Why Sequence Conifers?

Conifers represent an ancient and diverse branch in higher plant evolution. Some conifer species dominate modern-day ecosystems that are repositories for large amounts of terrestrial sequestered carbon, while others exist in populations numbering tens of individuals. Conifer forests are among the most productive in terms of annual lignocellulosic biomass generation, and coniferous trees are the preferred feedstock for much of the forest products industry, one of the most energy-intensive manufacturing sectors of the U.S. economy. Breeding programs to improve conifers have been in existence for more than 50 years, but progress has been slow because of the large size of the trees and their generally slow progress to sexual maturity.

Climate change and exotic forest pests are threatening certain conifer populations, but a general dearth of genomic resources and tools limits our capacity to address many of these issues and problems. One of the challenges of conifer genomics is that conifers do not have small genomes. Loblolly pine, for example, has a genome roughly seven times the size of the human genome. Thus, complete sequencing of the pine genome is unlikely until such time as sequencing and assembly costs are greatly reduced. Expressed sequence tags (ESTs), which represent the actively expressed portion of conifer genomes, are the most cost-effective route to identify the genes underpinning conifer growth, development, and response to the environment.

The proposed work will more than triple the number of publicly available ESTs for loblolly pine, the species currently serving as the primary reference species for conifer genomics. ESTs will also be generated for 22 other species, some of which have breeding programs and are of economic importance, but many of which have no existing genomic resources. New EST resources will be of immediate use in development of single-nucleotide polymorphism markers for ongoing association genetics studies and breeding for biomass accumulation, as well as for the development of improved oligonucleotide microarrays for functional genomics work. Comparative genomics studies performed using new sequences from previously unstudied conifers will facilitate phylogenetic analyses and greatly improve our understanding of higher plant evolution.

Principal Investigators: Jeffrey Dean (Univ. of Georgia), Glenn T. Howe (Oregon State Univ.), Kathleen D. Jermstad (U.S. Forest Service), David B. Neale and Deborah L. Rogers (Univ. of California, Davis)