Believing in MAGIC: Validation of a novel experimental breeding design

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Believing in MAGIC Validation of a novel
experimental breeding design

• Emma Huang, Ph.D.
• Biometrics on the Lake
• December 2, 2009

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Multiparent Advanced Generation Inter Cross
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Experimental crosses

• 2 parents
• BC
• F2
• ...

A
B
B
AB
AB
AB
4
4 Parents
A
C
B
D
AB
CD
ABCD
6 generations of selfing
Inbred individuals
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Final Result
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In theory...

• No genotyping for users after setup is complete
• Effective design for G x E
• Resource for large community - many traits
• Large population of RILs
• Large genetic (allelic) and phenotypic diversity
• Ability to map epistatic interactions
• High recombination ? high resolution

RIL final lines
Size
Diversity
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Vital resource for linkage mapping

• No physical map/sequence for wheat (yet)
• Previous maps developed for specific population
• Limited polymorphisms
• Would have to join maps across populations
• Possibly inconsistent estimates across maps
• Many markers have not been mapped
• MAGIC map is potentially
• More complete due to greater genetic diversity
• More accurate due to larger population size
• More precise due to many generations of
  recombination

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But... nontrivial

• Complex inheritance from founders
• Limited genotyping
• Population size/ markers computational burden
• Marker issues dominant markers, polyploidy,
  etc.

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Theory vs. Reality
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Linkage Map Construction

• Basic Strategy
• Filter and preprocess marker data
• Estimate pairwise recombination
• Group and order loci
• Refinement

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Step 2 Estimating Recombination Distance

• In standard designs, counting numbers of
  different genotypes
• This doesnt work for 4/8 way crosses
• Many generations of recombination
• No intermediate genotyping
• Ambiguous inheritance of alleles
• Instead maximize the likelihood

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Step 4 Refinement

• Start with framework map
• Position markers relative to fixed locations
• Maximize likelihood over grid of positions
• Compared to initial ordering
• Iterative and time-consuming
• Less sensitive to missing values
• Additional information about marker relationships

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MAGIC bag of tricks

• R package mpMap
• Simulate data, filter/process, generate linkage
  map, visual quality checks

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In a perfect world

• Nice data
• Fully informative markers
• No missing data
• No genotyping errors

Chr 6
Recombination fractions below diagonal scaled
LOD scores above
Chr 5
Chr 4
Chr 3
Chr 2
Chr 1
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Something closer to reality

• Typical data
• Biallelic markers
• 10 missing data
• 10 genotyping errors

• gt datbad lt- mp.sim(map, simped, seed1,
  error.prob.1, missing.prob.1)
• --------------------------------------------------
  -----
• Summary of mpcross object
• --------------------------------------------------
  -----
• 0 markers were removed with missing values in
  founders
• 0 markers were removed with non-polymorphic
  founder genotypes
• --------------------------------------------------
  -----
• 195 markers were biallelic.
• 0 markers were multiallelic.
• --------------------------------------------------
  -----
• 195 markers had gt5 missing data.
• 99 markers had gt10 missing data.
• 0 markers had gt20 missing data.
• --------------------------------------------------
  -----
• 49 markers had lt1e-5 p-value for segregation
  distortion
• 2 markers had lt1e-10 p-value for segregation
  distortion
• 0 markers had lt1e-15 p-value for segregation
  distortion

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4-parent MAGIC

• DArT SNP markers
• Constructed map
• 871 progeny
• 1148 markers
• 20/21 chromosomes
• 2010 5000 lines from 8-way cross

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Chromosome 6B
Genetic Map
Heat Map
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Looking to the future

• Improve the current map
• Starting from the least informative set of
  markers
• Further genotyping to fill in gaps
• QTL Mapping
• Testing different approaches
• Field trials
• Association Mapping
• Using constructed map for complex analysis

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CSIRO Mathematical and Information Sciences Emma
Huang Research Scientist Phone [phone]
2953 Email Emma.Huang_at_csiro.au
Thanks to Andrew George Colin Cavanagh Matthew
Morell
Thank you
Contact UsPhone 1300 363 400 or 61 3 9545
2176Email Enquiries_at_csiro.au Web www.csiro.au