David B Neale

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc PineSAP--sequence alignment and SNP identification pipeline
    Jill L Wegrzyn
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Bioinformatics 25:2609-10. 2009
  2. doi request reprint Forest tree genomics: growing resources and applications
    David B Neale
    Department of Plant Sciences, University of California, Davis, California 95616, USA
    Nat Rev Genet 12:111-22. 2011
  3. pmc Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests
    Elena Mosca
    Department of Plant Sciences, University of California at Davis Davis, CA, USA IASMA Research and Innovation Centre, Fondazione Edmund Mach, S Michele all Adige Italy
    Evol Appl 5:762-75. 2012
  4. pmc Evolution of disease response genes in loblolly pine: insights from candidate genes
    Elhan S Ersoz
    Department of Plant Sciences, University of California Davis, Davis, California, United States of America
    PLoS ONE 5:e14234. 2010
  5. pmc TreeGenes: A Forest Tree Genome Database
    Jill L Wegrzyn
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Int J Plant Genomics 2008:412875. 2008
  6. pmc Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine
    Emilie Chancerel
    INRA, UMR1202 BIOGECO, F 33610 Cestas, France
    BMC Genomics 12:368. 2011
  7. ncbi request reprint Association genetics of complex traits in conifers
    David B Neale
    Institute of Forest Genetics, USDA Forest Service and Department of Environmental Horticulture, University of California, Davis, CA, USA
    Trends Plant Sci 9:325-30. 2004
  8. doi request reprint Population, quantitative and comparative genomics of adaptation in forest trees
    David B Neale
    Department of Plant Sciences, University of California, Davis, Mail Stop 6 and Institute of Forest Genetics, Pacific Southwest Research Station, USDA Forest Service, Davis, CA 95616, USA
    Curr Opin Plant Biol 11:149-55. 2008
  9. ncbi request reprint Genomics to tree breeding and forest health
    David B Neale
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Curr Opin Genet Dev 17:539-44. 2007
  10. pmc Multilocus patterns of nucleotide diversity and divergence reveal positive selection at candidate genes related to cold hardiness in coastal Douglas Fir (Pseudotsuga menziesii var. menziesii)
    Andrew J Eckert
    Section of Evolution and Ecology, University of California, Davis, California 95616, USA
    Genetics 183:289-98. 2009

Collaborators

Detail Information

Publications27

  1. pmc PineSAP--sequence alignment and SNP identification pipeline
    Jill L Wegrzyn
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Bioinformatics 25:2609-10. 2009
    ..The use of machine learning in the SNP identifications extends the pipeline's application to any eukaryotic species where full genome sequence information is unavailable...
  2. doi request reprint Forest tree genomics: growing resources and applications
    David B Neale
    Department of Plant Sciences, University of California, Davis, California 95616, USA
    Nat Rev Genet 12:111-22. 2011
    ....
  3. pmc Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests
    Elena Mosca
    Department of Plant Sciences, University of California at Davis Davis, CA, USA IASMA Research and Innovation Centre, Fondazione Edmund Mach, S Michele all Adige Italy
    Evol Appl 5:762-75. 2012
    ..Some of these outliers encode proteins that are involved with plant stress responses and form the basis for further evolutionary enquiries...
  4. pmc Evolution of disease response genes in loblolly pine: insights from candidate genes
    Elhan S Ersoz
    Department of Plant Sciences, University of California Davis, Davis, California, United States of America
    PLoS ONE 5:e14234. 2010
    ..This burden is even greater if the generation time of the plant is much longer than the generation time of the pathogen...
  5. pmc TreeGenes: A Forest Tree Genome Database
    Jill L Wegrzyn
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Int J Plant Genomics 2008:412875. 2008
    ..TreeGenes was developed to provide a centralized web resource with analysis and visualization tools to support data storage and exchange...
  6. pmc Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine
    Emilie Chancerel
    INRA, UMR1202 BIOGECO, F 33610 Cestas, France
    BMC Genomics 12:368. 2011
    ..In this paper, we evaluated the potential of highly-multiplexed SNP genotyping for genetic mapping in maritime pine (Pinus pinaster Ait.), the main conifer used for commercial plantation in southwestern Europe...
  7. ncbi request reprint Association genetics of complex traits in conifers
    David B Neale
    Institute of Forest Genetics, USDA Forest Service and Department of Environmental Horticulture, University of California, Davis, CA, USA
    Trends Plant Sci 9:325-30. 2004
    ..Allele discovery using association approaches should lead to more-efficient methods of marker-assisted breeding and a deeper understanding of genetic adaptation in forest trees...
  8. doi request reprint Population, quantitative and comparative genomics of adaptation in forest trees
    David B Neale
    Department of Plant Sciences, University of California, Davis, Mail Stop 6 and Institute of Forest Genetics, Pacific Southwest Research Station, USDA Forest Service, Davis, CA 95616, USA
    Curr Opin Plant Biol 11:149-55. 2008
    ..This combined approach is identifying the most important genes that determine patterns of complex trait adaptation observed in many tree populations...
  9. ncbi request reprint Genomics to tree breeding and forest health
    David B Neale
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Curr Opin Genet Dev 17:539-44. 2007
    ..Population genetic neutrality tests have been applied to identify genes probably under natural selection and thus make good candidates for developing forest health diagnostic tools...
  10. pmc Multilocus patterns of nucleotide diversity and divergence reveal positive selection at candidate genes related to cold hardiness in coastal Douglas Fir (Pseudotsuga menziesii var. menziesii)
    Andrew J Eckert
    Section of Evolution and Ecology, University of California, Davis, California 95616, USA
    Genetics 183:289-98. 2009
    ....
  11. doi request reprint Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae)
    Andrew J Eckert
    Section of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA
    Mol Ecol 19:3789-805. 2010
    ....
  12. pmc Association genetics in Pinus taeda L. I. Wood property traits
    Santiago C González-Martínez
    Department of Plant Sciences, University of California, Davis, California 95616, USA
    Genetics 175:399-409. 2007
    ..This approach is of particular utility in species such as conifers, where genomewide strategies are limited by their large genomes...
  13. doi request reprint Association genetics of chemical wood properties in black poplar (Populus nigra)
    Fernando P Guerra
    Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
    New Phytol 197:162-76. 2013
    ....
  14. doi request reprint Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem
    Jill L Wegrzyn
    Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
    New Phytol 188:515-32. 2010
    ....
  15. pmc Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits
    Andrew J Eckert
    Section of Evolution and Ecology, University of California, Davis, 95616, USA
    Genetics 182:1289-302. 2009
    ..These associations provide insight into the genetic components of complex traits in coastal Douglas fir, as well as highlight the need for landscape genetic approaches to the detection of adaptive genetic diversity...
  16. pmc Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae)
    Andrew J Eckert
    US Department of Agriculture, Institute of Forest Genetics, Pacific Southwest Research Station, Davis, California 95616, USA
    Genetics 185:969-82. 2010
    ....
  17. pmc Nucleotide diversity and linkage disequilibrium in cold-hardiness- and wood quality-related candidate genes in Douglas fir
    Konstantin V Krutovsky
    Institute of Forest Genetics, Pacific Southwest Research Station, US Department of Agriculture Forest Service, Davis, CA 95616, USA
    Genetics 171:2029-41. 2005
    ..LD decayed relatively slowly but steadily within genes. Haploblock analysis was used to define haplotype tag SNPs (htSNPs). These data will help to select SNPs for association mapping, which is already in progress...
  18. pmc Nucleotide diversity and linkage disequilibrium in loblolly pine
    Garth R Brown
    Department of Environmental Horticulture, University of California, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 101:15255-60. 2004
    ....
  19. doi request reprint Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation
    Jill L Wegrzyn
    Department of Plant Sciences, University of California, Davis, California 95616
    Genetics 196:891-909. 2014
    ..Conifer genomes are full of repetitive DNA, with the most significant contributions from long-terminal-repeat retrotransposons. In depth analysis of the tandem and interspersed repetitive content yielded a combined estimate of 82%. ..
  20. doi request reprint CartograTree: connecting tree genomes, phenotypes and environment
    Hans A Vasquez-Gross
    Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
    Mol Ecol Resour 13:528-37. 2013
    ..The application provides a unique tool set to facilitate research on the ecology, physiology and evolution of forest tree species. CartograTree can be accessed at: http://dendrome.ucdavis.edu/cartogratree...
  21. pmc The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences
    Allen Kovach
    Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
    BMC Genomics 11:420. 2010
    ..The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda...
  22. pmc Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas fir. III. Quantitative trait loci-by-environment interactions
    Kathleen D Jermstad
    Institute of Forest Genetics, Pacific Southwest Research Station, U S Department of Agriculture Forest Service, Placerville, California 95667, USA
    Genetics 165:1489-506. 2003
    ..This is the first report of QTL interactions with specific environmental signals in forest trees and will assist in the identification of candidate genes controlling these important adaptive traits in perennial plants...
  23. pmc Comparative mapping in the Pinaceae
    Konstantin V Krutovsky
    Institute of Forest Genetics, Pacific Southwest Research Station, US Department of Agriculture Forest Service, Davis, California 95616, USA
    Genetics 168:447-61. 2004
    ..This study reports the first comparative map in forest trees at the family taxonomic level and establishes a framework for comparative genomics in Pinaceae...
  24. pmc Identification of quantitative trait loci influencing wood property traits in loblolly pine (Pinus taeda L.). III. QTL Verification and candidate gene mapping
    Garth R Brown
    Department of Environmental Horticulture, University of California Davis, 1 Shields Avenue, Davis, CA 95616, USA
    Genetics 164:1537-46. 2003
    ..Several candidate genes colocated with wood property QTL; however, these relationships must be verified in future experiments...
  25. doi request reprint DnaSAM: Software to perform neutrality testing for large datasets with complex null models
    Andrew J Eckert
    Section of Evolution and Ecology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA Center for Population Biology Department of Plant Sciences, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
    Mol Ecol Resour 10:542-5. 2010
    ..g. population bottlenecks). The output is a set of diversity and neutrality statistics with associated probability values under a user-specified null model that are stored in easy to manipulate text file...
  26. pmc Insights into the loblolly pine genome: characterization of BAC and fosmid sequences
    Jill L Wegrzyn
    Department of Plant Sciences, University of California Davis, Davis, California, United States of America
    PLoS ONE 8:e72439. 2013
    ..These discoveries, along with other genomic resources, will be used to annotate conifer genomes and address long-standing questions about gymnosperm evolution. ..
  27. ncbi request reprint Forest-tree population genomics and adaptive evolution
    Santiago C González-Martínez
    Department of Forest Systems and Resources, Center of Forest Research CIFOR INIA, 28040 Madrid, Spain
    New Phytol 170:227-38. 2006
    ....