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Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis
Large-scale genetic screens in Arabidopsis are a powerful approach for molecular dissection of complex signaling networks. However, map-based cloning can be time-consuming or even hampered due to low chromosomal recombination. Current strategies using next generation sequencing for molecular identif...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3348062/ https://www.ncbi.nlm.nih.gov/pubmed/22462410 http://dx.doi.org/10.1186/1746-4811-8-12 |
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author | Liu, Kun-hsiang McCormack, Matthew Sheen, Jen |
author_facet | Liu, Kun-hsiang McCormack, Matthew Sheen, Jen |
author_sort | Liu, Kun-hsiang |
collection | PubMed |
description | Large-scale genetic screens in Arabidopsis are a powerful approach for molecular dissection of complex signaling networks. However, map-based cloning can be time-consuming or even hampered due to low chromosomal recombination. Current strategies using next generation sequencing for molecular identification of mutations require whole genome sequencing and advanced computational devises and skills, which are not readily accessible or affordable to every laboratory. We have developed a streamlined method using parallel massive sequencing for mutant identification in which only targeted regions are sequenced. This targeted parallel sequencing (TPSeq) method is more cost-effective, straightforward enough to be easily done without specialized bioinformatics expertise, and reliable for identifying multiple mutations simultaneously. Here, we demonstrate its use by identifying three novel nitrate-signaling mutants in Arabidopsis. |
format | Online Article Text |
id | pubmed-3348062 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-33480622012-05-09 Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis Liu, Kun-hsiang McCormack, Matthew Sheen, Jen Plant Methods Methodology Large-scale genetic screens in Arabidopsis are a powerful approach for molecular dissection of complex signaling networks. However, map-based cloning can be time-consuming or even hampered due to low chromosomal recombination. Current strategies using next generation sequencing for molecular identification of mutations require whole genome sequencing and advanced computational devises and skills, which are not readily accessible or affordable to every laboratory. We have developed a streamlined method using parallel massive sequencing for mutant identification in which only targeted regions are sequenced. This targeted parallel sequencing (TPSeq) method is more cost-effective, straightforward enough to be easily done without specialized bioinformatics expertise, and reliable for identifying multiple mutations simultaneously. Here, we demonstrate its use by identifying three novel nitrate-signaling mutants in Arabidopsis. BioMed Central 2012-03-30 /pmc/articles/PMC3348062/ /pubmed/22462410 http://dx.doi.org/10.1186/1746-4811-8-12 Text en Copyright ©2012 Liu et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Liu, Kun-hsiang McCormack, Matthew Sheen, Jen Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis |
title | Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis |
title_full | Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis |
title_fullStr | Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis |
title_full_unstemmed | Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis |
title_short | Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis |
title_sort | targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in arabidopsis |
topic | Methodology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3348062/ https://www.ncbi.nlm.nih.gov/pubmed/22462410 http://dx.doi.org/10.1186/1746-4811-8-12 |
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