From traditional to genomic selection

Stefano Biffani (IBBA-CNR/PTP)
10th July 2014

Genetic Selection for lower environmental impact

Ruminomics Summer School

Dairy cattle Breeding

  • How the system used to work before Genomic Era
  • How the system works in the Genomic Era
  • What we can do in the Genomic era

Genetic improvement

  • Improving the genetic potential of individuals across generations

Genetic improvement

  • Improving the genetic potential of individuals across generations

  • Phenotype = Genotype + Environment + (G x E)

    1. Phenotype: what we observe
    2. Genotype: the set of genes which regulates trait's expression
    3. Environment: everything which is not genetic (feeding, age, farm…)

Genetic improvement

  • genes can be inherited but environment might change over time

How to do genetic improvement ?

  • Step 1 - Identify the breeding objective
    • Milk (yields/quality)
    • Functionality (Reproduction, Mastitis)
    • Reducing greenhouse gas emissions (Feed Efficiency)

How to do genetic improvement ?

  • Step 2 - Data recording
    • Animal ID
    • Phenotype

How to do genetic improvement ?

  • Step 3 - Data Analysis + breeding tools
    • estimate genetic parameters
      • How much of the variation in a trait is due to variation in genetic factors (h2) ?

How to do genetic improvement ?

  • Step 3 - Data Analysis + breeding tools
    • h2 (Heritability)
      • milk: .30
      • reproduction: .10
      • Enteric Methane Emission: .33

How to do genetic improvement ?

  • Step 3 - Data Analysis + breeding tools
    • h2 (Heritability)
      • milk: .30
      • reproduction: .10
      • Enteric Methane Emission: .33

NO GENETIC VARIATION, NO PARTY

How to do genetic improvement ?

  • Step 3 - Data Analysis + breeding tools
    • Estimated Breeding Value (EBV)
      • An animal's breeding value is the estimate of its genetic merit, half of which will be passed on to its progeny.

How to do genetic improvement ?

  • Step 3 - Data Analysis + breeding tools

    • Estimated Breeding Value (EBV)
      • EBVs are expressed in the units of measurement for each particular trait (e.g. Milk EBV +2000 kg)
    • Genetic & Genomic EBV

How to do genetic improvement ?

  • Step 4 - Using the results

    • setting up a breeding plan
    • selecting and mating
    • Generation Interval (aprox 5-6 years - NO genomics)

How to do genetic improvement ?

  • Step 4 - Using the results

    • GENETIC PROGRESS

The Genomic Revolution

1. A new terminology (SNP, gEBV…)

2. reduced Generation Interval

The Genomic Revolution

1. A new terminology (SNP, gEBV…)

2. reduced Generation Interval

3. Higher Accuracy (EBVs are estimates !!!!)

The Genomic Revolution

1. A new terminology (SNP, gEBV…)

2. reduced Generation Interval

3. Higher Accuracy (EBVs are estimates !!!!)

4. New Traits

What does Genomic mean?

Genomic: the study of the genome of living organisms:

  • structure
  • content
  • function
  • evolution

Genomic boosting

  • Genotyping & Sequencing

  • Technology (less time & money)

  • International Projects

  • Bioinformatic tools

What used to happen before the GR?

  • Breeding value estimation:

    • Phenotype + Pedigree (animal, sire, dam)
    • Progeny testing
      • estimating the genetic value of an individual using the performance of his/her offsprings (e.g. the EBV of a BULL)

Progeny Testing

Schefers and Weigel. January 2012, Vol. 2, No. 1 Animal Frontiers

What used to happen before the GR?

  • the paradox:
    • estimating the genetic value of an individual without using genes!

what does it happen now?

Nowadays it is possible to:

  • read the complete genome

  • discover areas of variations (SNPs)

what does it happen now?

Nowadays it is possible to:

  • read the complete genome

  • discover areas of variations (SNPs)

  • develop arrays to detect variation (SNP panels)

what does it happen now?

what does it happen now?

  • GENOMIC Breeding value estimation:

    • Phenotype + Pedigree + GENOMIC

what does it happen now?

  • GENOMIC Breeding value estimation:

    • Phenotype + Pedigree + GENOMIC
    • How can we estimate SNP effects?

How can we estimate SNP effects?

Let's make an example

I'm going to buy fruits in 4 different markets

market 1: 5 pears + 2 apples + 2 peaches + 3 kiwi = 23 €

market 2: 5 pears + 7 apples + 3 peaches + 6 kiwi = 18 €

market 3: 3 pears + 3 apples + 4 peaches + 3 kiwi = 15 €

market 4: 2 pears + 0 apples + 2 peaches + 2 kiwi = 20 €

How can we estimate SNP effects?

Let's make an example

I'm going to buy fruits in 4 different markets

market 1: 5 pears + 2 apples + 2 peaches + 3 kiwi = 23 € market 2: 5 pears + 7 apples + 3 peaches + 6 kiwi = 18 € market 3: 3 pears + 3 apples + 4 peaches + 3 kiwi = 15 € market 4: 2 pears + 0 apples + 2 peaches + 2 kiwi = 20 €

This is a set of equations that can be solved:

How can we estimate SNP effects?

market 1: 5 pears + 2 apples + 2 peaches + 3 kiwi = 23 € market 2: 5 pears + 7 apples + 3 peaches + 6 kiwi = 18 € market 3: 3 pears + 3 apples + 4 peaches + 3 kiwi = 15 € market 4: 2 pears + 0 apples + 2 peaches + 2 kiwi = 20 €

This is a set of equations that can be solved:

1 pear 1 apple 1 peach 1 kiwi
2.19 € 1.38 € 1.32 € 0.59 €

What can we do now?

  • Estimates = market expected cost

  • market selection !!!

  • the more markets we visit, the more accurate the estimates are

moving back to cattle

we have

bull 1: snp1 + snp2 … = 2500 (traditional EBV) bull 2: snp1 + snp2 … = 500 (traditional EBV) bull 3: snp1 + snp2 … =-1500 (traditional EBV) bull 4: snp1 + snp2 … = 1200 (traditional EBV)

moving back to cattle

we have

bull 1: snp1 + snp2 … = 2500 (traditional EBV) bull 2: snp1 + snp2 … = 500 (traditional EBV) bull 3: snp1 + snp2 … =-1500 (traditional EBV) bull 4: snp1 + snp2 … = 1200 (traditional EBV)

  1. We can estimate the value of any snp !!!

moving back to cattle

we have

bull 1: snp1 + snp2 … = 2500 (traditional EBV) bull 2: snp1 + snp2 … = 500 (traditional EBV) bull 3: snp1 + snp2 … =-1500 (traditional EBV) bull 4: snp1 + snp2 … = 1200 (traditional EBV)

  1. We can estimate the value of any snp !!!

  2. We can genotype an individual and estimate his genomic value

Benefit of genomics

  • Determine value of an animal at birth (…embryos)

  • Increase accuracy of selection

  • Reduce generation interval

Benefit of genomics

  • Increase selection intensity

  • Increase rate of genetic gain

What can we do beyond EBVs?

  • parentage testing
    • SNPs in place of microsatellites

What can we do beyond EBVs?

  • Identification and fine mapping of recessive defects

What can we do beyond EBVs?

  • Genome Wide Association Studies (GWAS) of complex traits

Lessons from genomics

  1. down to earth: we NEED phenotypes

Lessons from genomics

  1. down to earth: we NEED phenotypes

  2. extremely useful tools (bridging the gap)

Lessons from genomics

  1. down to earth: we NEED phenotypes

  2. extremely useful tools (bridging the gap)

  3. possibility to understand the relationship among traits

Lessons from genomics

  1. down to earth: we NEED phenotypes

  2. extremely useful tools (bridging the gap)

  3. possibility to understand the relationship among traits

  4. big data issue

Lessons from genomics

  1. down to earth: we NEED phenotypes

  2. extremely useful tools (bridging the gap) #

  3. possibility to understand the relationship among traits

  4. big data issue

  5. down to earth 2: develop “real” application

THANKS for the attention !!!

Do cows really cause pollution?

stefano.biffani0@alice.it