A White Campion (<it>Silene latifolia</it>) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping
<p>Abstract</p> <p>Background</p> <p>Expressed sequence tag (EST) databases represent a valuable resource for the identification of genes in organisms with uncharacterized genomes and for development of molecular markers. One class of markers derived from EST sequences...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2009-05-01
|
| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/10/243 |
| _version_ | 1828553495508156416 |
|---|---|
| author | Marais Gabriel AB Oger-Desfeux Christine Moccia Maria Widmer Alex |
| author_facet | Marais Gabriel AB Oger-Desfeux Christine Moccia Maria Widmer Alex |
| author_sort | Marais Gabriel AB |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Expressed sequence tag (EST) databases represent a valuable resource for the identification of genes in organisms with uncharacterized genomes and for development of molecular markers. One class of markers derived from EST sequences are simple sequence repeat (SSR) markers, also known as EST-SSRs. These are useful in plant genetic and evolutionary studies because they are located in transcribed genes and a putative function can often be inferred from homology searches. Another important feature of EST-SSR markers is their expected high level of transferability to related species that makes them very promising for comparative mapping. In the present study we constructed a normalized EST library from floral tissue of <it>Silene latifolia </it>with the aim to identify expressed genes and to develop polymorphic molecular markers.</p> <p>Results</p> <p>We obtained a total of 3662 high quality sequences from a normalized <it>Silene </it>cDNA library. These represent 3105 unigenes, with 73% of unigenes matching genes in other species. We found 255 sequences containing one or more SSR motifs. More than 60% of these SSRs were trinucleotides. A total of 30 microsatellite loci were identified from 106 ESTs having sufficient flanking sequences for primer design. The inheritance of these loci was tested via segregation analyses and their usefulness for linkage mapping was assessed in an interspecific cross. Tests for crossamplification of the EST-SSR loci in other <it>Silene </it>species established their applicability to related species.</p> <p>Conclusion</p> <p>The newly characterized genes and gene-derived markers from our <it>Silene </it>EST library represent a valuable genetic resource for future studies on <it>Silene latifolia </it>and related species. The polymorphism and transferability of EST-SSR markers facilitate comparative linkage mapping and analyses of genetic diversity in the genus <it>Silene</it>.</p> |
| first_indexed | 2024-12-12T05:19:34Z |
| format | Article |
| id | doaj.art-9cdf4b50eae743f9a40ca60d2e5ba423 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T05:19:34Z |
| publishDate | 2009-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-9cdf4b50eae743f9a40ca60d2e5ba4232022-12-22T00:36:40ZengBMCBMC Genomics1471-21642009-05-0110124310.1186/1471-2164-10-243A White Campion (<it>Silene latifolia</it>) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mappingMarais Gabriel ABOger-Desfeux ChristineMoccia MariaWidmer Alex<p>Abstract</p> <p>Background</p> <p>Expressed sequence tag (EST) databases represent a valuable resource for the identification of genes in organisms with uncharacterized genomes and for development of molecular markers. One class of markers derived from EST sequences are simple sequence repeat (SSR) markers, also known as EST-SSRs. These are useful in plant genetic and evolutionary studies because they are located in transcribed genes and a putative function can often be inferred from homology searches. Another important feature of EST-SSR markers is their expected high level of transferability to related species that makes them very promising for comparative mapping. In the present study we constructed a normalized EST library from floral tissue of <it>Silene latifolia </it>with the aim to identify expressed genes and to develop polymorphic molecular markers.</p> <p>Results</p> <p>We obtained a total of 3662 high quality sequences from a normalized <it>Silene </it>cDNA library. These represent 3105 unigenes, with 73% of unigenes matching genes in other species. We found 255 sequences containing one or more SSR motifs. More than 60% of these SSRs were trinucleotides. A total of 30 microsatellite loci were identified from 106 ESTs having sufficient flanking sequences for primer design. The inheritance of these loci was tested via segregation analyses and their usefulness for linkage mapping was assessed in an interspecific cross. Tests for crossamplification of the EST-SSR loci in other <it>Silene </it>species established their applicability to related species.</p> <p>Conclusion</p> <p>The newly characterized genes and gene-derived markers from our <it>Silene </it>EST library represent a valuable genetic resource for future studies on <it>Silene latifolia </it>and related species. The polymorphism and transferability of EST-SSR markers facilitate comparative linkage mapping and analyses of genetic diversity in the genus <it>Silene</it>.</p>http://www.biomedcentral.com/1471-2164/10/243 |
| spellingShingle | Marais Gabriel AB Oger-Desfeux Christine Moccia Maria Widmer Alex A White Campion (<it>Silene latifolia</it>) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping BMC Genomics |
| title | A White Campion (<it>Silene latifolia</it>) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping |
| title_full | A White Campion (<it>Silene latifolia</it>) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping |
| title_fullStr | A White Campion (<it>Silene latifolia</it>) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping |
| title_full_unstemmed | A White Campion (<it>Silene latifolia</it>) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping |
| title_short | A White Campion (<it>Silene latifolia</it>) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping |
| title_sort | white campion it silene latifolia it floral expressed sequence tag est library annotation est ssr characterization transferability and utility for comparative mapping |
| url | http://www.biomedcentral.com/1471-2164/10/243 |
| work_keys_str_mv | AT maraisgabrielab awhitecampionitsilenelatifoliaitfloralexpressedsequencetagestlibraryannotationestssrcharacterizationtransferabilityandutilityforcomparativemapping AT ogerdesfeuxchristine awhitecampionitsilenelatifoliaitfloralexpressedsequencetagestlibraryannotationestssrcharacterizationtransferabilityandutilityforcomparativemapping AT mocciamaria awhitecampionitsilenelatifoliaitfloralexpressedsequencetagestlibraryannotationestssrcharacterizationtransferabilityandutilityforcomparativemapping AT widmeralex awhitecampionitsilenelatifoliaitfloralexpressedsequencetagestlibraryannotationestssrcharacterizationtransferabilityandutilityforcomparativemapping AT maraisgabrielab whitecampionitsilenelatifoliaitfloralexpressedsequencetagestlibraryannotationestssrcharacterizationtransferabilityandutilityforcomparativemapping AT ogerdesfeuxchristine whitecampionitsilenelatifoliaitfloralexpressedsequencetagestlibraryannotationestssrcharacterizationtransferabilityandutilityforcomparativemapping AT mocciamaria whitecampionitsilenelatifoliaitfloralexpressedsequencetagestlibraryannotationestssrcharacterizationtransferabilityandutilityforcomparativemapping AT widmeralex whitecampionitsilenelatifoliaitfloralexpressedsequencetagestlibraryannotationestssrcharacterizationtransferabilityandutilityforcomparativemapping |