Genomics in Livestock Breeding

Question 1

Genomic information – the basic tools

Answer 1

• Microsatellites/Restriction Fragment Length Polymorphisms • No longer used as marker of choice
• Single Nucleotide Polymorphisms (SNPs) • Whole genome sequencing

Question 2

What are Single Nucleotide Polymorphisms (SNPs)?

Answer 2

• Single base pair positions in DNA at which different sequence alternatives (alleles) exist in a population
• Only considered to be SNPs if least abundant allele has a frequency of 1% or more (minor allele frequency – MAF)
• Frequency estimated to be 1/1000 base pairs

Question 3

Why are SNPs useful?

Answer 3

• Distributed throughout the genome – coding and non-coding DNA
• Potential of high density of markers
• Automated genotyping of SNP arrays – more cost
effective
BUT
• Only two alleles at any SNP (less variable that micro-satellites)
• SNP arrays only available for well characterised species (e.g. livestock)

Question 4

SNP arrays used in Livestock

Answer 4

• Low density (5K – 20K)
• 5-20 000 SNPs
• Low cost option
• Insufficient detail for many applications • Can be used with medium density arrays
• Medium density (40-50K) • 40-50 000 SNPs
• Used widely
• High density (700-800K) • Expensive
• Used for sires and research
Each SNP array is specific to one company

Question 5

Imputation of genotypes

Answer 5

Genotype imputation is a process of estimating missing genotypes from the haplotype or genotype reference panel. It can effectively boost the power of detecting single nucleotide polymorphisms (SNPs)

Question 6

Whole genome sequencing

Answer 6

• Original method - Sanger Sequencing
• Series of labelled single strands of DNA
• Separated by electrophoresis
• Used to construct a base by base copy of fragments of up to 1Kb
• Genome Assembly - overlap of fragments used to construct a whole genome sequence
• Usually only the non-repetitive DNA that is sequenced – but gaps are being filled in

Question 7

Genotyping by sequencing - GBS

Answer 7

• Efficient – high throughput sequencing
• Restriction enzymes digest DNA • PCR used to replicate fragments • 100 bp fragments sequenced
• Detailed genotyping of whole genome

Question 8

Parentage assignment and verification

Answer 8

• Maintain/verify accuracy of pedigree records
• Extensive systems – avoids handling at birth e.g
Deer and Sheep
• Animals to small to tag at birth e.g. Fish
• Multiple sire mating
• Parentage panels - SNPs are chosen because they are variable across many breeds/populations

Question 9

Single locus traits – e.g inherited disorders

Answer 9

Increasing number of genetic tests available:

Use individual SNPs known to be associated with locus

Question 10

Polygenic traits

Answer 10

Polygenic traits QUANTITATIVE

• Information from SNP arrays used to increase accuracy of Estimated Breeding Values

Question 11

Clues to an animal’s breeding value

Answer 11

• Own performance
• Repeated measures of
performance
• Performance of relatives
• Performance in related traits
•Genomic information

Question 12

Estimated Breeding Values

Answer 12

Best Linear Unbiased Prediction

Own performance
Repeated measures of
Performance
Performance in
related traits
Performance of relatives
Genomic information

Question 13

Genomic Breeding Values

Answer 13

• Uses Single Nucleotide Polymorphism (SNP) genotypes at thousands of sites across the genome
• 5K SNP chip – 5000 genotypes
• 700K SNP chip – 700 000 genotypes
• Increased accuracy of EBVs based on:
• Prediction equations that relate genotypic
variation to performance
• Better measure of genetic relationship between animals

Question 14

Reference population

Answer 14

• Increased accuracy based on prediction equations that relate genotypic variation to performance

Question 15

Genomic breeding values – increasing accuracy

Answer 15

Increased accuracy based on prediction equations that relate genotypic variation to performance
• Once prediction equations established 
• Genotypes from DNA sample can be
used to predict breeding value
DNA can be sampled from birth

Question 16

Genomic breeding values – accuracy

Answer 16

Accuracy will depend on:
• Heritability
• The size of the reference population
Accuracy may decrease over time - recombination

Question 17

Genomic breeding values – relationships

Answer 17

• Increased accuracy based on:
• Prediction equations that relate genotypic
variation to performance
• Better measure of genetic relationship between animals
Example:
ON average full sibs share half their genes
It actually varies from ~ 40 – 60% of their genes

More precise information on shared DNA
sequences gives more precise EBVs

Question 18

gEBVS

Answer 18

– useful for hard to measure traits
Can increase accuracy of EBVs for post slaughter traits
Example: Using phenotypic information from progeny with sire notified on the passport

Question 19

gEBVS – making use of commercial data

Answer 19

Can increase accuracy of EBVs in pure lines for improved performance of crossbred production stock

Question 20

What influences the rate of improvement?

Answer 20

• Heritability of the traits
• Selection pressure actually achieved
• Accuracy of selection
• Generation interval
• Genetic correlations with other traits

Question 21

Genomic information – the future?

Answer 21

• Better management of inbreeding based on shared genotypes
• Better mate selection
• Selection of crossing lines to achieve better heterosis?