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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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Eletronical eletrophoresis gel for 10 primers set design for Physcomitrella patens EST-SSR (SSRn) across Chlamydomonas reinhardtii (Chml) Oryza sativa (Os) and Arabidopsis thaliana (At) EST databases.
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Figure 11: Eletronical eletrophoresis gel for 10 primers set design for Physcomitrella patens EST-SSR (SSRn) across Chlamydomonas reinhardtii (Chml) Oryza sativa (Os) and Arabidopsis thaliana (At) EST databases.

Mentions: For the positive EST-SSRs found for the in silico transfer, ten sets of Physcomitrella EST-SSR primers were used to illustrate the transferability results using an electronic tool [56] to simulate gel electrophoresis (Figure 11). For the three tested EST-databases only two primers amplified a single locus in each species (SSR9 and SSR10). In the other sets 2, 3 and even 4 virtual amplicons were observed (Additional file 8). For Chlamydomonas, 70% of the tested primers resulted in one amplicon and 10% each resulted in 2, 3 or 4 amplifications. However, only 20% of amplicons obtained in this algae species are related to the EST-SSR sequence, suggesting that the majority of designed EST-SSR primers act as degenerate when applied to Chlamydomonas. For rice, 30%, 40% and 10% of tested primers resulted in one, two or three amplifications, respectively. In Arabidopsis 40%, 40% and 20% of tested primers results in one, two or three amplifications, respectively. For both flowering plants, 50% of tested primers amplified moss EST-SSR homologue sequences, showing a high rate of success for transferability across species. These results agree with other studies where the transfer success rates decrease with the increasing evolutionary distance [55,57-60]. The use of this molecular marker across distant taxonomical groups are not impossible, however our findings confirm that only a few retain their EST-SSR homologue sequences, making this effort hardly worthwhile [61].


In silico comparative analysis of SSR markers in plants.

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

Eletronical eletrophoresis gel for 10 primers set design for Physcomitrella patens EST-SSR (SSRn) across Chlamydomonas reinhardtii (Chml) Oryza sativa (Os) and Arabidopsis thaliana (At) EST databases.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 11: Eletronical eletrophoresis gel for 10 primers set design for Physcomitrella patens EST-SSR (SSRn) across Chlamydomonas reinhardtii (Chml) Oryza sativa (Os) and Arabidopsis thaliana (At) EST databases.
Mentions: For the positive EST-SSRs found for the in silico transfer, ten sets of Physcomitrella EST-SSR primers were used to illustrate the transferability results using an electronic tool [56] to simulate gel electrophoresis (Figure 11). For the three tested EST-databases only two primers amplified a single locus in each species (SSR9 and SSR10). In the other sets 2, 3 and even 4 virtual amplicons were observed (Additional file 8). For Chlamydomonas, 70% of the tested primers resulted in one amplicon and 10% each resulted in 2, 3 or 4 amplifications. However, only 20% of amplicons obtained in this algae species are related to the EST-SSR sequence, suggesting that the majority of designed EST-SSR primers act as degenerate when applied to Chlamydomonas. For rice, 30%, 40% and 10% of tested primers resulted in one, two or three amplifications, respectively. In Arabidopsis 40%, 40% and 20% of tested primers results in one, two or three amplifications, respectively. For both flowering plants, 50% of tested primers amplified moss EST-SSR homologue sequences, showing a high rate of success for transferability across species. These results agree with other studies where the transfer success rates decrease with the increasing evolutionary distance [55,57-60]. The use of this molecular marker across distant taxonomical groups are not impossible, however our findings confirm that only a few retain their EST-SSR homologue sequences, making this effort hardly worthwhile [61].

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