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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.


Mean repeat frequencies of different motif lengths. Repeat frequency refers to the number of times a motif is repeated. Letters above each category depict significantly different groupings according to DSCF posthoc comparisons. There is a significant decrease in repeat frequency as the motif length increases. Error bars represent the standard error of each mean.
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fig5: Mean repeat frequencies of different motif lengths. Repeat frequency refers to the number of times a motif is repeated. Letters above each category depict significantly different groupings according to DSCF posthoc comparisons. There is a significant decrease in repeat frequency as the motif length increases. Error bars represent the standard error of each mean.

Mentions: The motif region significantly differed among motif lengths (H = 28.4, P < 0.0001), but there was no consistent trend or relationship across the motif lengths (see Table 2, Fig. 4). Repeat frequencies across the different motif lengths showed very strong significant differences between groups, exhibiting an inverse relationship with the repeat frequency decreasing as motif length increased (H = 846.4, P < 0.0001; see Table 2, Fig. 5).


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)

Mean repeat frequencies of different motif lengths. Repeat frequency refers to the number of times a motif is repeated. Letters above each category depict significantly different groupings according to DSCF posthoc comparisons. There is a significant decrease in repeat frequency as the motif length increases. 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

fig5: Mean repeat frequencies of different motif lengths. Repeat frequency refers to the number of times a motif is repeated. Letters above each category depict significantly different groupings according to DSCF posthoc comparisons. There is a significant decrease in repeat frequency as the motif length increases. Error bars represent the standard error of each mean.
Mentions: The motif region significantly differed among motif lengths (H = 28.4, P < 0.0001), but there was no consistent trend or relationship across the motif lengths (see Table 2, Fig. 4). Repeat frequencies across the different motif lengths showed very strong significant differences between groups, exhibiting an inverse relationship with the repeat frequency decreasing as motif length increased (H = 846.4, P < 0.0001; see Table 2, Fig. 5).

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.