Our long term goal is to genetically dissect complex traits and understand the relationship between naturally occurring genetic and phenotypic variation in forest trees. In this project we will identify relationships between naturally occurring genetic and phenotypic variation in Pinus taeda L..

Loblolly pine, a gymnosperm, is well-positioned phylogenetically to help us understand the evolution of adaptive traits in land plants. To assign biological roles to genes of unknown function and to define gene networks of adaptive significance, a population genomic approach (association genetics) will be used to study how allelic sequence variation among individuals results in phenotypic differences. Specifically, we seek to:

1. Identify all common alleles in 5000 genes, creating a first-of-its-kind community resource of genomic sequence for loblolly pine.
2. Associate at 1000 loci allelic (SNP) variation with phenotypic variation.

Phenotypes will be measured in large populations of clonally propagated trees that represent the widest possible spectrum of genetic variation in the species. The traits will include chemical and anatomical wood properties, resistance to disease incited by biotrophic and necrotrophic fungi, gene expression measured in a 14k cDNA microarray, and expression of gene family members using real-time quantitative PCR. To aid interpretation of associations we will measure linkage disequilibrium in ten selected 100kb regions of the genome. This proposed research will leverage investments in EST projects and large insert library construction to support identification of alleles and relate them to natural phenotypic variation.

Our overarching goal of community coalescence will be accomplished by integrating loblolly pine genotyping, phenotyping and analytical efforts across the United States and making them available through the Treegenes database.

Identification of specific genes and alleles controlling naturally occurring phenotypic variation of complex traits is both biologically and economically relevant, providing:

1. A greater understanding of trait genetic architecture in plants
2. An indirect selection tool for tree breeders
3. A set of potentially useful genetic reagents for genetic modification.

By aggressively seeking to identify most of the major genes controlling specific wood property and disease related traits in loblolly pine, we anticipate a significant breakthrough in our understanding of the genetics of complex traits and the potential economic impact of indirect selection. Marker-aidedselection based on desired allelic variants in genes controlling economic traits can be used across pedigrees within both breeding and natural populations. Such a tool would have immediate and beneficial ramifications for applied tree improvement programs by dramatically reducing testing costs and breeding cycle times. Ultimately, such information could be useful in guiding gene conservation efforts and enhancing our ability to cope with the growing challenges of climate change, shifting habitats and evolving pest populations.