Title: "Association Genetics of Natural Genetic Variation and Complex Traits in Forest Trees"
Speaker: David B. Neale, Dept. Plant Sciences, University of California, Davis
Place: Electrical Engineering (EE) 270; April 10, 2007, Tuesday, 4:30pm


Economic and adaptive traits in forest trees are generally controlled by many genes, often with small individual effects on phenotypes. We have used a QTL mapping approach for many years to identify such genes. The number, position and size of effects can be estimated but the individual genes remain unknown. Positional cloning of QTLs in large genomes (20Gb) is not highly tractable. Thus, we have turned to the association genetics approach to identify genes underlying QTLs. The association genetics approach is rather amenable to conifers and other forest trees due to: (1) large, random mating and unstructured populations of forest trees, (2) moderate to high levels of nucleotide diversity, (2) precise evaluation of phenotype due to clonal or family-based testing and (4) the rapid decay of linkage disequilibrium. We have used this approach to detect associations between candidate gene SNPs and phenotypes in several trait groups (wood properties, disease resistance and biotic stresses). A limitation of these studies, however, has been the small number (<100) of candidate genes in association screens. Recently we have completed resequencing of ~8000 candidate genes and will begin genotyping SNPs in large association populations. This approach approximates a gene-space scan. These discoveries can be applied to marker-based breeding and for gene resource management in domesticated or natural populations.

Associated Reading:
Neale, D.B. and O. Savolainen (2004) Association genetics of complex traits in conifers. Trends in Plant Science. 9:325-330.

Peter, G. and D. Neale (2004) Molecular basis for the evolution of xylem lignification. Curr. Op. Plant Biol. 7:1-6.

Brown, G.R. et al. (2004) Nucleotide diversity and linkage disequilibrium in loblolly pine. Proc. Natl. Acad. Sci. U.S.A. 101:15255-15260.

Krutovsky,K.V. and D. B. Neale. (2005) Nucleotide diversity and linkage disequilibrium in cold-hardiness and wood quality related candidate genes in Douglas-fir. Genetics 171:2029-2041.

Gonzalez-Martinez, et al. (2006) Candidate genes for drought-stress response in Pinus taeda L. DNA sequence variation and natural selection. Genetics 172:1915-1926.

Gonzalez-Martinez, et al. (2006) Forest tree population genomics and adaptive evolution. New Phytologist 170:227-238.

Krutovsky, K. V., and D. B. Neale. (2006) Forest genomics and new molecular genetic approaches to measuring and conserving adaptive genetic diversity in forest trees. In: Th. Geburek & J. Turok (eds.) Conservation and Management of Forest Genetic Resources in Europe, Arbora Publishers, Zvolen.

Gonzalez-Martinez, S.C., et al. (2007) Association genetics in Pinus taeda L. I. Wood property traits. Genetics 175:399-409.

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