Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping
Abstract Background During the last decade, numerous microsatellite markers were developed for genotyping and to identify closely related plant genotypes. In citrus, previously developed microsatellite markers were arisen from genomic libraries and more often located in non coding DNA sequences. T...
| Main Authors: | , , , , , , , , |
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| Format: | Artículo |
| Language: | Inglés |
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Springer Nature
2020
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| Online Access: | http://hdl.handle.net/20.500.11939/6291 https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-287 |
| _version_ | 1855492054204809216 |
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| author | Luro, Francois Constantino, Gilles Terol, Javier Argout, Xavier Allario, Thierry Wincker, Patrick Talón, Manuel Ollitrault, Patrick Morillon, Raphael |
| author_browse | Allario, Thierry Argout, Xavier Constantino, Gilles Luro, Francois Morillon, Raphael Ollitrault, Patrick Talón, Manuel Terol, Javier Wincker, Patrick |
| author_facet | Luro, Francois Constantino, Gilles Terol, Javier Argout, Xavier Allario, Thierry Wincker, Patrick Talón, Manuel Ollitrault, Patrick Morillon, Raphael |
| author_sort | Luro, Francois |
| collection | ReDivia |
| description | Abstract
Background
During the last decade, numerous microsatellite markers were developed for genotyping and to identify closely related plant genotypes. In citrus, previously developed microsatellite markers were arisen from genomic libraries and more often located in non coding DNA sequences. To optimize the use of these EST-SSRs as genetic markers in genome mapping programs and citrus systematic analysis, we have investigated their polymorphism related to the type (di or trinucleotide) or their position in the coding sequences.
Results
Among 11000 unigenes from a Clementine EST library, we have found at least one microsatellite sequence (repeated units size ranged from 2 to 6 nucleotides) in 1500 unigenes (13.6%). More than 95% of these SSRs were di or trinucleotides. If trinucleotide microsatellites were encountered trough all part of EST sequences, dinucleotide microsatellites were preferentially (50%) concentrated in the 5' 100th nucleotides. We assessed the polymorphism of 41 EST-SSR, by PCR amplification droved with flanking primers among ten Citrus species plus 3 from other genera. More than 90% of EST-SSR markers were polymorphic. Furthermore, dinucleotide microsatellite markers were more polymorphic than trinucleotide ones, probably related to their distribution that was more often located in the 5' UnTranslated Region (UTR). We obtained a good agreement of diversity relationships between the citrus species and relatives assessed with EST-SSR markers with the established taxonomy and phylogeny. To end, the heterozygosity of each genotype and all dual combinations were studied to evaluate the percentage of mappable markers. Higher values (> 45%) were observed for putative Citrus inter-specific hybrids (lime lemon, or sour orange) than for Citrus basic true species (mandarin, pummelo and citron) (<30%). Most favorable combinations for genome mapping were observed in those involving interspecific hybrid genotypes. Those gave higher levels of mappable markers (>70%) with a significant proportion suitable for synteny analysis.
Conclusion
Fourty one new EST-SSR markers were produced and were available for citrus genetic studies. Whatever the position of the SSR in the ESTs the EST-SSR markers we developed are powerful to investigate genetic diversity and genome mapping in citrus. |
| format | Artículo |
| id | ReDivia6291 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Springer Nature |
| publisherStr | Springer Nature |
| record_format | dspace |
| spelling | ReDivia62912025-04-25T14:46:46Z Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping Luro, Francois Constantino, Gilles Terol, Javier Argout, Xavier Allario, Thierry Wincker, Patrick Talón, Manuel Ollitrault, Patrick Morillon, Raphael Gene Ontology Genomic SSRs F30 Plant genetics and breeding Clementines Sweet oranges Citrus Sour orange Abstract Background During the last decade, numerous microsatellite markers were developed for genotyping and to identify closely related plant genotypes. In citrus, previously developed microsatellite markers were arisen from genomic libraries and more often located in non coding DNA sequences. To optimize the use of these EST-SSRs as genetic markers in genome mapping programs and citrus systematic analysis, we have investigated their polymorphism related to the type (di or trinucleotide) or their position in the coding sequences. Results Among 11000 unigenes from a Clementine EST library, we have found at least one microsatellite sequence (repeated units size ranged from 2 to 6 nucleotides) in 1500 unigenes (13.6%). More than 95% of these SSRs were di or trinucleotides. If trinucleotide microsatellites were encountered trough all part of EST sequences, dinucleotide microsatellites were preferentially (50%) concentrated in the 5' 100th nucleotides. We assessed the polymorphism of 41 EST-SSR, by PCR amplification droved with flanking primers among ten Citrus species plus 3 from other genera. More than 90% of EST-SSR markers were polymorphic. Furthermore, dinucleotide microsatellite markers were more polymorphic than trinucleotide ones, probably related to their distribution that was more often located in the 5' UnTranslated Region (UTR). We obtained a good agreement of diversity relationships between the citrus species and relatives assessed with EST-SSR markers with the established taxonomy and phylogeny. To end, the heterozygosity of each genotype and all dual combinations were studied to evaluate the percentage of mappable markers. Higher values (> 45%) were observed for putative Citrus inter-specific hybrids (lime lemon, or sour orange) than for Citrus basic true species (mandarin, pummelo and citron) (<30%). Most favorable combinations for genome mapping were observed in those involving interspecific hybrid genotypes. Those gave higher levels of mappable markers (>70%) with a significant proportion suitable for synteny analysis. Conclusion Fourty one new EST-SSR markers were produced and were available for citrus genetic studies. Whatever the position of the SSR in the ESTs the EST-SSR markers we developed are powerful to investigate genetic diversity and genome mapping in citrus. 2020-01-08T09:47:25Z 2020-01-08T09:47:25Z 2008 article publishedVersion Luro, F. L., Costantino, G., Terol, J., Argout, X., Allario, T., Wincker, P., ... & Morillon, R. (2008). Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC genomics, 9(1), 287. 1471-2164 http://hdl.handle.net/20.500.11939/6291 10.1186/1471-2164-9-287 https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-287 en Atribución-NoComercial-SinDerivadas 3.0 España http://creativecommons.org/licenses/by-nc-nd/3.0/es/ Springer Nature electronico |
| spellingShingle | Gene Ontology Genomic SSRs F30 Plant genetics and breeding Clementines Sweet oranges Citrus Sour orange Luro, Francois Constantino, Gilles Terol, Javier Argout, Xavier Allario, Thierry Wincker, Patrick Talón, Manuel Ollitrault, Patrick Morillon, Raphael Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping |
| title | Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping |
| title_full | Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping |
| title_fullStr | Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping |
| title_full_unstemmed | Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping |
| title_short | Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping |
| title_sort | transferability of the est ssrs developed on nules clementine citrus clementina hort ex tan to other citrus species and their effectiveness for genetic mapping |
| topic | Gene Ontology Genomic SSRs F30 Plant genetics and breeding Clementines Sweet oranges Citrus Sour orange |
| url | http://hdl.handle.net/20.500.11939/6291 https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-287 |
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