BIO 321 : Genetics
RECOMBINATION AND
GENETIC MAPPING
Recombination
• Genes that are carried on the same chromosome are physically linked and, therefore,
do not segregate independently.
• However, linkage is not absolute; alleles on the same chromosome can be separated
genetically by recombination.
• Recombination is a physical exchange of pieces of chromosomes between
homologues when they pair during meiosis, (rarely: Mitosis).
• The physical process is referred to as cross over, while the genetic phenomenon is
referred to as recombination.
• Recombination is quite common, and the exchange is completely reciprocal down to
the base pair; there is no gain or loss of genetic information by either homologue.
• If recombination were not reciprocal, it would cause serious abnormalities. In fact
this does happen occasionally to generate chromosomal abnormalities as we will see
later.
Let us consider two linked genes A and B. Fig 5.2
With absolute linkage: AB/ab x ab/ab → ½ AB, ½ ab
With recombination:
AB/ab: A A a a A a A a A a A a
B B b b B B b b B B b b
(Each will get one copy of the ab/ab upon subsequent
fertilization)
We get all four possible progeny: AB, aaB, Abb, aabb
A a A a
B B b b
A a A a
B B b b
How then do we distinguish between linked genes and independent
assortment?
It is a matter of degree. Recombination occurs relatively infrequently
between genes that are close together on the chromosome.
AB/ab x ab/ab →90 AB, 90 ab, 10 Ab, 10 aB
In this case, it is clear that these genes are not assorting independently
because one set of phenotypes predominates over the other.
The major phenotype represents the nonrecombinants which reflect
the allelic configuration of the heterozygote parent's chromosomes.
The rarer phenotypes represent the recombinants.
• Recombination events occurs at random intervals along the homologues during
Prophase I of meiosis, and consequently, the chance that a recombination event
will occur between two genes is a function of the distance between them.
• The greater the distance between two genes, the more likely recombination will
occur between them during a single meiosis.
• Thus, if we score the phenotypes of a large number of progeny in the above cross,
the percent recombination is a measure of the distance between two genes.
• For A and B:
• % recombination = # aB + # Ab = 10+10 = 20/200 = 10%
Total Progeny 90+90+10+10
• Let’s suppose there is a third gene on this chromosome, C. We can determine its
distance from A as follows:
Ac/aC x ac/ac --- 10 AC, 141 aC, 141 Ac, 8 ac
• AC and ac are the recombinants; we can tell because we know the parental
configuration.
• But even if we weren't given the parental chromosomes, we
know that these must be the recombinant phenotypes because
they are rare.
• % recomb. = 10+8 = 18/300 = 6%
10+8+141+141
• From this we can conclude that A is closer to C than it is to B.
• In fact we use the percent recombination measured between
genes in these kind of genetic crosses as the distance along
chromosomes, and this serves as the basis for genetic mapping.
Recombination Frequencies Over Large Distances
• As genes that are farther and farther apart are considered, the frequency of
recombination between them increases.
• However, the greatest amount of recombination we ever observe in a cross is
50%. This is because of multiple crossovers.
• Consider that for genes that are far apart, and, therefore, the probability of a
single recombination between them is great, it is also probable that more than
one recombination event will occur.
• If one recombination event occurs, recombinant
gametes will be generated. But if two
recombination events occur, the gametes will
look like nonrecombinants.
• An odd number of events will generate
recombinant gametes, an even number of
events
will not.
• This essentially means that for genes that are far apart on the chromosome, and, therefore have a high probability of
having multiple recombinant events occur between them, ½ the gametes will be recombinants and ½ will be
nonrecombinants resulting in an equal number of all possible phenotypes.
• The percent recombination will be 50%, this is meaningless since it is the same distribution of phenotypes in the progeny
that we would expect for independent assortment in a heterozygote crossed by a homozygous recessive.
• The important implication here are:
• When we see independent assortment of two genes, it means that genes are either on different chromosomes, or very
far apart on the same chromosome.
• The percent recombination can never be over 50%. If it is, you made a mistake.
• How can we tell that genes are on the same chromosome if they are far apart?
• If we do a cross, we can determine that gene A is linked to gene B because they do not assort independently.
• In a second cross, we will find that gene B is linked to gene C by the same criterion.
• Further experiments of this type will show that gene c is linked to gene D, gene D is linked to gene E, and so on through
to gene Z.
• Gene A must be on the same chromosome as gene Z because we can trace their linkage in this way. However, if we do
the cross:
AaZz x aazz→ 200 AZ, 200 aZ, 200 Az, 200 az
• We get equal numbers of all phenotypes, 1/4 of each, which is 50% recombination or independent assortment.
• We can't define A-Z linkage in a cross between them, only by mapping the chromosome.
Genetic Mapping
• Let's go back to our A, B and C genes.
• AB/ab x ab/ab →90 AB, 90 ab, 10 Ab, 10 aB
• % recomb. = 10+10 = 20/200 = 10%
90+90+10+10
• Ac/aC x ac/ac ---10 AC, 141 aC, 141 Ac, 8 ac
• % recomb. = 10+8 = 18/300 = 6%
10+8+141+141
• If genes are located on linear chromosomes and DNA is a linear molecule, then genes might
well be arranged in a linear fashion along the DNA.
• If this is true, then we should be able to make a linear map, using recombinational distances, to
locate A, B, and C with respect to each other.
• There are two possible maps we can make with these data:
A C B
| | |
6 4
C A B
| | |
6 10
• To distinguish between these maps, we need to determine the distance between
C and B.
Bc/bC x bc/bc → 18 BC, 110 Bc, 100 bC, 22 bc
% recomb. = 18+22 = 40/250 = 16%
18+22+110+100
• This data is consistent with the second map.
• Results like these led to the conclusion that genes are arranged linearly on
chromosomes.
Three-Point Cross
• The above set of crosses represent two-point crosses, the analysis of two
genes in one cross.
• It is more efficient, and more accurate, to map the three genes in one cross.
• Let's look at a real cross:
cv - absence of cross veins in the wing
ct - sniped wing edges
v - vermilion or bright scarlet eye color
• Cross: cv ct v/+ + + x cv ct v/cv ct v
• Progeny Phenotypes
cv ct v Number
cv ct v 580
+ + + 592
cv + + 45
+ ct v 40
cv ct + 89
+ + v 94
cv + v 3
+ ct + 5
1448 Total Progeny
• To analyze these data, we treat these crosses two genes at a time.
• Consider cv and ct first:
The recombinants are cv + and + ct.
There are 45 + 40 + 3 + 5 = 93
Dividing this by total progeny: If we put these data together, it is clear
that cv and v are the outside genes
93/1448 = 6.4% because the distance is greatest between
them.
Consider ct and v:
The recombinants are + v and ct +. cv ct v
| | |
89 + 94 + 3 + 5 = 194 6.4 13.2
194/1448 = 13.2%
• Consider cv and v:
The recombinants are cv + and + v.
45 + 40 + 89 + 94 = 268
• There is a problem here. The numbers don't add up. There should be 19.6%
between cv and v, and we measured the distance as 18.5%
• The discrepancy arises from the exclusion of double cross overs (+ ct + and cv +
v) from the calculation of the distance between cv and v, while they were
included in the calculation of the shorter distances. Fig 5.6 (DCO are useful in
determining gene order, just compare with parental, odd one out is the middle
gene)
• For this reason, we use the additive distance between cv-ct and ct-v for the
distance between cv-v.
• Another interesting aspect to these double recombinants is that one can predict
the order of genes by bearing in mind that the rarest class of phenotypes are
those that arise from two recombination events.
• The probability of the double recombination occurring is the probability of one
occurring times the probability of the other occurring.
(0.132)(0.064) = 0.0084 predicted frequency
• this happens because once a cross over tales place in a region the
probability of another cross over taking place nearby is reduced
probably by physical interference caused by the breaking and
rejoining of chromatids (chromosomal interference).
• The degree of interference is expressed as a Coefficient of
Coincidence:
CC=observed DCO frequency/ expected DCO frequency
= 0.0055/0.0084= 0.65
• If we look for the rarest class, it must represent the double
recombinants and, therefore, predicts the order.
• One looks for the rare phenotypes, see which gene has been changed
alleles relative to the other two, and that must be the middle gene.
• One important practical point. Many students get into trouble when
confronted with a set of numbers of progeny by making assumptions
• In the cross AaBbCc/aabbcc, students will assume
that ABC and abc are the nonrecombinants.
• But this may not be true. If ABC and abc are the
largest classes it will be, but if AbC and aBc are
the most common class, then these are the
nonrecombinants.
• A student can't calculate the correct distances
using the wrong recombinants, and will get
recombination frequencies above 50%.
Large Map Distances
• Remember the A-Z chromosome we talked about previously.
• Let's assume we mapped distances and generated the following map:
A B C D E F G H I
| | | | | | | | | ...
10 15 21 8 12 6 22 14
• The distance between A and H is the additive distance 108%.
• But if we did the cross:
AI/ai x ai/ai
• We would not expect to get 108% of the Ai and aI (recombinants) phenotypes. Actually we
expect to get 50% recombinants of 1/4 of Ai and 1/4 of aI that occurs when genes are so far
apart they seem to assort independently because of multiple cross-overs.
• We will call the percentages between genes map units instead of percentages to reflect the
fact that we can have numbers much greater than 50 between genes when be build
complete maps.
• 1% = 1 map unit (mu) more or less...not very accurate over larger distances
because of multiple recombinations (30% recombination is around 40 mu).
More examples
• 1 ) Genes a and b are linked with 10% recombination . What would
be the phenotypes and the probability of each among progeny of
the following cross: a b+/a+ b x a b/a b?
• Answer: Recessive homozygous is silent: possible progeny are ab+,
a+b, a+b+, ab (last two are recombination events) frequency for
the first two are: 100-10=90/2=45% each. For the last two= 10/2+
5% each.
• 2 ) Genes and b are sex linked and are located 7 mu
apart on the X chromosome of Drosophila. A female
of genotype a+b/ab+ is mated with a wildtype male
(a+b+)
• a )What is the probability that one of her sons will be
either a+b+ or ab+ in phenotype?
• Answer: son gets the X from mother: a+b+ implies a
recombination event during meiosis in the mother=
7/2=3.5%. ab+ is the parental: 100-7=93/2=46.5. 46.5
+3.5=50%
• b)What is the probability that one of her daughters
will be a+b+ in phenotype:
• Answer: male is a+b+ (no possible recombination)
• Genes a b c are recessive. Females heterozygous at these three loci are crossed to males. The progeny is:
• Daughters: all + + +
• Sons:+ + + 23
abc 26
++c 45
ab+ 54
+bc 427
a++ 424
a+c 1
+ b+ 0
• What is known of the genotype of the females’ parents with respect to the three loci? Give gene order
and arrangement.
• Answer: the male progeny with the highest phenotypes represent the parentals (NON recombinants) .
These are the + b c and a + + thus the mother is : + b c/a + + .
• Compare a + + (parental) to a + c (Double recombinants), c is in the middle:
• What is known of the genotype of the male parent?
• Answer: since mother heterozygote only a wild type + + + male would generate a female progeny that is +
+ + ) (any other male genotype would result in recessive traits showing in some females).
• Map the three genes:
• Answer: for ac: (anything not +c or a+): 23+26 +1/1000=5mu
• For bc (anything not bc or + +) 54 + 45+1/1000= 10 mu
• a……..c……………….b
5 10
• 4 ) The following makes use of the following genetic map:
10 5 20 10 20 5
a k j b d m f
• Calculate:
• the frequency of jb gametes from a JB/jb genotype
Want parental: 100-20=80/2=40%
• The frequency of JBD gametes from a jBd/JbD genotype
Want the double recombination: for JB=0.2 and BD=0.1. So 0.2x0.1=0.02. half of that is JBD (other
is jbd)= 0.01 or 1%
• The frequency of jbd/jbd genotypes in a jBd/JbD x jBd/JbD mating
Same as b but squared since the double recombination should happen in each
parent=0.01x0.01=0.0001 or 0.01%
10 5 20 10 20 5
a k j b d m f
• The frequency of AM gametes from an aM/Am genotype: recombination, but the
distance is very large so sort like independent segregation: 25%
• The frequency of AkF gametes from an AKF/akf genotype.
We are looking for the double recombinant here: AK=0.1, KF is 0.5 (even though
they are more than 50 mu apart). So the DRec=0.1x0.5=0.05. Half are the aKf,
and half are the AkF=0.05/2=0.025 or 2.5%
