PBGMCB 620 – DNA fingerprinting
Fall 2012
Homework Problem
Tables 1 and 2 contain genotypic data for 10 wheat cultivars using two marker systems.
Table 1 contains genotypic data using simple sequence repeat (SSR or microsatellite)
markers (Roder et al., 1998; Song et al., 2005) and Table 2 contains DArt (Jaccoud et al.,
2001; Wenzl et al., 2004) marker data . Evaluate the informativeness of each marker
class (SSR vs. DArt) and use each dataset individually to assess genetic relatedness
among some wheat cultivars described below.
Perform the following calculations:
1. Calculate the number of alleles and allelic frequencies for each marker
2. Calculate the heterozygocity (Nei, 1978) and polymorphic information content
(Botstein, 1980) of each marker
3. Calculate the mean heterozygocity for the microsatellite dataset
4. Calculate the mean heterozygocity for the DArT dataset
5. Which marker class was the most informative? Explain your answer by referring
to your calculations.
6. Assess the genetic relatedness between the cultivars Weatherford, Madsen,
ORCF101, ORCF102, and Malcolm, treating the SSR and DArt datasets
separately, using the proportion-of-shared-alleles distance (Bowcock et al., 1994).
7. Assess the genetic relatedness between the cultivars Weatherford, Madsen,
ORCF101, ORCF102, and Malcolm, combining the SSR and DArt datasets. Use
the proportion-of-shared-alleles distance.
8. Were the estimates of genetic relatedness using different marker classes consistent
with each other and with the combined dataset? Explain some reasons for
consistency or lack of consistency in the analyses. Was any individual analysis
consistent with the combined analysis? Explain your answer using your
calculations in 6 and 7.
NOTE – Show your calculations or strategy for every step. You may use any computing
device or software for calculations except one that is specifically designed to do
phylogenetic analysis.
Table 1. Allele sizes (base-pairs) for 10 wheat cultivars screened with 10 microsatellitea (SSR) markers.
Cultivar
WEATHERFORD
MADSEN
TUBBS
HILL81
MALCOLM
YAMHILL
HYSLOP
ORCF101
ORCF102
FOOTE
a
barc169
119:119
119:119
119:119
119:119
119:119
119:119
116:116
119:119
119:119
116:116
barc228
172:172
179:179
172:176
172:179
176:176
172:179
179:179
176:176
172:179
172:179
barc57
236:236
224:224
224:236
230:230
236:236
224:224
230:230
224:224
224:224
215:215
gdm153
253:253
255:255
253:253
255:255
253:253
253:253
255:255
253:253
255:255
253:253
gwm11
203:203
197:197
197:197
197:197
197:197
197:197
197:197
201:201
197:197
197:197
gwm120
139:139
147:147
147:147
153:153
120:120
153:153
151:151
120:120
147:147
120:120
gwm219
182:182
182:182
182:182
190:190
147:147
182:182
190:190
147:147
147:147
147:147
gwm570
140:140
140:140
134:134
140:140
134:134
140:140
134:134
129:129
138:138
140:140
gwm95
117:117
117:117
117:117
115:115
117:117
115:115
117:117
117:117
117:117
117:117
wmc777
133:133
133:133
133:133
133:133
133:133
94:94
133:133
133:133
133:133
94:94
MIcrosatellites are described by Roder et al. (1998) and Song et al. (2005).
Table 2. Allelic constitution for 10 wheat cultivars screened with 10 bi-allelic (0 = allele A and 1 = allele B) DArTa markers.
MarkerName
WEATHERFORD
MADSEN
TUBBS
HILL81
MALCOLM
YAMHILL
HYSLOP
ORCF101
ORCF102
FOOTE
a
wPt0950
0
0
1
0
1
0
0
1
0
1
wPt1261
1
0
0
1
0
1
0
0
1
1
wPt1741
1
1
1
1
1
0
1
0
0
0
wPt2087
0
0
1
1
1
1
0
1
1
0
wPt2781
0
1
1
1
0
1
1
0
1
1
wPt2813
1
1
1
1
0
1
1
0
0
0
DArT marker technology is described by Jaccoud et al. (2001) and Wenzl et al. (2004).
wPt3524
0
1
0
1
0
1
0
1
0
1
wPt5234
1
0
0
0
1
0
1
1
0
1
wPt6975
0
1
0
0
0
1
0
0
1
1
wPt9664
1
1
1
0
1
0
1
1
1
0
References
Botstein, D., White, R.L, Skolnick, M., and Davis R.W. 1980. Construction of a genetic
linkage map in man using restriction fragment length polymorphisms. American
Journal of Human Genetics 32:314-331.
Bowcock, A.M., A. Ruiz-Linares, J. Tomfohrde, E. Minch, J.R. Kidd, and L.L. CavalliSforza. 1994. High resolution of human evolutionary trees with polymorphic
microsatellites 368:455-457.
Jaccoud, D., K. Peng, D. Feinstein, and A. Kilian. 2001. Diversity Arrays: a solid state
technology for sequence information independent genotyping. Nucleic Acids
Research 29:e25-.
Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small
number of individuals. Genetics 89:583-590.
Roder, M.S., V. Korzun, K. Wendehake, J. Plaschke, M.-H. Tixier, P. Leroy, and M.W.
Ganal. 1998. A microsatellite map of wheat. Genetics 149:2007-2023.
Song, Q.J., J.R. Shi, S. Singh, E.W. Fickus, J.M. Costa, J. Lewis, B.S. Gill, R. Ward, and
P.B. Cregan. 2005. Development and mapping of microsatellite (SSR) markers in
wheat. Theor Appl Genet 110:550-60.
Wenzl, P., J. Carling, D. Kudrna, D. Jaccoud, E. Huttner, A. Kleinhofs, and A. Kilian.
2004. Diversity Arrays Technology (DArT) for whole-genome profiling of barley.
Proceedings of the National Academy of Sciences USA 101:9915-9920.