GWAS Flashcards
What is a multigenic trait?
A trait controlled by multiple genes.
How does GWAS differ from QTL mapping?
GWAS allows sampling of diversity across the whole population.
GWAS doesn’t require an initial cross - just see what is present in the population.
When is GWAS most useful?
For organisms with where we cannot perform complex breeding programs for moral reasons or simply due to generation times.
How does GWAS work?
It is usually based on SNPs and requires SNP information from across the whole genome - SNP arrays. SNP frequencies and phenotypes are then compared across individuals in a population.
How are SNP arrays used?
1) Take genomic DNA from individual of interest and divide into fragments.
2) Label DNA fragments to make a probe.
3) Hybridise to the microarray slide.
4) When probe finds correct allele on array it binds more strongly so the spot on the array is brighter.
What is a Manhattan plot?
A type of scatter plot commonly used in genome-wide association studies (GWAS) to display significant SNPs.
What is shown on the X-axis of a Manhattan plot?
The chromosome and position along the chromosome of an SNP.
What is shown on the Y-axis of a Manhattan plot?
The log of the probability that SNP frequencies differ significantly between the 2 populations.
What does GWAS tell us?
A SNP may be the causal allele but is more likely a SNP close to the gene but not in the gene itself. The SNP must be close enough to the causal gene so recombinants are rare because otherwise it would become unlinked through recombination.
What are the reasons why SNPs may not give the full answer?
1) Each causal gene linked to a SNP may not be acting alone.
2) There may not be a SNP close enough to the causal gene.
3) Allele of the SNP + causal gene that causes the phenotype may be too rare.
