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what are quantitative or complex traits defined by

Interplay with the envrionment and many genes (polygneic)


what is a quantitative trait locus?

a genomic region that contains one or more genes affecting the phenotypic variation in a quantitative trait


how is an unknown QTL identified and localised?

by its linkage to one or more polymorphic genetic markers


what is QTL mapping?

form of linkage mapping based on recombination frequencies of the known marker loci


How do you begin QTL mapping

make two inbred lines which are homozygous for marker and trait.
F1 will be heterozygous.
by back crossing F1 with parentals and F2 sib mating get recombinant inbred lines (RIL)


what is an ideal makrer used in QTL mapping

- linked to controlling trait
- polymorphic so can see differences between individuals or species
- can be SNPs, microsatellites, strs etc.
- inherited in a mendelian fashion.
- neutral - not subject to selection.


How can you determine marker and QTL are linked

score the phenotype and marker genotype for all offspring.
if seemes to be an association
eg. M1M1 = heavier and M2M2 = lighter, can assume to be linked.
if not linked there would be no difference between marker genotype and mass.


how do you analyse offspring and marker relationsgip

offspring grouped according to marker genotype and phenotypes averaged for each marker genotype.
if group means vary significantly than a QTL resides in the vicinity of the marker. - same linkage block.


how can you verify that QTL resides in vicinity of marker?

repeated detection and QTL controlling trait under more than one set of environmental conditions. - must be stable across all environmetns and over years.


what frequencies are coupling and recombination expected to be at

coupling = highest freq
recombinant + coupling = second higher
recombinant/ recombinant = lowest.


how do you calculate marker means?

group into classes for each marker type
eg. marker homozygous 1, marker homozygous 2 and marker heterozygous.


if there is tight linkage what would you expect a high amount of?



what are the marker means a function of?

additive and or dominance effects.


what happens if group means vary significantly?

then a qtl resides in the vicinity of the makrer and the linkage block


what can you do if marker means differ

work out estimated values of a and d using genotypic scale of measurement for quantitative traits


why will estimated values be different to true values of a and d

due to recombination between QTL and marker


what will the frequency of gametes be if you cross two homozygotes of M1M1Q1Q1 and M2M2Q2Q2

frequency M1Q1 or M2Q2 = 1-r/2
frequency of M1Q2 or M2Q1 = r/2
r= recombination distance


how do you calculate the midpoint and what does it tell us

marker mean of heterozygote - marker means of biggest homo + smallest homo/2
if = 0 shows that heterozygote is equal to mid point and so no dominance - any other number shows dominance


what is the degree of dominance?



what is the QTL effect size

difference between homozygote marker means over different between largest and smallest range
accounts for percentage of phenotypic difference that between largest and smallest.


what are the advantages of single marker mapping?

genetic map not needed
can do anaylses using standard packages like anovva and t test


what are the disadvantages of single marker mapping

must exclude individuals lacking genotype info
need high density of markeers, markers throughout or might miss QTL


what is interval mapping with multiple markers?

where two marker loci are considered at the same time, to see if there is a QTL between them
uses mapped locations of pairs of adjacent or flanking markers to predict location of QTL
predictions are done in small intervals essentially creating a sliding window moving along chromosome from one end to another


what statistical analysis do we need to do to decide whether two homozygous marker means are different enough to indicate a QTL

threshold level of significance is determined by the LOD score or a permutation test.


how do you work out the ODDs?

probability of (data|QTL)/ probability of (data| no QTL)


what is taken into account when setting the threshold of significance for lods?

number of statistical comparisons to take into account false positives


what does threshold for significance vary with for lods?

permutation tests of the phenotypic data for individuals in presence or absence of QTL.


describe interval mapping

phenotypic data are evaluated directly without adjusting for possible genetic influences from outside the interval - probability of QTL lying between each marker
doesnt take into account anything outside of this interval - any epistasis, might over estimate effect.


describe composite interval mapping

intervals outside the interval of interest are considered as well, take into account regions either side


what are the draw backs of QTL mapping

cant identify causal gene of QTL as could be many
mapping studies localise QTL's to about 0-20cM which could contain 100's of genes
although higher marker density of linkage map gives more precise location the denser the map more likely false positives will be detected.