Frequency, type, and distribution of EST-SSRs from three genotypes of <it>Lolium perenne</it>, and their conservation across orthologous sequences of <it>Festuca arundinacea, Brachypodium distachyon</it>, and <it>Oryza sativa</it>
<p>Abstract</p> <p>Background</p> <p>Simple sequence repeat (SSR) markers are highly informative and widely used for genetic and breeding studies in several plant species. They are used for cultivar identification, variety protection, as anchor markers in genetic mappin...
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| Format: | Article |
| Language: | English |
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BMC
2007-07-01
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| Series: | BMC Plant Biology |
| Online Access: | http://www.biomedcentral.com/1471-2229/7/36 |
| _version_ | 1828523945491431424 |
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| author | Lübberstedt Thomas Nielsen Klaus K Didion Thomas Frei Ursula K Asp Torben |
| author_facet | Lübberstedt Thomas Nielsen Klaus K Didion Thomas Frei Ursula K Asp Torben |
| author_sort | Lübberstedt Thomas |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Simple sequence repeat (SSR) markers are highly informative and widely used for genetic and breeding studies in several plant species. They are used for cultivar identification, variety protection, as anchor markers in genetic mapping, and in marker-assisted breeding. Currently, a limited number of SSR markers are publicly available for perennial ryegrass (<it>Lolium perenne</it>). We report on the exploitation of a comprehensive EST collection in <it>L. perenne </it>for SSR identification. The objectives of this study were 1) to analyse the frequency, type, and distribution of SSR motifs in ESTs derived from three genotypes of <it>L. perenne</it>, 2) to perform a comparative analysis of SSR motif polymorphisms between allelic sequences, 3) to conduct a comparative analysis of SSR motif polymorphisms between orthologous sequences of <it>L. perenne</it>, <it>Festuca arundinacea, Brachypodium distachyon</it>, and <it>O. sativa</it>, 4) to identify functionally associated EST-SSR markers for application in comparative genomics and breeding.</p> <p>Results</p> <p>From 25,744 ESTs, representing 8.53 megabases of nucleotide information from three genotypes of <it>L. perenne</it>, 1,458 ESTs (5.7%) contained one or more SSRs. Of these SSRs, 955 (3.7%) were non-redundant. Tri-nucleotide repeats were the most abundant type of repeats followed by di- and tetra-nucleotide repeats. The EST-SSRs from the three genotypes were analysed for allelic- and/or genotypic SSR motif polymorphisms. Most of the SSR motifs (97.7%) showed no polymorphisms, whereas 22 EST-SSRs showed allelic- and/or genotypic polymorphisms. All polymorphisms identified were changes in the number of repeat units. Comparative analysis of the <it>L. perenne </it>EST-SSRs with sequences of <it>Festuca arundinacea</it>, <it>Brachypodium distachyon</it>, and <it>Oryza sativa </it>identified 19 clusters of orthologous sequences between these four species. Analysis of the clusters showed that the SSR motif generally is conserved in the closely related species <it>F. arundinacea</it>, but often differs in length of the SSR motif. In contrast, SSR motifs are often lost in the more distant related species <it>B. distachyon </it>and <it>O. sativa</it>.</p> <p>Conclusion</p> <p>The results indicate that the <it>L. perenne </it>EST-SSR markers are a valuable resource for genetic mapping, as well as evaluation of co-location between QTLs and functionally associated markers.</p> |
| first_indexed | 2024-12-11T20:38:16Z |
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| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-11T20:38:16Z |
| publishDate | 2007-07-01 |
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| spelling | doaj.art-e02d5fd70e0b46ebbb4c8252e27905582022-12-22T00:51:36ZengBMCBMC Plant Biology1471-22292007-07-01713610.1186/1471-2229-7-36Frequency, type, and distribution of EST-SSRs from three genotypes of <it>Lolium perenne</it>, and their conservation across orthologous sequences of <it>Festuca arundinacea, Brachypodium distachyon</it>, and <it>Oryza sativa</it>Lübberstedt ThomasNielsen Klaus KDidion ThomasFrei Ursula KAsp Torben<p>Abstract</p> <p>Background</p> <p>Simple sequence repeat (SSR) markers are highly informative and widely used for genetic and breeding studies in several plant species. They are used for cultivar identification, variety protection, as anchor markers in genetic mapping, and in marker-assisted breeding. Currently, a limited number of SSR markers are publicly available for perennial ryegrass (<it>Lolium perenne</it>). We report on the exploitation of a comprehensive EST collection in <it>L. perenne </it>for SSR identification. The objectives of this study were 1) to analyse the frequency, type, and distribution of SSR motifs in ESTs derived from three genotypes of <it>L. perenne</it>, 2) to perform a comparative analysis of SSR motif polymorphisms between allelic sequences, 3) to conduct a comparative analysis of SSR motif polymorphisms between orthologous sequences of <it>L. perenne</it>, <it>Festuca arundinacea, Brachypodium distachyon</it>, and <it>O. sativa</it>, 4) to identify functionally associated EST-SSR markers for application in comparative genomics and breeding.</p> <p>Results</p> <p>From 25,744 ESTs, representing 8.53 megabases of nucleotide information from three genotypes of <it>L. perenne</it>, 1,458 ESTs (5.7%) contained one or more SSRs. Of these SSRs, 955 (3.7%) were non-redundant. Tri-nucleotide repeats were the most abundant type of repeats followed by di- and tetra-nucleotide repeats. The EST-SSRs from the three genotypes were analysed for allelic- and/or genotypic SSR motif polymorphisms. Most of the SSR motifs (97.7%) showed no polymorphisms, whereas 22 EST-SSRs showed allelic- and/or genotypic polymorphisms. All polymorphisms identified were changes in the number of repeat units. Comparative analysis of the <it>L. perenne </it>EST-SSRs with sequences of <it>Festuca arundinacea</it>, <it>Brachypodium distachyon</it>, and <it>Oryza sativa </it>identified 19 clusters of orthologous sequences between these four species. Analysis of the clusters showed that the SSR motif generally is conserved in the closely related species <it>F. arundinacea</it>, but often differs in length of the SSR motif. In contrast, SSR motifs are often lost in the more distant related species <it>B. distachyon </it>and <it>O. sativa</it>.</p> <p>Conclusion</p> <p>The results indicate that the <it>L. perenne </it>EST-SSR markers are a valuable resource for genetic mapping, as well as evaluation of co-location between QTLs and functionally associated markers.</p>http://www.biomedcentral.com/1471-2229/7/36 |
| spellingShingle | Lübberstedt Thomas Nielsen Klaus K Didion Thomas Frei Ursula K Asp Torben Frequency, type, and distribution of EST-SSRs from three genotypes of <it>Lolium perenne</it>, and their conservation across orthologous sequences of <it>Festuca arundinacea, Brachypodium distachyon</it>, and <it>Oryza sativa</it> BMC Plant Biology |
| title | Frequency, type, and distribution of EST-SSRs from three genotypes of <it>Lolium perenne</it>, and their conservation across orthologous sequences of <it>Festuca arundinacea, Brachypodium distachyon</it>, and <it>Oryza sativa</it> |
| title_full | Frequency, type, and distribution of EST-SSRs from three genotypes of <it>Lolium perenne</it>, and their conservation across orthologous sequences of <it>Festuca arundinacea, Brachypodium distachyon</it>, and <it>Oryza sativa</it> |
| title_fullStr | Frequency, type, and distribution of EST-SSRs from three genotypes of <it>Lolium perenne</it>, and their conservation across orthologous sequences of <it>Festuca arundinacea, Brachypodium distachyon</it>, and <it>Oryza sativa</it> |
| title_full_unstemmed | Frequency, type, and distribution of EST-SSRs from three genotypes of <it>Lolium perenne</it>, and their conservation across orthologous sequences of <it>Festuca arundinacea, Brachypodium distachyon</it>, and <it>Oryza sativa</it> |
| title_short | Frequency, type, and distribution of EST-SSRs from three genotypes of <it>Lolium perenne</it>, and their conservation across orthologous sequences of <it>Festuca arundinacea, Brachypodium distachyon</it>, and <it>Oryza sativa</it> |
| title_sort | frequency type and distribution of est ssrs from three genotypes of it lolium perenne it and their conservation across orthologous sequences of it festuca arundinacea brachypodium distachyon it and it oryza sativa it |
| url | http://www.biomedcentral.com/1471-2229/7/36 |
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