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-)
