Browsing by Author "Smith, Kevin P"

Now showing 1 - 5 of 5
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    SNP Genotyping Data for the Barley Population in "Registration of the S2MET Barley Mapping Population for Multi-Environment Genomewide Selection"
    (2019-07-25) Neyhart, Jeffrey L; Smith, Kevin P; smith376@umn.edu; Smith, Kevin, P; University of Minnesota Barley-Oat-Silphium Breeding and Genetics Lab
    Two barley populations were genotyped for use in studies of genomewide selection: a training population of 183 individuals and a selection candidate population of 1200 individuals.
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    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 L
    Two 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.
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    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 Genetics
    Germplasm 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.
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    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 Rochester
    Targeted 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.
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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.