Cargando…
A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar
A small fast neutron (FN) mutant population has been established from Phaseolus vulgaris cv. Red Hawk. We leveraged the available P. vulgaris genome sequence and high throughput next generation DNA sequencing to examine the genomic structure of five P. vulgaris cv. Red Hawk FN mutants with striking...
Autores principales: | , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2013
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691542/ https://www.ncbi.nlm.nih.gov/pubmed/23805147 http://dx.doi.org/10.3389/fpls.2013.00210 |
_version_ | 1782274482185961472 |
---|---|
author | O'Rourke, Jamie A. Iniguez, Luis P. Bucciarelli, Bruna Roessler, Jeffrey Schmutz, Jeremy McClean, Phillip E. Jackson, Scott A. Hernandez, Georgina Graham, Michelle A. Stupar, Robert M. Vance, Carroll P. |
author_facet | O'Rourke, Jamie A. Iniguez, Luis P. Bucciarelli, Bruna Roessler, Jeffrey Schmutz, Jeremy McClean, Phillip E. Jackson, Scott A. Hernandez, Georgina Graham, Michelle A. Stupar, Robert M. Vance, Carroll P. |
author_sort | O'Rourke, Jamie A. |
collection | PubMed |
description | A small fast neutron (FN) mutant population has been established from Phaseolus vulgaris cv. Red Hawk. We leveraged the available P. vulgaris genome sequence and high throughput next generation DNA sequencing to examine the genomic structure of five P. vulgaris cv. Red Hawk FN mutants with striking visual phenotypes. Analysis of these genomes identified three classes of structural variation (SV); between cultivar variation, natural variation within the FN mutant population, and FN induced mutagenesis. Our analyses focused on the latter two classes. We identified 23 large deletions (>40 bp) common to multiple individuals, illustrating residual heterogeneity and regions of SV within the common bean cv. Red Hawk. An additional 18 large deletions were identified in individual mutant plants. These deletions, ranging in size from 40 bp to 43,000 bp, are potentially the result of FN mutagenesis. Six of the 18 deletions lie near or within gene coding regions, identifying potential candidate genes causing the mutant phenotype. |
format | Online Article Text |
id | pubmed-3691542 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-36915422013-06-26 A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar O'Rourke, Jamie A. Iniguez, Luis P. Bucciarelli, Bruna Roessler, Jeffrey Schmutz, Jeremy McClean, Phillip E. Jackson, Scott A. Hernandez, Georgina Graham, Michelle A. Stupar, Robert M. Vance, Carroll P. Front Plant Sci Plant Science A small fast neutron (FN) mutant population has been established from Phaseolus vulgaris cv. Red Hawk. We leveraged the available P. vulgaris genome sequence and high throughput next generation DNA sequencing to examine the genomic structure of five P. vulgaris cv. Red Hawk FN mutants with striking visual phenotypes. Analysis of these genomes identified three classes of structural variation (SV); between cultivar variation, natural variation within the FN mutant population, and FN induced mutagenesis. Our analyses focused on the latter two classes. We identified 23 large deletions (>40 bp) common to multiple individuals, illustrating residual heterogeneity and regions of SV within the common bean cv. Red Hawk. An additional 18 large deletions were identified in individual mutant plants. These deletions, ranging in size from 40 bp to 43,000 bp, are potentially the result of FN mutagenesis. Six of the 18 deletions lie near or within gene coding regions, identifying potential candidate genes causing the mutant phenotype. Frontiers Media S.A. 2013-06-25 /pmc/articles/PMC3691542/ /pubmed/23805147 http://dx.doi.org/10.3389/fpls.2013.00210 Text en Copyright © 2013 O'Rourke, Iniguez, Bucciarelli, Roessler, Schmutz, McClean, Jackson, Hernandez, Graham, Stupar and Vance. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc. |
spellingShingle | Plant Science O'Rourke, Jamie A. Iniguez, Luis P. Bucciarelli, Bruna Roessler, Jeffrey Schmutz, Jeremy McClean, Phillip E. Jackson, Scott A. Hernandez, Georgina Graham, Michelle A. Stupar, Robert M. Vance, Carroll P. A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar |
title | A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar |
title_full | A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar |
title_fullStr | A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar |
title_full_unstemmed | A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar |
title_short | A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar |
title_sort | re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691542/ https://www.ncbi.nlm.nih.gov/pubmed/23805147 http://dx.doi.org/10.3389/fpls.2013.00210 |
work_keys_str_mv | AT orourkejamiea aresequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT iniguezluisp aresequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT bucciarellibruna aresequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT roesslerjeffrey aresequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT schmutzjeremy aresequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT mccleanphillipe aresequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT jacksonscotta aresequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT hernandezgeorgina aresequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT grahammichellea aresequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT stuparrobertm aresequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT vancecarrollp aresequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT orourkejamiea resequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT iniguezluisp resequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT bucciarellibruna resequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT roesslerjeffrey resequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT schmutzjeremy resequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT mccleanphillipe resequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT jacksonscotta resequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT hernandezgeorgina resequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT grahammichellea resequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT stuparrobertm resequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar AT vancecarrollp resequencingbasedassessmentofgenomicheterogeneityandfastneutroninduceddeletionsinacommonbeancultivar |