title: Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean.
abstract: Fast neutron radiation has been used as a mutagen to develop extensive mutant collections. However, the genome-wide structural consequences of fast neutron radiation are not well understood. Here, we examine the genome-wide structural variants observed among 264 soybean [Glycine max (L.) Merrill] plants sampled from a large fast neutron-mutagenized population. While deletion rates were similar to previous reports, surprisingly high rates of segmental duplication were also found throughout the genome. Duplication coverage extended across entire chromosomes and often prevailed at chromosome ends. High-throughput resequencing analysis of selected mutants resolved specific chromosomal events, including the rearrangement junctions for a large deletion, a tandem duplication, and a translocation. Genetic mapping associated a large deletion on chromosome 10 with a quantitative change in seed composition for one mutant. A tandem duplication event, located on chromosome 17 in a second mutant, was found to cosegregate with a short petiole mutant phenotype, and thus may serve as an example of a morphological change attributable to a DNA copy number gain. Overall, this study provides insight into the resilience of the soybean genome, the patterns of structural variation resulting from fast neutron mutagenesis, and the utility of fast neutron-irradiated mutants as a source of novel genetic losses and gains.
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Yung-Tsi
authors.initials: YT
authors.lastname: Bolon
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Adrian O
authors.initials: AO
authors.lastname: Stec
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Michno
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Roessler
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Pudota B
authors.initials: PB
authors.lastname: Bhaskar
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Landon
authors.initials: L
authors.lastname: Ries
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Austin A
authors.initials: AA
authors.lastname: Dobbels
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Benjamin W
authors.initials: BW
authors.lastname: Campbell
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Nathan P
authors.initials: NP
authors.lastname: Young
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Justin E
authors.initials: JE
authors.lastname: Anderson
authors.affiliation: Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Ames, Iowa 50011.
authors.forename: David M
authors.initials: DM
authors.lastname: Grant
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: James H
authors.initials: JH
authors.lastname: Orf
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Seth L
authors.initials: SL
authors.lastname: Naeve
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Muehlbauer
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Plant Science Research Unit, United States Department of Agriculture-Agricultural Research Service, St. Paul, Minnesota 55108.
authors.forename: Carroll P
authors.initials: CP
authors.lastname: Vance
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 rstupar@umn.edu.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Stupar
mesh_terms: D020090:Chromosome Segregation / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D055028:Comparative Genomic Hybridization; D005214:Fast Neutrons; D018628:Gene Dosage; D017343:Genes, Plant; D018745:Genome, Plant; D056914:Genomic Structural Variation; D010641:Phenotype; D015203:Reproducibility of Results; D012639:Seeds / Q000235:genetics; D056916:Segmental Duplications, Genomic / Q000235:genetics*; D017384:Sequence Deletion; D013025:Glycine max / Q000235:genetics*
keywords: deletion; duplication; fast neutron; soybean; structural variation