LECTURES 13 & 14 (QTLs) Flashcards
What are QTLs?
they’re genomic regions (NOT GENES) that contribute to quantitative traits, they’re polygenic (determined by many genes) and there’s action of the environment into them
they contain several genes that affect the phenotypic variation of certain trai
How are QTLs localized in the genome?
they’re localized by t¡their linkage to polymorphic genetic markers , if we know where markers are located we can get an idea of where our QTL is placed.
what does an statistical analysis show?
it shows the different marker genotypes associated to the phenotype
What’s the principle of QTL analysis?
inbred parental strains to get F1 so the subsequent segregation of the parental genes can be correlated to phenotypic variation
What are the 6 requirements for a QTL analysis?
- mapping population
- markers
- framework linkage map to locate QTL
- easy to score phenotypes
- stats
- verification in different populations
explain in depth Requirement 1 (mapping population) for QTL analysis.
onion example: two parents big onion and small onion give a medium size onion (F1) and we also have markers associated with this.
once we have the F1 we can create the mapping population
F1xF1 or bacrosses with parent
What are RILs?
Recombinant inbred lines. you create them by crossing an F2 with a brother or a sister and inbreed for 20 generations
What are genetic markers? (4)
they represent the genetic difference bt individuals
they are polymorphic
they have a specific location within the chr
inherited in a mendelian way
What’s the ideal marker?
- essay to assay
- polymorphic (so we can see differences between lines)
- stable through time (although you need to keep checking markers against phenotypes bc mutations occur all the time)
- neutral ( they shouldn’t be subject to selection
- they must be located throughout the genome
Give
examples of good markers.
microsatellites(highly polymorphic) and SNP (less polymorphic, usually two variants major and minor depending the frequency at which they occur)
RFPL (restriction fragment length polymorphism) and isozymrd
How do we create a linkage map (requirement 3)
we do it by mapping techniques
the map should have evenly spaced markers and some anchor markers to form a integrated linkage map.
we know the location of the markers but not the location of the QTLs we use linkage to find where QTLs are located.
how do we know the relationship bt the marker and QTL?
we take all our individuals and group them into the marker categories, we plot them out (mean + standard deviation) and do stats
how do we analyze the QTLs?
if the means vary between the different markers there’s a QTL associated to the marker, the tighter the linkage the better the relationship.
How do we verify whether there’s a QTL associated with certain marker?
we do so by looking at different populations to see if we get the same results
single marker analysis, describe.
go to paper.
Were should the heterozygous marker be placed?
it should be in the middle but if there’s deviation that means partial dominance
what is â?
estimation of additive effect; the difference in homozygote marker class mean a(1-2r)
what’s ^d?
the estimation of dominance effect; the difference in hetero marker class mean with respect to the midpoint bt a+ and a-)
How is the % QTL effect determined?
Gmimi-Gm2m2/ PIL - PIS
what do we do if there’s recombination?
divide by either 1-2r or 1-2r)^2
what are the adv of single marker analysis?
- analysis can be done using stats
- simplicity
- can add complexity adding other varieties e.g sex
what’s the multiple marker analysis?
looking at various markers at a time
how’s r (distance bt QTL and marker) estimated?
through scoring the recombinants and non recombinants for the markers
How’s the position of a QTL estimated in multiple marker analysis?
the difference between the marker class means
how different do the means have to be to indicate a QTL?
this is established by the threshold level which is established by LOD score
what¡s LOD score?
logarithm of the odds = P(observing geno-pheny data for imdv given the presence of a QTL)/P(observing phony-geny data for imdv given the absence of a QTL)
this is calculated for each marker pair
What happens once the threshold significance is estates through the LOD?
everything above the threshold indicates a high probability of having a QTL
what’s interval mapping?
the use of map loci pairs of adjacent markers to predict the location of unseen QTLs
What are the two main types of interval mapping?
- interval mapping
- composite interval mapping.
describe normal interval mapping.
the phenotypic data is evaluated directlydoesn’t take to account anything occurring outside the interval (might overestimate the effect of a QTL)
describe composite interval mapping
it takes into account the regions at either side more realistic
what are ghost QTL?
when a QTL appears to be in between just because there¡re QTLs at either sides
where are more ghost QTLs?
in interval mapping but not in CIM.
Advantages of CIM and IM.
- more accurate
- easy to plot
- gets rid of the problem of recombination
Disadvantages of ICM and IM
- only considers one QTL at a time
requires software
what are the uses of QTL mapping?
- see effect sze
- see effects of one QTL into another
- location of QTL to focus in that region
- phenotype genotype association with implications in medicine.
What are the main limitations of QTL mapping?
detecting QTLs is very laborious
markers should be 20-30 cM apart
detecting QTLs depend on effect size
large population is needed.
difficult to find causal gene because there are so many genes involved
the denser the map the more false positives
the higher the marker density of the linkage map the more precise the location of the QTL
how far should be two markers?
at least 20-30 cM apart.
What does the effect size depend on?
it depends on the org you’re using
is it better a big or a small effect size?
a big, we want to find QTLs that have a lot of variation
what shape do QTL effect size resemble?
L shape distribution (mainly small)
what are the three main techniques used to map QTLs?
linkage mapping
association studies
and experimental pol
what are linkage mapping for finding and map QTLs?
look at genealogies of families (genotyped with many markers) look at recombination of the disease at some point good for single gene disorders but still markers have to be 20 cM apart
How can the causal gene be determined?
it’s very difficult to determine the causal gene bc 100sof genes involved but we can create congenic and isogenic lines and then screen the genes using bioinformatics, once a candidate gene has been established, we need to validate it .
What can we tell about QTLs (overall)
Almost all complex traits are affected by multiple QTLs
QTL effect size is L-shaped
QTL effects are sex and environment dependent
Epistatic effects amongst QTLs often seen
Pleiotropic effects often seen
what are congenic or isogenic lines?
only differ in a region of interst and can be done by BC
