PCR-based amplicon length polymorphisms(ALPs) at microsatellite loci and indels from non-coding DNA regions of cloned genes as a means of authenticating commercial Japanese green teas

2004 ◽  
Vol 84 (8) ◽  
pp. 895-902 ◽  
Author(s):  
Shiv Shankhar Kaundun ◽  
Satoru Matsumoto
Keyword(s):  
Microsatellite Loci ◽  
Length Polymorphisms ◽  
Amplicon Length

Classification of rice germplasm. II. Discrimination of indica from japonica via analysis of amplicon length polymorphisms

1998 ◽  
Vol 17 (8) ◽  
pp. 640-645 ◽  
Author(s):  
J. Xu ◽  
S. V. Constantino ◽  
G. Magpantay ◽  
J. Bennett ◽  
S. Sarkarung ◽  
...  
Keyword(s):  
Rice Germplasm ◽  
Length Polymorphisms ◽  
Amplicon Length

The use of DNA markers to map anthelmintic resistance loci in an intraspecific cross of Haemonchus contortus

Parasitology ◽  
2009 ◽  
Vol 137 (4) ◽  
pp. 705-717 ◽  
Author(s):  
P. W. HUNT ◽  
A. C. KOTZE ◽  
M. R. KNOX ◽  
L. J. ANDERSON ◽  
J. McNALLY ◽  
...  
Keyword(s):  
Dna Markers ◽  
Haemonchus Contortus ◽  
Anthelmintic Resistance ◽  
Field Isolate ◽  
Laboratory Strain ◽  
Drug Resistant ◽  
Drug Classes ◽  
Length Polymorphisms ◽  
Amplicon Length ◽  
Neutral Markers

SUMMARYThe use of DNA markers to track the development of anthelmintic resistance in parasites of livestock would allow informed choices for the management of this important problem. We describe a genetic mapping approach for the discovery of DNA markers for anthelmintic resistance in Haemonchus contortus. We crossed a multi-drug resistant field isolate of H. contortus with a well-characterized laboratory strain susceptible to 4 drug classes. The F2 were separately selected with 5 anthelmintics from 4 drug classes, producing drug-resistant populations carrying gene variants derived from both the field isolate and the laboratory strain. Individual F2 worms were analysed using amplicon length polymorphisms (ALPs). We looked for field isolate alleles over- or under-represented in F2 populations compared to the unselected F2 and/or the laboratory strain. The data we obtained suggest that marker association can be used to link neutral markers with resistance, but also that more markers and perhaps more inbred laboratory strains would make the procedure more likely to succeed.

scholarly journals A Generic Estimation of Population Subdivision Using Distances Between Alleles With Special Reference for Microsatellite Loci

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 1061-1064 ◽  
Author(s):  
Yannis Michalakis ◽  
Laurent Excoffier
Keyword(s):  
Special Reference ◽  
Genetic Markers ◽  
Fragment Length ◽  
Microsatellite Loci ◽  
Population Differentiation ◽  
Population Subdivision ◽  
Recent Past ◽  
Data Types ◽  
Length Polymorphisms ◽  
Restriction Fragment Length

Abstract Several estimators of population differentiation have been proposed in the recent past to deal with various types of genetic markers (i.e., allozymes, nucleotide sequences, restriction fragment length polymorphisms, or microsatellites). We discuss the relationships among these estimators and show how a single analysis of variance framework can accomodate these qualitatively different data types.

scholarly journals Unexpected vagaries of microsatellite loci inGlomus intraradices: length polymorphisms are rarely caused by variation in repeat number only

2008 ◽  
Vol 180 (3) ◽  
pp. 568-570 ◽  
Author(s):  
Natarajan Mathimaran ◽  
Laurent Falquet ◽  
Kurt Ineichen ◽  
Cyril Picard ◽  
Dirk Redecker ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Repeat Number ◽  
Length Polymorphisms

scholarly journals Isolation of Microsatellite Loci in Sceloporus grammicus (Squamata, Phrynosomatidae)

2004 ◽  
Vol 2 (4) ◽  
Author(s):  
Patrick Degnan ◽  
Elisabeth Arévalo
Keyword(s):  
Microsatellite Loci ◽  
Genomic Library ◽  
Chromosomal Rearrangements ◽  
Pcr Primers ◽  
Length Polymorphisms ◽  
Transitional Environment ◽  
Sceloporus Grammicus ◽  
Partial Genomic Library ◽  
Nucleotide Repeats ◽  
Flanking Regions

The mesquite lizard (Sceloporus grammicus) exhibits multiple Robertsonian chromosomal rearrangements (mainly centric fissions) resulting in several cytotypes. In a transitional environment from oak-pine forests to a drier xeric habitat in central Mexico, two cytotypes (F5: 2n = 34 and FM2: 2n = 46) are known to hybridize. A partial genomic library was constructed from S. grammicus genomic DNA and then screened for microsatellites. Microsatellites are short tandem nucleotide repeats that have near universal occurrence in all eukaryotic genomes. Microsatellites exhibit variable length polymorphisms that can be characterized and utilized as genetic markers for population studies. Thirteen microsatellite arrays were isolated from the S. grammicus genomic library and PCR primers were designed in the flanking regions for the amplification of these alleles. These microsatellite loci would be the primary tool used to answer behavioral, ecological, chromosomal and evolutionary questions that influence the maintenance of this hybrid zone.

A comparison of sequence and length polymorphism for genotyping Cryptosporidium isolates

Parasitology ◽  
2015 ◽  
Vol 142 (8) ◽  
pp. 1080-1085 ◽  
Author(s):  
G. WIDMER ◽  
S. M. CACCIÒ
Keyword(s):  
Distance Measures ◽  
Sequence Length ◽  
Weak Correlation ◽  
Nucleotide Substitutions ◽  
Simple Sequence Repeat Markers ◽  
Genotyping Method ◽  
Length Polymorphisms ◽  
Amplicon Length ◽  
Length Data ◽  
Simple Sequence

SUMMARYSimple sequence repeat markers have played an important role in elucidating the epidemiology of human and animal cryptosporidiosis. The drawback of sequence length polymorphisms is that nucleotide substitutions remain undetected. As some laboratories have opted for using length polymorphisms, while others have relied on sequencing, there is a need to compare both methods. We used a diversified set of unique length polymorphisms and matching nucleotide sequences to assess the ability of each genotyping protocol to discern clusters of related Cryptosporidium parvum isolates. We found a weak correlation between the two distance measures for individual markers. This analysis was extended to four-locus genotypes based on sequence length data or concatenated sequences from the same loci. We interrogated these data to assess whether one would reach the same conclusions regardless of the genotyping method. Clusters of isolates generated with the concatenated sequences were not observed with amplicon length, indicating that inferences on the structure of a Cryptosporidium population depend on the genotyping method. Moreover, isolate clusters derived from concatenated sequences were dependent on the algorithm used to calculate distances. These results emphasize the need for harmonizing genotyping tools, not only by selecting informative markers, but also by standardizing the entire genotyping method.

The isolation and characterization of 18 equine microsatellite loci, TKY272–TKY289

2000 ◽  
Vol 31 (2) ◽  
pp. 149-149 ◽  
Author(s):  
T Tozaki ◽  
H Kakoi ◽  
S Mashima ◽  
K Hirota ◽  
T Hasegawa ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Isolation And Characterization
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