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.

Identification of Two Duplicated Loci Controlling a Disease‐like Rugose Leaf Phenotype in Soybean

“…For example, among the four homologous genes of the Arabidopsis TERMINAL FLOWER gene (TFL1) in soybean, only one has been found to control growth habit; the other copies may have additional functions because they have shown different transcriptional patterns (Tian et al, 2010). Other studies, also using mutagenesis, have also identified and characterized mutations in members of gene families (Bolon et al, 2014). The d1d2 double recessive mutants inhibited chlorosis of soybean leaves, pods and, embryo, causing a mutated organism that retained the chlorophyll, called 'stay-green' (Chao et al, 1995).…”

Soybean Functional Genomics: Bridging the Genotype-to-Phenotype Gap

“…Combining forward genetic screens with next-generation sequencing, Hwang et al (2014) identified an 803 base pair deletion, including part of a peroxidase homolog Glyma15g05831, which likely results in the dwarf phenotype, a beneficial trait in extreme climates. Similarly, high-throughput genomics approaches including CGH arrays, exon capture, and next-generation sequencing have been used to identify and confirm changes in the genome likely underlying changes in plant architecture or seed quality (Bolon et al 2011(Bolon et al , 2014b. The entirety of the data assembled from this FN population including seeds, photographs of obvious phenotypic changes, and NIR data on seed composition has been collected and is publicly available at www.soybase.org/mutants/.…”

“…In addition, genome-wide association studies were used to identify genomic regions associated with oil content, plant height, and pubescence. Bolon et al (2014a) used genome re-sequencing to characterize FN radiation mutants. Rapid decreases in the cost of next-generation sequencing have also facilitated the adoption of de novo sequencing strategies for soybean.…”

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.…”

“…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).…”