Microsatellite markers in candidate genes for wood properties and its application in functional diversity assessment in Eucalyptus globulus
Background: Functional genetic markers have important implications for genetic analysis by providing direct estimation of functional diversity. Although high throughput sequencing techniques for functional diversity analysis are being developed nowadays, the use of already well established variable...
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2012
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paper:paper_07173458_v15_n2_p12_Acuna2023-06-08T15:43:01Z Microsatellite markers in candidate genes for wood properties and its application in functional diversity assessment in Eucalyptus globulus Acuña, Cintia Vanesa Hopp, Horacio Esteban Marcucci Poltri, Susana N. Functional markers Genetic diversity Lignin pathway SSR Wood density Breeding program Candidate genes Cellulose synthase Co-segregation Dinucleotides Diversity analysis Eucalyptus globulus Functional diversity Functional markers Genetic analysis Genetic diversity Genetic markers Genetic variation Glutathione-S-transferase High throughput Homocysteines Information contents Microsatellite markers Microsatellites Other applications Quantitative trait loci mappings Shikimate kinase SSR SSR markers Wood density Xyloglucans Biodiversity Biomarkers DNA sequences Forestry Plants (botany) Transcription factors Genes article cellulose synthase 3 gene cinnamoyl CoA reductase gene dinucleotide repeat Eucalyptus globulus exon gene locus genetic polymorphism genetic variability genotype glutathione S transferase gene homocysteine S methyltransferase gene intron microsatellite marker nonhuman nucleotide sequence plant gene promoter region shikimate kinase gene simple sequence repeat transcription factor LIM1 gene wood xyloglucan endotransglycosylase 2 gene Biodiversity Estimation Eucalyptus Globulus Forestry Functional Groups Genes Lignins Nucleic Acids Plants Wood Density Animalia Eucalyptus Eucalyptus globulus Background: Functional genetic markers have important implications for genetic analysis by providing direct estimation of functional diversity. Although high throughput sequencing techniques for functional diversity analysis are being developed nowadays, the use of already well established variable markers present in candidate genes is still an interesting alternative for mapping purposes and functional diversity studies. SSR markers are routinely used in most plant and animal breeding programs for many species including Eucalyptus. SSR markers derived from candidate genes (SSR-CG) can be used effectively in co-segregation studies and marker-assisted diversity management. Results: In the present study, eight new non reported SSRs were identified in seven candidate genes for wood properties in Eucalyptus globulus: cinnamoyl CoA reductase (CCR), homocysteine S-methyltransferase (HMT), shikimate kinase (SK), xyloglucan endotransglycosylase 2 (XTH2), cellulose synthase 3 (CesA3), glutathione S-transferase (GST) and the transcription factor LIM1. Microsatellites were located in promoters, introns and exons, being most of them CT dinucleotide repeats. Genetic diversity of these eight CG-derived SSR-markers was explored in 54 unrelated genotypes. Except for XTH2, high levels of polymorphism were detected: 93 alleles (mean of 13.1 sd 1.6 alleles per locus), a mean effective number of alleles (Ne) of 5.4 (sd 1.6), polymorphic information content values (PIC) from 0.617 to 0.855 and probability of Identity (PI) ranging from 0.030 to 0.151. Conclusions: This is the first report on the identification, characterization and diversity analysis of microsatellite markers located inside wood quality candidate genes (CG) from Eucalyptus globulus. This set of markers is then appropriate for characterizing genetic variation, with potential usefulness for quantitative trait loci (QTL) mapping in different eucalypts genetic pedigrees and other applications such as fingerprinting and marker assisted diversity management. © 2012 by Pontificia Universidad Católica de Valparaíso, Chile. Fil:Acuña, C.V. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Esteban Hopp, H. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Marcucci Poltri, S.N. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2012 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_07173458_v15_n2_p12_Acuna http://hdl.handle.net/20.500.12110/paper_07173458_v15_n2_p12_Acuna |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Functional markers Genetic diversity Lignin pathway SSR Wood density Breeding program Candidate genes Cellulose synthase Co-segregation Dinucleotides Diversity analysis Eucalyptus globulus Functional diversity Functional markers Genetic analysis Genetic diversity Genetic markers Genetic variation Glutathione-S-transferase High throughput Homocysteines Information contents Microsatellite markers Microsatellites Other applications Quantitative trait loci mappings Shikimate kinase SSR SSR markers Wood density Xyloglucans Biodiversity Biomarkers DNA sequences Forestry Plants (botany) Transcription factors Genes article cellulose synthase 3 gene cinnamoyl CoA reductase gene dinucleotide repeat Eucalyptus globulus exon gene locus genetic polymorphism genetic variability genotype glutathione S transferase gene homocysteine S methyltransferase gene intron microsatellite marker nonhuman nucleotide sequence plant gene promoter region shikimate kinase gene simple sequence repeat transcription factor LIM1 gene wood xyloglucan endotransglycosylase 2 gene Biodiversity Estimation Eucalyptus Globulus Forestry Functional Groups Genes Lignins Nucleic Acids Plants Wood Density Animalia Eucalyptus Eucalyptus globulus |
| spellingShingle |
Functional markers Genetic diversity Lignin pathway SSR Wood density Breeding program Candidate genes Cellulose synthase Co-segregation Dinucleotides Diversity analysis Eucalyptus globulus Functional diversity Functional markers Genetic analysis Genetic diversity Genetic markers Genetic variation Glutathione-S-transferase High throughput Homocysteines Information contents Microsatellite markers Microsatellites Other applications Quantitative trait loci mappings Shikimate kinase SSR SSR markers Wood density Xyloglucans Biodiversity Biomarkers DNA sequences Forestry Plants (botany) Transcription factors Genes article cellulose synthase 3 gene cinnamoyl CoA reductase gene dinucleotide repeat Eucalyptus globulus exon gene locus genetic polymorphism genetic variability genotype glutathione S transferase gene homocysteine S methyltransferase gene intron microsatellite marker nonhuman nucleotide sequence plant gene promoter region shikimate kinase gene simple sequence repeat transcription factor LIM1 gene wood xyloglucan endotransglycosylase 2 gene Biodiversity Estimation Eucalyptus Globulus Forestry Functional Groups Genes Lignins Nucleic Acids Plants Wood Density Animalia Eucalyptus Eucalyptus globulus Acuña, Cintia Vanesa Hopp, Horacio Esteban Marcucci Poltri, Susana N. Microsatellite markers in candidate genes for wood properties and its application in functional diversity assessment in Eucalyptus globulus |
| topic_facet |
Functional markers Genetic diversity Lignin pathway SSR Wood density Breeding program Candidate genes Cellulose synthase Co-segregation Dinucleotides Diversity analysis Eucalyptus globulus Functional diversity Functional markers Genetic analysis Genetic diversity Genetic markers Genetic variation Glutathione-S-transferase High throughput Homocysteines Information contents Microsatellite markers Microsatellites Other applications Quantitative trait loci mappings Shikimate kinase SSR SSR markers Wood density Xyloglucans Biodiversity Biomarkers DNA sequences Forestry Plants (botany) Transcription factors Genes article cellulose synthase 3 gene cinnamoyl CoA reductase gene dinucleotide repeat Eucalyptus globulus exon gene locus genetic polymorphism genetic variability genotype glutathione S transferase gene homocysteine S methyltransferase gene intron microsatellite marker nonhuman nucleotide sequence plant gene promoter region shikimate kinase gene simple sequence repeat transcription factor LIM1 gene wood xyloglucan endotransglycosylase 2 gene Biodiversity Estimation Eucalyptus Globulus Forestry Functional Groups Genes Lignins Nucleic Acids Plants Wood Density Animalia Eucalyptus Eucalyptus globulus |
| description |
Background: Functional genetic markers have important implications for genetic analysis by providing direct estimation of functional diversity. Although high throughput sequencing techniques for functional diversity analysis are being developed nowadays, the use of already well established variable markers present in candidate genes is still an interesting alternative for mapping purposes and functional diversity studies. SSR markers are routinely used in most plant and animal breeding programs for many species including Eucalyptus. SSR markers derived from candidate genes (SSR-CG) can be used effectively in co-segregation studies and marker-assisted diversity management. Results: In the present study, eight new non reported SSRs were identified in seven candidate genes for wood properties in Eucalyptus globulus: cinnamoyl CoA reductase (CCR), homocysteine S-methyltransferase (HMT), shikimate kinase (SK), xyloglucan endotransglycosylase 2 (XTH2), cellulose synthase 3 (CesA3), glutathione S-transferase (GST) and the transcription factor LIM1. Microsatellites were located in promoters, introns and exons, being most of them CT dinucleotide repeats. Genetic diversity of these eight CG-derived SSR-markers was explored in 54 unrelated genotypes. Except for XTH2, high levels of polymorphism were detected: 93 alleles (mean of 13.1 sd 1.6 alleles per locus), a mean effective number of alleles (Ne) of 5.4 (sd 1.6), polymorphic information content values (PIC) from 0.617 to 0.855 and probability of Identity (PI) ranging from 0.030 to 0.151. Conclusions: This is the first report on the identification, characterization and diversity analysis of microsatellite markers located inside wood quality candidate genes (CG) from Eucalyptus globulus. This set of markers is then appropriate for characterizing genetic variation, with potential usefulness for quantitative trait loci (QTL) mapping in different eucalypts genetic pedigrees and other applications such as fingerprinting and marker assisted diversity management. © 2012 by Pontificia Universidad Católica de Valparaíso, Chile. |
| author |
Acuña, Cintia Vanesa Hopp, Horacio Esteban Marcucci Poltri, Susana N. |
| author_facet |
Acuña, Cintia Vanesa Hopp, Horacio Esteban Marcucci Poltri, Susana N. |
| author_sort |
Acuña, Cintia Vanesa |
| title |
Microsatellite markers in candidate genes for wood properties and its application in functional diversity assessment in Eucalyptus globulus |
| title_short |
Microsatellite markers in candidate genes for wood properties and its application in functional diversity assessment in Eucalyptus globulus |
| title_full |
Microsatellite markers in candidate genes for wood properties and its application in functional diversity assessment in Eucalyptus globulus |
| title_fullStr |
Microsatellite markers in candidate genes for wood properties and its application in functional diversity assessment in Eucalyptus globulus |
| title_full_unstemmed |
Microsatellite markers in candidate genes for wood properties and its application in functional diversity assessment in Eucalyptus globulus |
| title_sort |
microsatellite markers in candidate genes for wood properties and its application in functional diversity assessment in eucalyptus globulus |
| publishDate |
2012 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_07173458_v15_n2_p12_Acuna http://hdl.handle.net/20.500.12110/paper_07173458_v15_n2_p12_Acuna |
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