scholarly journals Single Nucleotide Polymorphism Markers for Genetic Mapping in Drosophila melanogaster

2001 ◽  
Vol 11 (6) ◽  
pp. 1100-1113
Author(s):  
Roger A. Hoskins ◽  
Alexander C. Phan ◽  
Mohammed Naeemuddin ◽  
Felipa A. Mapa ◽  
David A. Ruddy ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Mapping ◽  
Physical Map ◽  
Molecular Genetic ◽  
Average Density ◽  
P Element ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Recombination Mapping ◽  
Resolution Mapping

For nearly a century, genetic analysis in Drosophila melanogaster has been a powerful tool for analyzing gene function, yet Drosophila lacks the molecular genetic mapping tools that recently have revolutionized human, mouse, and plant genetics. Here, we describe the systematic characterization of a dense set of molecular markers in Drosophila by using a sequence tagged site-based physical map of the genome. We identify 474 biallelic markers in standard laboratory strains of Drosophila that span the genome. Most of these markers are single nucleotide polymorphisms and sequences for these variants are provided in an accessible format. The average density of the new markers is one per 225 kb on the autosomes and one per megabase on the X chromosome. We include in this survey a set of P-element strains that provide additional use for high-resolution mapping. We show one application of the new markers in a simple set of crosses to map a mutation in the hedgehog gene to an interval of <1 Mb. This new map resource significantly increases the efficiency and resolution of recombination mapping and will be of immediate value to the Drosophila research community.

scholarly journals A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

2013 ◽  
Vol 164 (1) ◽  
pp. 412-423 ◽  
Author(s):  
R. Ariyadasa ◽  
M. Mascher ◽  
T. Nussbaumer ◽  
D. Schulte ◽  
Z. Frenkel ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Physical Map ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Single Nucleotide Polymorphisms in Genes Associated with Isoniazid Resistance in Mycobacterium tuberculosis

2003 ◽  
Vol 47 (4) ◽  
pp. 1241-1250 ◽  
Author(s):  
Srinivas V. Ramaswamy ◽  
Robert Reich ◽  
Shu-Jun Dou ◽  
Linda Jasperse ◽  
Xi Pan ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Single Nucleotide Polymorphisms ◽  
Molecular Genetic ◽  
Mycolic Acid ◽  
Genetic Group ◽  
Clinical Isolates ◽  
Central Component ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

ABSTRACT Isoniazid (INH) is a central component of drug regimens used worldwide to treat tuberculosis. Previous studies have identified resistance-associated mutations in katG, inhA, kasA, ndh, and the oxyR-ahpC intergenic region. DNA microarray-based experiments have shown that INH induces several genes in Mycobacterium tuberculosis that encode proteins physiologically relevant to the drug's mode of action. To gain further insight into the molecular genetic basis of INH resistance, 20 genes implicated in INH resistance were sequenced for INH resistance-associated mutations. Thirty-eight INH-monoresistant clinical isolates and 86 INH-susceptible isolates of M. tuberculosis were obtained from the Texas Department of Health and the Houston Tuberculosis Initiative. Epidemiologic independence was established for all isolates by IS6110 restriction fragment length polymorphism analysis. Susceptible isolates were matched with resistant isolates by molecular genetic group and IS6110 profiles. Spoligotyping was done with isolates with five or fewer IS6110 copies. A major genetic group was established on the basis of the polymorphisms in katG codon 463 and gyrA codon 95. MICs were determined by the E-test. Semiquantitative catalase assays were performed with isolates with mutations in the katG gene. When the 20 genes were sequenced, it was found that 17 (44.7%) INH-resistant isolates had a single-locus, resistance-associated mutation in the katG, mabA, or Rv1772 gene. Seventeen (44.7%) INH-resistant isolates had resistance-associated mutations in two or more genes, and 76% of all INH-resistant isolates had a mutation in the katG gene. Mutations were also identified in the fadE24, Rv1592c, Rv1772, Rv0340, and iniBAC genes, recently shown by DNA-based microarray experiments to be upregulated in response to INH. In general, the MICs were higher for isolates with mutations in katG and the isolates had reduced catalase activities. The results show that a variety of single nucleotide polymorphisms in multiple genes are found exclusively in INH-resistant clinical isolates. These genes either are involved in mycolic acid biosynthesis or are overexpressed as a response to the buildup or cellular toxicity of INH.

scholarly journals A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals

2020 ◽  
Vol 12 (4) ◽  
pp. 345-357 ◽  
Author(s):  
Niko Popitsch ◽  
Christian D Huber ◽  
Ilana Buchumenski ◽  
Eli Eisenberg ◽  
Michael Jantsch ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Single Nucleotide Polymorphisms ◽  
Genome Evolution ◽  
Rna Editing ◽  
Adaptive Evolution ◽  
Population Genomics ◽  
Common Type ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cellular Machinery

Abstract In animals, the most common type of RNA editing is the deamination of adenosines (A) into inosines (I). Because inosines basepair with cytosines (C), they are interpreted as guanosines (G) by the cellular machinery and genomically encoded G alleles at edited sites mimic the function of edited RNAs. The contribution of this hardwiring effect on genome evolution remains obscure. We looked for population genomics signatures of adaptive evolution associated with A-to-I RNA edited sites in humans and Drosophila melanogaster. We found that single nucleotide polymorphisms at edited sites occur 3 (humans) to 15 times (Drosophila) more often than at unedited sites, the nucleotide G is virtually the unique alternative allele at edited sites and G alleles segregate at higher frequency at edited sites than at unedited sites. Our study reveals that a significant fraction of coding synonymous and nonsynonymous as well as silent and intergenic A-to-I RNA editing sites are likely adaptive in the distantly related human and Drosophila lineages.

scholarly journals Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster

2020 ◽  
Vol 375 (1795) ◽  
pp. 20190341 ◽  
Author(s):  
Judit Salces-Ortiz ◽  
Carlos Vargas-Chavez ◽  
Lain Guio ◽  
Gabriel E. Rech ◽  
Josefa González
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Regulatory Networks ◽  
Regulation Of Gene Expression ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Organophosphate Insecticide ◽  
Single Nucleotide ◽  
Insecticide Exposure ◽  
Genomic Response

Most of the genotype–phenotype analyses to date have largely centred attention on single nucleotide polymorphisms. However, transposable element (TE) insertions have arisen as a plausible addition to the study of the genotypic–phenotypic link because of to their role in genome function and evolution. In this work, we investigate the contribution of TE insertions to the regulation of gene expression in response to insecticides. We exposed four Drosophila melanogaster strains to malathion, a commonly used organophosphate insecticide. By combining information from different approaches, including RNA-seq and ATAC-seq, we found that TEs can contribute to the regulation of gene expression under insecticide exposure by rewiring cis -regulatory networks. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

Association of molecular genetic markers and oxidative stress indices in workers in contact with asbestos dust

2020 ◽  
pp. 560-560
Author(s):  
L. M. Bezrukavnikova ◽  
N. N. Anokhin ◽  
E. S. Tsidilkovskaya
Keyword(s):  
Oxidative Stress ◽  
Lipid Peroxidation ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Markers ◽  
Molecular Genetic ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Stress Indices ◽  
Molecular Genetic Markers ◽  
And Oxidative Stress

The studied single-nucleotide polymorphisms EPHX1 (rs1051740), SAD2 (rs4880), MP9 (rs17576) in persons exposed to asbestos dust are associated with elevated levels of lipid peroxidation catabolites, which confirms their significance in the development of asbestos-related bronchopulmonary pathology.

scholarly journals Distinguishing Between Nile Tilapia Strains Using a Low-Density Single-Nucleotide Polymorphism Panel

2020 ◽  
Vol 11 ◽  
Author(s):  
Matthew G. Hamilton ◽  
Curtis E. Lind ◽  
Benoy K. Barman ◽  
Ravelina R. Velasco ◽  
Ma. Jodecel C. Danting ◽  
...  
Keyword(s):  
Nile Tilapia ◽  
Molecular Genetic ◽  
Genotyping By Sequencing ◽  
The Philippines ◽  
Primary Objective ◽  
Small Scale ◽  
Low Density ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genetically Improved

Nile tilapia (Oreochromis niloticus) is among the most important finfish in aquaculture, particularly in Asia. Numerous genetically improved strains of Nile tilapia have been developed and disseminated through formal and informal channels to hatcheries, many of which operate at a relatively small scale in developing countries. The primary objective of this study was to assess the extent to which molecular genetic tools can identify different and interrelated strains of Nile tilapia in Bangladesh and the Philippines, two globally significant producers. A tool was developed using a low-density panel of single-nucleotide polymorphisms (SNPs), genotyping-by-sequencing and discriminant analysis of principal components (DAPC). When applied to 2,057 samples from 205 hatcheries in Bangladesh and the Philippines, for hatcheries where the hatchery-identified strain was one of the sampled core populations used to develop the tool, hatchery-identified and DAPC-assigned hatchery-level strains were in agreement in 74.1% of cases in Bangladesh and 80.6% of cases in the Philippines. The dominant hatchery-identified and DAPC-assigned strains were GIFT, in Bangladesh, and GET-ExCEL—a composite strain partially derived from GIFT—in the Philippines.

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