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Title: A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar

Author
item O`Rourke, Jamie
item INIGUEZ, LUIS - Universidad Nacional Autonoma De Mexico
item Bucciarelli, Bruna
item ROESSLER, JEFFREY - University Of Minnesota
item SCHUMTZ, JEREMY - Hudsonalpha Institute For Biotechnology
item MCCLEAN, PHIL - North Dakota State University
item JACKSON, SCOTT - University Of Georgia
item HERNANDEZ, GEORGINA - Universidad Nacional Autonoma De Mexico
item Graham, Michelle
item STUPAR, ROBERT - University Of Minnesota
item Vance, Carroll

Submitted to: Frontiers in Plant Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/3/2013
Publication Date: 6/25/2013
Publication URL: https://handle.nal.usda.gov/10113/57034
Citation: O'Rourke, J.A., Iniguez, L.P., Bucciarelli, B., Roessler, J., Schumtz, J., McClean, P., Jackson, S.A., Hernandez, G., Graham, M.A., Stupar, R.M., Vance, C.P. 2013. A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar. Frontiers in Plant Genetics and Genomics. DOI:10.3389/fpls.2013.00210.

Interpretive Summary: Common bean, Phaseolus vulgaris L., is an important source of proteins and carbohydrates for over three million people world-wide. Identification of genes is currently underway, but gene function is still unknown. One way to learn about gene function is by studying mutants. We made a collection of common bean mutants using radiation. By sequencing the genomes of five mutant plants and a control we were able to identify regions where the radiation removed DNA of the mutant plants. In three of the mutant plants, these deletions might affect the expression of nearby genes causing visible changes in the plant. Analyzing the genome sequence of the mutant plants also found differences between the plants, not caused by radiation. These differences might be useful for plant breeders developing new cultivars. This paper demonstrates the utility of utilizing high throughput sequencing and the mutant population as a resource for the common bean research community.

Technical Abstract: 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 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 likely the result of fast neutron mutagenesis. Six of the 18 deletions resulting from mutagenesis lie near or within gene coding regions, identifying potential candidate genes causing the mutant phenotype.