Ordination of marker trait association profiles from long term international wheat trials
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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

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Ordination of marker trait association profiles from long term international wheat trials

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
Outline long-term international wheat trials

  • Motivation

  • Construction of the Wheat Phenome Atlas

  • Three-way Principal Component Analysis of marker-trait association profiles


The challenge
The Challenge long-term international wheat trials

  • 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
CIMMYT’s Wheat Program long-term international wheat trials

  • 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
Wheat Trials long-term international 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 long-term international wheat trials

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


Seed available
Seed Available long-term international wheat trials

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


Unique resource
Unique resource long-term international wheat trials

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


Enabling technologies
Enabling Technologies long-term international wheat trials

  • 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
Phenome Map long-term international wheat trials

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


Phenome atlas
Phenome Atlas long-term international wheat trials

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


Producing the wheat phenome atlas
Producing the long-term international wheat trialsWheat Phenome Atlas

  • Focus on the ESWYTs

    Elite Spring Wheat Yield Trials


Phenotypic data
Phenotypic data long-term international wheat trials

Advanced lines with high yield potential

  • 25 cycles from 1979/80 to 2004/05

  • 685 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
The Analysis long-term international wheat trials

  • 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
Genotypic data long-term international wheat trials

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 analysis1
The Analysis long-term international wheat trials

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
Wheat Phenome Atlas Version 1.0 long-term international wheat trials

  • 10 Phenome maps:

    • Overall

  • Population structures

    Pedigree data

    Phenotypic data

    Marker data

x 2 analytical methods

  • Environmental structures

    • Mega-environment

    • Phenotypic data

  • Combination of population and environmental structures

    • ESWYT cycle


A wheat phenome atlas

A wheat phenome atlas long-term international wheat trials

  • Phenome map: dense QTL map for a trait

  • Phenome atlas: collection and description of phenome maps


9 Other foliar diseases long-term international wheat trials

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)

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)

3 Rusts

Stem (SR)

Leaf (LR)

Stripe (YR)

Increasing blue colour = increasing significance of positive association

Increasing red colour = increasing significance of negative association


What did we find
What did we find? long-term international wheat trials

  • 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? long-term international wheat trials


Phenome maps: long-term international wheat trials

markers  traits

For selection:

genotypes  markers  traits

Three-way principal component analysis


  • A TAM block long-term international wheat trials

    • Markers in a linkage disequilibrium block showed significant association 

      • log score  4


Association: positive long-term international wheat trials

Marker : present

Association: negative

Marker : absent


Illustration 1 long-term international wheat trials


599 lines long-term international wheat trials 288 TAM blocks  16 traits


599 lines long-term international wheat trials 257 TAM blocks  15 traits


599 lines long-term international wheat trials 213 TAM blocks  14 traits


Illustration 2 long-term international wheat trials


ME2 long-term international wheat trials

ME1


599 lines long-term international wheat trials 202 TAM blocks  12 traits


599 lines long-term international wheat trials 218 TAM blocks  17 traits


Summary
Summary long-term international wheat trials

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


Our team
Our Team long-term international wheat trials

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


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