Presentation on theme: ""Implications of partitioned genetic diversity for linkage disequilibrium mapping in elite UK cereal germplasm". Donal O’Sullivan SGC Meeting, JIC, 6-7."— Presentation transcript:
"Implications of partitioned genetic diversity for linkage disequilibrium mapping in elite UK cereal germplasm". Donal O’Sullivan SGC Meeting, JIC, 6-7 th April 2006
Purpose Why use ‘elite’ varieties? Most familiar and obvious material Reasonable levels of diversity present Relevant to current markets Obtainable in quantity Extensive ‘historic series’ of robust field data for most relevant phenotypes To explore the prudent use of ‘populations’ of elite cereal varieties as LD mapping panels
Partitioning in 500+ Gediflux Barley varieties
Association mapping in wheat: proof of principle Gediflux data set: 499 genotyped varieties. 73 SSAPs, 42 SSRs, 72 NBS 1B1R, pinb haplotypes Historic trial data: 193 varieties with 18 phenotypes (incomplete ) yield +/- treated, hardness (113 lines) Lodging, disease, etc. Use pinb as a candidate with known phenotypic effect Use SSRs for structured association Analyse using “Structure” and “Strat” Use SSAPs for genomic control Analyse trait by trait by logistic regression
Mining historic endosperm texture data Historic NL trial data <2001
Structured association Structure: burn-in1 million iterations1 million No. populations (K) 8 No. replicate runs2
K = 8 cluster 1 vs cluster 5 Proportion of each individual in cluster 1. Proportion of each individual in cluster 5. Gediflux 500+ winter wheat
Pedigree of lines with highest ancestry in clusters 1 and 5. Cluster 1Cluster 5
Descendants of a cluster 5 founder
parents cluster 1cluster 5 progeny cluster cluster odds ratio82 p-value Parentage of lines for clusters 1 and 5. Cluster membership is genetic!
Association test using STRAT / structure Pinb and hardness testchi sqp-value Assuming no structure in population Corrected (run a) Corrected (run b)
STRAT and structure - QC Hardness and 55 SSAP markers, p-values <0.05 TestNo. <0.05 Assuming no pop. structure 14 Adjusted, run a 6 Adjusted, run b 6 Expected 3 May be under correcting.
Pedigree relationships between SBCMV resistant varieties Red = Tested R, Blue = Tested S, Grey = Untested
Genomic Control Method: use multilocus genotype data to detect and correct for stratification Premise: admixture operates over the whole genome but LD operates locally at short scales 18 traits 58 SSAP 1044 logistic regression analyses
Genomic control: p-values, pinb original GC Dry matter contenttreated Hagberg numbertreated Percent leaningtreated Percent lodgingtreated Protein contenttreated Specific weighttreated Straw lengthtreated Yieldtreated Brown rustnot treated Hagberg numbernot treated Percent leaningnot treated Percent lodgingnot treated Mildewnot treated Protein contentnot treated Septoria triticinot treated Specific weightnot treated Straw lengthnot treated Hardness
Test markers across all traits No. of tests1044 P-value <0.05 OBS original313 OBS GC34 EXP52 May be overcorrecting Genomic control: QC
Conclusions Population structure may be evident e.g. spring-winter/row number divide or less so –Carry out LD mapping within major sub-groups UK winter wheat shows cryptic population structure which groups varieties consistent with known pedigree Genomic control and/or structured association both effective in detecting known associations and reducing false +ves to realistic levels Roll on new phenotype and genotype data!