% gamete

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gamete gamete phenotype exp
obs e sp e sp
ebony spineless 250 430 e sp
wild type 250 440
e sp e ebony 250 59
e sp sp spineless 250 71
e tot sp 245 256 501
244 255 499 tot 489 511 1000
obs
exp
e tot sp 430 71 501
59 440 499 tot 489 511 1000
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Compare observed and expected numbers with a
goodness of fit chi-square test c dof
S
2
(observed number - expected number)2
(expected number)
c 3
2
(430-245)2 (71-256)2 (59-244)2
(440-255)2 245 256
244 255



139.7 133.7 134.7 134.2
542.3 p
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gamete gamete phenotype exp f
obs e sp e sp
ebony spineless 0.25 430 4
e sp wild type 0.25
440 4 e sp e ebony
0.25 59 1 e sp sp
spineless 0.25 71 1


effects of sample size !
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Calculated distance
RF 0.5
Actual distance
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Mapping function fi (e-m mi)/i! m
mean number of crossovers i actual
number of crossovers fi frequency of ith
crossover class but, only know the
no-crossover class (i 0) (e-m m0)/0!
e-m RF ½ (1 - e-m) solve for m m/2
corrected map distance
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1 2 3 4 5
Marker A B C D E F
G H I
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1 2 3 4 5
R P P P P
RF values 0.5 0.4 0.2
0.05 P 0.25 0.3 0.4 0.475 P 0.25
0.3 0.4 0.475 R 0.25 0.2 0.1
0.025 R 0.25 0.2 0.1 0.025
pr(independent assortment) .25 x .25 x
.25 x .25 .25 0.00098 pr (linkage, RF 0.2)
.1 x .4 x .4 x .4 x .4 0.00256
Likelihood ratio pr(indep assort)/pr(linkage)
0.00256/0.00098 2.61 Likelihood of
odds, Lod score log10(likelihood ratio)
0.42
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1 2 3 4 5
R P P P P
RF values 0.5 0.4 0.2
0.05 P 0.25 0.3 0.4 0.475 P 0.25
0.3 0.4 0.475 R 0.25 0.2 0.1
0.025 R 0.25 0.2 0.1 0.025
RF 0.5 0.4 0.2
0.05 Probability 0.00098 0.00162
0.00256 0.00127 Ratio 1
1.65 2.61 1.30 Lod 0
0.22 0.42 0.11
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Cm
M1 M2
0.8
minimal deletion
6.6
M3
2.0
M4
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Take-home points test for linkage by
statistical analysis of testcross offspring
(chi-square goodness of fit test, n number of
genotypes) linkage analysis is limited to
genes that are close together (non-linear
relationship between estimated and actual
distance mapping functions can improve
estimates of genetic distance linkage
analysis can be applied to pedigrees
phenotype can be associated with chromosome
regions if they are linked to molecular
markers molecular markers include VNTR loci
and microsatellites maximum likelihood is a
statistical method for inferring linkage