TITLE

PeakSeeker: a program for interpreting genotypes of mononucleotide repeats

AUTHOR(S)
Thompson, James M.; Salipante, Stephen J.
PUB. DATE
January 2009
SOURCE
BMC Research Notes;2009, Vol. 2, p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Mononucleotide repeat microsatellites are abundant, highly polymorphic DNA sequences, having the potential to serve as valuable genetic markers. Use of mononucleotide microsatellites has been limited by their tendency to produce "stutter", confounding signals from insertions and deletions within the mononucleotide tract that occur during PCR, which complicates interpretation of genotypes by masking the true position of alleles. Consequently, microsatellites with larger repeating subunits (dinucleotide and trinucleotide motifs) are used, which produce less stutter but are less genetically heterogeneous and less informative. A method to interpret the genotypes of mononucleotide repeats would permit the widespread use of those highly informative microsatellites in genetic research. Findings: We have developed an approach to interpret genotypes of mononucleotide repeats using a software program, named PeakSeeker. PeakSeeker interprets experimental electropherograms as the most likely product of signals from individual alleles. Because mononucleotide tracts demonstrate locus-specific patterns of stutter peaks, this approach requires that the genotype pattern from a single allele is defined for each marker, which can be approximated by genotyping single DNA molecules or homozygotes. We have evaluated the program's ability to discriminate various types of homozygous and heterozygous mononucleotide loci using simulated and experimental data. Conclusion: Mononucleotide tracts offer significant advantages over di- and tri-nucleotide microsatellite markers traditionally employed in genetic research. The PeakSeeker algorithm provides a high-throughput means to type mononucleotide tracts using conventional and widely implemented fragment length polymorphism genotyping. Furthermore, the PeakSeeker algorithm could potentially be adapted to improve, and perhaps to standardize, the analysis of conventional microsatellite genotypes.
ACCESSION #
42318795

 

Related Articles

  • Large-scale identification of polymorphic microsatellites using an in silico approach. Jifeng Tang; Baldwin, Samantha J.; Jacobs, Jeanne M. E.; van der Linden, C. Gerard; Voorrips, Roeland E.; Leunissen, Jack A. M.; van Eck, Herman; Vosman, Ben // BMC Bioinformatics;2008, Vol. 9, Special section p1 

    Background: Simple Sequence Repeat (SSR) or microsatellite markers are valuable for genetic research. Experimental methods to develop SSR markers are laborious, time consuming and expensive. In silico approaches have become a practicable and relatively inexpensive alternative during the last...

  • Microsatellites: simple sequences with complex evolution. Ellegren, Hans // Nature Reviews Genetics;Jun2004, Vol. 5 Issue 6, p435 

    Few genetic markers, if any, have found such widespread use as microsatellites, or simple/short tandem repeats. Features such as hypervariability and ubiquitous occurrence explain their usefulness, but these features also pose several questions. For example, why are microsatellites so abundant,...

  • Characterization of masson pine ( Pinus massoniana Lamb.) microsatellite DNA by 454 genome shotgun sequencing. Bai, Tian-Dao; Xu, Li-An; Xu, Meng; Wang, Zhang-Rong // Tree Genetics & Genomes;Apr2014, Vol. 10 Issue 2, p429 

    Microsatellites (simple sequence repeats, SSRs) are important genetic markers in tree breeding and conservation. Here we utilized high-throughput 454 sequencing technology to mine microsatellites from masson pine (MP) genomic DNA. First, we analyzed the characteristics of SSRs in all...

  • Development of soybean aphid genomic SSR markers using next generation sequencing. Jun, Tae-Hwan; Michel, Andrew P.; Mian, M.A. Rouf; Gustafson, Perry // Genome;May2011, Vol. 54 Issue 5, p360 

    Simple sequence repeats (SSRs) or microsatellites are very useful molecular markers, owing to their locus-specific codominant and multiallelic nature, high abundance in the genome, and high rates of transferability across species. The soybean aphid ( Matsumura) has become the most damaging...

  • Genetic analysis of salt-marsh sedge Carex scabrifolia Steud. populations using newly developed microsatellite markers. Hodoki, Yoshikuni; Ohbayashi, Kako; Kunii, Hidenobu // Conservation Genetics;Oct2009, Vol. 10 Issue 5, p1361 

    Nine microsatellite loci were isolated and characterized from the clonal salt-marsh sedge Carex scabrifolia, and genetic diversities within four populations were analyzed. The number of alleles per locus ranged from 2 to 7, with an average of 4.7. The observed and expected heterozygosities...

  • Description of three microsatellite loci of the Baikal omul Coregonus migratorius (Georgi). Gaikalov, I. V.; Ilyina, O. V.; Kirilchik, S. V.; Sukhanova, L. V. // Russian Journal of Genetics;Mar2008, Vol. 44 Issue 3, p365 

    Three new microsatellite loci found for the Baikal omul Coregonus migratorius (Georgi) are described.

  • New microsatellite markers for pigeonpea (cajanus cajan (L.) millsp.). Odeny, D. A.; B., Jayashree; Gebhardt, C.; Crouch, J. // BMC Research Notes;2009, Vol. 2, p1 

    Background: Pigeonpea is a nutritious tropical legume with several desirable characteristics but has been relatively neglected in terms of research. More efficient improvement can be achieved in this crop through molecular breeding but adequate molecular markers are lacking and no linkage map...

  • Development and characterization of new microsatellite markers for ginseng (Panax ginseng C. A. Meyer). Kyung-Ho Ma; Dixit, Anupam; Young-Chang Kim; Dong-Yun Lee; Tae-San Kim; Eun-Gi Cho; Park, Yong-Jin // Conservation Genetics;Dec2007, Vol. 8 Issue 6, p1507 

    Panax ginseng C.A. Meyer, commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. Its roots are highly prized for several medicinal properties. The present study describes development and characterization of twentytwo polymorphic microsatellite markers for this...

  • Development, inheritance, and linkage-group assignment of 60 novel microsatellite markers for the gray, short-tailed opossum Monodelphis domestica. Gouin, Nicolas; Westenberger, Scott J.; Mahaney, Susan M.; Lindley, Peter; VandeBerg, John L.; Samollow, Paul B.; Bell, J. B. // Genome;Dec2005, Vol. 48 Issue 6, p1019 

    Short-tandem-repeat (SSR) or microsatellite polymorphisms are some of the most extensively employed genetic markers in contemporary linkage mapping studies. To date, only a limited number of microsatellites have been isolated in the gray, short-tailed opossum Monodelphis domestica, a South...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics