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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...

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Detalles Bibliográficos
Autores principales: Liu, Kun-hsiang, McCormack, Matthew, Sheen, Jen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
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.
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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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