John Doebley

Summary

Affiliation: University of Wisconsin
Country: USA

Publications

  1. ncbi request reprint The molecular genetics of crop domestication
    John F Doebley
    Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
    Cell 127:1309-21. 2006
  2. pmc From many, one: genetic control of prolificacy during maize domestication
    David M Wills
    Department of Genetics, University of Wisconsin Madison, Madison, WI, USA
    PLoS Genet 9:e1003604. 2013
  3. ncbi request reprint Plant science. Unfallen grains: how ancient farmers turned weeds into crops
    John Doebley
    Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
    Science 312:1318-9. 2006
  4. ncbi request reprint The genetics of maize evolution
    John Doebley
    Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
    Annu Rev Genet 38:37-59. 2004
  5. pmc Linkage mapping of domestication loci in a large maize teosinte backcross resource
    William H Briggs
    Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
    Genetics 177:1915-28. 2007
  6. pmc The role of regulatory genes during maize domestication: evidence from nucleotide polymorphism and gene expression
    Qiong Zhao
    Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
    Genetics 178:2133-43. 2008
  7. pmc Genetic diversity and population structure of teosinte
    Kenji Fukunaga
    Laboratory of Genetics, University of Wisconsin, Madison, 53706, USA
    Genetics 169:2241-54. 2005
  8. pmc The genetic architecture of complex traits in teosinte (Zea mays ssp. parviglumis): new evidence from association mapping
    Allison L Weber
    University of Wisconsin, Madison, Wisconsin 53706, USA
    Genetics 180:1221-32. 2008
  9. ncbi request reprint Directional evolution for microsatellite size in maize
    Yves Vigouroux
    Department of Genetics, University of Wisconsin, Madison, USA
    Mol Biol Evol 20:1480-3. 2003
  10. ncbi request reprint Duplicate FLORICAULA/LEAFY homologs zfl1 and zfl2 control inflorescence architecture and flower patterning in maize
    Kirsten Bomblies
    Labortory of Genetics, University of Wisconsin, Madison, WI 53706, USA
    Development 130:2385-95. 2003

Research Grants

  1. MOLECULAR GENETICS OF VARIATION FOR COMPLEX TRAITS
    John Doebley; Fiscal Year: 1999
  2. MOLECULAR GENETICS OF VARIATION FOR COMPLEX TRAITS
    John Doebley; Fiscal Year: 2000
  3. MOLECULAR GENETICS OF VARIATION FOR COMPLEX TRAITS
    John Doebley; Fiscal Year: 2001
  4. MOLECULAR GENETICS OF VARIATION FOR COMPLEX TRAITS
    John Doebley; Fiscal Year: 2002
  5. Genetics of Variation for Complex Traits
    John Doebley; Fiscal Year: 2004
  6. Genetics of Variation for Complex Traits
    John Doebley; Fiscal Year: 2007
  7. Genetics of Variation for Complex Traits
    John Doebley; Fiscal Year: 2005
  8. Genetics of Variation for Complex Traits
    John Doebley; Fiscal Year: 2006

Collaborators

Detail Information

Publications31

  1. ncbi request reprint The molecular genetics of crop domestication
    John F Doebley
    Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
    Cell 127:1309-21. 2006
    ....
  2. pmc From many, one: genetic control of prolificacy during maize domestication
    David M Wills
    Department of Genetics, University of Wisconsin Madison, Madison, WI, USA
    PLoS Genet 9:e1003604. 2013
    ..This work shows how a subtle cis-regulatory change in tissue specific gene expression altered plant architecture in a way that improved the harvestability of maize. ..
  3. ncbi request reprint Plant science. Unfallen grains: how ancient farmers turned weeds into crops
    John Doebley
    Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
    Science 312:1318-9. 2006
  4. ncbi request reprint The genetics of maize evolution
    John Doebley
    Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
    Annu Rev Genet 38:37-59. 2004
    ....
  5. pmc Linkage mapping of domestication loci in a large maize teosinte backcross resource
    William H Briggs
    Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
    Genetics 177:1915-28. 2007
    ..The identification of four BC1 progeny with crossovers in a single gene, tb1, indicated that enough derived lines already exist to clone many QTL without the need to generate and identify additional crossovers...
  6. pmc The role of regulatory genes during maize domestication: evidence from nucleotide polymorphism and gene expression
    Qiong Zhao
    Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
    Genetics 178:2133-43. 2008
    ..We also analyzed expression profiles of genes in distinct maize tissues and observed that domestication genes are expressed on average at a significantly higher level than neutral genes in reproductive organs, including kernels...
  7. pmc Genetic diversity and population structure of teosinte
    Kenji Fukunaga
    Laboratory of Genetics, University of Wisconsin, Madison, 53706, USA
    Genetics 169:2241-54. 2005
    ..We defined core sets of collections of Z. mays ssp. mexicana and ssp. parviglumis that attempt to capture the maximum number of microsatellite alleles for given sample sizes...
  8. pmc The genetic architecture of complex traits in teosinte (Zea mays ssp. parviglumis): new evidence from association mapping
    Allison L Weber
    University of Wisconsin, Madison, Wisconsin 53706, USA
    Genetics 180:1221-32. 2008
    ..Candidate-gene-based association mapping appears to be a promising method for investigating the inheritance of complex traits in teosinte...
  9. ncbi request reprint Directional evolution for microsatellite size in maize
    Yves Vigouroux
    Department of Genetics, University of Wisconsin, Madison, USA
    Mol Biol Evol 20:1480-3. 2003
    ..The occurrence of directional evolution for microsatellite size indicates that the estimation of population parameters with microsatellite data in maize should be done with caution...
  10. ncbi request reprint Duplicate FLORICAULA/LEAFY homologs zfl1 and zfl2 control inflorescence architecture and flower patterning in maize
    Kirsten Bomblies
    Labortory of Genetics, University of Wisconsin, Madison, WI 53706, USA
    Development 130:2385-95. 2003
    ....
  11. pmc An analysis of genetic diversity across the maize genome using microsatellites
    Yves Vigouroux
    Department of Genetics, University of Wisconsin, Madison, 53706, USA
    Genetics 169:1617-30. 2005
    ..Overall, the pattern of genetic diversity at maize SSRs can be explained largely by a bottleneck effect with a smaller effect from selection...
  12. ncbi request reprint Rate and pattern of mutation at microsatellite loci in maize
    Yves Vigouroux
    Department of Genetics, University of Wisconsin, Madison 53706, USA
    Mol Biol Evol 19:1251-60. 2002
    ..The microsatellite-based estimate of the effective population size of maize is more than an order of magnitude less than previously reported values based on nucleotide sequence variation...
  13. pmc MADS-box genes of maize: frequent targets of selection during domestication
    Qiong Zhao
    Laboratory of Genetics, University of Wisconsin Madison, Madison, WI 53706, USA
    Genet Res (Camb) 93:65-75. 2011
    ..These results suggest that MADS-box genes were more frequent targets of selection during domestication than genes chosen at random from the genome...
  14. pmc Major regulatory genes in maize contribute to standing variation in teosinte (Zea mays ssp. parviglumis)
    Allison Weber
    Laboratory of Genetics, University of Wisconsin, Madison 53706, USA
    Genetics 177:2349-59. 2007
    ..Our data suggest that major regulatory genes in maize do play a role in the natural variation for complex traits in teosinte and that some of the minor variants we identified may have been targets of selection during domestication...
  15. pmc Identification of a functional transposon insertion in the maize domestication gene tb1
    Anthony Studer
    Department of Genetics, University of Wisconsin Madison, Madison, Wisconsin, USA
    Nat Genet 43:1160-3. 2011
    ..Molecular dating indicates that the Hopscotch insertion predates maize domestication by at least 10,000 years, indicating that selection acted on standing variation rather than new mutation...
  16. ncbi request reprint Population structure and genetic diversity of New World maize races assessed by DNA microsatellites
    Yves Vigouroux
    Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706 USA
    Am J Bot 95:1240-53. 2008
    ..We identify highland Mexico and the Andes as potential sources of genetic diversity underrepresented among elite lines used in maize breeding programs...
  17. ncbi request reprint A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture
    Richard M Clark
    Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
    Nat Genet 38:594-7. 2006
    ..Our findings show that the large stretches of noncoding DNA that comprise the majority of many plant genomes can be a source of variation affecting gene expression and quantitative phenotypes...
  18. ncbi request reprint A weak effect of background selection on trinucleotide microsatellites in maize
    Anne Céline Thuillet
    Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
    J Hered 99:45-55. 2008
    ..The fact that the same correlation is not confirmed for nucleotide diversity suggests that the strength of purifying selection at or near this class of microsatellites is higher than for nucleotide mutations...
  19. ncbi request reprint Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus
    Richard M Clark
    Laboratory of Genetics, University of Wisconsin, USA
    Mol Biol Evol 22:2304-12. 2005
    ..We use rate estimates from the tb1 region to estimate the timing of expansion of transposable elements in the maize genome and suggest that this expansion occurred primarily within the last million years...
  20. pmc A single domestication for maize shown by multilocus microsatellite genotyping
    Yoshihiro Matsuoka
    Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 99:6080-4. 2002
    ..We also found only modest evidence for postdomestication gene flow from teosinte into maize...
  21. pmc The origin of the naked grains of maize
    Huai Wang
    Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
    Nature 436:714-9. 2005
    ..Our results demonstrate that modest genetic changes in single genes can induce dramatic changes in phenotype during domestication and evolution...
  22. pmc Using association mapping in teosinte to investigate the function of maize selection-candidate genes
    Allison L Weber
    Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
    PLoS ONE 4:e8227. 2009
    ..The selection-candidate genes appear to be located closer in the genome to domestication QTL than expected by chance...
  23. pmc Pattern of diversity in the genomic region near the maize domestication gene tb1
    Richard M Clark
    Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 101:700-7. 2004
    ....
  24. ncbi request reprint Molecular evolution of FLORICAULA/LEAFY orthologs in the Andropogoneae (Poaceae)
    Kirsten Bomblies
    Department of Genetics, University of Wisconsin Madison, USA
    Mol Biol Evol 22:1082-94. 2005
    ..mays ssp. parviglumis), and found no evidence for selection pressure resulting from maize domestication within the zfl2-coding region...
  25. pmc Pleiotropic effects of the duplicate maize FLORICAULA/LEAFY genes zfl1 and zfl2 on traits under selection during maize domestication
    Kirsten Bomblies
    Department of Genetics, University of Wisconsin, Madison, Wisconsin, 53706, USA
    Genetics 172:519-31. 2006
    ..The results suggest that zfl2 activity is important for the QTL effect, supporting zfl2 as a candidate gene for a role in morphological evolution of maize...
  26. pmc Biography of John F. Doebley
    Christen Brownlee
    Proc Natl Acad Sci U S A 101:697-9. 2004
  27. ncbi request reprint The role of barren stalk1 in the architecture of maize
    Andrea Gallavotti
    Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093 0116, USA
    Nature 432:630-5. 2004
    ....
  28. ncbi request reprint The effects of artificial selection on the maize genome
    Stephen I Wright
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Science 308:1310-4. 2005
    ..If we assume that our sample of genes is representative, approximately 1200 genes throughout the maize genome have been affected by artificial selection...
  29. pmc A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement
    Masanori Yamasaki
    Division of Plant Sciences, University of Missouri, Columbia, Misssouri 65211, USA
    Plant Cell 17:2859-72. 2005
    ..Our large-scale screen for artificial selection allows identification of genes of potential agronomic importance even when gene function and the phenotype of interest are unknown...
  30. pmc Marcus rhoades, preferential segregation and meiotic drive
    James A Birchler
    Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
    Genetics 164:835-41. 2003
  31. ncbi request reprint A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
    Jianming Yu
    Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
    Nat Genet 38:203-8. 2006
    ..As this new method crosses the boundary between family-based and structured association samples, it provides a powerful complement to currently available methods for association mapping...

Research Grants8

  1. MOLECULAR GENETICS OF VARIATION FOR COMPLEX TRAITS
    John Doebley; Fiscal Year: 1999
    ..The long-term goal of this research is to understand how variation at the molecular level in gene expression/function produces variation for complex traits in natural populations. ..
  2. MOLECULAR GENETICS OF VARIATION FOR COMPLEX TRAITS
    John Doebley; Fiscal Year: 2000
    ..The long-term goal of this research is to understand how variation at the molecular level in gene expression/function produces variation for complex traits in natural populations. ..
  3. MOLECULAR GENETICS OF VARIATION FOR COMPLEX TRAITS
    John Doebley; Fiscal Year: 2001
    ..The long-term goal of this research is to understand how variation at the molecular level in gene expression/function produces variation for complex traits in natural populations. ..
  4. MOLECULAR GENETICS OF VARIATION FOR COMPLEX TRAITS
    John Doebley; Fiscal Year: 2002
    ..The long-term goal of this research is to understand how variation at the molecular level in gene expression/function produces variation for complex traits in natural populations. ..
  5. Genetics of Variation for Complex Traits
    John Doebley; Fiscal Year: 2004
    ..5) Finally, we will analyze the patterning of genetic diversity in genomic regions that have experienced recent and strong selective sweeps to understand how the genome responds to past selective pressure. ..
  6. Genetics of Variation for Complex Traits
    John Doebley; Fiscal Year: 2007
    ..5) Finally, we will analyze the patterning of genetic diversity in genomic regions that have experienced recent and strong selective sweeps to understand how the genome responds to past selective pressure. ..
  7. Genetics of Variation for Complex Traits
    John Doebley; Fiscal Year: 2005
    ..5) Finally, we will analyze the patterning of genetic diversity in genomic regions that have experienced recent and strong selective sweeps to understand how the genome responds to past selective pressure. ..
  8. Genetics of Variation for Complex Traits
    John Doebley; Fiscal Year: 2006
    ..5) Finally, we will analyze the patterning of genetic diversity in genomic regions that have experienced recent and strong selective sweeps to understand how the genome responds to past selective pressure. ..