Pine Genome Initiative (PGI) Scientific Benchmarks

Five year goals – each major area should proceed simultaneously and be performed in at least one conifer species.  Within the major areas the goals are listed in approximate order of accomplishment.

Genome Structure and Organization

• Develop BAC libraries of at least 3X coverage
• Obtain genomic sequence for 100% highly repetitive DNA and for significant portions of the mid-repetitive and low copy DNA
• Determine genomic spatial distribution of repetitive and low copy DNA through sequencing of BAC clones, macroarray analysis, cytomolecular mapping, etc
• Genetically and physically map ~20,000 genes
• Develop and support a genome browser that allows user-directed integration of multiple types of genomic data across species

Functional Genomics

• Obtain critical mass of EST sequence data over multiple libraries
• Obtain full length gene sequences for ~20,000 genes
• Construct gene expression microarrays representing ~30,000 unigenes
• Conduct microarray based studies to understand important biochemical and physiological processes
• Develop a robust, public domain DNA transformation system
• Develop and maintain a gene annotation database that allows user-directed integration of multiple types of transcriptional profiling data across species

Translational Genomics

• Develop, evaluate, and map ~60,000 SNPs
• Construct high density genotyping microarrays representing ~15,000 loci
• Develop computational methods for association and complex-pedigree mapping and for applying map information to selection and breeding programs
• Map QTLs and candidate genes for all important traits and evaluate G x E
• Develop and support a gene mapping database that allows user-directed integration of multiple types of mapping data across species

Genetic Stocks Development and Curation

• Develop and/or support a genetic stock center to archive, curate and distribute conifer genomic resources
• Establish and maintain multiple association and pedigree-based mapping populations
• Develop and support an online database system for tracking and distributing genetic stocks.

Funding timeline for the Pine Genome Initiative (million $US):

Research Area	FY 08	FY 09	FY 10	FY 11	FY 12
Genome Structure & Organization	4	12	12	12	12
Functional Genomics	2	8	8	8	8
Translational Genomics	2	8	8	8	8
Genetic Stocks Development & Curation	2	2	2	2	2
TOTAL	10	30	30	30	30

Summary of major areas having received or receiving funding

USDA has funded projects involved in genome mapping and QTL mapping especially for wood quality traits.  Several maps have been constructed and several QTL for wood traits have been mapped.

USDA provided some initial support for pine genome database development, but it was limited and short lived.

USDA funded a SNP discovery and evaluation project involving about 100 genes involved in wood formation and response to disease organisms.

DOE has funded some EST sequencing, marker development, and genome and QTL mapping.

DOE supported the development of a Populus genome sequence (6X coverage) through a Community Sequencing Project (CSP) at their Joint Genome Institute (JGI)

NSF has funded three pine EST sequencing projects (wood, embryogenesis, and response to environmental stress).  The later two of these projects involve microarray development and distribution and are currently ongoing.

NSF is currently funding two pine genome projects.  The first includes development of a 10X BAC library, development and analysis of Cot fractionated libraries, and a limited amount of genomic sequencing.  The second includes SNP discovery and evaluation for about 10000 genes involved in several important processes including wood formation and responses to abiotic and biotic stressors.