A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar
A small fast neutron 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 Phaseolus vulgaris cv. Red Hawk fast neutron mutants w...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2013-06-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2013.00210/full |
| _version_ | 1811225165966606336 |
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| author | Jamie A. O'Rourke Jamie A. O'Rourke Luis P. Iniguez Bruna eBucciarelli Bruna eBucciarelli Jeffrey eRoessler Jeremy eSchmutz Phillip E. McClean Scott A. Jackson Georgina eHernandez Michelle A. Graham Robert M. Stupar Carroll P. Vance Carroll P. Vance |
| author_facet | Jamie A. O'Rourke Jamie A. O'Rourke Luis P. Iniguez Bruna eBucciarelli Bruna eBucciarelli Jeffrey eRoessler Jeremy eSchmutz Phillip E. McClean Scott A. Jackson Georgina eHernandez Michelle A. Graham Robert M. Stupar Carroll P. Vance Carroll P. Vance |
| author_sort | Jamie A. O'Rourke |
| collection | DOAJ |
| description | A small fast neutron 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 Phaseolus vulgaris cv. Red Hawk fast neutron mutants with striking visual phenotypes. Analysis of these genomes identified three classes of structural variation; between cultivar variation, natural variation within the fast neutron mutant population, and fast neutron 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 structural variation 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 fast neutron mutagenesis. Six of the 18 deletions lie near or within gene coding regions, identifying potential candidate genes causing the mutant phenotype. |
| first_indexed | 2024-04-12T09:01:11Z |
| format | Article |
| id | doaj.art-1df7fde6dbc84965bfbb5b67460b1c1a |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-12T09:01:11Z |
| publishDate | 2013-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-1df7fde6dbc84965bfbb5b67460b1c1a2022-12-22T03:39:13ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2013-06-01410.3389/fpls.2013.0021051329A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivarJamie A. O'Rourke0Jamie A. O'Rourke1Luis P. Iniguez2Bruna eBucciarelli3Bruna eBucciarelli4Jeffrey eRoessler5Jeremy eSchmutz6Phillip E. McClean7Scott A. Jackson8Georgina eHernandez9Michelle A. Graham10Robert M. Stupar11Carroll P. Vance12Carroll P. Vance13USDA-Agricultural Research ServiceUniversity of MinnesotaUniversidad Nacional Autonoma de MexicoUSDA-Agricultural Research ServiceUniversity of MinnesotaUniversity of MinnesotaHudson Alpha Institute for BiotechnologyNorth Dakota State UniversityUniversity of GeorgiaUniversidad Nacional Autonoma de MexicoUSDA-Agricultural Research ServiceUniversity of MinnesotaUSDA-Agricultural Research ServiceUniversity of MinnesotaA small fast neutron 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 Phaseolus vulgaris cv. Red Hawk fast neutron mutants with striking visual phenotypes. Analysis of these genomes identified three classes of structural variation; between cultivar variation, natural variation within the fast neutron mutant population, and fast neutron 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 structural variation 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 fast neutron mutagenesis. Six of the 18 deletions lie near or within gene coding regions, identifying potential candidate genes causing the mutant phenotype.http://journal.frontiersin.org/Journal/10.3389/fpls.2013.00210/fullnatural variationcommon beanDNA-seqPhaseolus vulgarisstructural variationfast neutron mutation |
| spellingShingle | Jamie A. O'Rourke Jamie A. O'Rourke Luis P. Iniguez Bruna eBucciarelli Bruna eBucciarelli Jeffrey eRoessler Jeremy eSchmutz Phillip E. McClean Scott A. Jackson Georgina eHernandez Michelle A. Graham Robert M. Stupar Carroll P. Vance Carroll P. Vance A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar Frontiers in Plant Science natural variation common bean DNA-seq Phaseolus vulgaris structural variation fast neutron mutation |
| 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 | natural variation common bean DNA-seq Phaseolus vulgaris structural variation fast neutron mutation |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2013.00210/full |
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