Technique that utilizes low-stringency polymerase chain reaction (PCR) amplification with single primers of arbitrary sequence to generate strain-specific arrays of anonymous DNA fragments. RAPD technique may be used to determine taxonomic identity, assess kinship relationships, analyze mixed genome samples, and create specific probes.
Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.
Genotypic differences observed among individuals in a population.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The relationships of groups of organisms as reflected by their genetic makeup.
A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.
Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.
The science dealing with the earth and its life, especially the description of land, sea, and air and the distribution of plant and animal life, including humanity and human industries with reference to the mutual relations of these elements. (From Webster, 3d ed)
Any method used for determining the location of and relative distances between genes on a chromosome.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Procedures for identifying types and strains of fungi.
Any enterprise centered on the processing, assembly, production, or marketing of a line of products, services, commodities, or merchandise, in a particular field often named after its principal product. Examples include the automobile, fishing, music, publishing, insurance, and textile industries.
The systematic study of the complete DNA sequences (GENOME) of organisms.
The protection, preservation, restoration, and rational use of all resources in the total environment.
The variety of all native living organisms and their various forms and interrelationships.
A drug that has been used in various urinary syndromes and as an antispasmodic. Its therapeutic usefulness and its mechanism of action are not clear. It may have local anesthetic activity and direct relaxing effects on smooth muscle as well as some activity as a muscarinic antagonist.
A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)
MOLECULAR BIOLOGY techniques used in the diagnosis of disease.
Scientific study of human skeletal remains with the express purpose of identification. This includes establishing individual identity, trauma analysis, facial reconstruction, photographic superimposition, determination of time interval since death, and crime-scene recovery. Forensic anthropologists do not certify cause of death but provide data to assist in determination of probable cause. This is a branch of the field of physical anthropology and qualified individuals are certified by the American Board of Forensic Anthropology. (From Am J Forensic Med Pathol 1992 Jun;13(2):146)
The application of dental knowledge to questions of law.
Exclusive legal rights or privileges applied to inventions, plants, etc.
A method of differentiating individuals based on the analysis of qualitative or quantitative biological traits or patterns. This process which has applications in forensics and identity theft prevention includes DNA profiles or DNA fingerprints, hand fingerprints, automated facial recognition, iris scan, hand geometry, retinal scan, vascular patterns, automated voice pattern recognition, and ultrasound of fingers.
The application of genetic analyses and MOLECULAR DIAGNOSTIC TECHNIQUES to legal matters and crime analysis.
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
A plant species of the family FABACEAE used to study GENETICS because it is DIPLOID, self fertile, has a small genome, and short generation time.
A plant genus of the family FABACEAE. It is distinct from Sweet Clover (MELILOTUS), from Bush Clover (LESPEDEZA), and from Red Clover (TRIFOLIUM).
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
The encapsulated embryos of flowering plants. They are used as is or for animal feed because of the high content of concentrated nutrients like starches, proteins, and fats. Rapeseed, cottonseed, and sunflower seed are also produced for the oils (fats) they yield.
PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.
One or more types of plant seed proteins providing the large amounts of AMINO ACIDS utilized in GERMINATION and SEEDLING growth. As seeds are the major food source from AGRICULTURAL CROPS, seed storage proteins are a major source of DIETARY PROTEINS.
The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990)
Cleaved amplified polymorphic sequence Genetic marker "Random Amplified Polymorphic DNA (RAPD)". ... "rDNA: Random Amplification of Polymorphic DNA (RAPD)". Retrieved 2016-06-03. RAPD+Technique at the US National ... DNA fragments from PCR amplification of random segments of genomic DNA with a single primer of arbitrary nucleotide sequence ... Nearly all RAPD markers are dominant, i.e. it is not possible to distinguish whether a DNA segment is amplified from a locus ...
Random fragment length polymorphisms Amplified fragment length polymorphisms Random amplification of polymorphic DNA Single ... the mean number of alleles per locus, or the percentage of polymorphic loci. Genetic diversity determines the potential fitness ... Here the techniques to reduce inbreeding also help decrease the accumulation of deleterious mutations. These techniques have ... Another technique is using historic DNA for genetic analysis. Historic DNA is important because it allows geneticists to ...
... , or Strand-seq, is a technique for the selective sequencing of a daughter cell's ... These genomic assemblies integrate all forms of genetic variation including single nucleotide variants, indels and structural ... "Characterizing polymorphic inversions in human genomes by single-cell sequencing". Genome Res. 26 (11): 1575-1587. doi:10.1101/ ... However, non-random segregation of sister chromatids has been observed in mammalian cells ever since. There have been a few ...
They have a higher mutation rate than other areas of DNA leading to high genetic diversity. Microsatellites are often referred ... The use of PCR means that microsatellite length analysis is prone to PCR limitations like any other PCR-amplified DNA locus. A ... Random microsatellite primers can be developed by cloning random segments of DNA from the focal species. These random segments ... Unlike point mutations, which affect only a single nucleotide, microsatellite mutations lead to the gain or loss of an entire ...
For instance, NUMTs can be used not only as genetic markers but also as a tool for understanding the relative rate of mutation ... indicating that mtDNA can be amplified once inserted. Dayama et al. developed a high yield new technique for the exact ... been found between the fraction of noncoding DNA and NUMT abundance in the genome but NUMTs are also proven to have non-random ... They isolated and studied 21 nuclear mutants with different combinations of mutations in at least 12 nuclear loci called the ...
"Genetic diversity among wild forms and cultivated varieties of Discus (Symphysodon spp.) as revealed by Random Amplified ... evolutionary comparison of microsatellite and single-copy nuclear loci". Molecular Biology and Evolution. 15 (7): 798-808. doi: ... Polymorphic DNA (RAPD) fingerprinting". Aquaculture. 173 (1): 485-497. doi:10.1016/S0044-8486(98)00478-5. Kornfield I (1991) ... Mouthbrooding is a reproductive technique where the fish scoop up eggs and fry for protection. While this behavior differs from ...
They have a higher mutation rate than other areas of DNA[3] leading to high genetic diversity. Microsatellites are often ... The use of PCR means that microsatellite length analysis is prone to PCR limitations like any other PCR-amplified DNA locus. A ... Random microsatellite primers can be developed by cloning random segments of DNA from the focal species. These random segments ... Unlike point mutations, which affect only a single nucleotide, microsatellite mutations lead to the gain or loss of an entire ...
This method has been called Cleaved Amplified Polymorphic Sequence (CAPS). Alternatively, the amplified segment can be analyzed ... In molecular biology, restriction fragment length polymorphism (RFLP) is a technique that exploits variations in homologous DNA ... and in the characterization of genetic diversity or breeding patterns in animal populations. ... In allele a, restriction site 2 has been lost by a mutation, so the probe now detects the larger fused fragment running from ...
Cleaved amplified polymorphic sequence Genetic marker "Random Amplified Polymorphic DNA (RAPD)". ... "rDNA: Random Amplification of Polymorphic DNA (RAPD)". Retrieved 2016-06-03. RAPD+Technique at the US National ... DNA fragments from PCR amplification of random segments of genomic DNA with a single primer of arbitrary nucleotide sequence ... Nearly all RAPD markers are dominant, i.e. it is not possible to distinguish whether a DNA segment is amplified from a locus ...
Molecular finger printing techniques, such as random amplified polymorphic DNA (RAPD)-PCR, have revealed marked sequence ... pylori isolates exhibit genetic variability within single hosts. We examined H. pylori genetic diversity in a Mexican ... but the number of genetic loci affected was similar to the number reported previously (24 to 67 loci versus 44 loci). The ... The initially homogeneous population diversifies over time by mutation, and the genetic changes spread through the population ...
Dwarf Cavendish (AAA)) were studied using morphological and random amplified polymorphic DNA (RAPD) markers. Out of the 30 ... Both morphological and RAPD analyses successfully detected genetic variation within induced mutant clones, RAPD also detected ... Results were indicative that induced mutations bear a great potential in improving banana for salinity resistant. ... RAPDs established 106 major amplified products using 14 primers. Out of 106 markers, eight were monomorph, and the remaining ( ...
TALENs that are designed to target a W chromosome-specific sequence in a previously identified random amplified polymorphic DNA ... and radiation-induced chromosome rearrangements often result in mutations at multiple loci, which inevitably decrease strain ... 2002) Genetic sexing strains in medfly, Ceratitis capitata, sterile insect technique programmes. Genetica 116:5-13. ... The B. mori W chromosome is replete with repetitive DNA sequences, with only a single functional gene, fem, recently identified ...
... and the DNA-based molecular techniques for the diagnosis and genetic characterization of T. gondii. These techniques have ... Serotyping methods based on polymorphic polypeptides have the potential to become the choice for typing T. gondii in humans and ... Diagnosis of toxoplasmosis has been improved by the emergence of molecular technologies to amplify parasite nucleic acids. ... Among these, polymerase chain reaction (PCR)-based molecular techniques have been useful for the genetic characterization of T ...
Other marker techniques that have been developed for tomato include random amplified polymorphic DNA (RAPD) and amplified ... Assembling germplasm like landrace, wild types, improved and/or exotic types of tomatoes as sources of genetic diversity for ... MAB has become possible both for traits governed by single gene and quantitative trait loci (QTLs) [98]. The philosophy in ... A DNA marker is a fragment of DNA showing mutations/variations, which can be used to detect polymorphism between different ...
... amplified fragment length polymorphism (AFLP), random amplification of polymorphic DNA (RAPD), single strand conformation ... and ecosystem diversity [15]. As the names indicate, species diversity refers to the variety of species; genetic diversity is ... Similarly, the mitochondrial DNA in plants has a very high rate of structural mutations and thus can rarely be used as genetic ... development of genome-wide genetic markers for DNA profiling and marker assisted breeding, and quantitative trait loci (QTL) ...
Random fragment length polymorphisms Amplified fragment length polymorphisms Random amplification of polymorphic DNA Single ... the mean number of alleles per locus, or the percentage of polymorphic loci. Genetic diversity determines the potential fitness ... Here the techniques to reduce inbreeding also help decrease the accumulation of deleterious mutations. These techniques have ... Another technique is using historic DNA for genetic analysis. Historic DNA is important because it allows geneticists to ...
Detection and analysis of genetic variation can help us to understand the molecular basis of various biological phenomena in ... Genetic or DNA based marker techniques such as RFLP (restriction fragment length polymorphism), RAPD (random amplified ... Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics. ... Neff MM, Neff JD, Chory J, Pepper AE (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide ...
The polymorphic character of a sequence of the human genome comprising approximately 950 base pairs and methods for using it to ... These scanning and screening techniques provide one skilled in the art with the means to detect new mutations within the DNA ... shows that all of the diversity does not represent random mutations, but instead represents a mixture of individual base ... When two oligonucleotides differing by a single DNA base are supplied as primers in a reaction containing a single DNA or RNA ...
Female-male pairings appeared to be random and there was no evidence for mate choice by heterozygosity. There was some ... 274 individual worms were typed at seven microsatellite loci. Removal of individuals bearing duplicate MLGs (as a correction ... this is because of organotropic patterns in genetic variation and the tendency to sample from different organs in differently ... possibly the result of mutations occurring during the asexual (intramolluscan) phase of clonal expansion. Research has also ...
PCR of DNA from homozygous wild-type mice amplifies a single 170 bp band, whereas PCR of DNA from homozygous mutant mice have a ... Genetic mapping. The Dscamdel17 mutation arose spontaneously in the Balb/cJ mapping partner of an unrelated F1 mapping cross. ... The Dscam mutation was mapped by breeding to C57BL6/J and establishing linkage in F2 mice with polymorphic markers, and the ... In segregating genetic backgrounds containing BALB/c or 129 loci, these mice survive to adulthood and will breed as homozygotes ...
The development of molecular techniques for genetic analysis has led to a great augmentation in our knowledge of crop genetics ... stands for Random Amplification of Polymorphic DNA. It is a type of PCR reaction, but the segments of DNA that are amplified ... which may arise due to mutation or alteration in the genomic loci, that can be observed. A genetic marker may be a short DNA ... SFP (or Single feature polymorphism) • DArT (or Diversity Arrays Technology) They can be further categorized as dominant or co- ...
... using techniques such as phylogrouping, random amplified polymorphic DNA (RAPD) analysis, or multilocus sequence typing (MLST ... we used WGS as a single assay to sample genetic diversity in core and accessory genomes of E. coli in fecal samples taken from ... another gastrointestinal organism with a similar mutation rate but far less intrahost diversity (30, 31). The accessory genome ... In silico multilocus sequence typing.In silico MLST identified BLAST matches for all E. coli housekeeping loci in all 127 ...
Abbreviations: cM, centimorgan; kb, DNA kilobase pairs; PCR, polymerase chain reaction; RAPD, random amplified polymorphic DNA ... by allele quantification combined with melting curves analysis of single-nucleotide polymorphism loci ... DNA Analysis of Turfgrass Genetic Diversity. ... induced by chrysotile in the gpt delta transgenic mutation ... the bottleneck becomes apparent when used with new sequencing techniques.. TRADE NEWS: Complex Mixtures of Targeting ...
A series of Random Amplified Polymorphic DNA-based genetic studies mainly targeted at quantitative loci underlying resistance ... of the faba bean meta-transcriptome and has fueled development of extensive sets of Simple Sequence Repeat and Single ... A series of Random Amplified Polymorphic DNA-based genetic studies mainly targeted at quantitative loci underlying resistance ... Genetics of faba bean stretches back to the 1930s, but it was not until 1993 that DNA markers were used to construct genetic ...
As shown in Figure 1c, six F1 progeny that were randomly selected were all heterozygous for random-amplified polymorphic DNA ( ... To determine the genetic nature of this mutation, pollen from homozygotes M3 individuals were used for crosses into homozygous ... The mtapetala locus phenotype of M. truncatula closely resembles class B function mutations that have been cloned and ... After considering ease of use and the diversity of mutations possible, EMS, a base alkylating agent that generates point ...
Genotypic methods include several techniques, such as random amplified polymorphic DNA (RAPD) analysis (1, 10, 11), restriction ... Only loci with perfect repeat sequences were included in our analysis; imperfect repeats containing point mutations and/or ... Unfortunately, studies comparing different fingerprinting techniques for A. fumigatus show that, up to now, no single technique ... The Simpsons diversity index for the individual markers ranged from 0.77 to 0.97. The diversity index for the multiplex ...
Random Amplified Polymorphic DNA (RAPD) Introduction Random Amplified Polymorphic DNA (RAPD) markers are DNA fragments from PCR ... AMPLIFIED POLYMORPHISM DNA Genetic diversity characterization of Anthocepalus cadamba population revealed by Random Amplified ... The major histocompatibility complex (MHC) is a large locus on vertebrate DNA containing a set of closely linked polymorphic ... Single Nucleotide Polymorphisms or SNPs are a single nucleotide change in an area of an organisms DNA that is different in ...
Genetic variability: Genetic diversity obtained for five loci is shown in table 1. The total number of alleles per locus (Na) ... DNA extraction from the samples was performed with a slight modification of the guanidine isothiocyanate technique (Tri reagent ... are common in marine fish due to the effect of environmental conditions on larvae dispersion as well as random mutation ... Results of FST and RST suggest a single population with high genetic flow and no subpopulations. This could mean a low ...
Randomly amplified polymorphic DNA reveals fine-scale genetic structure in Pissodes strobi (Coleoptera: Curculionidae). ... Using multiple loci with high allelic diversity can give higher resolution than other techniques providing individual ... An analysis using Random Amplified Polymorphic DNA (RAPD) showed three populations: Vancouver Island, Interior BC and North ... Introduction A Single nucleotide polymorphism (SNP) is an alteration in a DNA sequence at a single base position. SNPs can be ...
... random amplified polymorphic DNA technique; specific combining ability; tetraploidy; yield components; United States. Abstract: ... genetic variation; genome; hybrids; karyotyping; loci; models; monosomics; plant breeding; progeny; rapeseed; ribosomal DNA; ... Resynthesized Brassica napus L. is an important source for broadening genetic diversity and producing lines with desired ... Oryza sativa; alleles; blast disease; crop production; disease resistance; frameshift mutation; genome mining; haplotypes; loci ...
An alternative technique for identifying molecular marks called random amplified polymorphic DNA (RAPD) has been developed ( ... Therefore, differences in markers from parents to offspring may be the result of DNA recombination, mutation, or random ... Williams et al., 1990). In this method, by using a single arbitrary primer (10 mer) and amplifying DNA by polymerase chain ... the paucity of isozyme loci restricts their usefulness in breeding (Helentjaris et al., 1986). DNA markers have been used to ...
1998 Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology ... Allelic variation arises from random nucleotide mutation, sometimes followed by selection, and from horizontal gene transfer ... The SNaPshot technique is based on addition of a single fluorescently labeled ddNTP to the 3′ end of an unlabeled specific ... 2000 Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria. J. ...
The great bulk of genetic variation at the nucleotide level may not be visible at the phenotypic level. It is this variation ... Potential use of random amplified polymorphic DNA (RAPD) technique to study the genetic diversity in Indian mustard (Brassica ... Restorer genes for different forms of Brassica cytoplasmic male sterility map to a single nucleus locus that modifies ... Schierholt A, Becker HC, Ecke W (2000) Mapping a high oleic acid mutation in winter oilseed rape (Brassica napus L.). Theor ...
... without prior DNA extraction. In the model demonstrated here, an example of derived cleaved amplified polymorphic sequence ... can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions ... The technique on creating gene deletion constructs is high throughput and could be easy to use in genome-wide single gene ... Cells are fixed and interacting loci are captured by covalent DNA-protein cross-links. To minimize non-specific noise and ...
Genetic Diversities of the Allelic Sex-Linked Genes in Actinidia. The Y-allelic sex-linked contigs (Supplemental Data Set 1A) ... The full-length SyGI genomic sequences, including the ∼1500-bp 5′ promoter region, were also amplified from genomic DNA of A. ... Integration of these segregation results with the previous fine genetic mapping of the sex-determining locus (Zhang et al., ... as proposed in the two-mutation model (Charlesworth, 2013, 2015). The two-mutation model would be also supported in this case ...
Reproducible genotypes Repeat genotyping of random 5 sample has lt1 discordance. Hardy Weinberg Single loci no significant ... Rapid, versatile, in vitro, method for amplifying defined target DNA sequences to yield multiple copies of specific region of ... Polymorphic regions of varying zygosity *Detected as Mendelian errors in HapMap *Behave (from a population genetic standpoint) ... block region of limited haplotype diversity and/or low LD 24. But there are unappealing aspects of the haplotype block idea* ...
... and random amplified polymorphic DNA (RAPD) analyses are supporting very well for nematode identification. However, ... Furthermore, choosing a DNA locus that provides a species-specific designation is still an open issue (Porazinska et al., 2009 ... DNA have been becoming the most reliable source of new information for enhancing our comprehension of evolutionary and genetic ... Techniques such as protein-based analysis, polymerase chain reaction (PCR), quantitative polymerase chain reaction (qPCR), ...
To assess genetic diversity by microarray, we used the same whole-genome amplified DNA from IQ07 and SalI described above. The ... B) We detected a strong mutation signal near codon 205 in pvdhps, which has not been previously described as polymorphic. (C) ... Sequencing Reveals Tens of Thousands of Mutations.. A major aim of resequencing in malaria parasites is to find single- ... genotyping confirmed the infection to be monoallelic at this locus (25). Total genomic DNA was subjected to whole-genome ...
  • Eleven of the 12 patients contained isolates with identical random amplified polymorphic DNA, amplified fragment length polymorphism, and vacA allele molecular footprints, whereas a single adult patient had two distinct profiles. (
  • The extent of polymorphism indicated the existence of considerable variation DNA level within induced mutant clones. (
  • Genetic or DNA based marker techniques such as RFLP (restriction fragment length polymorphism), RAPD (random amplified polymorphic DNA), SSR (simple sequence repeats) and AFLP (amplified fragment length polymorphism) are routinely being used in ecological, evolutionary, taxonomical, phylogenic and genetic studies of plant sciences. (
  • Alwala S, Suman A, Arro JA, Veremis JC, Kimbeng CA (2006) Target region amplification polymorphism (TRAP) for assessing genetic diversity in sugarcane germplasm collection. (
  • Though restriction fragments length polymorphism (RFLP) markers have been the basis for most of the work in crop plants, valuable markers have been generated from random amplification polymorphic DNA (RAPD) and amplified fragments length polymorphism (AFLP). (
  • A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites. (
  • In molecular biology, the term restriction fragment length polymorphism, or RFLP, (commonly pronounced "rif-lip") refers to a difference between two or more samples of homologous DNA molecules arising from differing locations of restriction sites, and to a related laboratory technique by which these segments can be distinguished. (
  • Amplified Fragment Length Polymorphism PCR (or AFLP-PCR or just AFLP) is a PCR-based tool used in genetics research, DNA fingerprinting, and in the practice of genetic engineering. (
  • This has permitted the reconstruction of the faba bean meta-transcriptome and has fueled development of extensive sets of Simple Sequence Repeat and Single Nucleotide Polymorphism (SNP) markers. (
  • Genotypic methods include several techniques, such as random amplified polymorphic DNA (RAPD) analysis ( 1 , 10 , 11 ), restriction fragment length polymorphism (RFLP) analysis ( 13 ), amplified fragment length polymorphism (AFLP) analysis ( 18 ), and microsatellite length polymorphism ( 2 ). (
  • The last technique is sometimes also called microsatellite polymorphism analysis ( 5 ) or polymorphic microsatellites marker analysis ( 8 ). (
  • Amplified Fragment Length Polymorphism (AFLP) Introduction Amplified Fragment Length Polymorphisms (AFLPs) are differences in restriction fragment lengths caused by SNPs or INDELs that create or abolish restriction endonuclease recognition sites. (
  • Key words: genetic polymorphism, leptin gene, Bali cattle, Kacang goat PENDAHULUAN Sapi Bali dan kambing Kacang merupakan sumber daya genetik yang perlu dikembang biakkan. (
  • 4. Association of genetic polymorphism in the calpastatin (CAST) gene with average daily gain was examined in Iranian purebred Kurdi sheep. (
  • Penelitian ini menggunakan metode Random Amplified Polymorphism DNA (RAPD). (
  • The acetylation polymorphism illustrates another genetic polymorphism of a drug-metabolizing enzyme studied in the early era of pharmacogenetics. (
  • In this context, and in light of the results from the loci sampled in this study, we can conclude … Genetic polymorphism and natural selection of Myanmar pfmsp-3 were analysed using the programs DNASTAR, MEGA6, and DnaSP 5.10.00. (
  • Genetic polymorphism is the cause of high interindividual variability for a given dose, for example in order to achieve a methadone plasma concentration of 250ng/mL, dosage of racemic methadone mixture may vary from 55 to 921mg per day for a 70kg patient without receiving any comedication [38]. (
  • In humans, a common genetic polymorphism is seen in arylamine NAT2, giving rise to rapid and slow acetylator phenotypes. (
  • 1986). DNA markers have been used to manipulate marker-assisted selection (MAS), and to guide the introgression of target genes from related species by restriction fragment length polymorphism (RFLP) in the past several years (Wolff et al. (
  • Techniques such as restriction fragment length polymorphism (RFLP), randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR), expressed sequence tags (EST), cleaved amplified polymorphic sequence (CAPS), sequence characterized amplified region (SCAR) and single nucleotide polymorphisms (SNP) have permitted rapid and precise analysis of germplasm, trait mapping, and marker-assisted breeding and selection. (
  • In a microsatellite development program, primers were designed for 248 SSR loci which were tested on a panel of 18 common bean genotypes to determine their potential as genetic markers finding higher average polymorphism information content for di-nucleotide repeat markers (0.3544) than for tri-nucleotide repeat markers (0.1536). (
  • Scientists use molecular markers such as SSR (simple sequence repeat), RAPD (random amplified polymorphic DNA), RFLP (restriction fragment length polymorphism), AFLP (amplified fragment length polymorphism), and ISSR (Intersimple sequence repeat) to reveal individual or group differences among aquatic plants. (
  • The low level of polymorphism found in this study is consistent with theoretical models of neutral mutations and background selection in highly self-fertilizing species. (
  • 1996 ) predict that in a selfer, DNA sequence polymorphism at a locus under balancing selection will far exceed that at a selectively neutral locus. (
  • The effort to build molecular genetic maps in A. thaliana has been impeded, however, by an apparent lack of nucleotide polymorphism. (
  • Based on the segregation of 294 amplified fragment length polymorphism markers, two mating type factors, and the sporeless trait, the linkage map consisted of 11 linkage groups with a total length of 837.2 centimorgans (cM). (
  • The gene region responsible for the sporeless trait was located in linkage group IX with 32 amplified fragment length polymorphism markers and the B mating type factor. (
  • We also identified eight markers closely linked (within 1.2 cM) to the sporeless locus using bulked-segregant analysis-based amplified fragment length polymorphism. (
  • One such amplified fragment length polymorphism marker was converted into two sequence-tagged site markers, SD488-I and SD488-II. (
  • 17 ], Restriction Fragment Length Polymorphism (RFLP) of ribosomal, mitochondrial, and anonymous nuclear DNA was used to determine the origin of N. coccinea var. (
  • Because the number of markers for D genome chromosomes in commercially available wheat single nucleotide polymorphism arrays is insufficient, we developed markers using a genome-specific amplicon sequencing strategy. (
  • In the first study, amplified fragment length polymorphism (AFLP) was scored for spores originating from a single pot of a cultured AMF isolate. (
  • Evaluation of heterozygous polymorphism and haplotype blocks revealed a high level of nucleotide diversity in Musa accessions. (
  • 2005. Real-time single-nucleotide polymorphism profiling using Taqman technology for rapid recognition of Campylobacter jejuni clonal complexes. (
  • Except for XTH2, high levels of polymorphism were detected: 93 alleles (mean of 13.1 sd 1.6 alleles per locus), a mean effective number of alleles (Ne) of 5.4 (sd 1.6), polymorphic information content values (PIC) from 0.617 to 0.855 and probability of Identity (PI) ranging from 0.030 to 0.151. (
  • Single nucleotide polymorphism is considered to be potentially useful in forensic human identification. (
  • It is very possible to reduce amp icon size from 100 to 450 bp ranges of the combined deoxyribonucleic acid index system (CODIS) loci to the 60-130 bp range when typing archaeological samples, showing that a single nucleotide polymorphism can be typed with a very short recognition sequence in the range of 55-45 BP. (
  • Single nucleotide polymorphism (SNP) markers are the method of choice for genetic analyses including diversity and quantitative trait loci (QTL) studies. (
  • The mean polymorphic information content (0.51) obtained from the microsatellites showed high polymorphism in accessing wide genetic diversity among the mutants and their parents. (
  • 9] characterized some mutant lines of cowpea using random amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphism (AFLP) markers. (
  • Amplified Fragment Length Polymorphism (AFLP)=== The AFLP technique (Vos et al. (
  • The introduction of DNA-based markers such as restriction fragment length polymorphism (RFLP), randomly amplified polymorphic DNA (RAPD), simple sequence repeats (SSR) and amplified fragment length polymorpshim (AFLP) caused genetic maps to become much more densely populated, generally into the range of several hundred to more than a thousand markers per genome. (
  • Molecular fingerprinting studies using RAPD ( 57 ), amplified fragment length polymorphisms (AFLP) ( 40 ), and sequence analysis of virulence-associated or housekeeping genes ( 20 , 46 ) with multiple single-colony isolates or cultures obtained from separate biopsy samples from single patients revealed that strains isolated from single patients were closely related but that there were subtle differences in the majority of patients. (
  • 1996). Because RAPD polymorphisms result from either a nucleotide base change that alters the primers binding site or from an insertion or deletion within the amplified region, polymorphisms usually result in the presence or absence of an amplification product from a single locus. (
  • Althoff DM, Gitzendanner MA, Segraves KA (2007) The utility of amplified fragment length polymorphisms in phylogenetics: a comparison of homology within and between genomes. (
  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. (
  • Single nucleotide polymorphisms, frequently called SNPs (pronounced "snips"), are the most common type of genetic variation among people. (
  • 1990). The advantages of RAPD is its simplicity, rapidity, the requirement for only a small quantity of DNA, and the ability to generate numerous polymorphisms (Cheng et al. (
  • To address this problem in a representative pathogen, 432 M. tuberculosis complex strains from global sources were genotyped on the basis of 230 synonymous (silent) single nucleotide polymorphisms (sSNPs) identified by comparison of four genome sequences. (
  • DNA-based molecular markers are the most powerful diagnostic tools used to detect genetic polymorphisms at the level of DNA. (
  • This analysis revealed over 18,261 single-nucleotide polymorphisms (SNPs), 6,257 of which were further validated using a tiling microarray. (
  • In this study, a sotol population was characterized through five elevational levels at one location in the Chihuahuan Desert in Mexico, using amplified fragment length polymorphisms (AFLP) markers. (
  • Core subset selection can be based on varying criteria including phenotypic traits or various forms of molecular marker data including, but not limited to, single nucleotide polymorphisms (SNP), amplified fragment length polymorphisms (AFLP), random amplified polymorphic DNA (RAPD), and simple sequence repeats (SSR). (
  • These risk factors include rare, inherited or de novo , smaller-scale "mistakes" in DNA sequence, such as single nucleotide loss-of-function variants (nonsense, splice site, and frameshift mutations predicted to abolish protein function), which also have a strong effect on disease risk, as well as more common but weaker inherited single nucleotide polymorphisms. (
  • Polymorphisms were surveyed in six varieties, and 31,542 polymorphic sites and 5,986 potential marker sites were detected in the D genome. (
  • Using quantitative single-cell PCR, we enumerated DNA polymorphisms in the symbionts of the reef-building coral Pocillopora damicornis , and applied a model selection approach to explore the potential for recombination between coexisting Symbiodinium populations. (
  • In the process of validating the method, we identified two single nucleotide polymorphisms that may be deleterious for the function of a gene putatively important for phototropism. (
  • We further applied a strategy for the simultaneous discovery of heterozygous and homozygous polymorphisms in diploid accessions to rapidly evaluate nucleotide diversity in accessions of the same genome type. (
  • Ecotilling is a high-throughput method for the discovery and characterization of single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels). (
  • Length polymorphisms of simple sequence repeat DNA in soybean. (
  • First, single-nucleotide polymorphisms (SNPs) are single-base changes in one sequence in comparison to another, related sequence. (
  • Single nucleotide polymorphisms (SNPs) have become the most widely used marker system for plant and animal genetic analyses. (
  • The position of the visualized probes on the membrane can detect DNA polymorphisms that change the RE cut site or the size of the fragments between cut sites. (
  • Polymorphisms in the number of repeats are observed as differences in the size of amplified fragments. (
  • The population structure of Scots pine was investigated on much of its Eurasian natural range using maternally inherited mitochondrial DNA polymorphisms. (
  • Random amplification of polymorphic DNA (RAPD), pronounced "rapid", is a type of polymerase chain reaction (PCR), but the segments of DNA that are amplified are random. (
  • The scientist performing RAPD creates several arbitrary, short primers (8-12 nucleotides), then proceeds with the PCR using a large template of genomic DNA, hoping that fragments will amplify. (
  • RAPD markers are decamer (10 nucleotides long) DNA fragments from PCR amplification of random segments of genomic DNA with a single primer of arbitrary nucleotide sequence and which are able to differentiate between genetically distinct individuals, although not necessarily in a reproducible way. (
  • Unlike traditional PCR analysis, RAPD does not require any specific knowledge of the DNA sequence of the target organism: the identical 10-mer primers will or will not amplify a segment of DNA, depending on positions that are complementary to the primers' sequence. (
  • Nearly all RAPD markers are dominant, i.e. it is not possible to distinguish whether a DNA segment is amplified from a locus that is heterozygous (1 copy) or homozygous (2 copies). (
  • Codominant RAPD markers, observed as different-sized DNA segments amplified from the same locus, are detected only rarely. (
  • Thus, the RAPD technique is notoriously laboratory dependent and needs carefully developed laboratory protocols to be reproducible. (
  • Molecular finger printing techniques, such as random amplified polymorphic DNA (RAPD)-PCR, have revealed marked sequence heterogeneity between strains from unrelated individuals ( 2 ). (
  • Dwarf Cavendish (AAA)) were studied using morphological and random amplified polymorphic DNA (RAPD) markers. (
  • Both morphological and RAPD analyses successfully detected genetic variation within induced mutant clones, RAPD also detected variation between the irradiated and non-irradiated clones, which were morphologically indistinguishable. (
  • Random amplified polymorphic DNA (RAPD) analysis is a polymerase chain reaction (PCR)-based technique, which uses random primers to generate DNA fragments. (
  • Here, we describe targeted gene integration of fluorescent marker expression cassettes into a randomly amplified polymorphic DNA (RAPD) marker region in the W chromosome of the lepidopteran model insect Bombyx mori using transcriptional activator-like effector nuclease (TALEN)-mediated genome editing. (
  • Techniques such as RAPD and AFLP are also being applied to cDNA-based templates to study patterns of gene expression and uncover the genetic basis of biological responses. (
  • Bardakci F (2001) Random amplified polymorphic DNA (RAPD) markers. (
  • Random Amplified Polymorphic DNA (RAPD) Introduction Random Amplified Polymorphic DNA (RAPD) markers are DNA fragments from PCR amplification of random segments of genomic DNA with single primer of arbitrary nucleotide sequence. (
  • Forty-five random primers were screened, of which twenty-two primers were selected to detect the molecular marker in three hybrid combinations of Chrysanthemum by using random amplified polymorphic DNA (RAPD). (
  • An alternative technique for identifying molecular marks called random amplified polymorphic DNA (RAPD) has been developed (Williams et al. (
  • The RAPD, SSR and AFLP techniques were successfully established under local conditions and found useful for characterizing banana and other Musa species. (
  • This report summarizes the results of our efforts to generate useful induced mutants of the Philippine banana cultivars, 'Latundan' and 'Lakatan' through irradiation, and to evaluate the usefulness of DNA marker techniques, such as RAPD, microsatellites or SSR, and AFLP, to characterize the genomic alterations in induced mutants of the two Philippine banana cultivars. (
  • Compared to arbitrary markers such as random amplified polymorphic DNA (RAPD), ISSR markers are highly reproducible due to the use of longer primers. (
  • Herein, three independent molecular methods, multilocus microsatellite typing (MLMT), random amplification of polymorphic DNA (RAPD) and simple sequence repeats-polymerase chain reaction (SSR-PCR), were used to evaluate the genetic diversity of 53 L. infantum isolates from five different endemic areas in Brazil. (
  • These include the amplification of DNA sequences of the parasite by specific polymerase chain reaction (PCR), the random amplification of polymorphic DNA (RAPD) (Hide et al. (
  • Random Amplified Polymorphic DNA(RAPD)markers were used to assess the genetic diversity of 587 individuals, belonging to 22 populations of Nothofagus nervosa that were distributed through the Coastal (38°S to 41 °S) and Andes Mountains in Central-Southern Chile (36°S to 40°S). The objective of this study was to complement the genetic inferences previously determined by isozyme analysis, in order to obtain more accurate genetic diversity estimations. (
  • Genetic structure, Nothofagus, RAPD markers. (
  • In the RAPD technique a single random 10 basepair primer is used to specify the sequence to be amplified. (
  • The main advantage of the RAPD technique is that no prior sequence information is needed, making it popular for minor crops where genomic tools (and sequence information) are limited. (
  • The disadvantages of phenotype-based assays can be overcome by direct identification of genotypes with DNA-based markers (Nsabimana and Staden, 2007). (
  • The products of these amplifications can be polymorphic and are useful as genetic markers (Vidal and de Garcia, 2000). (
  • Since the entire plant kingdom cannot be covered under sequencing projects, molecular markers and their correlation to phenotypes provide us with requisite landmarks for elucidation of genetic variation. (
  • The review details account of techniques used in identification of markers and their applicability in plant sciences. (
  • These molecular techniques, in particular the applications of molecular markers, have been used to scrutinize DNA sequence variation(s) in and among the crop species and create new sources of genetic variation by introducing new and favorable traits from landraces and related crop species. (
  • Markers can aid selection for target alleles that are not easily assayed in individual plants, minimize linkage drag around the target gene, and reduce the number of generations required to recover a very high percentage of the recurrent parent genetic background. (
  • Improvements in marker detection systems and in the techniques used to identify markers linked to useful traits, has enabled great advances to be made in recent years. (
  • For many years, gene mapping was limited in most organisms by traditional genetic markers which include genes that encode easily observable characteristics such as blood types or seed shapes. (
  • Dominant markers allow for analyzing many loci at one time, e.g. (
  • Co-dominant markers analyze one locus at a time. (
  • Genetics of faba bean stretches back to the 1930s, but it was not until 1993 that DNA markers were used to construct genetic maps. (
  • The Simpson's diversity index for the individual markers ranged from 0.77 to 0.97. (
  • The combination of all nine markers yielded a Simpson's diversity index of 0.9994, indicative of the high discriminatory power of these new loci. (
  • 1990). In this method, by using a single arbitrary primer (10 mer) and amplifying DNA by polymerase chain reaction (PCR), the resulting DNA markers easily can be separated on an agarose gel by electrophoresis (Williams et al. (
  • Molecular or DNA-based markers offer many advantages over conventional phenotypic markers. (
  • Gene-based markers appear to be very efficient at separating divergent wild and cultivated accessions as well as Andean and Mesoamerican genepools and therefore will be useful for diversity analyses and for comparative and transcript mapping in common bean. (
  • Currently, dozens of different molecular markers have been employed to assess genetic diversity for phylogenetic analysis and to identify germplasm. (
  • In the study of four Ruppia cirrhosa populations, 12 polymorphic markers (including 10 microsatellite loci and two more by cross amplification with those from R. maritima ) were developed to reveal population diversity and differentiation [ 9 ]. (
  • For instance, 10 microsatellite markers have been used to assess genetic diversity of Euryale ferox (Nymphaeaceae), a "vulnerable" species in Japan [ 10 ]. (
  • developed 10 microsatellite markers for Nymphoides peltata , another threatened clonal aquatic plant, which allowed evaluation of genetic diversity and conservation design in Japan [ 11 ] and assessment of genetic diversity within and between populations in China [ 12 ]. (
  • This analysis provides a data set for comparative analysis with important potential for identifying markers for global parasite diversity and drug resistance mapping studies. (
  • Although these single-gene approaches are often sufficient for determining polyclonal infections, they are not the ideal markers for studying parasite genetic diversity because they are highly variable. (
  • A non-radioactive silver staining technique for AFLP markers suitable for local laboratory conditions has been established. (
  • Microsatellite DNA markers are a useful DNA-based tool for monitoring the genetic variation of pen shell populations. (
  • In this study, 20 polymorphic microsatellite (MS) DNA markers were identified from a partial genomic pen shell DNA library enriched in CA repeats, and used to compare allelic variation between wild and hatchery pen shell populations in Korea. (
  • This allows to genotype thousands of genetic markers on populations with hundreds of individuals. (
  • Approximately 80% of the designed pri- mers successfully amplified D genome-specific products, suggesting that by concentrating on a specific subgenome, we were able to design successful markers as efficiently as could be done in a diploid species. (
  • All five microsatellite markers were found to be polymorphic. (
  • The narrow genetic base could be one of the reasons for the low yield of polymorphic markers in the study. (
  • The molecular genetic techniques have been adopted for the management and manipulation of plant genomes DNA markers are the most powerful and widely used because they can portray genome sequence composition [ 4 ]. (
  • More particularly, the invention relates to soybean quantitative trait loci (QTL) for tolerance to protoporphyrinogen oxidase inhibitors, to soybean plants possessing these QTLs, which map to a novel chromosomal region, and to genetic markers that are indicative of phenotypes associated with protoporphyrinogen oxidase inhibitor tolerance. (
  • 2. The method of claim 1, wherein said quantitative trait locus is localized to a chromosomal interval defined by and including markers SATT495 and SATT613 on linkage group L. (
  • The foreground selection was carried out in F 1 and BC n F 1 generations with 22 polymorphic markers. (
  • Development and Application of Genetic Markers for Population Structure Analysis of the Blue Coral Reef Starfish, Linckia laevigata (Linn. (
  • Microsatellites have been preferred as the most popular molecular markers and proven effective in estimating population size, paternity test, genetic diversity for the critically endangered species. (
  • Modern molecular biology is the continuous source of new techniques that can be applied to obtain genetic markers, including, first of all, molecular (DNA) markers. (
  • Then, due to the importance of hybrid individual identification, we explore several of the tools (morphological, chemical, DNA based markers) that have been employed for this purpose. (
  • Functional genetic markers have important implications for genetic analysis by providing direct estimation of functional diversity. (
  • Although high throughput sequencing techniques for functional diversity analysis are being developed nowadays, the use of already well established variable markers present in candidate genes is still an interesting alternative for mapping purposes and functional diversity studies. (
  • SSR markers derived from candidate genes (SSR-CG) can be used effectively in co-segregation studies and marker-assisted diversity management. (
  • Genetic diversity of these eight CG-derived SSR-markers was explored in 54 unrelated genotypes. (
  • This is the first report on the identification, characterization and diversity analysis of microsatellite markers located inside wood quality candidate genes (CG) from Eucalyptus globulus . (
  • This set of markers is then appropriate for characterizing genetic variation, with potential usefulness for quantitative trait loci (QTL) mapping in different eucalypts genetic pedigrees and other applications such as fingerprinting and marker assisted diversity management. (
  • From the point previously mentioned, within- and between- populations genetic diversity based on genetic markers is of the essence for future conservation plans (Al-Qamashoui et al . (
  • In this regard, many techniques have been used recently, but microsatellite markers are one of the best techniques to determine genetic diversity and relations in poultry populations (Liao et al . (
  • 2007) reported that accurate results for diversity studies could be obtained by using 20 microsatellite markers and 24 birds. (
  • these markers are useful in genetic mapping studies (Budowle et al. (
  • Various genetic tools have been successfully used to study the genetic diversity of plant species, including morphological, cytological, biochemical, and molecular markers. (
  • DNA markers have enormous potential to improve the efficiency and precision of conventional plant breeding via marker-assisted selection (MAS). (
  • Owing to genetic linkage, DNA markers can be used to detect the presence of allelic variation in the genes underlying these traits. (
  • By using DNA markers to assist in plant breeding, efficiency and precision could be greatly increased. (
  • We have tested allele specific polymerase chain reaction (PCR), tetra markers and a genotyping tool based on the single strand specific nuclease CEL-I to verify randomly selected SNP markers identified previously either with a SNP array or by genotyping by sequencing in rice and mungbean, respectively. (
  • Quantitative trait loci (QTL) analyses may yield a considerable number of markers that require verification of their correctness and diagnostic capacity to predict a phenotype. (
  • Conversion of SNP markers to cleaved amplified polymorphic sequence (CAPS) markers is often used as a PCR-based method to genotype SNP markers [ 4 ], but similar to commercial kits, the method might not be practical for SNP validation. (
  • Microsatellites has been widely used as reliable molecular markers to study the genetic relationship of different populations and for indirect measures of inbreeding. (
  • Heterozygosity (the occurrence of two different alleles at a specific locus) scored at neutral microsatellite markers has generally been assumed to reflect genome wide heterozygosity. (
  • Because it is often infeasible to genotype individuals across all available loci, researchers generally rely on subsets of markers. (
  • The geographic distribution of previous studies using these markers provides a greater degree of confidence regarding the robustness to common sources of error related to amplification anomalies, such as null alleles, relative to loci with more limited use. (
  • The past two decades have seen a proliferation of genetic markers that can be used to study the genetic characteristics of species with little or no a priori knowledge regarding the sequence of an organism's genome. (
  • Perhaps no class of genetic markers has seen more use in the last 15 years than microsatellite loci. (
  • [5] The increasing availability of DNA amplification by PCR at the beginning of the 1990s triggered a large number of studies using the amplification of microsatellites as genetic markers for forensic medicine, for paternity testing, and for positional cloning to find the gene underlying a trait or disease. (
  • Therefore genetic diversity of some cowpea mutant lines was studied using simple sequence repeats (SSR) markers. (
  • The present study proved that SSR markers are useful for the genetic diversity assessment of cowpea mutants. (
  • Traditional characterization and selection technique depends on the application of morphological markers to reveal phenotypic variations in the plant population. (
  • PCR-based DNA markers are efficient tools used in plant breeding and genetics to estimate very precisely the genetic diversity [8] and differentiate among genotypes at species and sub-species level. (
  • Based on genetic criteria, including linkage disequilibrium, discrimination power, and molecular criteria as polymerase chain reaction conditions of loci multiplexing, we proposed a key identification set using six microsatellite markers to discriminate all genotypes present in the ex situ collection. (
  • Generally, single copy probes were selected for RFLP analysis, resulting in co-dominant markers in diploid species. (
  • RFLPs were very useful markers, but the need for large amounts of high quality DNA, low throughput, the need for prior sequence information and the inability to automate the procedure (Table 12.1) means that it is now rarely used. (
  • Each AFLP run yields many fragments per individual and like RAPDs, these markers are scored as present of absent, with each fragment scored as a single locus. (
  • Here we use genetic linkage mapping to construct a consensus map containing 28644 GBS markers. (
  • The identified genes can then be explored as genetic markers to be used in genomic applications in wheat breeding. (
  • Genetic linkage maps began with just a few to several tens of phenotypic markers obtained one by one by observing morphological and biochemical variations of an organism, mainly following mutation. (
  • It relies on inference from two main sources of information, i) macrofossils and pollen in sediment profiles, ii) population structure in DNA markers ideally inferred at the sequence level. (
  • Among all different classes of molecular markers available for evaluating genetic diversity, microsatellites or simple sequence repeats (SSRs) [ 4 , 5 ] are well known for their potentially high information content and versatility as molecular tools [ 6 ]. (
  • We resampled 13 populations in 6 regions along a 1600 km long latitudinal gradient from northern France to central Norway after 5 years, and assessed population genetic diversity with 9 microsatellite markers. (
  • Several mechanisms, such as point mutations, intragenic recombination, and introduction of foreign (African) alleles, sequenced two housekeeping genes ( glmM and hspA ). (
  • Developed in the early 1990's by Keygene[1], AFLP uses restriction enzymes to cut genomic DNA, followed by ligation of adaptors to the sticky ends of the restriction fragments. (
  • En este estudio una población de sotol fue caracterizada a través de cinco niveles altitudinales de una localidad del desierto chihuahuense en México, usando marcadores de polimorfismos de fragmentos amplificados (AFLP). (
  • In this study single-spore Neonectria isolates originating from both the same and from different perithecia, apple cultivars and apple orchards in Sweden and Belgium, were evaluated for AFLP- and SSR-based genetic similarity and for mating system. (
  • Seven SSR loci produced a total of 31 alleles with an average of 4 alleles per locus, while 11 AFLP primer combinations produced an average of 35 fragments per primer combination and 71 % polymorphic fragments. (
  • AFLP-based Jaccard's similarity coefficients were the highest when single-ascospore isolates obtained from the same perithecium were compared, medium-high for isolates from different perithecia on the same tree, and lowest when isolates from different trees were compared. (
  • Since AFLP profiles differed also when single-ascospore isolates from the same perithecium were compared, the mating system of N. ditissima is most likely heterothallic. (
  • whether this diversity represents diversification of a founding strain or a mixed infection with distinct strain populations is not clear. (
  • The one patient with distinct profiles contained two strain populations differing at 113 gene loci, including the cag pathogenicity island virulence genes. (
  • The two strain populations in this single host had different spatial distributions in the stomach and exhibited very limited genetic exchange. (
  • Genetic variability influences both the health and long-term survival of populations because decreased genetic diversity has been associated with reduced fitness, such as high juvenile mortality, diminished population growth, reduced immunity, and ultimately, higher extinction risk. (
  • Extinction risk has been associated with low genetic diversity and several researchers have documented reduced fitness in populations with low genetic diversity. (
  • This lower heterozygosity (i.e. low genetic diversity) renders small populations more susceptible to the challenges mentioned above. (
  • Previous investigations have also detected near-identical multilocus genotypes in populations of adult worms - possibly the result of mutations occurring during the asexual (intramolluscan) phase of clonal expansion. (
  • Finally, evidence for heterozygote deficiency caused by small sample size, calls for carefully designed random and comprehensive sampling strategies for S. japonicum in China, where control efforts have greatly fragmented parasite populations. (
  • Knowledge of the weevil genetic structure on a small-scale stand level is extremely important in developing strategies that decrease the possible development of tolerance in P. strobi populations to resistant trees. (
  • Genetic structure of local weevil populations differed over stand age in both interior and Sitka spruce plantations. (
  • The younger and older plots had more single populations associated with individual trees than did middle aged plots. (
  • For example, SSR analysis of an aquatic macrophyte Sparganium emersum revealed significant genotypic diversity between populations in two rivers, the Swalm and Rur. (
  • However, the number of vegetative propagation cycles for the shoot-tip technique used may not be sufficient to eliminate chimeras completely in the mutated populations. (
  • A total of 438 alleles were detected at the 20 MS loci in the two populations. (
  • Statistical analysis of fixation index ( F ST ) and analysis of molecular variance (AMOVA) showed minor, but significant, genetic differences between the wild and hatchery populations ( F ST = 0.0106, CI 95% = 0.003-0.017). (
  • Further studies with additional pen shell samples are needed to conclusively determine the genetic diversity between the wild and hatchery populations. (
  • This chapter considers the complementary approaches necessary for identifying morphospecies, geographical populations characterized by distinct genetic lineages, and sympatric sibling species reproductively isolated by courtship behavior. (
  • Interestingly, we found no association between geographical distance between populations and genetic distance. (
  • The reduction in nucleotide diversity is not expected to be equally apportioned within and among populations. (
  • These results provide a foundation of knowledge for understanding the genetic diversity in sotol populations growing in the Chihuahuan Desert mountains. (
  • These Santa Ana Mountains pumas show strong evidence of a genetic bottleneck and isolation from other populations in California. (
  • Philornis downsi populations have high connectivity within and between islands, with low levels of genetic differentiation between Floreana and the other two islands examined. (
  • In the second study, clonal reproduction in AMF was suggested by complete linkage of alleles at three loci among spores of field populations. (
  • We compared TE loads among populations of D. pulex where sex occurs regularly (cyclical parthenogens or 'sexuals') with those in which the ability to reproduce sexually has been completely lost (obligate 'asexuals') for six different families of DNA transposons. (
  • We investigated the impact of recombination on TE dynamics in natural populations by surveying six families of DNA transposons among populations of Daphnia pulex , an aquatic microcrustacean. (
  • Following all parameters and to avoid the chance of contamination we independently extracted and sequenced the DNA in two different labs and measured the cranial variability in all hominid skulls using 128 cranial landmarks, compiled 3D morphometrics, genetic data of ancient DNA samples and analyzed the admixture and genetic affinities of above three populations. (
  • We first time report any kind of population study on Burmese populations and with the genetic affinity of Burmese with East Asian, East Indian (Including Gadhwal region of Himalaya) and Bangladeshi populations, we found significant admixture with West Eurasians. (
  • The three populations in the present study are quite different in their genetic structure but 3D morphometric study using huge number of landmarks explains a close homology among these populations and this can be explained by the role of climatic signature on these populations. (
  • For example, some researchers assumed that wild populations might have low genetic variability [ 9 - 11 ], while Lu et al. (
  • 5 ] concluded that wild populations might maintain high genetic variation. (
  • Hybridization is considered an important evolutionary force since it may lead to (1) an increase of the intraspecific genetic diversity of the participating populations, (2) the creation of new species, (3) species extinction through genetic assimilation, and (4) the generation of highly invasive genotypes. (
  • In clonal microorganisms, populations consist of one to several distinct clones or lineages, sexual reproduction is absent or limited, and evolution occurs only through the accumulation of favorable spontaneous mutations within independent lineages ( 28 , 43 , 44 , 50 ). (
  • In sexually reproducing populations, favorable combinations of mutations arising in different lineages may be lost through subsequent recombination ( 30 ). (
  • Previous genome-wide ancient DNA studies from the Near East have revealed that at the time when agriculture developed, populations from Anatolia, Iran, and the Levant were approximately as genetically differentiated from each other as present-day Europeans and East Asians are today 24 , 25 . (
  • Prolonged geographical isolation in ecologically similar environments may lead to the fixation of alternate, incompatible mutations in allopatric populations under uniform selection (mutation-order speciation), or genetic drift could facilitate differentiation and speciation, at least when founding populations are small [ 4 , 6 - 9 ]. (
  • In developing countries, the risk of losing genetic diversity and/or particular characteristics of indigenous chicken populations due to inbreeding or crossbreeding has become a serious problem (FAO, 2011). (
  • 2007). To protect genetic diversity, the chicken breeds, strains and populations all over the globe should be genetically characterized. (
  • 2014). Molecular data can be used to provide more accurate information on population structures, genetic variation and breeding patterns of chicken populations for future evaluations (Abebe et al . (
  • The current population genetic structure of a taxon is the result of many factors such as the dispersal capacity of the organism, the degree to which individuals of different populations recognize each other as potential mates, the connectivity of suitable habitats, historical events that impose geographical isolation (e.g. glaciations or elevation of mountains) and interactions with ecologically similar species or predators [ 1 - 4 ]. (
  • Gene flow among populations is fundamentally related to genetic variability within populations. (
  • One major use of DNA techniques is to reveal genetic diversity within and between populations or species. (
  • A discriminant analysis revealed three geographically defined groups and showed that 14 loci explained 87.2% of the genetic differentiation among N. nervosa populations. (
  • The unavoidable mating of related animals in closed populations leads to accumulation of inbreeding and a reduced genetic diversity. (
  • Heterozygosity and allelic diversities can be lost from small, closed, selected populations at a rapid rate. (
  • In order to study the role of the parasite diversity in the pathogenesis of Chagas disease, a comprehensive characterization of the populations found in nature is crucial. (
  • Genetic and paleobotanical evidences indicate that these populations have contributed much to Holocene recolonization of more northern latitudes. (
  • From 986 trees distributed among 54 populations, four distinct multi-locus mitochondrial haplotypes (mitotypes) were detected based on the three nad7 intron 1 haplotypes and two previously reported size variants for nad1 intron B/C. Population differentiation was high ( G ST = 0.657) and the distribution of the mitotypes was geographically highly structured, suggesting at least four genetically distinct ancestral lineages. (
  • RFLP analysis was also the basis for early methods of genetic fingerprinting , useful in the identification of samples retrieved from crime scenes, in the determination of paternity , and in the characterization of genetic diversity or breeding patterns in animal populations. (
  • Nonetheless, moderate founder effects concerning population genetic composition (allele frequencies) were evident, especially for smaller populations. (
  • Advanced marker techniques tend to amalgamate advantageous features of several basic techniques. (
  • The advanced marker techniques also utilize newer class of DNA elements such as retrotransposons, mitochondrial and chloroplast based microsatellites, thereby revealing genetic variation through increased genome coverage. (
  • A genetic marker is a gene or DNA sequence with a known location on a chromosome and associated with a particular gene or trait. (
  • A primer amplifying a dominant marker could amplify at many loci in one sample of DNA with one PCR reaction. (
  • A primer amplifying a co-dominant marker would yield one targeted product. (
  • Thus, as ever higher density molecular marker coverage and dense genetic and even complete genome sequence maps of key crop and model species emerged through the 1990s and early 2000s, genetic and genome knowledge of Vicia faba lagged far behind other grain legumes such as soybean, common bean and pea. (
  • The results obtained could provide a sound basis for the successful application of mutation and molecular marker techniques to improve bananas in the Philippines. (
  • In banana, several DNA marker techniques have been used to investigate genetic relationships between Musa accessions, and to determine differences in somaclonal variants and radiation-induced mutants. (
  • In this study, using a sporeless P. eryngii strain, we constructed a genetic linkage map to introduce a molecular breeding program like marker-assisted selection. (
  • Although the cost of genetic studies that involve genetic mapping, genome-wide association sequencing is decreasing, sequencing the whole genome remains pro- studies, phylogenetic analyses, marker-assisted selection (MAS) and ge- hibitively expensive, particularly in species with large genomes. (
  • Furthermore, this technique is useful in controlling the distri- sites simultaneously and tend to be robust marker platforms. (
  • Microsatellite combines several features of an ultimate molecular marker and they are used increasingly in various plant genetic studies and applications. (
  • andb) selecting the soybean plant or germplasm comprising the at least one allele of one or more marker locus, thereby selecting a soybean plant with tolerance or improved tolerance to herbicides that inhibit protoporphyrinogen oxidase function. (
  • What's more, a universal individual identification method was established and the genetic diversity were analysed in this study as the applications of this marker system. (
  • The review of marker techniques, both those already applied and as yet not applied for study on oilseed rape, is presented here. (
  • Development of a SCAR (sequence characterised amplified region) marker for molecular tagging of the dwarf BREIZH (Bzh) gene in Brassica napus L. Theor. (
  • Marker-assisted increase of genetic diversity in a double-low seed quality winter oilseed rape genetic background. (
  • The genetic variability of four species of the genus Zoysia collected from South Korea was analyzed using an inter-simple sequence repeat (ISSR) marker system. (
  • Considering the potentials of the ISSR marker based genetic diversity analysis, the present study aimed to evaluate the extent of genetic diversity and phylogenetic relationships among four species of genus Zoysia collected from Korea. (
  • The large number of quantitative trait loci (QTLs) mapping studies for diverse crops species have provided an abundance of DNA marker-trait associations. (
  • One area of biotechnology, DNA marker technology, derived from research in molecular genetics and genomics, offers great promise for plant breeding. (
  • Marker choice can bias inferences made using disparate suites of loci. (
  • DNA barcoding marker, ribulose-1,5-bisphosphate carboxylase(rbcL) of the chloroplast DNA (cpDNA) was also used for characterization and identification of the mutants to species level. (
  • Therefore, molecular marker-base characterization has been found very useful complement to phenotypic characterization of new mutants for the purpose of crop improvement and genetic studies. (
  • High density genetic maps facilitate many biological studies including map-based cloning, association genetics and marker assisted breeding. (
  • Molecular marker technology has proved to be an efficient tool for plant genetic resource characterization, conservation, and management. (
  • The use of fluorescently labeled microsatellite marker panels greatly increases the capacity of semiautomated genotyping of a large number of accessions, allowing for a faster and highly informative characterization of genetic resources. (
  • Microsatellites are often referred to as short tandem repeats ( STRs ) by forensic geneticists and in genetic genealogy , or as simple sequence repeats ( SSRs ) by plant geneticists. (
  • No knowledge of the DNA sequence of the targeted genome is required, as the primers will bind somewhere in the sequence, but it is not certain exactly where. (
  • The genome-wide extent of sequence diversity has been determined in exquisite detail by whole-genome sequencing of three unrelated clinical isolates, isolates 26695, J99, and HPAG1 ( 3 , 39 , 53 ). (
  • Development of silkworm strains with ubiquitous female-specific fluorescence for convenient genetic sorting or complete female-specific embryonic lethality for male-only rearing provides a successful example of targeting an insect sex chromosome with genome editing tools, which should assist future sterile insect technique development for pest insects. (
  • A diploid individual with the same maternal and paternal grandfather, for example, will have a much higher chance of being homozygous at any loci inherited from the paternal copies of each of their parents' genomes than would an individual with unrelated maternal and paternal grandfathers (each diploid individual inherits one copy of their genome from their mother and one from their father). (
  • The polymorphic character of a sequence of the human genome comprising approximately 950 base pairs and methods for using it to determine human identification and parentage are disclosed. (
  • In addition to genetic fingerprinting, RFLP was an important tool in genome mapping, localization of genes for genetic disorders, determination of risk for disease, and paternity testing. (
  • SNPs occur in the DNA in 1 out of every 300 nucleotides.In the human genome, this means that there are at least 1 million SNPs in the human's 3 million-nucleotide genome. (
  • The genetic recombination process mediated by crossing over (CO) events is not random along chromosomes and its occurrence can drive molecular evolution and genome organization. (
  • As exemplified above, the evolution of separate sexes can originate from an initial gene, or whole-genome, duplication event, resulting in a situation more permissive of gain-of-function mutations, possibly required for this transition. (
  • Gene-based (genic) microsatellites are a useful tool for plant genetics and simple sequence repeat loci can often be found in coding regions of the genome. (
  • In contrast, genomic microsatellites are usually developed by screening of random DNA fragments from throughout the genome, most of which is non-transcribed. (
  • A single isolate of P. vivax obtained from a febrile patient with clinical malaria from Peru was subjected to whole-genome sequencing (30× coverage). (
  • Because P. vivax cannot be easily propagated in vitro, obtaining genomic DNA sufficient for whole-genome studies is difficult and in the past has required primate infections. (
  • Genome-sequencing efforts required P. vivax isolate Salvador I (SalI) to be amplified in primates to generate enough genomic DNA for sequencing at 10× coverage. (
  • Although the availability of the genome sequence provides new opportunities to discover drug and vaccine targets and to perform gene expression ( 13 , 14 ) and proteomic studies, the lack of worldwide genetic diversity data has hampered population studies. (
  • In brief, a GBS protocol starts with a digestion of the DNA using one or more known restriction enzymes, aiming to reduce the complexity of the genome to be sequenced. (
  • In recent years, we have dramatically changed our view of human genome, from a collection of DNA base pairs that was largely quite stable to one whose very structure can change. (
  • One of the most intriguing types of DNA rearrangements is copy-number variants (CNVs), deletions or duplications of parts of the genome. (
  • Here, to test the hypothesis that the advent and decline of this culture was influenced by movements of people, we generated genome-wide ancient DNA from 22 individuals from Peqi'in Cave, Israel. (
  • The gene of the S-layer protein was amplified from the genome of L. brevis by polymerase chain reaction with oligonucleotides, synthesized according to the N-terminal amino acid sequences, as primers. (
  • They are marks that are readily amplified using primers binding them in a conserved part of the genome flanking the repeat section. (
  • Due to the short primer sequence, many fragments of the genome will be amplified. (
  • Because they do not require whole genome sequencing and require relatively small expenditures for data acquisition, high density genetic linkage maps are currently of great interest. (
  • A novel polymorphic region of the Scots pine mitochondrial genome has been identified, the intron 1 of nad7 , with three variants caused by insertions-deletions. (
  • In the first schematic, a small segment of the genome is being detected by a DNA probe (thicker line). (
  • Analysis of RFLP variation in genomes was formerly a vital tool in genome mapping and genetic disease analysis. (
  • This study aimed to analyze the efficiency of three new microsatellite multiplex panels, which were designed to evaluate a total of 16 loci of the rice genome, based on single PCR reactions of each panel. (
  • These are stretches of at least 200 basepairs (bp) of DNA in the human genome that match identically with corresponding regions in the mouse and rat genomes. (
  • 2004). Induced mutation has been utilized as a tool to generate variation and breeding in a number of vegetatively propagated crops such as banana (Hautea et al. (
  • 2006) and genetic diversity due to somaclonal variation (Lakshmanan et al. (
  • Detection and analysis of genetic variation can help us to understand the molecular basis of various biological phenomena in plants. (
  • this is because of organotropic patterns in genetic variation and the tendency to sample from different organs in differently sized hosts. (
  • It can be described as a variation, which may arise due to mutation or alteration in the genomic loci, that can be observed. (
  • The bottleneck in associating genes and their functions has therefore moved from locating gene candidates to validating their function and the last part of this review covers mutagenesis and genetic transformation, two complementary routes to validating gene function and unlocking novel trait variation for the improvement of this important grain legume. (
  • and Mycobacterium tuberculosis ) have very restricted unselected allelic variation in structural genes, which hinders study of the genetic relationships among strains and strain-trait correlations. (
  • Trait-lineage relationships exist, in part, because pathogenic bacterial species often have a level of genetic diversity far in excess of the variation present in higher eukaryotic organisms such as humans. (
  • Genetic variation in bacteria is due to differences in gene content and nucleotide variation in or between structural genes. (
  • The great bulk of genetic variation at the nucleotide level may not be visible at the phenotypic level. (
  • Barret P, Delourme R, Renard M, Domergue F, Lessire L Delseny M, Roscoe TJ (1998b) A rape-seed FAE1 gene is linked to the El locus associated with variation in the content of erucic acid. (
  • It can also detect variation in DNA profiles of induced mutant clones which are otherwise morphologically indistinguishable, and detect variation between the induced mutant parent clones and their derived suckers. (
  • Induced mutation (either by chemicals or irradiation), coupled with in vitro propagation technique such as shoot-tip culture, has been established as a tool to generate variation in a number of vegetatively propagated crops [2-4]. (
  • Induced mutation (either by chemicals or irradiation) has been established as a tool to generate variation in a number of seed- and vegetatively propagated crops [2-4]. (
  • Where there is intraspecific variation in the degree of domestication, it is possible to study the genetic control of traits of the domestication syndrome in segregating generations of appropriate intraspecific crosses. (
  • Based on the estimated parameters, the middle elevational level had the highest genetic variation. (
  • Information about the amount and partitioning of genetic variation of this fungus could be helpful for improving orchard management strategies and for breeding apple cultivars with high levels of genetically determined resistance. (
  • These surveys revealed a large amount of copy number variation (at least 12,000 CNVs overlapping more than 1,000 genes), most of which represent benign polymorphic changes. (
  • Characterization of mungbean genotypes on the basis of DNA fingerprinting has become an efficient tool to link genotypic variation. (
  • The assessment of genetic variation is a major concern of plant breeders and population genetics. (
  • Adaptation may occur in Symbiodinium through selection acting on both existing genetic variation [ 19 , 20 ] and new genetic variation arising through somatic mutations [ 21 ] and/or genetic recombination. (
  • Characterization and diversity studies on a small collection of Napier grasses have identified a moderate level of genetic variation and highlighted the availability of some good agronomic traits, particularly high biomass production, as a forage crop. (
  • Genetic variation, heritability and genetic gains for growth and stem form traits in open-pollinated progenies test of Eucalyptus cloeziana. (
  • Performance of genetic variation among and within Gallesia integrifolia Vell. (
  • Genetic variation, herdabilities and gains in selection for growth traits in progeny test of Pinus caribaea var. (
  • 2005 ). Such methods provide overall measures of genomic diversity but do not readily provide information on variation at the nucleotide level for gene-coding sequences. (
  • The population structure and biology of a microbial species are determined by the extent, if any, to which recombination contributes to its genetic variation. (
  • Interlocus variation in within-species genetic diversity ( H S ) was low (0.170). (
  • On a per-locus basis, the proportion of total genetic variation due to differences among species (G ST ) was 0.601. (
  • Thus, about 39.9 of genetic variation was within species. (
  • In conclusion, the ISSR assay was useful for detecting genetic variation in the genus Zoysia , and its discriminatory power was comparable to that of other genotyping tools. (
  • In this context, it raises the question of whether the variation in the pathogenicity of the parasite and clinical features of VL may be related to its genetic diversity. (
  • Watterson's neutrality test and Ohta's two-locus analysis of linkage disequilibrium (LD) both suggested that stochastic demographic and environmental factors can partially explain the loci variation observed in the RAPDs. (
  • The role of the last glaciations, as well as some conservation and breeding strategies, may have influenced current genetic variation and fragmentation in this species. (
  • This process has the potential to broaden functional diversity and generate new phenotypic variation that eventually can play a critical role in the origin of new adaptations and important agronomic traits. (
  • Previous work has suggested that both the proximal 5′ flanking region and a polymorphic microsatellite element within that region of the vole Avpr1a gene are associated with variation in V1a receptor (V1aR) distribution and behavior, but neither has been causally linked. (
  • In Caenorhabditis elegans , for example, variation in a single nucleotide of npr-1 , which alters the neuropeptide receptor protein structure , has been shown to be responsible for strain differences in social feeding behavior [9] . (
  • Sequencing of genomic and complementary DNA from affected mice revealed a 38-bp deletion in exon 17, causing a frame shift resulting in ten unique amino acids followed by a premature stop codon ( Supplementary Fig. 1 ). (
  • This question can be answered using various tools, but one of the long-lasting gold standards is to sequence 16S ribosomal RNA (rRNA) gene amplicons generated by domain-level PCR reactions amplifying from genomic DNA. (
  • Detecting somatic mutations from plasma DNA in advanced cancer patients may be potentially preferable when repeated tumor biopsies are not feasible and genomic analysis of archival tumor is deemed insufficient [ 9 ]. (
  • NGSEP includes a module to translate genotype calls to some of the most widely used input formats for integration with several tools to perform downstream analyses such as population structure analysis, construction of genetic maps, genetic mapping of complex traits and phenotype prediction for genomic selection. (
  • Until recently, there has been a general lack of genetic and genomic tools to study species outside of a few model organisms (e.g. (
  • The genomic mechanisms that give rise to phenotypic diversity across species or among individuals within a species are not well understood. (
  • The name "satellite" DNA refers to the early observation that centrifugation of genomic DNA in a test tube separates a prominent layer of bulk DNA from accompanying "satellite" layers of repetitive DNA. (
  • After digesting the genomic DNA with a RE, the DNA fragments are separated by agarose gel electrophoresis, and transferred to a nylon membrane via Southern Blotting (Southern, 1975). (
  • For the UCEs, resequencing of genomic DNA from 72 diploid human samples was performed by the sequencing center at Washington Univer- sity using conventional capillary electrophoresis (CE) methods. (
  • Examples include variable number tandem repeats and highly polymorphic genes such as some surface structure and virulence genes. (
  • The 11 remaining loci were highly polymorphic, exhibited low frequencies of null alleles, and were easy to interpret with the aid of allele binning software. (
  • It is used to analyze the genetic diversity of an individual by using random primers. (
  • RAPDs established 106 major amplified products using 14 primers. (
  • B. subjecting the DNA to an amplification process primed by the set of primers of step (A). (
  • A subset of the restriction fragments are then amplified using primers complementary to the adaptor and part of the restriction site fragments (as described in detail below). (
  • Five primers amplified efficiently presenting between six and 28 alleles per locus. (
  • To address this, amplicons derived from 16S-rDNA were generated from chicken caecal content DNA using different annealing temperatures, primers and different DNA extraction procedures. (
  • In conclusion, existing primers and standard annealing temperatures captured as much diversity as lower annealing temperatures and shorter primers. (
  • The environmental DNA is first amplified by PCR using primers that contain sequencing adapters and barcodes. (
  • Begins with DNA containing a sequence to be amplified and a pair of synthetic oligonucleotide primers that flank the sequence. (
  • Rapidly cool the DNA (37-65˚C) and anneal primers to complementary single-straned sequences flanking the target DNA. (
  • Extend primers at 70-75˚C using a heat-resistant DNA polymerase such as Taq polymerase derived from Thermus aquaticus. (
  • This method uses two locus-specific outer primers that asymmetrically flank the SNP under investigation, and two allele-specific inner primers, which produce a larger fragment for one allele, and a smaller fragment for the second allele. (
  • complementary DNA primers, DNA polymerase, and temperature cycling of the reaction. (
  • The repeat region is amplified using primers homologous to the sequences flanking these repeats (Fig. 12.3). (
  • Its resolving power is much lower than targeted, species-specific DNA comparison methods, such as short tandem repeats. (
  • Insect sex is determined genetically and shows high diversity among different species. (
  • Sex separation methods are critical for commercial aspects of rearing silkworms, and genetic-sexing systems also could serve as the basis for adaptation to sterile insect techniques for pest lepidopteran species. (
  • Toxoplasma gondii has been considered a single species in the genus Toxoplasma . (
  • Genetic diversity is the variability of genes in a species. (
  • The diploid annual legume Medicago truncatula has been developed as a tractable genetic system for studying biological questions that are unique to, or well suited for study in legume species. (
  • nevertheless, there is no available information on the genetic identification on fish stocks of this species in the region. (
  • G ut 2001 ), they provide useful targets for large-scale molecular population genetic studies examining evolutionary relationships among bacterial strains, especially in strongly clonal species. (
  • In addition, the findings of genetic diversity based on SSR analysis may contribute to establishing conservation programs for some endangered species. (
  • Additional cell free DNA species, such as cell-free mitochondrial DNA (mtDNA) are also under evaluation for clinical relevance [ 5 ]. (
  • Adamson RE, Ward RD, Feliciangeli MD, Maingon R (1993) The application of random amplified polymorphic DNA for sandfly species identification. (
  • THE estimation of nucleotide diversity in highly self-fertilizing species ( H amrick and G odt 1989 ) is of considerable theoretical interest to population geneticists. (
  • The large number of spores released by these cultivars also gives rise to various other problems, such as damage to cultivation facilities, reduced commercial value (due to spores deposited on the mushrooms), and depletion of genetic diversity in the natural population of the mushroom species cultivated ( 11 , 34 ). (
  • Genetic diversity, demography, and abundance - biological characteristics that influence population viability - can vary across a species' distribution. (
  • Both the mitochondrial and microsatellite data were consistent with there being a single species across islands. (
  • Arbuscular mycorrhizal fungi (AMF) are important symbionts of most plant species, promoting plant diversity and productivity. (
  • Furthermore, the material originated for each species from a single pot culture and the fungi may not have had the opportunity to recombine with other genotypes from a field. (
  • Hybridization and polyploidization of several (sub)species, combined with vegetative propagation and human selection have produced a complex genetic history. (
  • Estimates from molecular data for the fraction of new nonsynonymous mutations that are adaptive vary strongly across plant species. (
  • However, because of the lack of clear evidence (experimental or biological confirmation) of sexuality in Leishmania parasites, until today it has been suggested and even accepted that Leishmania species were mainly clonal with infrequent genetic recombination (see [1] for review). (
  • Four diversity indices, one of them newly proposed here, are compared in terms of their response to changes in the numbers of individuals and species, in the distribution of the individuals among the species, and in spatial aggregation. (
  • One application of these specific molecular techniques is in defining species and sub-species of salmonids. (
  • This paper puts forth the view that diversity is an average property of a community and identifies that property as species rarity. (
  • Microsatellite loci have been used extensively over the past two decades to study the genetic characteristics of non-model species. (
  • The purpose was to consolidate the numerous genetic resources for this species into a manageable panel and to provide a uniform methodology that improves comparisons between past and future studies. (
  • Certain genes exhibit notable diversity in their expression patterns both within and between species. (
  • This is the first direct evidence that polymorphic microsatellite elements near behaviorally relevant genes can contribute to diversity in brain gene expression profiles, providing a mechanism for generating behavioral diversity both at the individual and species level. (
  • Due to the high homogeneity demonstrated by DNA-DNA hybridisation studies, it was suggested that the entire genus should be one species [ 4 ]. (
  • Our selected SSR loci set can be used for larger genetic studies of fig germplasm, and a similar approach can be adopted for other fruit species. (
  • The molecular epidemiology of the isolates was investigated using two different typing methods: PCR-based amplification of the species-specific repetitive polymorphic CKRS-1 sequence and multilocus sequence typing. (
  • This diversity originates ed 107 Helicobacter pylori clones from biopsied specimens from both the clonal nature of the species and interstrain taken from both parents and four children. (
  • The observation that many alien species become invasive despite low genetic diversity has long been considered the 'genetic paradox' in invasion biology. (
  • Despite the initially low genetic diversity, this species seems to be successful at persisting across its invaded range, and will likely continue to build up higher genetic diversity at the local scale. (
  • This clearly illustrates how temporal dynamics affect genetic diversity patterns of invasive aliens species after initial invasion, which can, in turn, determine the long-term success of these species in their invaded range [ 3 ]. (
  • Furthermore, since not only the invasive species' fitness and population persistence, but also its long-term ecosystem impacts and success of potential eradication or control measures are dependent on its population genetic diversity, it is important to understand how these temporal dynamics will affect its population genetic structure [ 3 , 15 , 16 ]. (
  • Development and diversity of Andean-derived, gene-based microsatellites for common bean (Phaseolus vulgaris L. (
  • In the latter case, alleles of genic microsatellites can be associated with structural mutations that lead to novel proteins that are larger or smaller than those of the original alleles and which can have substituted or repeated amino acids. (
  • A total of 160 primer pairs were designed to screen for polymorphic microsatellites using the selected tetranucleotide microsatellite sequences. (
  • A total of 154,677 tetranucleotide microsatellites were identified and 15 of them were discovered as the polymorphic and stable loci. (
  • Here we combine population genetic methods (microsatellites) with phylogenetic information (mtDNA) to define genetic population clusters of the wide-spread Neotropical túngara frog ( Physalaemus pustulosus ). (
  • Microsatellites and their longer cousins, the minisatellites , together are classified as VNTR (variable number of tandem repeats ) DNA. (
  • Other microsatellites are located in regulatory flanking or intronic regions of genes, or directly in codons of genes - microsatellite mutations in such cases can lead to phenotypic changes and diseases, notably in triplet expansion diseases such as fragile X syndrome and Huntington's disease . (
  • Among these, polymerase chain reaction (PCR)-based molecular techniques have been useful for the genetic characterization of T. gondii . (
  • The impacts of early DNA-based approaches are summarized, but most molecular examples refer to methods based on polymerase chain reaction. (
  • Inter simple sequence repeat (ISSR) technique is a polymerase chain reaction (PCR) based technique, reported by Zietkiewicz et al. (
  • A number of means can express the level of genetic diversity: observed heterozygosity, expected heterozygosity, the mean number of alleles per locus, or the percentage of polymorphic loci. (
  • It can also improve our understanding about microevolution through a better understanding of selection, mutation, assertive matting, and recombination. (
  • However, even very low levels of recombination can effectively prevent the process of genetic degeneration observed in non-recombining chromosomes (Haddrill et al. (
  • Conclusive evidence for inter-lineage recombination and introgression in this genus will require either direct observational evidence or a single-cell genotyping approach targeting multiple, single-copy loci. (
  • We addressed the question of recombination in the AMF Glomus intraradices by sequencing 11 polymorphic nuclear loci in 40 morphologically identical isolates from one field. (
  • Recombination was detected among sequence variants present within single isolates. (
  • Genetic diversity was found among spores but no evidence of recombination. (
  • Ideally, a much larger number of polymorphic loci should be investigated to draw conclusions about recombination. (
  • Recombination provides a mechanism by which the rate of both TE gain and loss can be accelerated, a duality that has long intrigued many biologists interested in the influence of sex on mutation accumulation. (
  • Asexuals, however, have proportionally more singletons (loci occupied in a single isolate), which differs from previous studies where selfing and outcrossing were used as a proxy for high and low recombination. (
  • Here, we applied population genetic approaches to demonstrate that a population of C. neoformans serotype A clinical isolates from Botswana contains an unprecedented proportion of fertile MAT a isolates and exhibits evidence of both clonal expansion and recombination within two partially genetically isolated subgroups. (
  • Indeed, the first study experimentally evidenced genetic recombination and proposed that Leishmania parasites are capable of having a sexual cycle consistent with meiotic processes inside the insect vector. (
  • It is also used in identification of recombination rate in the loci between restriction sites. (
  • Arus P, Orton TJ (1983) Inheritance and linkage relationships of isozyme loci in Brassica oleracea . (
  • Understanding of the genetic control of elements of the domestication syndrome is improving as a result of the development of saturated linkage maps for major crops, identification and mapping of quantitative trait loci, cloning and sequencing of genes or parts of genes, and discoveries of widespread orthologies in genes and linkage groups within and between families. (
  • Inheritance and linkage relationships of isozyme loci in Brassica oleracea. (
  • Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. (
  • They are also used in genetic linkage analysis to locate a gene or a mutation responsible for a given trait or disease. (
  • Introduction Genetic linkage mapping dates back to the early 20th century when scientists began to understand the recombinational nature and cellular behavior of chromosomes. (
  • In 1913 Sturtevant studied the first genetic linkage map of chromosome X of Drosophila melanogaster [1]. (
  • If researchers were trying to initially determine the chromosomal location of a particular disease gene, they would analyze the DNA of members of a family afflicted by the disease, and look for RFLP alleles that show a similar pattern of inheritance as that of the disease (see genetic linkage ). (
  • This makes the method popular for comparing the DNA of biological systems that have not had the attention of the scientific community, or in a system in which relatively few DNA sequences are compared (it is not suitable for forming a cDNA databank). (
  • The analysis of 16S-rDNA sequences to assess the bacterial community composition of a sample is a widely used technique that has increased with the advent of high throughput sequencing. (
  • Out of 886 high quality sequences, 497 had complete microsatellite loci that were not truncated by the sequencing reaction and of these tri-nucleotide repeats were more common than di-nucleotide repeats. (
  • We've learned that higher-order structural features, such as specific configurations of repeated base pair sequences, can predispose for DNA rearrangements. (
  • Alternative explanations such as recurrent mutations or sequences from contaminating microorganisms could also explain these results because the AMF were not cultivated in clean culture prior to analysis. (
  • PCR, "discovered" in 1983 by Kary Mullis, enables the amplification (or duplication) of millions of copies of any DNA sequence with known flanking sequences. (
  • A large number of SNPs between two sequences may indicate a more distant genetic relationship. (
  • The amplified atpD coding sequences were inserted into the pCRT7/CT-TOPO vector using TA-cloning strategy and transformed in Escherichia coli. (
  • SSR, also known as microsatellite, is most widely used in the study of genetic diversity of aquatic plants due to its high abundance, high variability, and codominance. (
  • All loci were easily amplified and demonstrated allelic variability, with the number of alleles ranging from 5 to 35 in the wild population and from 5 to 22 in the farmed population. (
  • Genetic analysis is important to identify genetic variability in organisms inhabiting a specific region. (
  • The optimum sample size to determine genetic variability in sotol was from 24 to 26 plants. (
  • Although microsatellite loci analyses [ 3 - 8 ] have been used to assess the genetic variability and evaluate the population size for giant pandas, the genetic status of the giant panda is still matters of significant controversy. (
  • this allows them to accumulate mutations unhindered over the generations and gives rise to variability that can be used for DNA fingerprinting and identification purposes. (
  • C. in each of the samples, separating by size the DNA fragments generated in step (B). (
  • In RFLP analysis the DNA sample is broken into pieces (digested) by restriction enzymes and the resulting restriction fragments are separated according to their lengths by gel electrophoresis. (
  • To begin, both mosquito and microbial small and large subunit rRNA fragments are amplified from a metagenomic community DNA sample. (
  • The central component of all these protocols is the digestion of the initial DNA with known restriction enzymes, to generate sequencing fragments at predictable and reproducible sites. (
  • bacterial artificial chromosome (BAC) Artificial chromosome vector derived from bacteria used for cloning relatively large DNA fragments. (
  • In contrast, CEL-I digestion of mixed fragments produced from test and reference DNA reliably pinpointed the correct genotypes, yet scoring of the genotypes became complicated when multiple SNPs were present in the PCR fragments. (
  • These amplified fragments can then be separated through agarose gel electrophoresis (Fig 12.1). (
  • In RFLP analysis , a DNA sample is digested into fragments by one or more restriction enzymes , and the resulting restriction fragments are then separated by gel electrophoresis according to their size. (
  • The DNA fragments produced by the digest are then separated by length through a process known as agarose gel electrophoresis and transferred to a membrane via the Southern blot procedure. (
  • Hybridization of the membrane to a labeled DNA probe then determines the length of the fragments which are complementary to the probe. (
  • Our data suggest that humans are infected with a population of closely related strains that vary at a small number of gene loci, that this population of strains may already be present when an infection is acquired, and that even during superinfection genetic exchange among distinct strains is rare. (
  • Early studies on the parasite strains from North America and Europe identified limited genetic diversity, which were classified into genetic types I, II, and III [ 16 ]. (
  • sSNP genotyping rapidly delineates relationships among closely related strains of pathogenic microbes and allows construction of genetic frameworks for examining the distribution of biomedically relevant traits such as virulence, transmissibility, and host range. (
  • for estimating genetic relationships among M. tuberculosis strains and for studying relationships between strain genotype and patient phenotype. (
  • Furthermore, the use of multilocus sequence typing indicated similar results and divided strains of V. vulnificus into genetic lineages ( 24 ). (
  • Some differences in genetic content between strains can be explained by the presence of polynucleotide tracts in hypervariable loci, including those encoding the lipo-oligosaccharide (LOS), flagellar biosynthesis, and the polysaccharide capsule ( 60 ). (
  • Finally, the presence/absence of specific loci can be found in both distantly and closely related strains. (
  • 2008. Phylogenetic backgrounds and virulence profiles of atypical enteropathogenic Escherichia coli strains from a case-control study using multilocus sequence typing and DNA microarray analysis. (
  • Efforts should be made to incorporate the other local chicken strains as unique genetic resources into conservation programmes. (
  • Brasil Morpho-biological diversity of Trypanosoma cruzi has been known since Chagas first works in Several further studies confirmed the morphological differences among the parasite strains, which were isolated from different reservoirs and vectors, as well as from human beings. (
  • T. cruzi genotypic characterization, initially carried out by schizodeme analysis and more recently by various other techniques, has shown a great diversity of the parasite strains. (
  • We report elucidation of a novel regulatory function for interleukin receptor-associated kinase (IRAK)-1 binding protein 1 (IRAK1BP1, also known as SIMPL) through quantitative trait locus mapping of the TLR response in wild-derived mouse strains. (
  • Furthermore, these results show that the genetic diversity of wild-derived mouse strains makes them a valuable model of important human gene functions that have been lost in some laboratory-inbred strains. (
  • Among the ∼450 established inbred mouse strains, most descended from a restricted number of founder animals derived from the Mus musculus group of subspecies, and thus have rather limited genetic diversity. (
  • To assess the genetic strated that strains have circulated within the family. (
  • The values of genetic difference indicate an absence of population structure (F ST =0.0075 and R ST =0.016, p=0.051) and similarity in the allele frequencies, defined by Nei's index (0.805). (
  • A total number of 182 alleles were detected with an average value of 9.1 allele per locus. (
  • The SNP has advantages, among them: having zero rate of recurring mutation, the likelihood of mutation is negligible due to automated typing, the nature of Dialogic means that allele is a qualitative issue, but not a quantitative issue, and because of that, it is more amenable to automation. (
  • Each fragment length is considered an allele , whether it actually contains a coding region or not, and can be used in subsequent genetic analysis. (
  • In allele a , restriction site 2 has been lost by a mutation , so the probe now detects the larger fused fragment running from sites 1 to 3. (
  • I aggregated the small number of polymorphic sites found in more than 300 UCEs and analyzed the result- ing derived allele frequency (DAF) spectrum to show that the UCEs as a whole are under negative (purifying) selection that is much stronger than that in protein coding genes. (
  • Removal of individuals bearing duplicate MLGs (as a correction for presumed clonal expansion) had an impact on both HWP and organotropic genetic differentiation. (
  • Middle-aged plots had increased beetle movement regardless of the number of weevil larvae per leader, increased number of females ovipositing per tree and less weevil genetic differentiation between trees. (
  • We found low genetic differentiation between islands and strong evidence for inter-island gene flow, or shared recent ancestry among individuals. (
  • There was no evidence of genetic differentiation between habitats and molecular variance was mainly attributable to within individuals. (
  • Genetic differentiation (Fst) values were found in the ranges 0.443 to 0.747 with an average of 0.686 and gene flow (Nm) values ranged from 0.085 to 0.314 with an average of 0.237. (
  • I found a remarkable hierarchical structure of differentiation mechanisms in space and time: neutral and mutation-order processes are older and occur mainly between regions, whereas more recent adaptive processes are the main driver of genetic differentiation and reproductive isolation within regions. (
  • We furthermore observe that I. glandulifera experiences significant among-population gene flow, gradually resulting in higher genetic diversity and lower overall genetic differentiation through time. (
  • The method is based on restriction enzyme (RE) digestion and DNA hybridization. (
  • The basic technique for the detection of RFLPs involves fragmenting a sample of DNA with the application of a restriction enzyme , which can selectively cleave a DNA molecule wherever a short, specific sequence is recognized in a process known as a restriction digest . (
  • The results obtained from both morphological and molecular analyses show that more point mutations were generated by irradiation with fast neutrons than with gamma rays. (
  • Using microsatellite data in Bayesian clustering and landscape genetic analyses, we examine gene flow and dispersal in P. downsi between three islands and across habitats (highlands, lowlands) and examine for the presence of population bottlenecks. (
  • Ancient DNA analyses on the remains of the Hunnu people had shown some clues to this problem. (
  • The Northern genetic lineage (NW Costa Rica) is genetically homogenous while the Southern lineage (SW Costa Rica and Panama) is sub-divided into three population clusters by both microsatellite and mtDNA analyses. (
  • Genetic diversity and phylogenetic analyses are important tools for plant breeding and genetic research because they provide information that forms the basis for conservation and utilization of genetic resources in crop improvement. (
  • Heterozygosity, a fundamental measurement of genetic diversity in population genetics, plays an important role in determining the chance of a population surviving environmental change, novel pathogens not previously encountered, as well as the average fitness of a population over successive generations. (
  • Female-male pairings appeared to be random and there was no evidence for mate choice by heterozygosity. (
  • Population genetic diversity, polymorphic loci, Nei's unbiased heterozygosity, average and effective number of alleles, and optimum number of samples were determined. (
  • Genetic diversity determines the potential fitness of a population and ultimately its long-term persistence, because genes encode phenotypic information. (
  • As the modes of action of the genes involved in domestication and the metabolic pathways leading to particular phenotypes become better understood, it should be possible to determine whether similar phenotypes have similar underlying genetic controls, or whether human selection in genetically related but independently domesticated taxa has fixed different mutants with similar phenotypic effects. (
  • Genetic resources stored in gene banks are usually sampled with the purpose of evaluating and utilizing them efficiently, as well as studying phenotypic and genotypic diversity, identifying duplicate accessions, and forming core subsets. (
  • Inbreeding has a deleterious effect on additive genetic variance as well as on phenotypic values and also affects fitness traits by accumulation of deleterious recessive alleles in the population ( Falconer and Mackay, 1996 ). (
  • Domesticated forms of wheat demonstrate an incredible level of phenotypic diversity and the ability to adapt to various habitats. (
  • Behavior is a trait that is particularly well suited for exploring genetic mechanisms underlying phenotypic plasticity, as it is an evolutionarily labile trait. (
  • However, it is likely that a significant portion of phenotypic diversity is derived from mutations that alter gene expression [10] - [13] . (
  • Application of molecular tools for characterization and diversity assessment has been found useful to complement phenotypic evaluation of plant population. (
  • The development of molecular techniques for genetic analysis has led to a great augmentation in our knowledge of crop genetics and our understanding of the structure and behavior of various crop genomes. (
  • Although now largely obsolete, RFLP analysis was the first DNA profiling technique cheap enough to see widespread application. (
  • 1997). Therefore, it has been a powerful technique for genetic analysis (Chapco et al. (
  • A common theme that has emerged from molecular population genetic analysis of pathogenic bacteria is that biomedically relevant traits, such as host range and virulence, are nonrandomly distributed among phylogenetic lineages ( M usser 1996 ). (
  • Non-DNA techniques include multilocus enzyme electrophoresis and cuticular hydrocarbon analysis. (
  • Landscape genetic analysis identified two genetic clusters: one encompassing Santa Cruz and Isabela, and one on Floreana Island. (
  • However, the in hospite population genetic structure of Symbiodinium is poorly understood and mostly based on analysis of bulk DNA extracted from thousands to millions of cells. (
  • The diversity of this organism has been observed by a number of techniques including pulsed-field gel electrophoresis (PFGE) ( 82 ), subtractive hybridization ( 2 ), microarray analysis ( 16 , 42 , 61 , 64 , 65 ), and multilocus sequence typing (MLST) ( 71 ). (
  • Cool to 4˚C and store or use amplified PCR product for analysis. (
  • The individual identification method and the genetic diversity analysis method in this study provided adequate material for the future study of giant panda. (
  • The methods include pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), multilocus variable-number tandem repeat (VNTR) analysis, DNA microarrays, and mass spectrometry. (
  • 2009. Multiple-locus variable-number tandem repeat analysis for subtyping of Salmonella enterica subsp. (
  • They are widely used for DNA profiling in cancer diagnosis , in kinship analysis (especially paternity testing ) and in forensic identification. (
  • Sequence analysis revealed insertions/deletions (InDels) and base substitutions as the two main classes of mutations induced in the plastid DNA of the mutants studied. (
  • Diversity Analysis in Ocimum Sp. (
  • The technique for RFLP analysis is, however, slow and cumbersome. (
  • A sample of 548 accessions of traditional upland rice landraces collected in Brazil in the last 25 years was genotyped, a database of allelic frequencies was established, estimates of genetic parameters were performed and analysis of genetic structure of the collection was developed. (
  • Genetic structure analysis of the collection using a Bayesian approach detected three possible major clusters, with an overall F ST value of 0.177. (
  • The three multiplex panels described here represent a powerful tool for rice genetic analysis, offering a rapid and efficient option for rice germplasm characterization. (
  • SNPs typically arise through sporadic mutation, so they represent a means of measuring random genetic drift. (
  • About 1% and 24% of discovered SNPs were loss-of-function and non-synonymous mutations, respectively. (
  • Four-cutter RFLP data were collected at one mitochondrial and three nuclear loci from 115 isolines representing 11 worldwide population collections, as well as from seven commonly used ecotypes. (
  • Our present study is the first to recover, amplify and sequence (HVR and coding regions of mtDNA) inadequately preserved and highly degraded (1.5 Ky to ≤1.0 Ky ago) hominids mitochondrial DNA of three most intriguing and indigenous ancient population of South and South-East Asia (Myanmar=20 Buried individuals, Nicobar Islands=15 and Andaman Island=6). (
  • Therefore, these arrays have been widely used for germplasm charac- Genotyping by multiplexing amplicon sequencing (GBMAS) (Lab 5-12 terization and quantitative trait locus (QTL) mapping. (
  • We conclude that Ecotilling is suitable for diversity studies in Musa , that it can be considered for functional genomics studies and as tool in selecting germplasm for traditional and mutation breeding approaches. (
  • In this article, we proposed six simple sequence repeat (SSR) loci as a sufficient tool to characterize fig ( Ficus carica L.) germplasm in Morocco maintained in an ex situ collection. (
  • It contributes to the advancement of research on large scale characterization and management of germplasm banks, as well as identification, protection and assessments of genetic relationship of rice germplasm. (
  • Domestication is generally considered to be the end-point of a continuum that starts with exploitation of wild plants, continues through cultivation of plants selected from the wild but not yet genetically different from wild plants, and terminates in fixation, through human selection, of morphological and hence genetic differences distinguishing a domesticate from its wild progenitor. (
  • Genetic diversity study is also important in crop breeding for the purpose of selecting genetically distant lines that are suitable for the production of heterotic hybrids [4] as well as for characterization and conservation of mutant lines. (
  • Our study suggests sufficiently high numbers of genetically diverse founders during population re-establishment, which prevent the erosion of local genetic diversity. (
  • The diagnosis and genetic characterization of T. gondii infection is crucial for the surveillance, prevention and control of toxoplasmosis. (
  • In this review, we summarize conventional non-DNA-based diagnostic methods, and the DNA-based molecular techniques for the diagnosis and genetic characterization of T. gondii . (
  • The molecular dissection of plant growth and development in model plants such as Arabidopsis has largely relied on genetic approaches involving the isolation and subsequent characterization of mutants affected in specific biological processes. (
  • Characterization of the genetic capacity and functionality of the gut community will provide insight into the effects of gut microbiota on mosquito life traits. (
  • It is, therefore, an ideal material for genetic characterization based on molecular technology. (
  • Therefore, if a mutation has occurred in the template DNA at the site that was previously complementary to the primer, a PCR product will not be produced, resulting in a different pattern of amplified DNA segments on the gel. (
  • [34] . ISSR technique involves PCR amplification of DNA using a single primer composed of a microsatellite sequence. (
  • Here, we describe a W chromosome-based, genetic-sexing system combining transcriptional activator-like effector nucleases and CRISPR/Cas9 technologies in B. mori . (
  • More recently, SNP-based genetic maps have permitted chromosome intervals of interest to be aligned to collinear segments of sequenced legume genomes such as the model legume Medicago truncatula , which in turn opens up the possibility for hypotheses on gene content, order and function to be translated from model to crop. (
  • banding The differential staining of a chromosome by a variety of techniques that results in a specific pattern of positively and negatively stained bands for each chromosomal pair. (
  • The Y chromosome diversity is well associated with linguistic families in East Asia. (
  • Also, we review some of the tools employed for hybrid recognition and their pattern of expression in hybrid individuals (morphological, chemical, chromosome number, and DNA fingerprinting techniques). (
  • We emphasize that even when chromosome number, morphological characters, and chemical characters are of limited use for hybrid recognition in the absence of DNA fingerprinting techniques, their exploration may give insights of the ecological performance of hybrids. (
  • We estimated the allelic diversity of 20 isolates taken bers showed natural mixed infection. (
  • Eight major clusters of related genotypes were identified in M. tuberculosis sensu stricto, including a single cluster representing organisms responsible for several large outbreaks in the United States and Asia. (
  • Moreover, sSNP genotypes can be readily analyzed with computational tools developed over decades of population genetic research. (
  • Over all Nei's genetic distance value (D) obdervedfrom nil to 2.706 among 861accessions pair resulting as a means of permutation combination of 42 mungbean genotypes. (
  • The UPGMA dendogram based on Nei's genetic distance separated the genotypes, BARI mung-1 and BD6906 from other 40 genotype. (
  • Local breeding goals, including collection, evaluation and conservation of such chicken genotypes as genetic resources, are needed to permit selection for unforeseen requirements in the future and to serve as a source of research materials (Tadano et al . (
  • A measure of genetic diversity of genotypes to be used as parents is imperative to use them prudently in crop improvement. (
  • Eighteen very similar genotypes were detected by MLMT, most of them differed in only one locus and no correlation was found between MLMT profiles, geographical origin or the estimated population structure. (
  • Eighty-five alleles with a mean number of six alleles per locus were observed in 62 distinct genotypes. (
  • To examine this issue, we analyzed multiple single-colony isolates from two to four separate stomach biopsies of eight adult and four pediatric patients from a high-incidence Mexican population. (
  • The total genetic divergence and pairwise genetic divergence between isolates from adults and isolates from children were not statistically different. (
  • We also analyzed isolates obtained 15 and 90 days after experimental infection of humans and found no evidence of genetic divergence, indicating that transmission to a new host does not induce rapid genetic changes in the bacterial population in the human stomach. (
  • Molecular tools may provide a better understanding of the genetic and the epidemiological relationships between environmental and clinical isolates and thereby allow assessment of potential routes of transmission. (
  • Genetic similarity among the studied isolates was illustrated with a principal coordinate analyseis (PCoA) and a dendrogram. (
  • Finally, nucleotide sequencing of the flgR gene revealed the presence of a single residue that was different in the FlgR proteins of the C. jejuni Turkey and CS isolates. (
  • Such genetic diversity has been problematic in studies attempting to distinguish pathogenic from nonpathogenic isolates. (
  • Aeschbacher and Piffaretti ( 1 ) reported that there was no clustering of animal and human isolates based on multilocus enzyme electrophoresis using nine polymorphic loci. (
  • Interestingly, despite this genetic homogeneity, most of the isolates clustered according to their geographical origin. (
  • clinical heterogeneity Refers here to the production of clinically different phenotypes from mutation in the same gene. (
  • Such information is likely to have a profound effect on the success of genetic improvement and completes information from phenotypes and biometric measurements of the domestic chickens in Egypt. (
  • Estimates of genetic parameters and gains from selection for growth traits in Pinus caribaea var. (
  • This diversity has been successfully used to map traits such as flavivirus ( 19 ) and Salmonella typhimurium susceptibility ( 20 ), as well as resistance to lethal shock induced by TNF-α ( 21 ). (
  • Insight into such interactions is critical to understanding large-scale patterns of organismal diversity. (
  • We analyzed DNA samples from 97 pumas sampled between 2001 and 2012. (
  • The diversity index for the multiplex combination of di-, tri-, and tetranucleotide repeats ranged from 0.9784 to 0.9968. (
  • Interpopulation nucleotide diversity was also consistently low among the loci, averaging 0.0014. (
  • 2004 ). First described for Arabidopsis ecotypes (hence Ecotilling) it has since been shown to be an accurate, low-cost and high-throughput method for the discovery and evaluation of nucleotide diversity in humans, switchgrass, poplar, melon and other organisms (Gilchrist et al. (
  • 2004), PCR-RFLP of kinetoplast DNA (kDNA) minicircles (Morales et al. (
  • RFLP tests require much larger samples of DNA than do short tandem repeat (STR) tests. (
  • These microsatellite loci may be valuable for future aquaculture and population genetic studies for developing conservation and management plans. (
  • Theory predicts that the number of seeds during re-establishment, and the levels of among-population gene flow can strongly affect recolonization dynamics, resulting in either an erosion or build-up of population genetic diversity through time. (
  • This study focuses on temporal changes in the population genetic structure of the annual invasive plant Impatiens glandulifera across Europe. (
  • It requires a large amount of sample DNA, and the combined process of probe labeling, DNA fragmentation, electrophoresis, blotting, hybridization, washing, and autoradiography can take up to a month to complete. (
  • 1993), the paucity of isozyme loci restricts their usefulness in breeding (Helentjaris et al. (
  • A series of Random Amplified Polymorphic DNA-based genetic studies mainly targeted at quantitative loci underlying resistance to a series of biotic and abiotic stresses were conducted during the 1990's and early 2000s. (
  • At present, many P. vivax studies still rely on a small set of polymorphic antigens such as circumsporozoite protein, merozoite surface proteins, and apical membrane antigen (AMA-1) to assess diversity ( 15 - 20 ). (
  • Many recent studies have established an important role for rare CNVs, both inherited and de novo (arising as new mutations in the parental germline), in the origin of neurodevelopmental disorders such as autism spectrum disorders, intellectual dysfunction, epilepsy, and attention deficit disorder, as well as psychiatric disorders, most notably schizophrenia. (
  • In the case of schizophrenia, for example, a recent collaborative study including most of the data generated in all genetic studies of schizophrenia to date found definitive evidence for eight such CNV risk loci, which collectively, are carried by a small fraction (1-2 percent) of people with schizophrenia. (
  • This study confirms the finding of previous studies that túngara frogs diverged into two allopatric genetic lineages north and south of the gap in the distribution in central Costa Rica several million years ago. (
  • The ISSR has mild technical difficulty, good reproducibility and reasonable cost, permitting its use for genetic studies of population. (
  • Here, we use the geographic distribution of previous studies to identify microsatellite loci for white-tailed deer ( Odocoileus virginianus ) with the potential for widespread use, and we evaluate the effectiveness of this panel in a portion of the range where few previous studies have been conducted. (
  • This review article focuses on the applications of advanced genomics mainly demographic, adaptive genetic variations, inbreeding, hybridization and introgression, and disease susceptibilities, in the conservation of threatened biota. (
  • Aransay AM, Scoulica E, Tselentis Y, Ready PD (2000) Phylogenetic relationships of phlebotomine sandflies inferred from small subunit nuclear ribosomal DNA. (
  • The recessive mutation arose in the BALB/cByJ genetic background and caused an overt neurological phenotype. (