Phenotypic and Genomic Analyses of a Fast Neutron Mutant Population Resource in Soybean    

Abstract

Mutagenized populations have become indispensable resources for introducing variation and studying gene function in plant genomics research. In this study, fast neutron (FN) radiation was used to induce deletion mutations in the soybean (Glycine max) genome. Approximately 120,000 soybean seeds were exposed to FN radiation doses of up to 32 Gray units to develop over 23,000 independent M2 lines. Here, we demonstrate the utility of this population for phenotypic screening and associated genomic characterization of striking and agronomically important traits. Plant variation was cataloged for seed composition, maturity, morphology, pigmentation, and nodulation traits. Mutants that showed significant increases or decreases in seed protein and oil content across multiple generations and environments were identified. The application of comparative genomic hybridization (CGH) to lesion-induced mutants for deletion mapping was validated on a midoleate x-ray mutant, M23, with a known FAD2-1A (for fatty acid desaturase) gene deletion. Using CGH, a subset of mutants was characterized, revealing deletion regions and candidate genes associated with phenotypes of interest. Exome resequencing and sequencing of PCR products confirmed FN-induced deletions detected by CGH. Beyond characterization of soybean FN mutants, this study demonstrates the utility of CGH, exome sequence capture, and next-generation sequencing approaches for analyses of mutant plant genomes. We present this FN mutant soybean population as a valuable public resource for future genetic screens and functional genomics research.

Bringing New Plant Varieties to Market: Plant Breeding and Selection Practices Advance Beneficial Characteristics while Minimizing Unintended Changes

“…Breeders then select for agriculturally desirable genetic changes while selecting against the many unintended or unwanted changes that can occur with these methods (Bolon et al, 2011). Over 3000 plant varieties, mostly vegetables, fruits, grains, and ornamentals (IAEA-MVD, 2017), have been developed via mutagenesis.…”

Identification of Homogentisate Dioxygenase as a Target for Vitamin E Biofortification in Oilseeds

“…In order to identify the causative gene lesion responsible for the observed phenotype, we utilized comparative genome hybridization (CGH) analysis, a microarray-based method for high-throughput identification of induced genomic deletions and additions (Bolon et al, 2011(Bolon et al, , 2014Haun et al, 2011). CGH analysis of five brown-seeded BC 1 F 2 plants detected a total of eight deleted DNA segments present in at least one of the plants analyzed (Fig.…”

“…For each CGH dataset, the average and SD values for corrected log 2 ratios of the 696,139 unique probes were obtained. Significant CNV events were called following previously set criteria (Bolon et al, 2011), namely, segments with an average corrected log 2 ratio values greater than or less than three SD from the array mean were identified as additions or deletions, respectively. Likewise, if a gap between potential segments was less than half the size of the total distance covered by neighboring segments, then the entire region was considered a single CNV event.…”

“…CGH was performed using a 696,139-feature soybean CGH microarray (Bolon et al, 2011;Haun et al, 2011). The oligonucleotide probes are 50-to 70-mers spaced at approximately 1.1 kb intervals and were designed by Roche NimbleGen based on the sequenced Williams 82 genome.…”

“…A major challenge in soybean, as with other crop plants, is assigning function to each these genes or at least identifying those that contribute to agronomic traits. We therefore developed a large number of soybean mutants by fast neutron irradiation, a mutagen known to induce genetic deletions and segmental duplications (Li et al, 2001;Rogers et al, 2009;Bolon et al, 2011Bolon et al, , 2014. A major advantage of this approach is that these genetic lesions can be easily defined using array-based hybridization methods (Bruce et al, 2009;Bolon et al, 2011Bolon et al, , 2014Haun et al, 2011).…”