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In silico comparative analysis of SSR markers in plants.

Victoria FC, da Maia LC, de Oliveira AC - BMC Plant Biol. (2011)

Bottom Line: The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots.With this in silico study we confirm several microsatellite plant survey results made with available bioinformatics tools.The comparative studies of EST-SSR markers among all plant lineages is well suited for plant evolution studies as well as for future studies of transferability of molecular markers.

View Article: PubMed Central - HTML - PubMed

Affiliation: Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, RS, Brasil.

ABSTRACT

Background: The adverse environmental conditions impose extreme limitation to growth and plant development, restricting the genetic potential and reflecting on plant yield losses. The progress obtained by classic plant breeding methods aiming at increasing abiotic stress tolerances have not been enough to cope with increasing food demands. New target genes need to be identified to reach this goal, which requires extensive studies of the related biological mechanisms. Comparative analyses in ancestral plant groups can help to elucidate yet unclear biological processes.

Results: In this study, we surveyed the occurrence patterns of expressed sequence tag-derived microsatellite markers for model plants. A total of 13,133 SSR markers were discovered using the SSRLocator software in non-redundant EST databases made for all eleven species chosen for this study. The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots. With this in silico study we confirm several microsatellite plant survey results made with available bioinformatics tools.

Conclusions: The comparative studies of EST-SSR markers among all plant lineages is well suited for plant evolution studies as well as for future studies of transferability of molecular markers.

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Predicted amino acid occurrences in SSR loci within plant groups studied.
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Figure 9: Predicted amino acid occurrences in SSR loci within plant groups studied.

Mentions: The predicted amino acid content for the SSR loci detected in the eleven species studied is shown in Figure 9. The amino acids arginine (Arg), alanine (Ala) and Serine (Ser) were predominant for all species. Alanine was predominant for the majority of cryptogams, ranging from 14.85% to 29.7%. Exceptions were observed for Adiantum, Mesostigma and Physcomitrella, in which serine (Ser), glutamic acid (Glu) and leucine (Leu) were the predominant amino acid (up to 17%). Serine (up to 11%) was predominant for fern species and for Gnetum and Arabidopsis, Pinus and Oryza showed arginine as the predominant amino acid (10.46% and 23.31%, respectively). Tyrosine (Tyr), asparagine (Asp), aspartic acid (Asn) were the amino acids found at lower frequencies among SSR loci for all species and were practically absent in the algae species surveyed. In bryophytes, methionine was only found in Physcomitrella, but at a small frequency (1.7%). For all higher plant species databases used in this survey, arginine, alanine, serine, glutamic acid, proline (Pro) and leucine were among the predominant amino acids, agreeing with previous reports for flowering plants [11,3,22,42-45]. No reports were found for amino acid distribution in SSR loci in lower plants.


In silico comparative analysis of SSR markers in plants.

Victoria FC, da Maia LC, de Oliveira AC - BMC Plant Biol. (2011)

Predicted amino acid occurrences in SSR loci within plant groups studied.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3037304&req=5

Figure 9: Predicted amino acid occurrences in SSR loci within plant groups studied.
Mentions: The predicted amino acid content for the SSR loci detected in the eleven species studied is shown in Figure 9. The amino acids arginine (Arg), alanine (Ala) and Serine (Ser) were predominant for all species. Alanine was predominant for the majority of cryptogams, ranging from 14.85% to 29.7%. Exceptions were observed for Adiantum, Mesostigma and Physcomitrella, in which serine (Ser), glutamic acid (Glu) and leucine (Leu) were the predominant amino acid (up to 17%). Serine (up to 11%) was predominant for fern species and for Gnetum and Arabidopsis, Pinus and Oryza showed arginine as the predominant amino acid (10.46% and 23.31%, respectively). Tyrosine (Tyr), asparagine (Asp), aspartic acid (Asn) were the amino acids found at lower frequencies among SSR loci for all species and were practically absent in the algae species surveyed. In bryophytes, methionine was only found in Physcomitrella, but at a small frequency (1.7%). For all higher plant species databases used in this survey, arginine, alanine, serine, glutamic acid, proline (Pro) and leucine were among the predominant amino acids, agreeing with previous reports for flowering plants [11,3,22,42-45]. No reports were found for amino acid distribution in SSR loci in lower plants.

Bottom Line: The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots.With this in silico study we confirm several microsatellite plant survey results made with available bioinformatics tools.The comparative studies of EST-SSR markers among all plant lineages is well suited for plant evolution studies as well as for future studies of transferability of molecular markers.

View Article: PubMed Central - HTML - PubMed

Affiliation: Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, RS, Brasil.

ABSTRACT

Background: The adverse environmental conditions impose extreme limitation to growth and plant development, restricting the genetic potential and reflecting on plant yield losses. The progress obtained by classic plant breeding methods aiming at increasing abiotic stress tolerances have not been enough to cope with increasing food demands. New target genes need to be identified to reach this goal, which requires extensive studies of the related biological mechanisms. Comparative analyses in ancestral plant groups can help to elucidate yet unclear biological processes.

Results: In this study, we surveyed the occurrence patterns of expressed sequence tag-derived microsatellite markers for model plants. A total of 13,133 SSR markers were discovered using the SSRLocator software in non-redundant EST databases made for all eleven species chosen for this study. The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots. With this in silico study we confirm several microsatellite plant survey results made with available bioinformatics tools.

Conclusions: The comparative studies of EST-SSR markers among all plant lineages is well suited for plant evolution studies as well as for future studies of transferability of molecular markers.

Show MeSH
Related in: MedlinePlus