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.

Microsatellite loci in the phytoparasitic nematode Globodera

Genome ◽  
2000 ◽  
Vol 43 (1) ◽  
pp. 160-165 ◽  
Author(s):  
M Thiéry ◽  
D Mugniéry
Keyword(s):  
Microsatellite Loci ◽  
Related Species ◽  
Genomic Library ◽  
Globodera Pallida ◽  
Allele Polymorphism ◽  
Dna Templates ◽  
Closely Related Species ◽  
Species Specific ◽  
Flanking Regions ◽  
Phytoparasitic Nematode

A Globodera pallida genomic library, population Guiclan (Pa2/3), was screened for TG and TC microsatellite motifs. Screening of 50 000 clones revealed 48 positive matches. After sequencing, primers were designed to amplify 14 microsatellite loci. The specificity of the loci was tested with DNA templates of other populations of G. pallida, and also on other species of Globodera. Appearance of amplification products on several of these DNA templates showed that the microsatellite flanking regions are relatively conserved between G. pallida populations as well as between Globodera species. Evidence for allele polymorphism between individuals was demonstrated by using nine loci primers, in G. pallida population Guiclan and from a population of a closely related species G. "mexicana". Some alleles appeared to be species specific. Key words: Globodera, microsatellites, nematodes, phytoparasite, allele frequency.

scholarly journals Developing Microsatellite DNA Markers in Pecan

2003 ◽  
Vol 128 (3) ◽  
pp. 374-380 ◽  
Author(s):  
L.J. Grauke ◽  
Muhammad J. Iqbal ◽  
Avutu S. Reddy ◽  
Tommy E. Thompson
Keyword(s):  
Dna Markers ◽  
Microsatellite Dna ◽  
Southern Hybridization ◽  
Genomic Library ◽  
Carya Illinoinensis ◽  
Enriched Library ◽  
Microsatellite Dna Markers ◽  
Ssr Primers ◽  
Nucleotide Repeats ◽  
Simple Sequence

A microsatellite-enriched library was developed from `Halbert', a native pecan [Carya illinoinensis (Wangenh.) K. Koch] selection from Coleman County, Texas. A genomic library enriched for simple sequence repeats (SSR) containing 6144 clones was archived in 384 well plates for screening. In total, 439 clones were identified after Southern hybridization using di- and tri-nucleotide repeats as probes. In total, 125 positive clones were sequenced and primers were designed for 24 repeats. The SSR markers chosen for analysis include di-(CT and GA) and tri-nucleotide repeats (CTT, GAA and GAT). Of the 24 primer pairs tested, 19 successfully amplified microsatellites from `Halbert'. DNA was isolated from 48 pecan and hickory accessions selected to strategically represent the genetic diversity of the National Clonal Germplasm Repository (NCGR) Carya collections. The 19 SSR primers that produced good amplification products in `Halbert' were used to evaluate the collection, with 11 revealing polymorphism. The number of fragments amplified with different primer combinations ranged from 4 to 32 in the 48 genotypes tested. Evaluation of the data confirms the utility of the microsatellites in delimiting known relationships.

scholarly journals RPA-PCR couple: an approach to expedite plant diagnostics and overcome PCR inhibitors

BioTechniques ◽  
2020 ◽  
Vol 69 (4) ◽  
pp. 270-280 ◽  
Author(s):  
Mustafa Ahmad Munawar ◽  
Frank Martin ◽  
Anna Toljamo ◽  
Harri Kokko ◽  
Elina Oksanen
Keyword(s):  
Reaction Kinetics ◽  
Dna Extraction ◽  
Pcr Primers ◽  
Sybr Green ◽  
Recombinase Polymerase Amplification ◽  
Pcr Inhibitors ◽  
Plant Dna ◽  
Pcr Assays ◽  
Flanking Regions

DNA extraction can be lengthy and sometimes ends up with amplification inhibitors. We present the potential of recombinase polymerase amplification (RPA) to replace plant DNA extraction. In our rapid ‘RPA-PCR couple’ concept, RPA is tuned to slower reaction kinetics to promote amplification of long targets. RPA primers amplify target and some flanking regions directly from simple plant macerates. Then PCR primers exponentially amplify the target directly from the RPA reaction. We present the coupling of RPA with conventional, TaqMan and SYBR Green PCR assays. We applied the concept to strawberry Phytophthora pathogens and the Phytophthora identification marker atp9-nad9. We found RPA-PCR couple specific, sensitive and reliable. The approach may also benefit other difficult samples such as food, feces and ancient samples.

scholarly journals Isolation and characterization of 21 novel microsatellite loci in sailfish Istiophorus platypterus Shaw 1792 from a shotgun genomic library

2018 ◽  
Vol 34 (4) ◽  
pp. 974-976
Author(s):  
G. G. Rubio-Castro ◽  
A. Munguia-Vega ◽  
C. Quiñonez-Velázquez ◽  
F. J. García-Rodríguez
Keyword(s):  
Microsatellite Loci ◽  
Genomic Library ◽  
Istiophorus Platypterus ◽  
Isolation And Characterization
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