A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study
<p<Abstract</p< <p<Background</p< <p<Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for <it<Quercus robur </it<and <it<Quercus pe...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Cherubini Marcello [verfasserIn] Mattioni Claudia [verfasserIn] Villani Fiorella [verfasserIn] Koelewijn Hans-Peter [verfasserIn] Gailing Oliver [verfasserIn] Buonamici Anna [verfasserIn] Sebastiani Federico [verfasserIn] Vendramin Giovanni [verfasserIn] Frigerio Jean-Marc [verfasserIn] Chancerel Emilie [verfasserIn] Bodénès Catherine [verfasserIn] Durand Jérôme [verfasserIn] Goicoechea Pablo G [verfasserIn] Herrán Ana [verfasserIn] Ikaran Ziortza [verfasserIn] Cabané Cyril [verfasserIn] Ueno Saneyoshi [verfasserIn] Alberto Florian [verfasserIn] Dumoulin Pierre-Yves [verfasserIn] Guichoux Erwan [verfasserIn] de Daruvar Antoine [verfasserIn] Kremer Antoine [verfasserIn] Plomion Christophe [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2010 |
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| Übergeordnetes Werk: |
In: BMC Genomics - BMC, 2003, 11(2010), 1, p 570 |
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| Übergeordnetes Werk: |
volume:11 ; year:2010 ; number:1, p 570 |
| Links: |
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| DOI / URN: |
10.1186/1471-2164-11-570 |
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| Katalog-ID: |
DOAJ008333084 |
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| 520 | |a <p<Abstract</p< <p<Background</p< <p<Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for <it<Quercus robur </it<and <it<Quercus petraea </it<provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in <it<Castanea sativa </it<(chestnut).</p< <p<Results</p< <p<A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of <it<Quercus robur</it<. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.</p< <p<Conclusion</p< <p<We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.</p< | ||
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10.1186/1471-2164-11-570 doi (DE-627)DOAJ008333084 (DE-599)DOAJ029fd579421c4b9ba304c2feeabdc084 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Cherubini Marcello verfasserin aut A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for <it<Quercus robur </it<and <it<Quercus petraea </it<provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in <it<Castanea sativa </it<(chestnut).</p< <p<Results</p< <p<A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of <it<Quercus robur</it<. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.</p< <p<Conclusion</p< <p<We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.</p< Biotechnology Genetics Mattioni Claudia verfasserin aut Villani Fiorella verfasserin aut Koelewijn Hans-Peter verfasserin aut Gailing Oliver verfasserin aut Buonamici Anna verfasserin aut Sebastiani Federico verfasserin aut Vendramin Giovanni verfasserin aut Frigerio Jean-Marc verfasserin aut Chancerel Emilie verfasserin aut Bodénès Catherine verfasserin aut Durand Jérôme verfasserin aut Goicoechea Pablo G verfasserin aut Herrán Ana verfasserin aut Ikaran Ziortza verfasserin aut Cabané Cyril verfasserin aut Ueno Saneyoshi verfasserin aut Alberto Florian verfasserin aut Dumoulin Pierre-Yves verfasserin aut Guichoux Erwan verfasserin aut de Daruvar Antoine verfasserin aut Kremer Antoine verfasserin aut Plomion Christophe verfasserin aut In BMC Genomics BMC, 2003 11(2010), 1, p 570 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:11 year:2010 number:1, p 570 https://doi.org/10.1186/1471-2164-11-570 kostenfrei https://doaj.org/article/029fd579421c4b9ba304c2feeabdc084 kostenfrei http://www.biomedcentral.com/1471-2164/11/570 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1, p 570 |
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10.1186/1471-2164-11-570 doi (DE-627)DOAJ008333084 (DE-599)DOAJ029fd579421c4b9ba304c2feeabdc084 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Cherubini Marcello verfasserin aut A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for <it<Quercus robur </it<and <it<Quercus petraea </it<provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in <it<Castanea sativa </it<(chestnut).</p< <p<Results</p< <p<A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of <it<Quercus robur</it<. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.</p< <p<Conclusion</p< <p<We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.</p< Biotechnology Genetics Mattioni Claudia verfasserin aut Villani Fiorella verfasserin aut Koelewijn Hans-Peter verfasserin aut Gailing Oliver verfasserin aut Buonamici Anna verfasserin aut Sebastiani Federico verfasserin aut Vendramin Giovanni verfasserin aut Frigerio Jean-Marc verfasserin aut Chancerel Emilie verfasserin aut Bodénès Catherine verfasserin aut Durand Jérôme verfasserin aut Goicoechea Pablo G verfasserin aut Herrán Ana verfasserin aut Ikaran Ziortza verfasserin aut Cabané Cyril verfasserin aut Ueno Saneyoshi verfasserin aut Alberto Florian verfasserin aut Dumoulin Pierre-Yves verfasserin aut Guichoux Erwan verfasserin aut de Daruvar Antoine verfasserin aut Kremer Antoine verfasserin aut Plomion Christophe verfasserin aut In BMC Genomics BMC, 2003 11(2010), 1, p 570 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:11 year:2010 number:1, p 570 https://doi.org/10.1186/1471-2164-11-570 kostenfrei https://doaj.org/article/029fd579421c4b9ba304c2feeabdc084 kostenfrei http://www.biomedcentral.com/1471-2164/11/570 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1, p 570 |
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10.1186/1471-2164-11-570 doi (DE-627)DOAJ008333084 (DE-599)DOAJ029fd579421c4b9ba304c2feeabdc084 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Cherubini Marcello verfasserin aut A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for <it<Quercus robur </it<and <it<Quercus petraea </it<provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in <it<Castanea sativa </it<(chestnut).</p< <p<Results</p< <p<A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of <it<Quercus robur</it<. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.</p< <p<Conclusion</p< <p<We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.</p< Biotechnology Genetics Mattioni Claudia verfasserin aut Villani Fiorella verfasserin aut Koelewijn Hans-Peter verfasserin aut Gailing Oliver verfasserin aut Buonamici Anna verfasserin aut Sebastiani Federico verfasserin aut Vendramin Giovanni verfasserin aut Frigerio Jean-Marc verfasserin aut Chancerel Emilie verfasserin aut Bodénès Catherine verfasserin aut Durand Jérôme verfasserin aut Goicoechea Pablo G verfasserin aut Herrán Ana verfasserin aut Ikaran Ziortza verfasserin aut Cabané Cyril verfasserin aut Ueno Saneyoshi verfasserin aut Alberto Florian verfasserin aut Dumoulin Pierre-Yves verfasserin aut Guichoux Erwan verfasserin aut de Daruvar Antoine verfasserin aut Kremer Antoine verfasserin aut Plomion Christophe verfasserin aut In BMC Genomics BMC, 2003 11(2010), 1, p 570 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:11 year:2010 number:1, p 570 https://doi.org/10.1186/1471-2164-11-570 kostenfrei https://doaj.org/article/029fd579421c4b9ba304c2feeabdc084 kostenfrei http://www.biomedcentral.com/1471-2164/11/570 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1, p 570 |
| allfieldsGer |
10.1186/1471-2164-11-570 doi (DE-627)DOAJ008333084 (DE-599)DOAJ029fd579421c4b9ba304c2feeabdc084 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Cherubini Marcello verfasserin aut A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for <it<Quercus robur </it<and <it<Quercus petraea </it<provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in <it<Castanea sativa </it<(chestnut).</p< <p<Results</p< <p<A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of <it<Quercus robur</it<. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.</p< <p<Conclusion</p< <p<We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.</p< Biotechnology Genetics Mattioni Claudia verfasserin aut Villani Fiorella verfasserin aut Koelewijn Hans-Peter verfasserin aut Gailing Oliver verfasserin aut Buonamici Anna verfasserin aut Sebastiani Federico verfasserin aut Vendramin Giovanni verfasserin aut Frigerio Jean-Marc verfasserin aut Chancerel Emilie verfasserin aut Bodénès Catherine verfasserin aut Durand Jérôme verfasserin aut Goicoechea Pablo G verfasserin aut Herrán Ana verfasserin aut Ikaran Ziortza verfasserin aut Cabané Cyril verfasserin aut Ueno Saneyoshi verfasserin aut Alberto Florian verfasserin aut Dumoulin Pierre-Yves verfasserin aut Guichoux Erwan verfasserin aut de Daruvar Antoine verfasserin aut Kremer Antoine verfasserin aut Plomion Christophe verfasserin aut In BMC Genomics BMC, 2003 11(2010), 1, p 570 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:11 year:2010 number:1, p 570 https://doi.org/10.1186/1471-2164-11-570 kostenfrei https://doaj.org/article/029fd579421c4b9ba304c2feeabdc084 kostenfrei http://www.biomedcentral.com/1471-2164/11/570 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1, p 570 |
| allfieldsSound |
10.1186/1471-2164-11-570 doi (DE-627)DOAJ008333084 (DE-599)DOAJ029fd579421c4b9ba304c2feeabdc084 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Cherubini Marcello verfasserin aut A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for <it<Quercus robur </it<and <it<Quercus petraea </it<provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in <it<Castanea sativa </it<(chestnut).</p< <p<Results</p< <p<A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of <it<Quercus robur</it<. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.</p< <p<Conclusion</p< <p<We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.</p< Biotechnology Genetics Mattioni Claudia verfasserin aut Villani Fiorella verfasserin aut Koelewijn Hans-Peter verfasserin aut Gailing Oliver verfasserin aut Buonamici Anna verfasserin aut Sebastiani Federico verfasserin aut Vendramin Giovanni verfasserin aut Frigerio Jean-Marc verfasserin aut Chancerel Emilie verfasserin aut Bodénès Catherine verfasserin aut Durand Jérôme verfasserin aut Goicoechea Pablo G verfasserin aut Herrán Ana verfasserin aut Ikaran Ziortza verfasserin aut Cabané Cyril verfasserin aut Ueno Saneyoshi verfasserin aut Alberto Florian verfasserin aut Dumoulin Pierre-Yves verfasserin aut Guichoux Erwan verfasserin aut de Daruvar Antoine verfasserin aut Kremer Antoine verfasserin aut Plomion Christophe verfasserin aut In BMC Genomics BMC, 2003 11(2010), 1, p 570 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:11 year:2010 number:1, p 570 https://doi.org/10.1186/1471-2164-11-570 kostenfrei https://doaj.org/article/029fd579421c4b9ba304c2feeabdc084 kostenfrei http://www.biomedcentral.com/1471-2164/11/570 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1, p 570 |
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Cherubini Marcello @@aut@@ Mattioni Claudia @@aut@@ Villani Fiorella @@aut@@ Koelewijn Hans-Peter @@aut@@ Gailing Oliver @@aut@@ Buonamici Anna @@aut@@ Sebastiani Federico @@aut@@ Vendramin Giovanni @@aut@@ Frigerio Jean-Marc @@aut@@ Chancerel Emilie @@aut@@ Bodénès Catherine @@aut@@ Durand Jérôme @@aut@@ Goicoechea Pablo G @@aut@@ Herrán Ana @@aut@@ Ikaran Ziortza @@aut@@ Cabané Cyril @@aut@@ Ueno Saneyoshi @@aut@@ Alberto Florian @@aut@@ Dumoulin Pierre-Yves @@aut@@ Guichoux Erwan @@aut@@ de Daruvar Antoine @@aut@@ Kremer Antoine @@aut@@ Plomion Christophe @@aut@@ |
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The availability of ESTs for <it<Quercus robur </it<and <it<Quercus petraea </it<provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in <it<Castanea sativa </it<(chestnut).</p< <p<Results</p< <p<A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of <it<Quercus robur</it<. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.</p< <p<Conclusion</p< <p<We have generated a bin map for oak comprising 256 EST-SSRs. 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Cherubini Marcello |
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TP248.13-248.65 QH426-470 A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study |
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A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study |
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Cherubini Marcello Mattioni Claudia Villani Fiorella Koelewijn Hans-Peter Gailing Oliver Buonamici Anna Sebastiani Federico Vendramin Giovanni Frigerio Jean-Marc Chancerel Emilie Bodénès Catherine Durand Jérôme Goicoechea Pablo G Herrán Ana Ikaran Ziortza Cabané Cyril Ueno Saneyoshi Alberto Florian Dumoulin Pierre-Yves Guichoux Erwan de Daruvar Antoine Kremer Antoine Plomion Christophe |
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fast and cost-effective approach to develop and map est-ssr markers: oak as a case study |
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A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study |
| abstract |
<p<Abstract</p< <p<Background</p< <p<Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for <it<Quercus robur </it<and <it<Quercus petraea </it<provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in <it<Castanea sativa </it<(chestnut).</p< <p<Results</p< <p<A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of <it<Quercus robur</it<. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.</p< <p<Conclusion</p< <p<We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.</p< |
| abstractGer |
<p<Abstract</p< <p<Background</p< <p<Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for <it<Quercus robur </it<and <it<Quercus petraea </it<provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in <it<Castanea sativa </it<(chestnut).</p< <p<Results</p< <p<A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of <it<Quercus robur</it<. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.</p< <p<Conclusion</p< <p<We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.</p< |
| abstract_unstemmed |
<p<Abstract</p< <p<Background</p< <p<Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for <it<Quercus robur </it<and <it<Quercus petraea </it<provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in <it<Castanea sativa </it<(chestnut).</p< <p<Results</p< <p<A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of <it<Quercus robur</it<. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.</p< <p<Conclusion</p< <p<We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.</p< |
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A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study |
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https://doi.org/10.1186/1471-2164-11-570 https://doaj.org/article/029fd579421c4b9ba304c2feeabdc084 http://www.biomedcentral.com/1471-2164/11/570 https://doaj.org/toc/1471-2164 |
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Mattioni Claudia Villani Fiorella Koelewijn Hans-Peter Gailing Oliver Buonamici Anna Sebastiani Federico Vendramin Giovanni Frigerio Jean-Marc Chancerel Emilie Bodénès Catherine Durand Jérôme Goicoechea Pablo G Herrán Ana Ikaran Ziortza Cabané Cyril Ueno Saneyoshi Alberto Florian Dumoulin Pierre-Yves Guichoux Erwan de Daruvar Antoine Kremer Antoine Plomion Christophe |
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10.1186/1471-2164-11-570 |
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