Research Topics
| David B NealeSummaryAffiliation: University of California Country: USA Publications
| Collaborators
|
Detail Information
Publications
PineSAP--sequence alignment and SNP identification pipelineJill L Wegrzyn
Department of Plant Sciences, University of California, Davis, CA 95616, USA
Bioinformatics 25:2609-10. 2009..AVAILABILITY: All code used for this pipeline is freely available at the Dendrome project website (http://dendrome.ucdavis.edu/adept2/resequencing.html)..
Forest tree genomics: growing resources and applicationsDavid B Neale
Department of Plant Sciences, University of California, Davis, California 95616, USA
Nat Rev Genet 12:111-22. 2011....- Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pineEmilie 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... 
Association genetics of complex traits in conifersDavid 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...- Population, quantitative and comparative genomics of adaptation in forest treesDavid 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... - Genomics to tree breeding and forest healthDavid 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... - 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.... - 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.... - Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylemJill L Wegrzyn
Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
New Phytol 188:515-32. 2010.... - Association genetics in Pinus taeda L. I. Wood property traitsSantiago 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... - 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.... - Nucleotide diversity and linkage disequilibrium in cold-hardiness- and wood quality-related candidate genes in Douglas firKonstantin 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... - Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traitsAndrew 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... - The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequencesAllen 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... - Nucleotide diversity and linkage disequilibrium in loblolly pineGarth R Brown
Department of Environmental Horticulture, University of California, Davis, CA 95616, USA
Proc Natl Acad Sci U S A 101:15255-60. 2004.... - Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas fir. III. Quantitative trait loci-by-environment interactionsKathleen 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... - Comparative mapping in the PinaceaeKonstantin 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... - 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.... - DnaSAM: Software to perform neutrality testing for large datasets with complex null modelsAndrew 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... - Contrasting patterns of nucleotide diversity for four conifers of Alpine European forestsElena 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... - Evolution of disease response genes in loblolly pine: insights from candidate genesElhan 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... - Identification of quantitative trait loci influencing wood property traits in loblolly pine (Pinus taeda L.). III. QTL Verification and candidate gene mappingGarth 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... - CartograTree: connecting tree genomes, phenotypes and environmentHans 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... - TreeGenes: A Forest Tree Genome DatabaseJill 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... - Forest-tree population genomics and adaptive evolutionSantiago C González-Martínez
Department of Forest Systems and Resources, Center of Forest Research CIFOR INIA, 28040 Madrid, Spain
New Phytol 170:227-38. 2006....