Table 5

Haplotypes found in nineteen tetraploid potato individuals and resulting genotype model

Individual

H1

H2

H3

H4

H5

H6

H7

H8

H9

H10

Genotype model

χ²-value

p-value

S9

19

2

3

1/1/2/5

8.25

0.02

S25

21

27

4/4/8/8

0.75

0.39

S50

18

3

3

1/1/3/6

6.00

0.05

S73

18

14

1/1/8/8

0.50

0.48

S83

26

2

1/1/1/5

4.76

0.03

S89

7

2

14

8/8/5/7

3.26

0.20

S93

26

8/8/8/8

0

1

B1

7

17

8/8/8/5

0.22

0.64

B4

4

19

8/8/8/5

0.71

0.40

B26

24

0

1

B30

79

5/5/5/5

0

1

B37

7

16

8/8/8/1

0.36

0.55

B43

28

2

1/1/1/3

5.38

0.02

B52

9

14

1/1/8/8

1/8/8/8

1.09 or 2.45

0.30 0.12

B63

2

17

2

8

5/8/9/10

20.79

0.0001

B75

2

9

13

10/10/5/8

4.25

0.12

B80

10

12

1/1/5/5

0.18

0.67

B86

5

19

8/8/8/5

0.22

0.64

B108

20

3

1/1/1/5

1.75

0.19

For nineteen individuals, the number of clones obtained per individual for each of the ten haplotypes (Table 4) and the resulting genotype model are shown. For each genotype model, the goodness of fit (chi-square) and the p-values for the deviation of the number of observed clones from the expectation based on the genotype model are calculated. Genotype models which do not significantly deviate from the observed haplotype distribution are shown in bold (significance level: 5%). It is assumed that haplotype frequencies deviate χ² distributed from the genotype model, with # of different alleles -1 degrees of freedom. In the first row of Table 5, the χ²-value is calculated as follows: . The p-value represents the probability of obtaining haplotype frequencies at least as extreme as the observed ones, given that the genotype model (null hypothesis) is true.

Neigenfind et al. BMC Genomics 2008 9:356   doi:10.1186/1471-2164-9-356