Download - 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 DavisGary Peter, John Davis, Dudley Huber, Matias Kirst, George Casella – U FloridaBarry Goldfarb & Bailian Li – North Carolina State Carol Loopstra & Tom Byram – Texas A&M
ADEPT 2: Team MembersUC 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 MembersUF
• 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 MembersTAMU
• Carol Loopstra– Gene expression phenotyping
• Tom Byram– Forest genetics
• 2 PhD students
NCSU• Barry Goldfarb
– Verification population & wood property phenotyping
• Bailian Li– Forest genetics
• 1 PhD student– Patrick Cumbie
• Nick Wheeler– Outreach
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.
Timeline
• 4 Year project 2005-2009• Official project start July 2005• Resequencing 2006-2007• SNP Genotyping 2008• Disease phenotyping 2006-2008• GE phenotyping 2006-2008• Wood phenotyping 2006-2008• Association testing 2008-2009
Databases
Phenotypic Data
Genetic Architectureof Traits
Identification of Genes thatControl Complex Traits
Genotypic Data
Allele Discovery
Candidate Alleles
Candidate Gene Selection
Allele Selection
Primer Design & Genomic Sequencing
Primer
Allele
Phenotype
SNP Genotyping
Information forGene & Allele
Selection
Genotype
Genetic Analyses
Gene ExpressionAnalyses
Association Tests
TraitPheno-typing
Sequence
Databases
UC Davis
UF & TAMU
UF & NCSU
UF
NCSU
UFUC Davis
Assoc. Pop.
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
• Wood Properties
• Water Deficit
• Disease Resistance
Specific Deliverables • 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 • 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).
o Chromatogramso Alignmentso SNP calls
• Custom software for DNA sequence manipulation and summarization.
• Population genetic summaries of data by locus.
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.
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:
o Gene expression (TAMU)o Metabolites (UCD)o Wood quality (UF)o Drought-tolerance (NCSU)o Disease resistance (UF)
• Genotype-phenotype associations.
Deliverables TimelineObjective 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.
Deliverables TimelineObjective 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.
http://dendrome.ucdavis.edu
http://dendrome.ucdavis.edu/treegenes
http://dendrome.ucdavis.edu/interface
http://dendrome.ucdavis.edu/TGPlone
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• ADEPT2 Project 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
241,796 reads submitted to Trace Archive
Trace Archive Accessions:2072163883-2072419182
6,178 PopSets submitted via Sequin to NCBIAccessions: FJ043059-FJ147084
Dendrome Plone – ADEPT2
Dendrome
Dendrome Website and Related Web Resources Encompasses 6,754 Pages
Detailed Usage Statistics Available @ http://dendrome.ucdavis.edu/awstats/awstats.pl
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Collaborators Institution Species/Project
Shirley Luckhart UCDavis Mosquito
Nicholas Wheeler NCSU Fagaceae
Patricia Faivre Rampant INRA-URGV Populus nigra
Janice Cooke University of Alberta Mountain Pine Beetle
Rich Shuren & Brian Stanton Greenwood Resources Populus nigra
Shannon Dillon CSIRO Pinus radiata
Outi Savolainen & Sonja Kujala University of Oulu Pinus sylvestris
Santiago Gonzalez Martinez ICIFOR - INIA Pinus pinaster & Populus alba
Delphine Grivet ICIFOR - INIA Pinus pinaster
Kathleen Jermstad IFG Pinus lambertiana & Pseudotsuga menziesii
Glenn Howe OSU Pseudotsuga menziesii
Marta Scalfi IASMA Picea abies
Dudley Huber UF Pinus elliottii
Kermit Ritland UBC Picea glauca
Martin Lascoux Uppsala University Picea abies
Cristophe Plomion INIA Pinus pinaster
Rich Cronn USFS-PNW North American white pines
Aaron Liston OSU North American white pines
John Syring Linfield College North American white pines