Angela Flashcards
In most cases, how many loci affect one trait?
many
What does QTL detection stand for?
Quantitative trait loci detection
What is the goal for QTL detection?
to find a polymorphism in the genome that is associated with a distinct difference in phenotype
What is a polymorphism
variation in the dna sequence
How are QTL’s discovered?
markers (an unimportant polymorphism)
What is a quantitative trait locus?
a region within the genome which is associated with a specific trait that varies in the population
What are the two types of approaches for QTL detection?
- candidate gene approach
- anonymous marker panel approach
What is the candidate gene approach?
- selecting a gene for physiological or biochemical reasons in order to identify a polymorphism within a gene
- done one at a time
- very selective and targeted
What is the anonymous marker panel approach?
- most common
- don’t know genes or loci where the polymorphism is, try to identify which markers are associated with which QTL
- developing a panel of markers
- scan a region/chromosome/genome of multiple markers
What are the two technologies used under the candidate gene approach?
- PCR
- Sequencing specific gene/markers
What are the two technologies used under the anonymous marker panel approach?
- high density marker panels
- whole genome sequencing
What is the genotyping individuals by PCR method?
Candidate gene approach
a restriction endonuclease cleaves dna at a specific sequence and the differences are coded as alleles
What is the genotyping individuals by sequencing specific gene/markers technology?
Candidate gene approach
identifying polymorphisms
What is the high density marker panels technology
Anonymous marker panel approach
photo etching a glass slides, and building velcro tags, tags are used the grab matching animal dna, grabbed dna lights up spots = genotype
What will you see if the QTL and the marker are linked?
MM and mm will both be normal distributions with an overlap
What are two factors that affect QTL detection?
Inheritance
- crosses of divergent lines (multimodal dist)
- offspring parent resemblance
(deviation from parent avg)
- segregation analysis
(expected inheritance using pedigree)
Population design
- inbred line cross
- outbred population
What does eQTL stand for?
Expression quantitative trait loci
What is the goal of eQTL?
find a polymorphism in the genome that is associated with the gene expression phenotype
What are the two approaches of eQTL detection?
same as QTL, candidate gene and anonymous marker panel
What are the two technologies used for eQTL detection?
microarrays - anonymous marker panel approach
qPCR - candidate gene approach
What is a cis vs a trans eQTL?
cis - eQTL is close to the gene
trans - eQTL is far away from the gene or on another chromosome
What is an eQTL hotspot?
genomic regions with eQTL regulating more than four genes
What is single locus selection?
- select based on preferred alleles
- directly influence allele frequency
- track progess by change in allele frequency
- qualitative trait
What is phenotypic selection?
- selection based on preferred phenotype
- indirectly influence allele frequency
- track progress by change in phenotype
- quantitative trait
