linkage 1,2- lecture 12,13 Flashcards
linkage
The tendency for genes or segments of DNA closely positioned along a chromosome to segregate together at meiosis, and therefore be inherited together
(opposite of independent assortment)
Manhattan plot
A Manhattan plot, which plots the association statistical significance as –log10(p-value) in the y-axis against chromosomes in the x-axis, is a good way of displaying millions of genetic variants in one figure. One can easily spot regions of the genome that cross a particular significance threshold
x linked genes
men inherit baldness from their maternal lineage
sex influenced autosomal trait
(dominant in males and recessive in females) or vice versa, differently expressed due to hormonal environments
centimorgan
A centimorgan (abbreviated cM) is a unit of measure for the frequency of genetic recombination. One centimorgan is equal to a 1% chance that two markers on a chromosome will become separated from one another due to a recombination event durin g meiosis (which occurs during the formation of egg and sperm cells).
recombinant frequency
number of recombinant progeny/total number of progeny *100
recombination
Genetic recombination is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent
genetic maps reflect distance based on how
often, on average, recombination occurs between two loci. The further
apart two loci are the higher the chance that a crossing over will take
place and thus the greater the genetic distance between them.
Conversely, if two loci are located very close together, there is very little
chance for crossing over to take place. Thus, there is a correlation
between physical and genetic distance, but that correlation is not perfect
(more on this point later). Thus, when using genetic maps to identify the
location of a gene we are taking advantage of the normal cellular
process of recombination
There are two types of maps used in locating genes: name them and explain how they are similar and different
genetic and physical maps.
Both maps contain useful, but different, information and thus complement one another.
A physical map measures distance between two loci in the genome in base pairs (e.g., determined by DNA sequencing), while a genetic map measures distances in the frequency of recombination events
complete linkage
no recombination occurs between the two genes
complete independence
independent assortment
testcross
is a cross between a heterozygous and a homozygous recessive individual, the latter is also referred to as the tester. Testcrosses are useful as you can determine offspring genotype simply by observing phenotype (as the offspring inherit only recessive alleles from the tester parent).
partial linkage
the proportion of recombinant progeny will fall somewhere in between 0 and 0.5 (or 0 to 50%). The proportion of recombinant progeny
can then be used to determine the genetic distance between the loci of
interest
phase
refers to the particular arrangement of alleles on a chromosome
recombinant frequency
The frequency with which a single chromosomal crossing occurs between two genes during meiosis
number of recombinant progeny/total progeny * 100
results of a test cross with complete linkage, independent assortment, linkage with crossing over
what influences the probability of recombination
distance between genes
what breaks up linkage between genes
recombination
in a test cross what is the maximum frequency of recombinant gametes
50%
recombination
the rearrangement of genetic material, especially by crossing over in chromosomes or by the artificial joining of segments of DNA from different organisms.
complete (or absolute) linkage
In genetics, complete (or absolute) linkage is defined as the state in which two loci are so close together that alleles of these loci are virtually never separated by crossing over. The closer the physical location of two genes on the DNA, the less likely they are to be separated by a crossing-over event.
independent assortment
The idea behind independent assortment is that genes are inherited independently of one another. In other words, the genetic factors that control crest and sex are physically separate. Because the genetic factors are physically separate, they segregate independently during gamete (egg and sperm) formation.
chi square test usage
testing for independent assortment
contingency table
2 by 2 table of the number of progeny with each genotype
worked problem contingency table
what is the physical distance between genes related to
the rate of recombination between them
3 point cross question
determining the order of genes
deletion mapping
Deletion mapping is a process by which a DNA feature (mutation, DNA polymorphism, or MIC-limited DNA segment) can be genetically mapped to a segment of a MIC chromosome, defined by deletion ends, using a panel of deletion homozygotes.
hemizygous
Simply stated, homozygous describes two identical alleles or DNA sequences at one locus, heterozygous describes two different alleles at one locus, and hemizygous describes the presence of only a single copy of the gene in an otherwise diploid organism.
phase
Phase refers to the particular arrangement of alleles on a chromosome
three major points to remember about crossing over
(1) crossing over breaks up the physical linkage between
alleles/genes
(2) the distance between any two loci influences the
probability of crossing over (i.e., the further apart two loci are, the higher
the chance there is of a recombination event occur between them)
(3) the maximum frequency of recombination between any two loci is
50%. This final point stems from the fact that only two of the four sister
chromatids are involved in crossing over
recombination frequency (RF)
(Number of recombinant progeny / total number of progeny) * 100
the percentage of recombinant progeny produced in a cross. The RF ranges from 0%, in the case of complete linkage, to 50% in the case of independent assortment. The fewer recombinant progeny produced, the lower the RF, and the tighter the association between two genes. Note, when performing these calculations, there will be two types of recombinant progeny and two types of parental progeny
