APPENDIX E Major Components of a Poplar Genomics Initiative

If the U.S. Department of Energy decides to focus more of its resources on the biotechnology of feedstock crops, genomics would be a logical subject for research. In the following discussion, the tools, type of experiments, and target traits for a major genomics project in a bioenergy crop are outlined using poplars as an example. These structural genomics studies would provide the tools for mapping and isolating a large number of genes. With this foundation, many different kinds of traits could be studied, and experiments could be performed to determine their roles and use them in breeding or genetic engineering. All of the options outlined below do not have to be undertaken to make progress in this area; however, a significant program to study a single feedstock species is likely to entail a recurring annual cost of at least $2 million for a number of years.

A comprehensive genomics project should have the following components: structural genomics, materials for studying trait variation and expression, and functional genomics.

  • Structural Genomics. The establishment of tools for studying and mapping genes, such as large sequence databanks, genome maps, and high-efficiency transformation methods.

  • Materials for Studies of Trait Variation and Expression. The development of large, carefully designed pedigrees and field experiments and other experimental materials based on trait expression, in which genes for key traits can be either mapped or directly identified via differential expression.

  • Functional Genomics. Experiments for mapping and isolating genes for valuable traits via fine-mapping, intensive studies of gene expression via microarray panels, synteny comparisons to model organisms, and high-throughput transformation.

STRUCTURAL GENOMICS

The following components could be included in the area of structural genomics:

  • dense microsatellite-based genetic marker maps

  • dense expressed sequence tag sequence banks

  • physical mapping via bacterial artificial chromosomes

  • expression chips (microarrays) of the majority of genes in the genome

  • physical map synteny relationships with Arabidopsis

  • high-throughput transformation methods

  • high-throughput single-nucleotide polymorphism map arrays

MATERIALS FOR STUDY OF TRAIT VARIATIONS AND EXPRESSIONS

Research on materials for the study of trait variations and expressions could include the following subjects:

  • traits on segregating pedigrees and field trials in hybrid and intraspecific pedigrees

  • ribonucleic acids from tissues with contrasting trait expression (e.g., distinct tissues and ages)

  • phenotypic targets of economic importance and distinct expression in woody plants-heterosis and yield



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Review of the Research Strategy for Biomass-Derived Transportation Fuels APPENDIX E Major Components of a Poplar Genomics Initiative If the U.S. Department of Energy decides to focus more of its resources on the biotechnology of feedstock crops, genomics would be a logical subject for research. In the following discussion, the tools, type of experiments, and target traits for a major genomics project in a bioenergy crop are outlined using poplars as an example. These structural genomics studies would provide the tools for mapping and isolating a large number of genes. With this foundation, many different kinds of traits could be studied, and experiments could be performed to determine their roles and use them in breeding or genetic engineering. All of the options outlined below do not have to be undertaken to make progress in this area; however, a significant program to study a single feedstock species is likely to entail a recurring annual cost of at least $2 million for a number of years. A comprehensive genomics project should have the following components: structural genomics, materials for studying trait variation and expression, and functional genomics. Structural Genomics. The establishment of tools for studying and mapping genes, such as large sequence databanks, genome maps, and high-efficiency transformation methods. Materials for Studies of Trait Variation and Expression. The development of large, carefully designed pedigrees and field experiments and other experimental materials based on trait expression, in which genes for key traits can be either mapped or directly identified via differential expression. Functional Genomics. Experiments for mapping and isolating genes for valuable traits via fine-mapping, intensive studies of gene expression via microarray panels, synteny comparisons to model organisms, and high-throughput transformation. STRUCTURAL GENOMICS The following components could be included in the area of structural genomics: dense microsatellite-based genetic marker maps dense expressed sequence tag sequence banks physical mapping via bacterial artificial chromosomes expression chips (microarrays) of the majority of genes in the genome physical map synteny relationships with Arabidopsis high-throughput transformation methods high-throughput single-nucleotide polymorphism map arrays MATERIALS FOR STUDY OF TRAIT VARIATIONS AND EXPRESSIONS Research on materials for the study of trait variations and expressions could include the following subjects: traits on segregating pedigrees and field trials in hybrid and intraspecific pedigrees ribonucleic acids from tissues with contrasting trait expression (e.g., distinct tissues and ages) phenotypic targets of economic importance and distinct expression in woody plants-heterosis and yield

OCR for page 47
Review of the Research Strategy for Biomass-Derived Transportation Fuels wood chemistry and structure disease resistance shoot phenology and stress tolerance maturation, flowering onset and sterility, and rootability FUNCTIONAL GENOMICS Research on functional genomics could include studies in the following areas: high-precision quantitative trait loci analysis and synteny-based candidate gene selection transformation tests of candidate genes selected from expressed sequence tag banks complementation, suppression, and overexpression tests of identified genes via transformation large population of activation-tagged transgenic trees to directly identify genes for diverse traits additional bacterial artificial chromosome libraries for trait-specific experiments