Jan Dvorak

Summary

Affiliation: University of California
Country: USA

Publications

  1. doi request reprint The origin of spelt and free-threshing hexaploid wheat
    Jan Dvorak
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    J Hered 103:426-41. 2012
  2. pmc Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS
    Delphine Fleury
    Australian Centre for Plant Functional Genomics, University of Adelaide, PMB1, Glen Osmond SA 5064, Australia
    BMC Genomics 11:382. 2010
  3. pmc A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat
    Yong Q Gu
    1Genomics and Gene Discovery Research Unit, USDA ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
    BMC Genomics 10:496. 2009
  4. pmc Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)
    Shiaoman Chao
    USDA ARS Genotyping Laboratory, Biosciences Research Laboratory, Fargo, ND, USA
    BMC Genomics 11:727. 2010
  5. pmc Discovery and mapping of wheat Ph1 suppressors
    J Dvorak
    Department of Plant Sciences, University of California, Davis, California 95616, USA
    Genetics 174:17-27. 2006
  6. ncbi request reprint Molecular characterization of a diagnostic DNA marker for domesticated tetraploid wheat provides evidence for gene flow from wild tetraploid wheat to hexaploid wheat
    Jan Dvorak
    Department of Plant Sciences, University of California, Davis, USA
    Mol Biol Evol 23:1386-96. 2006
  7. pmc Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing aegilops species
    J Dvorak
    Department of Agronomy and Range Science, University of California, Davis 95616, USA
    Genetics 148:423-34. 1998
  8. pmc Tempos of gene locus deletions and duplications and their relationship to recombination rate during diploid and polyploid evolution in the Aegilops-Triticum alliance
    Jan Dvorak
    Department of Plant Sciences, University of California, Davis, California 95616, USA
    Genetics 171:323-32. 2005
  9. pmc Deletion polymorphism in wheat chromosome regions with contrasting recombination rates
    Jan Dvorak
    Department of Plant Sciences, University of California, Davis, California 95616, USA
    Genetics 168:1665-75. 2004
  10. pmc Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence
    Frank M You
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    BMC Genomics 12:59. 2011

Collaborators

Detail Information

Publications35

  1. doi request reprint The origin of spelt and free-threshing hexaploid wheat
    Jan Dvorak
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    J Hered 103:426-41. 2012
    ..It is proposed that the tetraploid parent of hexaploid wheat was not hulled emmer but a free-threshing form of tetraploid wheat...
  2. pmc Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS
    Delphine Fleury
    Australian Centre for Plant Functional Genomics, University of Adelaide, PMB1, Glen Osmond SA 5064, Australia
    BMC Genomics 11:382. 2010
    ..aestivum since it is only slightly larger than the ancestor wheat D genome. Gene co-linearity between the grasses can be exploited by extrapolating from rice and Brachypodium distachyon to Ae. tauschii or barley, and then to wheat...
  3. pmc A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat
    Yong Q Gu
    1Genomics and Gene Discovery Research Unit, USDA ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
    BMC Genomics 10:496. 2009
    ..A BAC-based physical map is one of them. A physical map will facilitate analysis of genome structure, comparative genomics, and assembly of the entire genome sequence...
  4. pmc Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)
    Shiaoman Chao
    USDA ARS Genotyping Laboratory, Biosciences Research Laboratory, Fargo, ND, USA
    BMC Genomics 11:727. 2010
    ..Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico...
  5. pmc Discovery and mapping of wheat Ph1 suppressors
    J Dvorak
    Department of Plant Sciences, University of California, Davis, California 95616, USA
    Genetics 174:17-27. 2006
    ..ucd-5S may primarily regulate recombination between homologous chromosomes...
  6. ncbi request reprint Molecular characterization of a diagnostic DNA marker for domesticated tetraploid wheat provides evidence for gene flow from wild tetraploid wheat to hexaploid wheat
    Jan Dvorak
    Department of Plant Sciences, University of California, Davis, USA
    Mol Biol Evol 23:1386-96. 2006
    ..A cline of the 2 haplotype frequencies exists across Euro-Asia in T. aestivum. It is suggested that T. aestivum in eastern Asia conserved the gene pool of the original T. aestivum more than wheat elsewhere...
  7. pmc Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing aegilops species
    J Dvorak
    Department of Agronomy and Range Science, University of California, Davis 95616, USA
    Genetics 148:423-34. 1998
    ..This relationship was not found among the more distantly related species...
  8. pmc Tempos of gene locus deletions and duplications and their relationship to recombination rate during diploid and polyploid evolution in the Aegilops-Triticum alliance
    Jan Dvorak
    Department of Plant Sciences, University of California, Davis, California 95616, USA
    Genetics 171:323-32. 2005
    ..The significance of these findings for genome evolution at the diploid and polyploid level is discussed...
  9. pmc Deletion polymorphism in wheat chromosome regions with contrasting recombination rates
    Jan Dvorak
    Department of Plant Sciences, University of California, Davis, California 95616, USA
    Genetics 168:1665-75. 2004
    ..The rate of diploidization of polyploid wheat by deletions was estimated and was shown to have proceeded faster in the distal, high-recombination interval than in the proximal, low-recombination interval...
  10. pmc Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence
    Frank M You
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    BMC Genomics 12:59. 2011
    ....
  11. pmc RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development
    Frank M You
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Nucleic Acids Res 38:W313-20. 2010
    ..02 Gb, providing an almost unlimited source of molecular markers for mapping large and complex genomes. A web-based server and a command line-based pipeline for RJPrimers are both available at http://wheat.pw.usda.gov/demos/RJPrimers/...
  12. pmc A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor
    Ming Cheng Luo
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 110:7940-5. 2013
    ..tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions...
  13. pmc BatchPrimer3: a high throughput web application for PCR and sequencing primer design
    Frank M You
    Department of Plant Sciences, University of California, CA 95616, USA
    BMC Bioinformatics 9:253. 2008
    ..In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded...
  14. pmc A new implementation of high-throughput five-dimensional clone pooling strategy for BAC library screening
    Frank M You
    Department of Plant Sciences, University of California, Davis, CA 95516, USA
    BMC Genomics 11:692. 2010
    ..However, this strategy occasionally needs manual PCR to deconvolute pools and identify truly positive clones...
  15. pmc ConservedPrimers 2.0: a high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery
    Frank M You
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    BMC Bioinformatics 10:331. 2009
    ..To date, no suitable high-throughput tool is available for this purpose...
  16. ncbi request reprint Mechanisms and rates of birth and death of dispersed duplicated genes during the evolution of a multigene family in diploid and tetraploid wheats
    Eduard D Akhunov
    Department of Plant Sciences, University of California, Davis, USA
    Mol Biol Evol 24:539-50. 2007
    ..The evolution of the ALP family shows that repeated elements facilitate both gene duplication and expression of duplicated genes and highlights their importance for the evolution of gene repertoire in large plant genomes...
  17. pmc Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms
    Frank M You
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    BMC Genomics 13:354. 2012
    ..Here we updated this pipeline for SNP discovery in outcrossing (allogamous) species and demonstrated its efficacy in SNP discovery in walnut (Juglans regia L.)...
  18. ncbi request reprint Comparative genetic maps reveal extreme crossover localization in the Aegilops speltoides chromosomes
    Ming Cheng Luo
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Theor Appl Genet 111:1098-106. 2005
    ..monococcum maps. The wheat B genome and the genome of Ae. longissima, a close relative of Ae. speltoides, do not show the extreme localization of crossovers observed in Ae. speltoides...
  19. pmc Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay
    Eduard Akhunov
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Theor Appl Genet 119:507-17. 2009
    ....
  20. pmc A high-throughput strategy for screening of bacterial artificial chromosome libraries and anchoring of clones on a genetic map constructed with single nucleotide polymorphisms
    Ming Cheng Luo
    Department of Plant Sciences, University of California, Davis, CA 95616
    BMC Genomics 10:28. 2009
    ..It is hypothesized that this impediment can be overcome by screening multidimensional pools of BAC clones using the highly parallel Illumina GoldenGate assay...
  21. pmc Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species
    Ming Cheng Luo
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    BMC Genomics 11:122. 2010
    ....
  22. pmc Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes
    Eduard D Akhunov
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    BMC Genomics 11:702. 2010
    ..dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat...
  23. ncbi request reprint Genome plasticity a key factor in the success of polyploid wheat under domestication
    Jorge Dubcovsky
    Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA
    Science 316:1862-6. 2007
    ..Frequent gene deletions and disruptions generated by a fast replacement rate of repetitive sequences are buffered by the polyploid nature of wheat, resulting in subtle dosage effects on which selection can operate...
  24. pmc The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms
    Eduard D Akhunov
    Department of Agronomy and Range Science, University of California, Davis, California 95616, USA
    Genome Res 13:753-63. 2003
    ....
  25. pmc Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates
    Eduard D Akhunov
    Department of Agronomy and Range Science, University of California, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 100:10836-41. 2003
    ..Synteny perturbations were characterized in 31 paralogous sets of loci with perturbed synteny. Both insertions and deletions of loci were detected and both preferentially occurred in high recombination regions of chromosomes...
  26. ncbi request reprint High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis
    Ming Cheng Luo
    Department of Agronomy and Range Science, University of California at Davis, Davis, CA, 95616, USA
    Genomics 82:378-89. 2003
    ....
  27. doi request reprint A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus
    Monika K Michalak de Jimenez
    Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108 6050, USA
    Funct Integr Genomics 13:19-32. 2013
    ..Indeed, these observations advocate the evolutionary importance of this locus as suggested by "Maan's scs hypothesis."..
  28. doi request reprint Characterizing the walnut genome through analyses of BAC end sequences
    Jiajie Wu
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Plant Mol Biol 78:95-107. 2012
    ..This study is an initial characterization of the walnut genome and provides the largest genomic resource currently available; as such, it will be a valuable tool in studies aimed at genetically improving walnut...
  29. ncbi request reprint GenoProfiler: batch processing of high-throughput capillary fingerprinting data
    Frank M You
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Bioinformatics 23:240-2. 2007
    ....
  30. doi request reprint Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat
    Jirui Wang
    Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
    New Phytol 198:925-37. 2013
    ..tauschii chromosomes with recombination rates. Gene flow from A. tauschii was an important source of wheat genetic diversity and shaped its distribution along the D-genome chromosomes...
  31. pmc Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae
    M C Luo
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 106:15780-5. 2009
    ..tauschii chromosomes, suggesting that the dependence of synteny erosion on gene location along the centromere-telomere axis either evolved recently in the Triticeae phylogenetic lineage or its evolution was recently accelerated...
  32. pmc Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii
    Ajay Kumar
    Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA
    BMC Genomics 13:597. 2012
    ..Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported...
  33. doi request reprint Biolistic transformation of Schistosoma mansoni: Studies with modified reporter-gene constructs containing regulatory regions of protease genes
    Jan Dvorak
    Sandler Center for Basic Research in Parasitic Diseases, California Institute for Quantitative Biosciences QB3, 1700 4th St, University of California, San Francisco, CA 94158 2550, USA
    Mol Biochem Parasitol 170:37-40. 2010
    ..Electroporation of the same constructs was also weakly efficient (1-10% positives per experiment). However, reporter signals were found in tissues other than the gut, which may represent dysregulated transcription...
  34. ncbi request reprint Differential use of protease families for invasion by schistosome cercariae
    Jan Dvorak
    Sandler Center for Basic Research in Parasitic Diseases, California Institute for Quantitative Biomedical Research QB3, 1700 4th Street, University of California, San Francisco, CA 94158 2550, USA
    Biochimie 90:345-58. 2008
    ..Computational analysis of serine protease phylogeny revealed an extraordinarily distant relationship between S. mansoni serine proteases and other members of the Clan PA family S1 proteases...
  35. ncbi request reprint The structure of wild and domesticated emmer wheat populations, gene flow between them, and the site of emmer domestication
    M C Luo
    Department of Plant Sciences, University of California, Davis, CA, 95616, USA
    Theor Appl Genet 114:947-59. 2007
    ..Durum wheat is closely related to domesticated emmer in the eastern Mediterranean and likely originated there...