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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.


Related in: MedlinePlus

Group comparisons of major taxonomic groups. A (shown in black), He (light gray), and Ho (gray) are shown for each major taxonomic group. The cladogram was drawn with similar taxonomic relationships as those supported by the Angiosperm Phylogeny Group (Stevens, 2001). The percentages in parentheses next to each group name indicate the proportion of entries in the database that comprise each clade. Error bars represent the standard error of each mean.
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fig6: Group comparisons of major taxonomic groups. A (shown in black), He (light gray), and Ho (gray) are shown for each major taxonomic group. The cladogram was drawn with similar taxonomic relationships as those supported by the Angiosperm Phylogeny Group (Stevens, 2001). The percentages in parentheses next to each group name indicate the proportion of entries in the database that comprise each clade. Error bars represent the standard error of each mean.

Mentions: There was no significant difference between monocots and dicots in any of the measures of genetic variation (A, He, and Ho). The monocots did, however, have significantly larger motif regions compared to dicots (H = 17.3, P < 0.0001; see Table 3). Across the different plant taxonomic clades, the gymnosperms exhibited a significantly greater number of alleles than most other plant taxonomic clades, whereas the eudicots, asterids, and rosids had significantly reduced heterozygosity and number of alleles than most of their evolutionarily older counterparts, with the exception of the Nymphaeales (Table 3, Fig. 6).


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)

Group comparisons of major taxonomic groups. A (shown in black), He (light gray), and Ho (gray) are shown for each major taxonomic group. The cladogram was drawn with similar taxonomic relationships as those supported by the Angiosperm Phylogeny Group (Stevens, 2001). The percentages in parentheses next to each group name indicate the proportion of entries in the database that comprise each clade. 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

fig6: Group comparisons of major taxonomic groups. A (shown in black), He (light gray), and Ho (gray) are shown for each major taxonomic group. The cladogram was drawn with similar taxonomic relationships as those supported by the Angiosperm Phylogeny Group (Stevens, 2001). The percentages in parentheses next to each group name indicate the proportion of entries in the database that comprise each clade. Error bars represent the standard error of each mean.
Mentions: There was no significant difference between monocots and dicots in any of the measures of genetic variation (A, He, and Ho). The monocots did, however, have significantly larger motif regions compared to dicots (H = 17.3, P < 0.0001; see Table 3). Across the different plant taxonomic clades, the gymnosperms exhibited a significantly greater number of alleles than most other plant taxonomic clades, whereas the eudicots, asterids, and rosids had significantly reduced heterozygosity and number of alleles than most of their evolutionarily older counterparts, with the exception of the Nymphaeales (Table 3, Fig. 6).

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.


Related in: MedlinePlus