Genetic Basis of Agronomic Traits
Connecting Phenotype to Genotype
Rely on co-inheritance of functional polymorphism and DNA variant
Traditional F2 QTL Mapping
Association Mapping
Correlate molecular with phenotypic variation, rely on many
Use
recombination
eventsrecombination,
in F2 to narrowphenotype
trait of interest
to a may
generations
of historical
of interest
genomic
regionwith a smaller chromosomal segment
be associated
Yu and Buckler (2006); Zhu et al. (2008)
Association Mapping Workflow
Choose lines to include
in mapping population to capture
as much diversity as possible
Genome-wide association mapping
Candidate/targeted gene approach
1. Germplasm
2. Genotyping
2. Phenotyping
3. Association
Testing
Grow and measure traits in
replicated trials
Correlate phenotypic variation
with genotypic variation
Association Mapping Considerations
• Extent of linkage disequilibrium
– Informs genotyping strategy
– Amount of resolution
• Degree of population structure
– Can lead to false associations
Sunflower Association Mapping
(SAM) Objectives
1. Population genetics of the sunflower germplasm,
select lines for inclusion
2. Investigate the structure of LD within the association
mapping population
3. Grow and characterize the population for
wide variety of traits + genotype
4. Test for associations between molecular
polymorphisms and variation in key traits
SAM Population Line Selection
433 Cultivated Sunflower Lines
Core 12
(~50% of allelic diversity)
Core 48
(~60% of allelic diversity)
Core 96
(~70% of allelic diversity)
Core 192
(~80% of allelic diversity)
Core 288
(~90% of allelic diversity)
Mandel et al., TAG 2011
SAM Genetic Diversity
Mandel et al., PLoS Genetics 2013
SAM Genetic Relationships
HA X RHA
10k SNPs
Mandel et al., PLoS Genetics 2013
Genome-Wide Patterns of FST
RHA vs. HA
10k SNPs
Mandel et al., PLoS Genetics 2013
Genome-Wide Patterns of LD
Linkage Group 1
10k SNPs
Mandel et al., PLoS Genetics 2013
Genome-Wide Patterns of LD
Linkage Group 10
10k SNPs
Mandel et al., PLoS Genetics 2013
Genome-Wide Patterns of LD
10k SNPs
Mandel et al., PLoS Genetics 2013
Background Genomic Diversity
• Substantial SNP genetic variation
• Population structure RHA vs. HA
– Somewhat restricted to linkage groups
• LD also varies extensively across the genome
• Phenotypic measurements
SAM Field Locations
Plant > 20K seeds
288 inbred lines
4 plants per line
2 replicates
3 locations
7,200 plants
15 people
SAM Phenotyping/Genotyping
Phenotyping:
- Flowering time
- Plant architecture
- Pigmentation
- Leaf traits
- Seed size/shape
- Oil-related traits
- Dormancy/germination
- Wood-related traits
- Total biomass
- Leaf C and N
Genotyping strategies:
- Entire SAM re-sequencing
- 10k SNP Infinium array
- GBS approach, ~ 40k SNPs
Flowering Time SNP associations
10k SNP Array
10k SNPs
Mandel et al., PLoS Genetics 2013
Visualizing Associations – LG 10
No Branching
Branching
Recessive
apical
branching
Mandel et al., PLoS Genetics 2013
10k SNPs
Elevated LD and Potential
Targets of Selection
Downy Mildew
Branching/Flowering
Sunflower Rust
Black Stem
Downy Mildew
Mandel et al., PLoS Genetics 2013
10k SNPs
Co-Localization of QTL and
SNP Associations
10k SNPs
Days to Flower
Mandel et al., PLoS Genetics 2013
Total Branching
Cell-wall Chemistry SNP Associations
GBS, Lignin at GA location
~40k SNPs
SAM Re-Sequencing Efforts
• Entire SAM population of 288 lines
• South Africa ARC, Genome Canada/Quebec,
and INRA
• Illumina Hi-Seq, 1 or 2 samples per lane
SAM Re-Sequencing
Data Analysis Workflow
Adam Bewick and Ben Hsieh
• Sunflower genome
– Version: Nov22k22.scf.split.fasta
• Read-trimming with prinseq-lite
• Alignment with BWA
• Produce VCF files with samtools
SAM Re-Sequencing Coverage
Adam Bewick
LR, NO-I, O-I, OPV, NO, O
191/288 lines have been run through the pipeline
SAM Re-Sequencing Next Steps
• Next step is to assay genetic variation
– Structural Variation: CNV – Adam’s talk
– SNPs
• Use data for genome-wide investigations of
genetic variation, association mapping, and
evolutionary analyses
Association Genetics Summary
• Mapping panel is very diverse
• LD varies across the genome
• Association testing and SNPs and genomic
regions as candidates
• Created permanent mapping resource
• Sequenced genome and 288 re-sequenced
lines: GREAT resource!
Acknowledgments
Members of the:
Burke Lab
Leebens-Mack Lab
Rieseberg Lab
Raj Ayyampalayam
Undergrad Teams
Adam Bewick
Ben Hsieh
John Bowers
Mark Chapman
Laura Marek
Jenny Dechaine
Savithri Nambeesan
Ed McAssey
Steve Knapp
Eleni Bachlava