisconsin Copyright ©2020; Do not upload without permission What about organisms that do not have sexual reproduction? In prokaryotes: Horizontal gene transfer (HGT): Also termed Lateral Gene Transfer - the lateral transmission of genes between individual cells, either directly or indirectly. Could include transformation, transduction, and conjugation. This transfer of genes between organisms occurs in a manner distinct from the vertical transmission of genes from parent to offspring via sexual reproduction. These mechanisms not only generate new gene assortments, they also help move genes throughout populations and from species to species. HGT has been shown to be an important factor in the evolution of many organisms. From some basic background on prokaryotic genome architecture Smaller Population Size • Differences in genome architecture (noncoding, nonfunctional) (regulatory sequence) (transcribed sequence) General Principles • Most conserved feature of Prokaryotes is the operon • Gene Order: Prokaryotic gene order is not conserved (aside from order within the operon), whereas in Eukaryotes gene order tends to be conserved across taxa • Intron-exon genomic organization: The distinctive feature of eukaryotic genomes that sharply separates them from prokaryotic genomes is the presence of spliceosomal introns that interrupt protein-coding genes Small vs. Large Genomes 1. Compact, relatively small genomes of viruses, archaea, bacteria (typically, <10Mb), and many unicellular eukaryotes (typically, <20 Mb). In these genomes, protein-coding and RNA-coding sequences occupy most of the genomic sequence. 2. Expansive, large genomes of multicellular and some unicellular eukaryotes (typically, >100 Mb). In these genomes, the majority of the nucleotide sequence is non-coding. -
Genetic Recombination Promote Genetic Diversity in Prokaryotes
CAMPBELL TENTH BIOLOGY EDITION Reece • Urry • Cain • Wasserman • Minorsky • Jackson 27 Bacteria and Archaea Lecture Presentation by Nicole Tunbridge and Kathleen Fitzpatrick © 2014 Pearson Education, Inc. Masters of Adaptation . Utah’s Great Salt Lake can reach a salt concentration of 32% . Its pink color comes from living prokaryotes © 2014 Pearson Education, Inc. Figure 27.1 © 2014 Pearson Education, Inc. Prokaryotes thrive almost everywhere, including places too acidic, salty, cold, or hot for most other organisms . Most prokaryotes are microscopic, but what they lack in size they make up for in numbers . There are more in a handful of fertile soil than the number of people who have ever lived . Prokaryotes are divided into two domains: bacteria and archaea © 2014 Pearson Education, Inc. Concept 27.1: Structural and functional adaptations contribute to prokaryotic success . Earth’s first organisms were likely prokaryotes . Most prokaryotes are unicellular, although some species form colonies . Most prokaryotic cells are 0.5–5 µm, much smaller than the 10–100 µm of many eukaryotic cells . Prokaryotic cells have a variety of shapes . The three most common shapes are spheres (cocci), rods (bacilli), and spirals © 2014 Pearson Education, Inc. Figure 27.2 1 µm 1 µm 3 µm (a) Spherical (b) Rod-shaped (c) Spiral © 2014 Pearson Education, Inc. Figure 27.2a 1 µm (a) Spherical © 2014 Pearson Education, Inc. Figure 27.2b 1 µm (b) Rod-shaped © 2014 Pearson Education, Inc. Figure 27.2c 3 µm (c) Spiral © 2014 Pearson Education, Inc. Cell-Surface Structures . An important feature of nearly all prokaryotic cells is their cell wall, which maintains cell shape, protects the cell, and prevents it from bursting in a hypotonic environment . -
Development of Novel SNP Assays for Genetic Analysis of Rare Minnow (Gobiocypris Rarus) in a Successive Generation Closed Colony
diversity Article Development of Novel SNP Assays for Genetic Analysis of Rare Minnow (Gobiocypris rarus) in a Successive Generation Closed Colony Lei Cai 1,2,3, Miaomiao Hou 1,2, Chunsen Xu 1,2, Zhijun Xia 1,2 and Jianwei Wang 1,4,* 1 The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China; [email protected] (L.C.); [email protected] (M.H.); [email protected] (C.X.); [email protected] (Z.X.) 2 University of Chinese Academy of Sciences, Beijing 100049, China 3 Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510663, China 4 National Aquatic Biological Resource Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China * Correspondence: [email protected] Received: 10 November 2020; Accepted: 11 December 2020; Published: 18 December 2020 Abstract: The complex genetic architecture of closed colonies during successive passages poses a significant challenge in the understanding of the genetic background. Research on the dynamic changes in genetic structure for the establishment of a new closed colony is limited. In this study, we developed 51 single nucleotide polymorphism (SNP) markers for the rare minnow (Gobiocypris rarus) and conducted genetic diversity and structure analyses in five successive generations of a closed colony using 20 SNPs. The range of mean Ho and He in five generations was 0.4547–0.4983 and 0.4445–0.4644, respectively. No significant differences were observed in the Ne, Ho, and He (p > 0.05) between the five closed colony generations, indicating well-maintained heterozygosity. -
A Mechanism for Genetic Recombination Generating One Parent and One Recombinant* by Thierry Boon and Norton D
A MECHANISM FOR GENETIC RECOMBINATION GENERATING ONE PARENT AND ONE RECOMBINANT* BY THIERRY BOON AND NORTON D. ZINDER ROCKEFELLER UNIVERSITY, NEW YORK Communicated August 18, 1969 Abstract.-A mechanism is proposed for generating one parental and one re- combinant genome in a single recombination event between two DNA mole- cules. Three stages of the event are described: initiation, replication, and re- turn. Initiation requires breakage and joining of strands. Replication pro- ceeds through a biparental "replication fork" generated in initiation. Return also involves breakage and joining of strands. Some of the implications of such a mechanism for genetic recombination are discussed. Introduction.-We have undertaken a study of the products of recombination of bacteriophage fil under conditions in which the parental genomes cannot replicate in the cell prior to recombination. The results obtained suggest that the products of one recombination event between two parental genomes are one parental genome and one recombinant genome. Previous studies of genetic recombination in bacteriophage did not demon- strate a correlation between the yields of reciprocal recombinants produced in single cells.2-5 Similarly, recombination between closely linked markers is often nonreciprocal in Neurospora and other fungi.6' 7 Although the results with phage f, are still preliminary, we wish to propose a mechanism of recom- bination having main features that are compatible with such nonreciprocal events. This mechanism involves breakage and joining of DNA strands and also requires DNA synthesis. Description of the Mechanism. -The DNA of phage f1 (similar to M13 and fd) is single stranded and circular.8 It has a molecular weight of about 1.7 X 106.9 After entrance into the host cell this DNA is transformed into a circular double-stranded form.10' 11 As the mechanism to be proposed is primarily aimed at understanding the recombina- tion events in phage fl, we describe it, using two double-stranded circular DNA molecules as parents. -
Genetic Linkage Analysis
BASIC SCIENCE SEMINARS IN NEUROLOGY SECTION EDITOR: HASSAN M. FATHALLAH-SHAYKH, MD Genetic Linkage Analysis Stefan M. Pulst, MD enetic linkage analysis is a powerful tool to detect the chromosomal location of dis- ease genes. It is based on the observation that genes that reside physically close on a chromosome remain linked during meiosis. For most neurologic diseases for which the underlying biochemical defect was not known, the identification of the chromo- Gsomal location of the disease gene was the first step in its eventual isolation. By now, genes that have been isolated in this way include examples from all types of neurologic diseases, from neu- rodegenerative diseases such as Alzheimer, Parkinson, or ataxias, to diseases of ion channels lead- ing to periodic paralysis or hemiplegic migraine, to tumor syndromes such as neurofibromatosis types 1 and 2. Arch Neurol. 1999;56:667-672 With the advent of new genetic markers tin gene, diagnosis using flanking mark- and automated genotyping, genetic map- ers requires the analysis of several family ping can be conducted extremely rap- members. idly. Genetic linkage maps have been gen- erated for the human genome and for LINKAGE OF GENES model organisms and have provided the basis for the construction of physical maps When Mendel observed an “independent that permit the rapid mapping of disease assortment of traits” (Mendel’s second traits. law), he was fortunate to have chosen traits As soon as a chromosomal location that were not localized close to one an- for a disease phenotype has been estab- other on the same chromosome.1 Subse- lished, genetic linkage analysis helps quent studies revealed that many genes determine whether the disease pheno- were indeed linked, ie, that traits did not type is only caused by mutation in a assort or segregate independently, but that single gene or mutations in other genes traits encoded by these linked genes were can give rise to an identical or similar inherited together. -
Integrating Genetic Linkage Maps with Pachytene Chromosome Structure in Maize
Copyright 2004 by the Genetics Society of America Integrating Genetic Linkage Maps With Pachytene Chromosome Structure in Maize Lorinda K. Anderson,*,1 Naser Salameh,† Hank W. Bass,‡ Lisa C. Harper,§ W. Z. Cande,§ Gerd Weber† and Stephen M. Stack* *Department of Biology, Colorado State University, Fort Collins, Colorado 80523, †Department of Plant Breeding and Biotechnology, University of Hohenheim, D-70593 Stuttgart, Germany, ‡Department of Biological Science, Florida State University, Tallahassee, Florida 32306 and §Department of Molecular and Cell Biology, University of California, Berkeley, California 94720 Manuscript received November 4, 2003 Accepted for publication January 9, 2004 ABSTRACT Genetic linkage maps reveal the order of markers based on the frequency of recombination between markers during meiosis. Because the rate of recombination varies along chromosomes, it has been difficult to relate linkage maps to chromosome structure. Here we use cytological maps of crossing over based on recombination nodules (RNs) to predict the physical position of genetic markers on each of the 10 chromosomes of maize. This is possible because (1) all 10 maize chromosomes can be individually identified from spreads of synaptonemal complexes, (2) each RN corresponds to one crossover, and (3) the frequency of RNs on defined chromosomal segments can be converted to centimorgan values. We tested our predic- tions for chromosome 9 using seven genetically mapped, single-copy markers that were independently mapped on pachytene chromosomes using in situ hybridization. The correlation between predicted and observed locations was very strong (r2 ϭ 0.996), indicating a virtual 1:1 correspondence. Thus, this new, high-resolution, cytogenetic map enables one to predict the chromosomal location of any genetically mapped marker in maize with a high degree of accuracy. -
Genetic Engineering and Protein Synthesis
Key: Yellow highlight = required component Genetic Engineering and Protein Synthesis Subject Area(s) Biology Life Science Curricular Unit Title What does DNA do? Header Image 1 Image file: DNA.gif ADA Description: A computer generated model of DNA Source/Rights: Copyright © Spiffistan, Wikimedia Commons (http://commons.wikimedia.org/wiki/File:Bdna_cropped.gif) Caption: Double Stranded DNA structure Grade Level 9 (9-12) Summary This unit begins with an introduction to genetic engineering to grab the students attention before moving on to some basic biology topics. The entire gene expression process is covered, focusing on DNA transcription/translation and how this relates to protein synthesis. Mutations are also covered at the end of this unit to emphasize that changes to DNA are not always intentional. Multiple activities are included to help the students better understand the lessons. Engineering Connection Version: August 2013 1 Genetic engineering is a field with a growing number of practical applications. Engineers have developed genetic recombination techniques to manipulate gene sequences to have organisms express specific traits. It is integral that genetic engineers understand how traits are expressed and what effects will be produced by altering the DNA of an organism. Gene expression is a result of the protein synthesis process which reads DNA as a set of instructions for building specific proteins. Once this process is well understood, and genes are classified based on the desired trait, engineers develop ways to alter the genes to create a net benefit to us or the organism. This could include anything such as larger cows that produce more meat, pest resistant crops, or bacteria that produce fuel. -
Section 4. Guidance Document on Horizontal Gene Transfer Between Bacteria
306 - PART 2. DOCUMENTS ON MICRO-ORGANISMS Section 4. Guidance document on horizontal gene transfer between bacteria 1. Introduction Horizontal gene transfer (HGT) 1 refers to the stable transfer of genetic material from one organism to another without reproduction. The significance of horizontal gene transfer was first recognised when evidence was found for ‘infectious heredity’ of multiple antibiotic resistance to pathogens (Watanabe, 1963). The assumed importance of HGT has changed several times (Doolittle et al., 2003) but there is general agreement now that HGT is a major, if not the dominant, force in bacterial evolution. Massive gene exchanges in completely sequenced genomes were discovered by deviant composition, anomalous phylogenetic distribution, great similarity of genes from distantly related species, and incongruent phylogenetic trees (Ochman et al., 2000; Koonin et al., 2001; Jain et al., 2002; Doolittle et al., 2003; Kurland et al., 2003; Philippe and Douady, 2003). There is also much evidence now for HGT by mobile genetic elements (MGEs) being an ongoing process that plays a primary role in the ecological adaptation of prokaryotes. Well documented is the example of the dissemination of antibiotic resistance genes by HGT that allowed bacterial populations to rapidly adapt to a strong selective pressure by agronomically and medically used antibiotics (Tschäpe, 1994; Witte, 1998; Mazel and Davies, 1999). MGEs shape bacterial genomes, promote intra-species variability and distribute genes between distantly related bacterial genera. Horizontal gene transfer (HGT) between bacteria is driven by three major processes: transformation (the uptake of free DNA), transduction (gene transfer mediated by bacteriophages) and conjugation (gene transfer by means of plasmids or conjugative and integrated elements). -
Inference and Analysis of Population Structure Using Genetic Data and Network Theory
| INVESTIGATION Inference and Analysis of Population Structure Using Genetic Data and Network Theory Gili Greenbaum,*,†,1 Alan R. Templeton,‡,§ and Shirli Bar-David† *Department of Solar Energy and Environmental Physics and †Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990 Midreshet Ben-Gurion, Israel, ‡Department of Biology, Washington University, St. Louis, Missouri 63130, and §Department of Evolutionary and Environmental Ecology, University of Haifa, 31905 Haifa, Israel ABSTRACT Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance- based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition’s modularity, a network theory measure indicating the quality of community partitions. -
Genetic Linkage of the Huntington's Disease Gene to a DNA Marker James F
LE JOURNAL CANADIEN DES SCIENCES NEUROLOG1QUES SPECIAL FEATURE Genetic Linkage of the Huntington's Disease Gene to a DNA Marker James F. Gusella ABSTRACT: Recombinant DNA techniques have provided the means to generate large numbers of new genetic linkage markers. This technology has been used to identify a DNA marker that coinherits with the Huntington's Disease (HD) gene in family studies. The HD locus has thereby been mapped to human chromosome 4. The discovery of a genetic marker for the inheritance of HD has implications both for patient care and future research. The same approach holds considerable promise for the investigation of other genetic diseases, including Dystonia Musculorum Deformans. RESUME: Les techniques d'ADN recombine ont fourni le moyen de g£nerer un grand nombre de nouveux marqueurs a liason g6n£tique. Cette technologie a He employe" afin d'identifier un marqueur d'ADN qui co-herite avec le gene de la maladie de Huntington (MH) dans les etudes familiales. Le lieu du gene de la MH a ainsi 6te localise sur le chromosome humain numero 4. La d6couverte d'un marqueur g6n6tique pour I'her6dit6 de MH a des implications pour la soin de patients ainsi que pour la recherche dans le futur. La meme approche semble pleine de promesses pour l'investigation d'autres maladies g6ndtiques, incluant la dystonie musculaire deTormante. Can. J. Neurol. Sci. 1984; 11:421-425 Huntington's Disease currently no effective therapy to cure this devastating disease, Huntington's disease (HD) is a genetic neurodegenerative or to slow its inexorable progression. disorder first described by George Huntington in 1873 (Hunting ton, 1972;Hayden, 1981;Chaseetal., 1979). -
Cancer Genomics Terminology
Cancer Genomics Terminology Acquired Susceptibility Mutation: A mutation in a gene that occurs after birth from a carcinogenic insult. Allele: One of the variant forms of a gene. Different alleles may produce variation in inherited characteristics. Allele Heterogeneity: A phenotype that can be produced by different genetic mechanisms. Amino Acid: The building blocks of protein, for which DNA carries the genetic code. Analytical Sensitivity: The proportion of positive test results correctly reported by the laboratory among samples with a mutation(s) that the laboratory’s test is designed to detect. Analytic Specificity: The proportion of negative test results correctly reported among samples when no detectable mutation is present. Analytic Validity: A test’s ability to accurately and reliably measure the genotype of interest. Apoptosis: Programmed cell death. Ashkenazi: Individuals of Eastern European Jewish ancestry/decent (For example-Germany and Poland). Non-assortative mating occurred in this population. Association: When significant differences in allele frequencies are found between a disease and control population, the disease and allele are said to be in association. Assortative Mating: In population genetics, selective mating in a population between individuals that are genetically related or have similar characteristics. Autosome: Any chromosome other than a sex chromosome. Humans have 22 pairs numbered 1-22. Base Excision Repair Gene: The gene responsible for the removal of a damaged base and replacing it with the correct nucleotide. Base Pair: Two bases, which form a “rung on the DNA ladder”. Bases are the “letters” (Adenine, Thymine, Cytosine, Guanine) that spell out the genetic code. Normally adenine pairs with thymine and cytosine pairs with guanine.