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An empirical review: Characteristics of plant microsatellite markers that confer higher levels of genetic variation.

Merritt BJ, Culley TM, Avanesyan A, Stokes R, Brzyski J - Appl Plant Sci (2015)

Bottom Line: There were significant differences between imperfect and perfect repeat types in A and H e.Dinucleotide motifs exhibited significantly higher A, H e, and H o than most other motifs.In conclusion, researchers should carefully consider marker characteristics so they can be tailored to the desired application.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Science, University of Cincinnati, 614 Rieveschl Hall, Cincinnati, Ohio 45221-0006 USA.

ABSTRACT
During microsatellite marker development, researchers must choose from a pool of possible primer pairs to further test in their species of interest. In many cases, the goal is maximizing detectable levels of genetic variation. To guide researchers and determine which markers are associated with higher levels of genetic variation, we conducted a literature review based on 6782 genomic microsatellite markers published from 1997-2012. We examined relationships between heterozygosity (H e or H o) or allele number (A) with the following marker characteristics: repeat type, motif length, motif region, repeat frequency, and microsatellite size. Variation across taxonomic groups was also analyzed. There were significant differences between imperfect and perfect repeat types in A and H e. Dinucleotide motifs exhibited significantly higher A, H e, and H o than most other motifs. Repeat frequency and motif region were positively correlated with A, H e, and H o, but correlations with microsatellite size were minimal. Higher taxonomic groups were disproportionately represented in the literature and showed little consistency. In conclusion, researchers should carefully consider marker characteristics so they can be tailored to the desired application. If researchers aim to target high genetic variation, dinucleotide motif lengths with large repeat frequencies may be best.

No MeSH data available.


Database compilation/modification workflow. This workflow depicts the general origins, compilations, and modifications of each individual entry into the database with a general “binning” of different variables based on the nature of the measurements and the appropriate statistical analyses used.
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fig1: Database compilation/modification workflow. This workflow depicts the general origins, compilations, and modifications of each individual entry into the database with a general “binning” of different variables based on the nature of the measurements and the appropriate statistical analyses used.

Mentions: The primer information within the database for each locus consisted of the following information whenever possible: the reported locus name or merit ID (those entries without either of these criteria were assigned a unique number), the primer motif, the number of alleles (A), expected heterozygosity (He), and observed heterozygosity (Ho). We only included data for the species in which the primer was originally designed, as nonspecific primers have shown tendencies to amplify poorly or inconsistently in closely related species (Rubinsztein et al., 1995; Primmer et al., 1996; Whitton et al., 1997; Morin et al., 1998). Within each study, any missing value for a genetic parameter (A, He, or Ho) was represented as a value but reported zero values were maintained. Figure 1 depicts a schematic workflow of the database compilation.


An empirical review: Characteristics of plant microsatellite markers that confer higher levels of genetic variation.

Merritt BJ, Culley TM, Avanesyan A, Stokes R, Brzyski J - Appl Plant Sci (2015)

Database compilation/modification workflow. This workflow depicts the general origins, compilations, and modifications of each individual entry into the database with a general “binning” of different variables based on the nature of the measurements and the appropriate statistical analyses used.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4542939&req=5

fig1: Database compilation/modification workflow. This workflow depicts the general origins, compilations, and modifications of each individual entry into the database with a general “binning” of different variables based on the nature of the measurements and the appropriate statistical analyses used.
Mentions: The primer information within the database for each locus consisted of the following information whenever possible: the reported locus name or merit ID (those entries without either of these criteria were assigned a unique number), the primer motif, the number of alleles (A), expected heterozygosity (He), and observed heterozygosity (Ho). We only included data for the species in which the primer was originally designed, as nonspecific primers have shown tendencies to amplify poorly or inconsistently in closely related species (Rubinsztein et al., 1995; Primmer et al., 1996; Whitton et al., 1997; Morin et al., 1998). Within each study, any missing value for a genetic parameter (A, He, or Ho) was represented as a value but reported zero values were maintained. Figure 1 depicts a schematic workflow of the database compilation.

Bottom Line: There were significant differences between imperfect and perfect repeat types in A and H e.Dinucleotide motifs exhibited significantly higher A, H e, and H o than most other motifs.In conclusion, researchers should carefully consider marker characteristics so they can be tailored to the desired application.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Science, University of Cincinnati, 614 Rieveschl Hall, Cincinnati, Ohio 45221-0006 USA.

ABSTRACT
During microsatellite marker development, researchers must choose from a pool of possible primer pairs to further test in their species of interest. In many cases, the goal is maximizing detectable levels of genetic variation. To guide researchers and determine which markers are associated with higher levels of genetic variation, we conducted a literature review based on 6782 genomic microsatellite markers published from 1997-2012. We examined relationships between heterozygosity (H e or H o) or allele number (A) with the following marker characteristics: repeat type, motif length, motif region, repeat frequency, and microsatellite size. Variation across taxonomic groups was also analyzed. There were significant differences between imperfect and perfect repeat types in A and H e. Dinucleotide motifs exhibited significantly higher A, H e, and H o than most other motifs. Repeat frequency and motif region were positively correlated with A, H e, and H o, but correlations with microsatellite size were minimal. Higher taxonomic groups were disproportionately represented in the literature and showed little consistency. In conclusion, researchers should carefully consider marker characteristics so they can be tailored to the desired application. If researchers aim to target high genetic variation, dinucleotide motif lengths with large repeat frequencies may be best.

No MeSH data available.