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NSF Plant Genome Program: Association Genetics and Natural Variation of Complex Traits in Pine

NSF Plant Genome Program: Association Genetics and Natural Variation of Complex Traits in Pine. David Neale & Chuck Langley – UC Davis Gary Peter, John Davis, Dudley Huber, Matias Kirst , George Casella – U Florida Barry Goldfarb & Bailian Li – North Carolina State

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NSF Plant Genome Program: Association Genetics and Natural Variation of Complex Traits in Pine

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  1. NSF Plant Genome Program: Association Genetics and Natural Variation of Complex Traits in Pine David Neale & Chuck Langley – UC Davis Gary Peter, John Davis, Dudley Huber, MatiasKirst, George Casella – U Florida Barry Goldfarb & BailianLi – North Carolina State Carol Loopstra & Tom Byram – Texas A&M

  2. UC Davis David Neale – Project Leader SNP discovery, genotyping, association testing, databases 2 PhD students Bioinformatics Chuck Langley-Population geneticist Association testing & population genetics ADEPT 2: Team Members

  3. UF George Casella Association testing & new methods for multilocus testing John Davis Disease phenotyping & association testing Dudley Huber Association testing in structured populations Matias Kirst Gene expression phenotyping & association testing Gary Peter Wood property phenotyping & association testing, UF PM 4 Graduate Students Disease Tania Quesada Gene expression Wood properties Xiaobo Li, SFRC; Association testing pipeline & methods Jessica Li, Statistics ADEPT 2: Team Members

  4. TAMU Carol Loopstra Gene expression phenotyping Tom Byram Forest genetics 2 PhD students NCSU Barry Goldfarb Verification population & wood property phenotyping BailianLi Forest genetics 1 PhD student Patrick Cumbie Nick Wheeler Outreach ADEPT 2: Team Members

  5. Over Arching Goal & Approach • Goal • Discover genes/alleles that control wood property, disease resistance, and gene expression traits in loblolly pine • Approach • Association genetics is a population level survey used to identify trait-marker relationships. • Association genetics takes advantage of the evolutionary history of recombination within a species, and that all of the phenotypic and genotypic variation within a species is present in a single experiment.

  6. Timeline • 4 Year project 2005-2009 • Official project start July 2005 • Resequencing 2006-2007 • SNP Genotyping 2008 • Disease phenotyping2006-2008 • GE phenotyping2006-2008 • Wood phenotyping2006-2008 • Association testing 2008-2009

  7. Candidate Gene Selection Information forGene & Allele Selection Databases Sequence Primer Design & Genomic Sequencing Primer Gene Expression Analyses Allele Discovery Allele UF & TAMU Allele Selection Assoc. Pop. NCSU Databases Trait Pheno- typing Candidate Alleles Phenotype Phenotypic Data SNP Genotyping Genetic Analyses UF & NCSU Genotype Genotypic Data Genetic Architectureof Traits Association Tests UC Davis UF UC Davis UF Identification of Genes thatControl Complex Traits

  8. Community Deliverables • Primer database with 10,000 tested primers • Genomic sequences of 5000 genes • SNP database for 5000 genes • Genotypic data for CCLONES & NCSU for ~1000 SNPs/haplotypes • Phenotypic data for CCLONES & NCSU populations • Novel association testing methods • Candidates for additional functional studies

  9. Wood Properties • Water Deficit • Disease Resistance

  10. Objective 1: Bioinformatics – To identify 5,000 target candidate genes for wood property and disease resistance traits through the integration of loblolly pine genomic resources and the development of primer databases for SNP discovery, SNP genotyping, and RT-PCR. • Deliverables: • List of candidate genes including gene annotation information. • Online primer database (TreeGenes). Specific Deliverables

  11. Specific Deliverables • Objective 2: Discover alleles for 5,000 candidate genes using a high-throughput sequencing pipeline at Agencourt Bioscience Corporation. • Deliverables: • Resequencing data (6924 genes) including data deposition to public databases (NCBI GenBank and TreeGenes). • Chromatograms • Alignments • SNP calls • Custom software for DNA sequence manipulation and summarization. • Population genetic summaries of data by locus.

  12. Specific Deliverables • Objective 3: To estimate the extent of linkage disequilibrium in genomic regions around a small number (~10) of candidate genes and discover 5’ regulatory (promoter) SNPs. • Deliverables: • Sequences of 10 BACs. • Custom software for BAC annotation in non-model organisms. • BAC-specific SNPs and linkage disequilibrium (LD) estimates across large physical distances.

  13. Specific Deliverables • Objective 4: Association Genetics – To detect and verify associations between SNPs in ~1000 candidate genes and a suite of whole plant wood property phenotypes, disease resistance phenotypes and gene expression phenotypes. • Deliverables: • Illumina 7600 SNP genotyping chips for loblolly pine (UCD). • Genotyping results for three association populations and two pedigrees (UCD). • Phenotypes across five categories: • Gene expression (TAMU) • Metabolites (UCD) • Wood quality (UF) • Drought-tolerance (NCSU) • Disease resistance (UF) • Genotype-phenotype associations.

  14. Deliverables Timeline Objective 1: • 100% - List of candidate genes including gene annotation information. • 100% - Online primer database (TreeGenes). Objective 2: • 100% - Resequencing data acquisition, base calling, alignments and SNP identification. • 67% - Data deposition to public repositories (dbSNP remains). • 100% - Development of custom software for DNA sequence manipulation and summarization (3 publications: 2 in print or press; 1 in review). • 33%- Population genetic summaries by locus.

  15. Deliverables Timeline Objective 3: • 100% - Acquisition of DNA sequences for 10 BACs. • 33% - Assembly and annotation of 10 BACs. • 33% - Development of custom software for BAC annotation in non-model organisms. • 0% - BAC-specific SNPs and linkage disequilibrium (LD) estimates across large physical distances. Objective 4: • 100% - Design of loblolly pine Illumina genotyping chip (~7600 SNPs). • 100% - Genotyping results for three association and two linkage mapping populations. • 90% - Phenotypes across five categories. • 20%- Genotype-phenotype associations.

  16. http://dendrome.ucdavis.edu/treegenes http://dendrome.ucdavis.edu/TGPlone http://dendrome.ucdavis.edu http://dendrome.ucdavis.edu/interface

  17. ADEPT2 BioinformaticsProject Resources • PineSAP – High throughput Pine Alignment and SNP calling Pipeline • Alignments, SNP calls, Genotype file generation, and Data Submissions • DNASam – High throughput sequence analysis tool • ADEPT2Project Website • Portal to research summaries, software packages, and collaborative tools • Dendrome Plone – Content Management System • Full content management for analysis and collaborations • Full management of public database accounts and user permissions • TreeGenes Database – 10 modules to store genotypic and phenotypic data • DiversiTree – extensive workspace interface to enable users to query information from TreeGenes

  18. 241,796 reads submitted to Trace ArchiveTrace Archive Accessions:2072163883-2072419182

  19. 6,178 PopSets submitted via Sequin to NCBIAccessions: FJ043059-FJ147084

  20. Dendrome Plone – ADEPT2

  21. Dendrome

  22. Dendrome Website and Related Web Resources Encompasses 6,754 Pages Detailed Usage Statistics Available @ http://dendrome.ucdavis.edu/awstats/awstats.pl

  23. Select data type to search Retrieve search results Display one or more entries from search Create lists Display linked data DiversiTree Interface

  24. Site Statisticswww.forestrycareers.org • Forestrycareers.org is a recruitment tool for the forestry and natural resource disciplines • It has been marketed through NAUFRP (National Ass. Univ. with Forestry and Nat. Res. Programs • Number of visitors and site hits has increased continuously since it was rolled out in June, 08

  25. Selected Feedback on Recruitment Website “I just wanted to let you know I use this web site all the time!  It really is a great resource, and I am so thankful that it was created!”  Student and Careers Services Center, University of Georgia. “Please let those who were associated with putting the forestry and natural resources web site together that they did a wonderful job.  The Cal Poly NRM Dept. will link to it from our NRM web site.  Please pass along our appreciation for a job well done!!!” “This is a great addition to our recruitment efforts for the college” Virginia Tech

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