Population genetic variation of microsatellite markers developed for Siberian fir ( Abies sibirica Ledeb.) and European silver fir ( Abies alba Mill.) using whole genome sequencing data
The article presents the results of the search for microsatellite or simple sequence repeat (SSR) loci with tri-, tetra-, penta- and hexanucleotide tandem repeat motifs in the draft de novo assembly of the Siberian fir ( Abies sibirica Ledeb.) genome and the development of convenient relatively high...
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| Veröffentlicht in: | Plant genetic resources: characterization and utilization 2023-04, Vol.21 (2), p.149-158 |
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| creator | Oreshkova, Natalia V. Bondar, Eugenia I. Sharov, Vadim V. Dhungana, Sudha P. Gailing, Oliver Krutovsky, Konstantin V. |
| description | The article presents the results of the search for microsatellite or simple sequence repeat (SSR) loci with tri-, tetra-, penta- and hexanucleotide tandem repeat motifs in the draft
de novo
assembly of the Siberian fir (
Abies sibirica
Ledeb.) genome and the development of convenient relatively highly and moderately polymorphic markers that can be easily genotyped even by simple gel electrophoresis. In total, 64 pairs of oligonucleotide polymerase chain reaction (PCR) primers for 32 detected microsatellite loci were designed and tested. Based on the testing results, 10 most promising polymorphic loci were selected and genotyped in eight natural populations of Siberian fir. Homologous microsatellite loci in the genome of European silver fir (
Abies alba
Mill.) were also identified by mapping Siberian fir contigs, containing SSR loci to the European silver fir genome assembly. A multiplex panel of 14 universal microsatellite loci was developed and genotyped in samples from four natural populations of
A. alba
and a small sample of eight Nordmann fir (
Abies nordmanniana
(Steven) Spach) trees. |
| doi_str_mv | 10.1017/S1479262123000552 |
| format | Article |
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de novo
assembly of the Siberian fir (
Abies sibirica
Ledeb.) genome and the development of convenient relatively highly and moderately polymorphic markers that can be easily genotyped even by simple gel electrophoresis. In total, 64 pairs of oligonucleotide polymerase chain reaction (PCR) primers for 32 detected microsatellite loci were designed and tested. Based on the testing results, 10 most promising polymorphic loci were selected and genotyped in eight natural populations of Siberian fir. Homologous microsatellite loci in the genome of European silver fir (
Abies alba
Mill.) were also identified by mapping Siberian fir contigs, containing SSR loci to the European silver fir genome assembly. A multiplex panel of 14 universal microsatellite loci was developed and genotyped in samples from four natural populations of
A. alba
and a small sample of eight Nordmann fir (
Abies nordmanniana
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de novo
assembly of the Siberian fir (
Abies sibirica
Ledeb.) genome and the development of convenient relatively highly and moderately polymorphic markers that can be easily genotyped even by simple gel electrophoresis. In total, 64 pairs of oligonucleotide polymerase chain reaction (PCR) primers for 32 detected microsatellite loci were designed and tested. Based on the testing results, 10 most promising polymorphic loci were selected and genotyped in eight natural populations of Siberian fir. Homologous microsatellite loci in the genome of European silver fir (
Abies alba
Mill.) were also identified by mapping Siberian fir contigs, containing SSR loci to the European silver fir genome assembly. A multiplex panel of 14 universal microsatellite loci was developed and genotyped in samples from four natural populations of
A. alba
and a small sample of eight Nordmann fir (
Abies nordmanniana
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de novo
assembly of the Siberian fir (
Abies sibirica
Ledeb.) genome and the development of convenient relatively highly and moderately polymorphic markers that can be easily genotyped even by simple gel electrophoresis. In total, 64 pairs of oligonucleotide polymerase chain reaction (PCR) primers for 32 detected microsatellite loci were designed and tested. Based on the testing results, 10 most promising polymorphic loci were selected and genotyped in eight natural populations of Siberian fir. Homologous microsatellite loci in the genome of European silver fir (
Abies alba
Mill.) were also identified by mapping Siberian fir contigs, containing SSR loci to the European silver fir genome assembly. A multiplex panel of 14 universal microsatellite loci was developed and genotyped in samples from four natural populations of
A. alba
and a small sample of eight Nordmann fir (
Abies nordmanniana
(Steven) Spach) trees.</abstract><cop>Cambridge</cop><pub>Cambridge University Press</pub><doi>10.1017/S1479262123000552</doi><tpages>10</tpages><orcidid>https://orcid.org/0000-0002-8819-7084</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Plant genetic resources: characterization and utilization, 2023-04, Vol.21 (2), p.149-158 |
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| language | eng |
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| source | Cambridge University Press Journals Complete |
| subjects | Abies alba Abies sibirica Annealing Assembly Design Electrophoresis Gene mapping Gene sequencing Genetic diversity Genetic markers Genomes Laboratories Loam soils Microsatellites Natural populations Nucleotide sequence Oligonucleotides Polymerase chain reaction Population genetics Populations Whole genome sequencing |
| title | Population genetic variation of microsatellite markers developed for Siberian fir ( Abies sibirica Ledeb.) and European silver fir ( Abies alba Mill.) using whole genome sequencing data |
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