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Recombination frequency, RF = [(NPD + 1/2T) / total number of tetrads] x 100. In our example, this is ([3 + 1/2(70)]/200) x 100 = 19 map units.
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LECTURE 7: TETRAD ANALYSIS; GENE CONVERSION, continued
Reading: Ch. 5, p 142-151; Ch. 6, p 192-
Problems: Ch. 5, solved problem III, also 28a, 29ab, 30, 32, 34, 35; Ch. 6, #30, 31
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First, let’s review how to calculate map distance in yeast:
Consider and example of two linked genes, ARG3 and URA.
P: arg3 ura2 x ARG3 URA
Diploid: arg3 ura2 / ARG3 URA
Meiotic products:
PD ( arg3 ura2 ; arg3 ura2 ; ARG3 URA2 ; ARG3 URA2 ) = 127
NPD ( arg3 URA2 ; arg3 URA2 ; ARG3 ura2 ; ARG3 ura2 ) = 3
T: ( arg3 ura2 ; arg3 URA2 ; ARG3 ura2 ; ARG3 URA2 ) = 70
Recombination frequency, RF = [(NPD + 1/2T) / total number of tetrads] x 100. In our example,
this is ([3 + 1/2(70)]/200) x 100 = 19 map units. We will modify the equation to obtain a better
estimate of map distance. If you draw out the possible crossover events between two linked
genes, you can see the different tetrads that result; see Fig. 5.17 (p. 147).
No crossovers --------> PD
Single crossover --------> T
Double crossover (2-strand) --------> PD
Double crossover (3-strand) --------> T
Double crossover (3-strand) --------> T
Double crossover (4-strand) --------> NPD
You can see how we can modify the equation to make it more accurate. Remember that half
(2/4) the strands recombine if there is a single crossover event and that 4 strands recombine if
there is a double crossover event (even if all of the strands don’t participate, some participate
more than once.)
Map distance = (total rec. events / total tetrads) x 100 = [(1/2[SCO] + DCO) / total tetrads] x 100
Map distance = ([1/2 (T – 2 NPD) + 4 NPD]/ total tetrads) x 100
Map distance = (1/2 T + 3 NPD) / total tetrads x 100
For our example above, map distance = ([1/2 (70) + 3 (3)] / 200) x 100 = 22 map units
This modified equation makes 2 assumptions: (1) there are no more than two crossovers in the
interval and (2) there is no chromosomal interference (all types of DCOs occur with equal
frequency.
In Neurospora crassa , meiosis occurs within the tight confines of a narrow ascus, resulting in the
formation of ordered tetrads. Because of the precise positioning of each meiotic product within
the ascus, one can infer the arrangement (and segregation) of each chromatid of homologous
chromosomes during Meiosis I and II. This gives information about the distance between the
gene and its centromere. (Meiosis II is followed by mitosis; each pair of genetically identical
daugthers sits adjacent to one another. Each ascus is thus made of up 8 haploid ascospores.)
Consider a gene required for ascospore color (ws
gives black spores and ws gives white
spores):
P: ws
x ws
Diploid: ws
/ ws (immediately undergoes meiosis)
If no recombination between ws gene and the centromere occurs, then the resulting ascospores
are arranged in a neat array with black and white spores clearly segregated from one another
(they separated during meiosis I), each type cleanly segregated to either side of the imaginary
line separating the 4
th
and 5
th
ascospores. This is called a first division segregation pattern.
Since the daughters of the mitotic division lie right next to one another, we can simplify the two
possible configurations to:
(ws
ws
ws ws)
(ws ws ws
ws
If recombination occurs between ws and the centromere, then a second division segregation
pattern is observed. Now, both types of spores are found on either side of the imaginary line
between the 4
th
and 5
th
ascospores. Now there are four possible configurations:
(ws
ws ws
ws)
(ws ws
ws
ws)
(ws
ws ws ws
(ws ws
ws ws
When an ascus shows a second division segregation pattern, we know that half of the chromatids
are recombinant and the other half have not participated in crossovers. Thus, we can calculate
the distance of a gene from its centromere simply by dividing the percentage of second division
octads by 2.
Gene-centromere distance = ([# of second division octads / total octads] x 100) / 2
To examine linkage of two genes in Neurospora, we can use the same formulas as we did for
Baker’s yeast.