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Browsing by Author "Stupar, Robert M"

Now showing 1 - 3 of 3
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    Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans
    (2016-09-26) Anderson, J; Kono, Thomas J Y; Stupar, Robert M; Kantar, Michael B; Morrell, Peter L; kant0063@umn.edu; Kantar, Michael B
    Understanding the genetics basis of adaption is a fundamental goal of biological research. The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs, to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses.
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    Fast neutron mutagenesis in soybean creates frameshift mutations
    (2021-12-01) Wyant, Skylar R; Rodriguez, Fernanda M; Carter, Corey K; Parrott, Wayne A; Jackson, Scott A; Stupar, Robert M; Morrell, Peter L; pmorrell@umn.edu; Morrell, Peter L; University of California Department of Ecology and Evolutionary Biology; University of Minnesota Department of Agronomy and Plant Genetics; University of Georgia Department of Crop and Soil Sciences
    The mutagenic effects of ionizing radiation have been used for decades to create novel variants in experimental populations. Fast neutron (FN) bombardment as a mutagen has been especially widespread in plants, with extensive reports describing the induction of large structural variants, i.e., deletions, insertions, inversions, and translocations. However, the full spectrum of FN-induced mutations is poorly understood. We contrast small insertions and deletions (indels) observed in 27 soybean lines subject to FN irradiation with the standing indels identified in 107 diverse soybean lines. We use the same populations to contrast the nature and context (bases flanking a nucleotide change) of single nucleotide variants. The rate of accumulation of new single nucleotide changes in FN lines is marginally higher than expected based on spontaneous mutation. In both FN treated lines and in standing variation, C→T transitions and the corresponding reverse complement G→A transitions are the most abundant and occur most frequently in a CpG local context. These data indicate that most SNPs identified in FN lines are likely derived from spontaneous de novo processes that occurred in subsequent generations following mutagenesis, rather than from the FN irradiation mutagen. However, small indels in FN lines differ from standing variants. Short insertions, from 1 – 6 base pairs, are less abundant than in standing variation, and short deletions are more abundant and more prone to induce frameshift mutations that should disrupt the structure and function of encoded proteins. These findings indicate that FN irradiation generates numerous small indels in the genome, increasing the abundance of loss of function mutations that will impact single genes.
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    Variants from "The role of deleterious substitutions in crop genomes"
    (2016-07-26) Kono, Thomas J Y; Fu, Fengli; Mohammadi, Mohsen; Hoffman, Paul J; Liu, Chaochih; Stupar, Robert M; Smith, Kevin P; Tiffin, Peter; Fay, Justin C; Morrell, Peter L; konox006@umn.edu; Kono, Thomas J Y
    SNP calls in protein coding regions were obtained from 15 barley and 8 soybean lines. Non synonymous SNPs were predicted to be deleterious or not using three approaches.