Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing
<p>Abstract</p> <p>Background</p> <p>Rise of temperatures and shortening of available water as result of predicted climate change will impose significant pressure on long-lived forest tree species. Discovering allelic variation present in drought related genes of two Au...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-04-01
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| Series: | BMC Research Notes |
| Online Access: | http://www.biomedcentral.com/1756-0500/5/175 |
| _version_ | 1818064908758024192 |
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| author | Homolka Andreas Eder Thomas Kopecky Dieter Berenyi Maria Burg Kornel Fluch Silvia |
| author_facet | Homolka Andreas Eder Thomas Kopecky Dieter Berenyi Maria Burg Kornel Fluch Silvia |
| author_sort | Homolka Andreas |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Rise of temperatures and shortening of available water as result of predicted climate change will impose significant pressure on long-lived forest tree species. Discovering allelic variation present in drought related genes of two Austrian oak species can be the key to understand mechanisms of natural selection and provide forestry with key tools to cope with future challenges.</p> <p>Results</p> <p>In the present study we have used Roche 454 sequencing and developed a bioinformatic pipeline to process multiplexed tagged amplicons in order to identify single nucleotide polymorphisms and allelic sequences of ten candidate genes related to drought/osmotic stress from sessile oak (<it>Quercus robur</it>) and sessile oak (<it>Q. petraea</it>) individuals. Out of these, eight genes of 336 oak individuals growing in Austria have been detected with a total number of 158 polymorphic sites. Allele numbers ranged from ten to 52 with observed heterozygosity ranging from 0.115 to 0.640. All loci deviated from Hardy-Weinberg equilibrium and linkage disequilibrium was found among six combinations of loci.</p> <p>Conclusions</p> <p>We have characterized 183 alleles of drought related genes from oak species and detected first evidences of natural selection. Beside the potential for marker development, we have created an expandable bioinformatic pipeline for the analysis of next generation sequencing data.</p> |
| first_indexed | 2024-12-10T14:43:29Z |
| format | Article |
| id | doaj.art-4c2b96305b244615933e3e83d2b1150d |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-12-10T14:43:29Z |
| publishDate | 2012-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-4c2b96305b244615933e3e83d2b1150d2022-12-22T01:44:38ZengBMCBMC Research Notes1756-05002012-04-015117510.1186/1756-0500-5-175Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencingHomolka AndreasEder ThomasKopecky DieterBerenyi MariaBurg KornelFluch Silvia<p>Abstract</p> <p>Background</p> <p>Rise of temperatures and shortening of available water as result of predicted climate change will impose significant pressure on long-lived forest tree species. Discovering allelic variation present in drought related genes of two Austrian oak species can be the key to understand mechanisms of natural selection and provide forestry with key tools to cope with future challenges.</p> <p>Results</p> <p>In the present study we have used Roche 454 sequencing and developed a bioinformatic pipeline to process multiplexed tagged amplicons in order to identify single nucleotide polymorphisms and allelic sequences of ten candidate genes related to drought/osmotic stress from sessile oak (<it>Quercus robur</it>) and sessile oak (<it>Q. petraea</it>) individuals. Out of these, eight genes of 336 oak individuals growing in Austria have been detected with a total number of 158 polymorphic sites. Allele numbers ranged from ten to 52 with observed heterozygosity ranging from 0.115 to 0.640. All loci deviated from Hardy-Weinberg equilibrium and linkage disequilibrium was found among six combinations of loci.</p> <p>Conclusions</p> <p>We have characterized 183 alleles of drought related genes from oak species and detected first evidences of natural selection. Beside the potential for marker development, we have created an expandable bioinformatic pipeline for the analysis of next generation sequencing data.</p>http://www.biomedcentral.com/1756-0500/5/175 |
| spellingShingle | Homolka Andreas Eder Thomas Kopecky Dieter Berenyi Maria Burg Kornel Fluch Silvia Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing BMC Research Notes |
| title | Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing |
| title_full | Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing |
| title_fullStr | Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing |
| title_full_unstemmed | Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing |
| title_short | Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing |
| title_sort | allele discovery of ten candidate drought response genes in austrian oak using a systematically informatics approach based on 454 amplicon sequencing |
| url | http://www.biomedcentral.com/1756-0500/5/175 |
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