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...

Descripción completa

Detalles Bibliográficos
Autores principales: 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.
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