Browsing by Author "Morrell, Peter L"
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Item Barley Genotyping SNPs Annotated using SNPMeta(2016-07-18) Kono, Thomas J Y; Kiran, Seth; Poland, Jesse A; Morrell, Peter L; konox006@umn.edu; Kono, Thomas J YSNPs annotations were derived from publicly available DNA sequences in GenBank using BLAST. Gene name, functional impact, and other information are returned using the program SNPMeta available for download at https://github.com/MorrellLAB/SNPMeta.Item Comparative genomics approaches accurately predict deleterious variants in plants(2018-07-03) Kono, Thomas John Y; Lei, Li; Shih, Ching-Hua; Hoffman, Paul J; Morrell, Peter L; Fay, Justin C; pmorrell@umn.edu; Morrell, Peter L; University of Minnesota Department of Agronomy and Plant Genetics; University of Rochester Department of BiologyRecent advances in genome resequencing have led to increased interest in prediction of the functional consequences of genetic variants. Variants at phylogenetically conserved sites are of particular interest, because they are more likely than variants at phylogenetically variable sites to have deleterious effects on fitness and contribute to phenotypic variation. Numerous comparative genomic approaches have been developed to predict deleterious variants, but they are nearly always judged based on their ability to identify known disease-causing mutations in humans. Determining the accuracy of deleterious variant predictions in nonhuman species is important to understanding evolution, domestication, and potentially to improving crop quality and yield. To examine our ability to predict deleterious variants in plants we generated a curated database of 2,910 Arabidopsis thaliana mutants with known phenotypes. We evaluated seven approaches and found that while all performed well, the single best-performing approach was a likelihood ratio test applied to homologs identified in 42 plant genomes. Although the approaches did not always agree, we found only slight differences in performance when comparing mutations with gross versus biochemical phenotypes, duplicated versus single copy genes, and when using a single approach versus ensemble predictions. We conclude that deleterious mutations can be reliably predicted in A. thaliana and likely other plant species, but that the relative performance of various approaches can depend on the organism to which they are applied.Item 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 BUnderstanding 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.Item Environmental association identifies candidates for tolerance to low temperature and drought(2019-02-11) Lei, Li; Poets, Ana M; Liu, Chaochih; Wyant, Skylar R; Hoffman, Paul J; Carter, Corey K; Trantow, Richard M; Shaw, Brian G; Li, Xin; Muehlbauer, Gary J; Katagiri, Fumiaki; Morrell, Peter L; pmorrell@umn.edu; Morrell, Peter L; University of Minnesota Department of Plant and Microbial Biology; University of Minnesota Department of Agronomy and Plant GeneticsBarley is cultivated from the equator to the Arctic Circle. The wild progenitor species, Hordeum vulgare ssp. spontaneum, occupies a relatively narrow latitudinal range (~30 - 40˚ N) primarily at low elevation, < 1500 m. Adaptation to the range of cultivation has occurred over ~8,000 years. The genetic basis of this adaptation is amenable to study through environmental association. Using genotyping from 7,864 SNPs in 784 barley landraces, we perform mixed model association analysis relative to bioclimatic variables and analysis of allele frequency differentiation across multiple partitions of the data. Using resequencing data from a subset of the landraces, we test for linkage disequilibrium (LD) between SNPs queried in genotyping and SNPs in neighboring loci. We identify seven loci previously reported to contribute to adaptive differences to flowering time and abiotic stress in barley and four loci previously identified in other plant species. In many cases, patterns of LD are consistent with the causative variant occurring in the immediate vicinity of the queried SNP. The identification of barley orthologs to well characterized genes may provide new understanding of the nature of adaptive variation and could permit a more targeted use of potentially adaptive variants in barley breeding and germplasm improvement.Item 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 SciencesThe 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.Item SNP Genotyping Data from the Barley Experimental Population from "Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley"(2016-07-19) Fang, Zhou; Gonzales, Ana M; Clegg, Michael T; Smith, Kevin P; Muehlbauer, Gary J; Steffenson, Brian J; Morrell, Peter L; pmorrell@umn.edu; Morrell, Peter LTwo Barley Oligo Pool Assay chips (BOPA 1 and 2) were genotyped from the Wild Barley Diversity Collection. Due to its broad geographic distribution and ecological adaptation, this collection is a valuable source of potentially useful genes.Item Supporting data for Development of a multi-parent population for genetic mapping and allele discovery in six-row barley(2019-08-12) Hemshrot, Alex; Poets, Ana M; Tyagi, Priyanka; Lei, Li; Carter, Corey; Hirsch, Candice N; Li, Lin; Brown-Guedira, Gina; Morrell, Peter L; Muehlbauer, Gary J; Smith, Kevin P; llei@umn.edu; Lei, Li; University of Minnesota Department of Plant and Microbial Biology; HuaZhong Agricultural University Department of Genetics, College of Plant Science and Technology; USDA Eastern Regional Small Grains Genotyping Laboratory; University of Minnesota Department of Agronomy & Plant GeneticsGermplasm collections hold valuable allelic diversity for crop improvement and genetic mapping of complex traits. To gain access to the genetic diversity within the USDA National Small Grain Collection (NSGC), we developed the Barley Recombinant Inbred Diverse Germplasm Population (BRIDG6), a six-row spring barley multi-parent population (MPP) with 88 cultivated accessions ranging from landrace to cultivars crossed to a common parent (Rasmusson). The parents were randomly selected from a core subset of the NSGC that represents the genetic diversity of landrace and breeding accessions. In total, we generated 6,160 F5 recombinant inbred lines (RILs) with an average of 69 and a range of 37-168 RILs per family genotyped with 7,773 SNPs. The number of segregating SNPs per family range from 956 to 6,775, with an average of 3,889 SNPs per family. Using BRIDG6, we detected 23 QTL contributing to flowering time. Five QTL were within five megabase pairs of previously described flowering time genes. For the major QTL detected near HvPpd-H1, a flowering time gene that affects photoperiod, we observed both positive and negative allele effects ranging from +4 to –3 days relative to Rasmusson among the 79 families segregating for the SNP. Haplotype-based analysis of HvPpd-H1 identified private alleles to families of Asian origin conferring both positive and negative effects, providing the first observation of flowering time-related alleles private to Asian accessions. We evaluate several subsampling strategies to determine their effect on the power of QTL detection and found that for flowering time in barley, a sample size larger than 50 families or 3,000 individuals results in the highest QTL detection. This MPP will be useful for uncovering large and small effect QTL for traits of interest and identifying and utilizing valuable alleles from the NSGC for barley improvement.Item Supporting data for The Fate of Deleterious Variants in a Barley Genomic Prediction Population(2019-10-21) Morrell, Peter L; Smith, Kevin P; Vonderharr, Emily E; Kono, Thomas John Y; Fay, Justin C; Koenig, Daniel; pmorrell@umn.edu; Morrell, Peter L; Department of Agronomy and Plant Genetics, University of Minnesota; Department of Botany & Plant Sciences, University of California, Riverside; Department of Biology, University of RochesterTargeted identification and purging of segregating deleterious genetic variants has been proposed as a novel approach to plant breeding. This approach is motivated in part by the observation that demographic events and strong selection associated with cultivated species pose a “cost of domestication.” This includes an increase in the proportion of genetic variants at phylogenetically-constrained sites where a mutation is likely to reduce fitness. Recent advances in DNA resequencing technology and sequence constraint-based approaches to predict the functional impact of a mutation now permit the identification of putatively deleterious SNPs (dSNPs) on a genome-wide scale. Using exome capture resequencing of 21 barley 6-row spring breeding lines, we identify 3,855 dSNPs among 497,754 total SNPs. The dSNPs are more frequent in portions of the genome with a higher recombination rate, as measured by cM/Mb, than in pericentromeric regions with lower recombination rate and gene density. Using 5,215 progeny from a genomic prediction experiment, we examine the fate of dSNPs over three breeding cycles. Average derived allele frequency is lower for dSNPs than any other class of variants. Adjusting for frequency, derived alleles at dSNPs reduce in frequency or are lost more frequently than other classes of SNPs. Using a linear mixed model applied to 677 lines phenotyped at 5 year-locations, we find that a genomic region with the strongest association with a fungal disease resistance trait that was selected for in the population also negatively impacts yield. Finally, the highest yielding lines in the experiment, as chosen by standard genomic prediction approaches, carry fewer homozygous dSNPs than randomly selected lines.Item Two genomic regions contribute disproportionately to geographic differentiation in wild barley(Genes, Genomes, Genetics, 2014-07) Fang, Zhou; Gonzales, Ana M; Clegg, Michael T; Smith, Keven P; Muehlbauer, Gary J; Steffenson, Brian; Morrell, Peter LGenetic differentiation in natural populations is driven by geographic distance and by ecological or physical features within and between natural habitats that reduce migration. The primary population structure in wild barley differentiates populations east and west of the Zagros Mountains. Genetic differentiation between eastern and western populations is uneven across the genome and is greatest on linkage groups 2H and 5H. Genetic markers in these two regions demonstrate the largest difference in frequency between the primary populations and have the highest informativeness for assignment to each population. Previous cytological and genetic studies suggest there are chromosomal structural rearrangements (inversions or translocations) in these genomic regions. Environmental association analyses identified an association with both temperature and precipitation variables on 2H and with precipitation variables on 5H.Item 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 YSNP 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.