Ordination of marker-trait association profiles from long- term international wheat trials Vivi Arief, Pieter Kroonenberg, Ian Delacy, Mark Dieters, Jose Crossa and Kaye Basford

Outline Motivation Construction of the Wheat Phenome Atlas Three-way Principal Component Analysis of marker-trait association profiles

The Challenge To develop a detailed understanding of the heritable variation in the wheat genome To directly translate this knowledge into gains in wheat breeding

CIMMYT’s Wheat Program Targets wheat breeding in 6 agro- ecological regions around the world Contains a vast accumulation of knowledge, data and genetic resources Is publicly available

Wheat Trials 40 years of trials With 10 or more international nurseries per year And 50 to 400 entries per nursery At 50 or more locations around the world → 17m phenotypic data points on >80 traits across 13k lines evaluated in >10k field trials (data worth >US$500m)

Pedigree Pedigree information tracing the history of all 13k lines in the breeding programs

Seed Available Retained seed in storage from all trials available for low-cost high throughput genotyping (can give 26m marker data points)

Unique resource No other crop (to our knowledge) has this resource publicly available

Enabling Technologies ASREML (in the last 10 years) –An analysis program that can deal with the 17m unbalanced data points ICIS (in the last 5 years) –Database to capture the pedigree, phenotype and marker data DArTs (since 2006) –The first of high through-put affordable marker systems –US$45 a DNA sample gives ~1,500 data points

Phenome Map Diagrammatic representation of the regions of a genome that influence heritable phenotypic variation for a trait

Phenome Atlas The integration of all phenome maps and a description of the methodologies that were used to produce the maps

Producing the Wheat Phenome Atlas Focus on the ESWYTs Elite Spring Wheat Yield Trials

Phenotypic data Advanced lines with high yield potential 25 cycles from 1979/80 to 2004/ unique lines 1445 trials across 400 locations Phenotypic data for 20 traits –8 agronomic traits (including grain yield) –3 rusts (leaf, stripe and stem) –9 other foliar diseases

The Analysis Obtained BLUPs using ASREML Fitted a separate residual and design for each trial –ESWYT 1 to 13: RCB –ESWYT 14 to 25:  -lattice Fitted separate models for combined association analysis and structured association analysis –Combined association analysis: G model –Family structure: G model –Spatial structure: GGL model –Temporal structure: GGY model

Genotypic data DArTs (Diversity Arrays Technology) Dominant markers 1; 0; X 1447 markers ~1.4 million data points 645 genotypes  599 unique genotypes (some are replicated)

The Analysis Association analyses Simple t-test –for each trait –for each marker –for each structure Marker order ESWYT disequilibrium map –No existing map shared more than 50% common markers with ESWYT –Obtained using ESWYT dataset

Wheat Phenome Atlas Version 1.0 Population structures Pedigree data Phenotypic data Marker data Combination of population and environmental structures ESWYT cycle Environmental structures Mega-environment Phenotypic data 10 Phenome maps: Overall x 2 analytical methods

A wheat phenome atlas Phenome map: dense QTL map for a trait Phenome atlas: collection and description of phenome maps

Increasing blue colour = increasing significance of positive association Increasing red colour = increasing significance of negative association 3 Rusts Stem (SR) Leaf (LR) Stripe (YR) 8 Agronomic traits Grain Yield (GY) Kernel Size (KS) Plant Height (PH) Days to Heading (DH) Test Weight (TW) Grain Protein (GP) Lodging (LG) Shattering (SH) 9 Other foliar diseases Stripe rust on the spike (YS) Septoria tritici blotch (ST) Septoria nodurum blotch (SN) Spot blotch (SB) Powdery mildew (PM) Barley yellow dwarf (BYD) Fusarium leaf blotch (FN) Tan spot (TS) Xanthomonas (XT)

What did we find? Many Trait Associated Markers (TAMs) for a trait Multiple traits for a TAM Association identified depend on: – what germplasm included – where tested – when examined

What about the genotypes?

Phenome maps: markers  traits For selection: genotypes  markers  traits Three-way principal component analysis

A TAM block Markers in a linkage disequilibrium block showed significant association  log score  4

Association: positive Marker : present Association: negative Marker : absent

Illustration 1

599 lines  288 TAM blocks  16 traits

599 lines  257 TAM blocks  15 traits

599 lines  213 TAM blocks  14 traits

Illustration 2

ME1 ME2

599 lines  202 TAM blocks  12 traits

599 lines  218 TAM blocks  17 traits

Three-way ordination: Summarizes genotype  TAM block  trait data Reveals pattern in genotype  TAM block  trait data Parental selection Genotype screening Prediction of selection outcome Observed patterns depend on the genotype  TAM block  trait arrays used Summary

Our Team Vivi Arief Ian DeLacy Hailemichael Desmae Christopher Lambrides Jacqueline Batley David Edwards Mark Dieters Ian Godwin Kaye Basford Jose Crossa Susanne Dreisigacker Tom Payne Ravi Singh Etienne Duveiller Guy Davenport Yann Manes Marilyn Warburton Graham McLaren Hans-Joachim Braun Jonathan Crouch Rodomiro Ortiz Peter Wenzel Eric Huttner Andrzej Kilian Also