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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.


Comparison of expected and observed levels of heterozygosity across different motif lengths. Letters above each category depict significantly different groupings for either Ho or He, according to DSCF posthoc comparisons. Groupings indicate that dinucleotide repeats (2) are significantly greater than all other motif lengths in He, with the exception of hexanucleotide repeats (6) for Ho. Imperfect motifs are included for side-by-side comparison but were not included in statistical analysis. Error bars represent the standard error of each mean.
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fig3: Comparison of expected and observed levels of heterozygosity across different motif lengths. Letters above each category depict significantly different groupings for either Ho or He, according to DSCF posthoc comparisons. Groupings indicate that dinucleotide repeats (2) are significantly greater than all other motif lengths in He, with the exception of hexanucleotide repeats (6) for Ho. Imperfect motifs are included for side-by-side comparison but were not included in statistical analysis. Error bars represent the standard error of each mean.

Mentions: Compared with imperfect motifs, perfect motifs as a group exhibited significantly higher levels of A and He (H = 4.36 and 5.06; P = 0.037 and 0.025, respectively; see Table 2); however, there were no significant differences in Ho (H = 0.04; P = 0.8513). Within perfect motifs, motif lengths differed significantly from one another for A, He, and Ho (H = 107.89, 132.96, and 82.08; P < 0.0001, respectively; see Table 2). The dinucleotide repeat motifs exhibited significantly higher He than any other motif length, and significantly higher A and Ho than the tri-, tetra-, and pentanucleotide repeats (see Table 2, Figs. 2 and 3). Although these significant differences could be a function of the different sample sizes within each motif length group, this is unlikely as the tests incorporate sample size in the calculation.


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)

Comparison of expected and observed levels of heterozygosity across different motif lengths. Letters above each category depict significantly different groupings for either Ho or He, according to DSCF posthoc comparisons. Groupings indicate that dinucleotide repeats (2) are significantly greater than all other motif lengths in He, with the exception of hexanucleotide repeats (6) for Ho. Imperfect motifs are included for side-by-side comparison but were not included in statistical analysis. Error bars represent the standard error of each mean.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

fig3: Comparison of expected and observed levels of heterozygosity across different motif lengths. Letters above each category depict significantly different groupings for either Ho or He, according to DSCF posthoc comparisons. Groupings indicate that dinucleotide repeats (2) are significantly greater than all other motif lengths in He, with the exception of hexanucleotide repeats (6) for Ho. Imperfect motifs are included for side-by-side comparison but were not included in statistical analysis. Error bars represent the standard error of each mean.
Mentions: Compared with imperfect motifs, perfect motifs as a group exhibited significantly higher levels of A and He (H = 4.36 and 5.06; P = 0.037 and 0.025, respectively; see Table 2); however, there were no significant differences in Ho (H = 0.04; P = 0.8513). Within perfect motifs, motif lengths differed significantly from one another for A, He, and Ho (H = 107.89, 132.96, and 82.08; P < 0.0001, respectively; see Table 2). The dinucleotide repeat motifs exhibited significantly higher He than any other motif length, and significantly higher A and Ho than the tri-, tetra-, and pentanucleotide repeats (see Table 2, Figs. 2 and 3). Although these significant differences could be a function of the different sample sizes within each motif length group, this is unlikely as the tests incorporate sample size in the calculation.

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.