Genomic Prediction

Eli Gacasan

Overview

  1. What is genomic selection?
  2. History
  3. What is linkage disequilibrium
  4. Some aspects of quantitative genetics
  5. Tutorial
  6. Gap filling?

What is genomic selection?

André Eggen, The development and application of genomic selection as a new breeding paradigm, Animal Frontiers, Volume 2, Issue 1, January 2012, Pages 10–15, https://doi.org/10.2527/af.2011-0027

History

timeline
  title  
  1950s-1990 :  Development and adoption of BLUP in plant and animal selection
  1990s : Marker Assisted Selection 
  2000s : Genomic Selection 
  2010s-Present : Increased adoption of genomic selection : Incorporation of sophisticated statistical methods

History

timeline
  title 
  section 1950s-1990 Development and adoption of BLUP in plant and animal selection
    Estimation of Variance and Variance Components (Henderson, 1953) 
    BLUE and BLUP under a Selection Model (Henderson, 1973)
    BLUP of Breeding Values Not in the Model for Records (Henderson, 1977)

  1. Selection using phenotype data and pedigree data.
  2. BLUP and BLUEs adopted in animal breeding and then adopted in plant breeding.

History

timeline
   
  1950s-1990 :  Development and adoption of BLUP in plant and animal selection
  1990s : Marker Assisted Selection

  1. Marker Assisted Selection (MAS) uses DNA markers to select for candidates with desired traits.
  2. Traditionally requires a marker detection step to select significant markers and use the significant markers for prediction of breeding value of a candidate.

History

timeline
   
  1950s-1990 :  Development and adoption of BLUP in plant and animal selection
  1990s : Marker Assisted Selection 
  2000s : Genomic Selection

  1. All markers of the genome are used to help predict the breeding value of a candidate (regardless if the effect sizes)
  2. Introduced by Meuwisson (2001)

History

SNPs

Single nucleotide polymorphisms are widely used, genotyped with high throughput machines. The recombination events are of major biological importance - inheritance of whole genomic segments from paternal and maternal side. Non-independent inheritance contradicts mendel’s law of independent assortment. Mendel’s law is valid if the genes are far from one another or for example on separate chromosomes. But it is not valid when the SNPs or genes are close to eachother.

Linkage disequilibrium

When we have non-independent assortment is caused by recombination, the degree of recombination is measured by the recombination rate

Linkage disequilibrium

A parameter (characteristic) of the population. You can determine the LD between two loci in a population, linkage disequilibrium is a non random association of loci within populations and can be measured. So we can tell whether two loci are strongly linked or weakly linked together or not linked at all together. In other words LD it tells something about the strength about the correlation of an allele in a certain location and the occurance of another allele on another locus.

Why is LD important

Shows association strength between observed SNP and the unobserved genes-qtl. LD defines how far we are allowed to look from the detected markers when we look for causality on the genome (genes or qtl)

What is LD

A parameter that quantifies the non random association between loci Shows if the frequency of different alles between two loci is higher or lower than what would be expected if the loci were independent from each other and associated randomly

Overall Summary

SNP markers allow us to track associations between parts of the genome, such associations can be non random especially if the SNPs are close. Linkage disequilibrium can measure those associations

Implementation of genomic selection

flowchart LR
  A[Training dataset] --> B[Build a model] 
  B --> C[Testing dataset]
  C --> D[Get prediction accuracy from testing dataset] 
  D --> E[Done?]

M.E. Goddard, B.J. Hayes. Genomic Selection (2007)

Implementation of genomic selection

flowchart LR
  A[Training dataset] --> B[Build a model] 
  B --> C[Testing dataset]
  C --> D[Get prediction accuracy from testing dataset] 
  D --> E[Done?]

Training Data

Training Data

Marker Data

Phenotypic Data

References

Symposium review: How to implement genomic selection

Linkage disequilibrium — understanding the evolutionary past and mapping the medical future

Genomic selection: A paradigm shift in animal breeding

Genomic selection M.E. Goddard & B.J. Hayes

Genomic BLUP Decoded: A Look into the Black Box of Genomic Prediction

Course Notes ‘QTL Mapping, MAS, and Genomic Selection’ (Hayes, 2007)

Genomic selection in plant breeding: from theory to practice

Genome-wide association and genomic selection in animal breeding (Ben Hayes and Mike Goddard)

Will genomic selection be a practical method for plant breeding?

Progress and perspectives on genomic selection models for crop breeding

Genomic selection in plant breeding: Key factors shaping two decades of progress

The development and application of genomic selection as a new breeding paradigm (nice illustration)