Genetics: Bio 140 Dr.

WS Turner Chapter 4 July 2nd, 2013

Class Quiz 4
1. 2. 3. 4. What does RF stand for? What is a single nucleotide polymorphism? Is a centromere a gene? What is the Perkins formula used for?

Reginald C. Punnet

William Bateson

Predicted Phenotype Ratios

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L)

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L)

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L) + P(RRLl) = P(R)P(R)P(L)P(l) + P(R)P(R)P(l)P(L)

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L) + P(RRLl) = P(R)P(R)P(L)P(l) + P(R)P(R)P(l)P(L) + P(RrLl) = P(R)P(r)P(L)P(l) + P(R)P(r)P(l)P(L) + P(r)P(R)P(L)P(l) + P(r)P(R)P(l)P(L)

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L) + P(RRLl) = P(R)P(R)P(L)P(l) + P(R)P(R)P(l)P(L) + P(RrLl) = P(R)P(r)P(L)P(l) + P(R)P(r)P(l)P(L) + P(r)P(R)P(L)P(l) + P(r)P(R)P(l)P(L)

P(RRll) = P(R)P(R)P(l)P(l) + P(Rrll) = P(R)P(r)P(l)P(l) + P(r)P(R)P(l)P(l)

Probability of Purple flower and round pollen

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L) + P(RRLl) = P(R)P(R)P(L)P(l) + P(R)P(R)P(l)P(L) + P(RrLl) = P(R)P(r)P(L)P(l) + P(R)P(r)P(l)P(L) + P(r)P(R)P(L)P(l) + P(r)P(R)P(l)P(L)

P(RRll) = P(R)P(R)P(l)P(l) + P(Rrll) = P(R)P(r)P(l)P(l) + P(r)P(R)P(l)P(l)

Probability of Purple flower and round pollen

P(rrLL) = P(r)P(r)P(L)P(L) + P(rrLl) = P(r)P(r)P(L)P(l) + P(r)P(r)P(l)P(L)

Probability of red flower and Long pollen

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L) + P(RRLl) = P(R)P(R)P(L)P(l) + P(R)P(R)P(l)P(L) + P(RrLl) = P(R)P(r)P(L)P(l) + P(R)P(r)P(l)P(L) + P(r)P(R)P(L)P(l) + P(r)P(R)P(l)P(L)

P(RRll) = P(R)P(R)P(l)P(l) + P(Rrll) = P(R)P(r)P(l)P(l) + P(r)P(R)P(l)P(l)

Probability of Purple flower and round pollen

P(rrLL) = P(r)P(r)P(L)P(L) + P(rrLl) = P(r)P(r)P(L)P(l) + P(r)P(r)P(l)P(L)

Probability of red flower and Long pollen

P(rrll) = P(r)P(r)P(l)P(l)

Probability of red flower and round pollen

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) = (0.5)(0.5)(0.5)(0.5) = 0.0625 + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L) + P(RRLl) = P(R)P(R)P(L)P(l) + P(R)P(R)P(l)P(L) + P(RrLl) = P(R)P(r)P(L)P(l) + P(R)P(r)P(l)P(L) + P(r)P(R)P(L)P(l) + P(r)P(R)P(l)P(L)

P(RRll) = P(R)P(R)P(l)P(l) + P(Rrll) = P(R)P(r)P(l)P(l) + P(r)P(R)P(l)P(l)

Probability of Purple flower and round pollen

P(rrLL) = P(r)P(r)P(L)P(L) + P(rrLl) = P(r)P(r)P(L)P(l) + P(r)P(r)P(l)P(L)

Probability of red flower and Long pollen

P(rrll) = P(r)P(r)P(l)P(l)

Probability of red flower and round pollen

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) = (0.5)(0.5)(0.5)(0.5) = 0.0625 + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L) = 2(0.0625) + P(RRLl) = P(R)P(R)P(L)P(l) + P(R)P(R)P(l)P(L) + P(RrLl) = P(R)P(r)P(L)P(l) + P(R)P(r)P(l)P(L) + P(r)P(R)P(L)P(l) + P(r)P(R)P(l)P(L)

P(RRll) = P(R)P(R)P(l)P(l) + P(Rrll) = P(R)P(r)P(l)P(l) + P(r)P(R)P(l)P(l)

Probability of Purple flower and round pollen

P(rrLL) = P(r)P(r)P(L)P(L) + P(rrLl) = P(r)P(r)P(L)P(l) + P(r)P(r)P(l)P(L)

Probability of red flower and Long pollen

P(rrll) = P(r)P(r)P(l)P(l)

Probability of red flower and round pollen

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) = (0.5)(0.5)(0.5)(0.5) = 0.0625 + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L) = 2(0.0625) + P(RRLl) = P(R)P(R)P(L)P(l) + P(R)P(R)P(l)P(L) = 2(0.0625) + P(RrLl) = P(R)P(r)P(L)P(l) + P(R)P(r)P(l)P(L) + P(r)P(R)P(L)P(l) + P(r)P(R)P(l)P(L)

P(RRll) = P(R)P(R)P(l)P(l) + P(Rrll) = P(R)P(r)P(l)P(l) + P(r)P(R)P(l)P(l)

Probability of Purple flower and round pollen

P(rrLL) = P(r)P(r)P(L)P(L) + P(rrLl) = P(r)P(r)P(L)P(l) + P(r)P(r)P(l)P(L)

Probability of red flower and Long pollen

P(rrll) = P(r)P(r)P(l)P(l)

Probability of red flower and round pollen

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) = (0.5)(0.5)(0.5)(0.5) = 0.0625 + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L) = 2(0.0625) + P(RRLl) = P(R)P(R)P(L)P(l) + P(R)P(R)P(l)P(L) = 2(0.0625) + P(RrLl) = P(R)P(r)P(L)P(l) + P(R)P(r)P(l)P(L) + P(r)P(R)P(L)P(l) + P(r)P(R)P(l)P(L) = 4(0.0625)

P(RRll) = P(R)P(R)P(l)P(l) + P(Rrll) = P(R)P(r)P(l)P(l) + P(r)P(R)P(l)P(l)

Probability of Purple flower and round pollen

P(rrLL) = P(r)P(r)P(L)P(L) + P(rrLl) = P(r)P(r)P(L)P(l) + P(r)P(r)P(l)P(L)

Probability of red flower and Long pollen

P(rrll) = P(r)P(r)P(l)P(l)

Probability of red flower and round pollen

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) = (0.5)(0.5)(0.5)(0.5) = 0.0625 + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L) = 2(0.0625) + P(RRLl) = P(R)P(R)P(L)P(l) + P(R)P(R)P(l)P(L) = 2(0.0625) + P(RrLl) = P(R)P(r)P(L)P(l) + P(R)P(r)P(l)P(L) + P(r)P(R)P(L)P(l) + P(r)P(R)P(l)P(L) = 4(0.0625)

= 9(0.0625) = .5625
Probability of Purple flower and round pollen

P(RRll) = P(R)P(R)P(l)P(l) + P(Rrll) = P(R)P(r)P(l)P(l) + P(r)P(R)P(l)P(l)

P(rrLL) = P(r)P(r)P(L)P(L) + P(rrLl) = P(r)P(r)P(L)P(l) + P(r)P(r)P(l)P(L)

Probability of red flower and Long pollen

P(rrll) = P(r)P(r)P(l)P(l)

Probability of red flower and round pollen

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) = (0.5)(0.5)(0.5)(0.5) = 0.0625 + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L) = 2(0.0625) + P(RRLl) = P(R)P(R)P(L)P(l) + P(R)P(R)P(l)P(L) = 2(0.0625) + P(RrLl) = P(R)P(r)P(L)P(l) + P(R)P(r)P(l)P(L) + P(r)P(R)P(L)P(l) + P(r)P(R)P(l)P(L) = 4(0.0625)

= 9(0.0625) = .5625
Probability of Purple flower and round pollen

P(RRll) = P(R)P(R)P(l)P(l) + P(Rrll) = P(R)P(r)P(l)P(l) + P(r)P(R)P(l)P(l)

= 3(.0625) = .1875
Probability of red flower and Long pollen

P(rrLL) = P(r)P(r)P(L)P(L) + P(rrLl) = P(r)P(r)P(L)P(l) + P(r)P(r)P(l)P(L)

P(rrll) = P(r)P(r)P(l)P(l)

Probability of red flower and round pollen

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) = (0.5)(0.5)(0.5)(0.5) = 0.0625 + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L) = 2(0.0625) + P(RRLl) = P(R)P(R)P(L)P(l) + P(R)P(R)P(l)P(L) = 2(0.0625) + P(RrLl) = P(R)P(r)P(L)P(l) + P(R)P(r)P(l)P(L) + P(r)P(R)P(L)P(l) + P(r)P(R)P(l)P(L) = 4(0.0625)

= 9(0.0625) = .5625
Probability of Purple flower and round pollen

P(RRll) = P(R)P(R)P(l)P(l) + P(Rrll) = P(R)P(r)P(l)P(l) + P(r)P(R)P(l)P(l)

= 3(.0625) = .1875
Probability of red flower and Long pollen

P(rrLL) = P(r)P(r)P(L)P(L) + P(rrLl) = P(r)P(r)P(L)P(l) + P(r)P(r)P(l)P(L)

= 3(.0625) = .1875
Probability of red flower and round pollen

P(RRll) = P(r)P(r)P(l)P(l)

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) = (0.5)(0.5)(0.5)(0.5) = 0.0625 + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L) = 2(0.0625) + P(RRLl) = P(R)P(R)P(L)P(l) + P(R)P(R)P(l)P(L) = 2(0.0625) + P(RrLl) = P(R)P(r)P(L)P(l) + P(R)P(r)P(l)P(L) + P(r)P(R)P(L)P(l) + P(r)P(R)P(l)P(L) = 4(0.0625)

= 9(0.0625) = .5625
Probability of Purple flower and round pollen

P(RRll) = P(R)P(R)P(l)P(l) + P(Rrll) = P(R)P(r)P(l)P(l) + P(r)P(R)P(l)P(l)

= 3(.0625) = .1875
Probability of red flower and Long pollen

P(rrLL) = P(r)P(r)P(L)P(L) + P(rrLl) = P(r)P(r)P(L)P(l) + P(r)P(r)P(l)P(L)

= 3(.0625) = .1875
Probability of red flower and round pollen

P(RRll) = P(r)P(r)P(l)P(l)

= 0.0625

Observed Purple Flowers Long Pollen Purple Flowers Round Pollen + Red Flowers Long Pollen + Red Flowers Round Pollen 55 381 21 284 + 21

Expected

R = purple flower r = red flower

L = long pollen l = round pollen

RrLl x RrLl
Probability of Purple flower and Long pollen

P(RRLL) = P(R)P(R)P(L)P(L) = (0.5)(0.5)(0.5)(0.5) = 0.0625 + P(RrLL) = P(R)P(r)P(L)P(L) + P(r)P(R)P(L)P(L) = 2(0.0625) + P(RRLl) = P(R)P(R)P(L)P(l) + P(R)P(R)P(l)P(L) = 2(0.0625) + P(RrLl) = P(R)P(r)P(L)P(l) + P(R)P(r)P(l)P(L) + P(r)P(R)P(L)P(l) + P(r)P(R)P(l)P(L) = 4(0.0625)

= 9(0.0625) = .5625
Probability of Purple flower and round pollen

P(RRll) = P(R)P(R)P(l)P(l) + P(Rrll) = P(R)P(r)P(l)P(l) + P(r)P(R)P(l)P(l)

= 3(.0625) = .1875
Probability of red flower and Long pollen

P(rrLL) = P(r)P(r)P(L)P(L) + P(rrLl) = P(r)P(r)P(L)P(l) + P(r)P(r)P(l)P(L)

= 3(.0625) = .1875
Probability of red flower and round pollen

P(RRll) = P(r)P(r)P(l)P(l)

= 0.0625

Observed Purple Flowers Long Pollen Purple Flowers Round Pollen + Red Flowers Long Pollen + Red Flowers Round Pollen 55 381 21 284 + 21

Expected .5625(381) = 214.31

.1875(381) =

71.44

.1875(381) =

71.44

.0625(381) =

23.81 381

Observed Purple Flowers Long Pollen Purple Flowers Round Pollen Red Flowers Long Pollen Red Flowers Round Pollen 284

Expected 214.31

2 = (O-E)2 E ( 284 - 214.31 )2 = 22.66 214.31 ( 21 - 71.44 )2 71.44 ( 21 - 71.44 )2 71.44 ( 55 - 23.81 )2 23.81 Sum is = 35.61

21

71.44

21

71.44

= 35.61

55

23.81

= 40.86 134.74

Observed Purple Flowers Long Pollen Purple Flowers Round Pollen Red Flowers Long Pollen Red Flowers Round Pollen 284

Expected 214.31

2 = (O-E)2 E ( 284 - 214.31 )2 = 22.66 214.31 ( 21 - 71.44 )2 71.44 ( 21 - 71.44 )2 71.44 ( 55 - 23.81 )2 23.81 Sum is = 35.61

21

71.44

21

71.44

= 35.61

55

23.81

= 40.86 134.74

pr = purple eyes pr+ = red eyes (wildtype)

vg = vestigal wings vg+ = wildtype wings

pr/pr vg/vg X pr+/ pr+ vg+/vg+

pr+/pr vg+/vg Testcross pr+/pr vg+/vg

female

pr/pr vg/vg
male

dihybrid

tester

Testcross pr+/pr vg+/vg

female

pr/pr vg/vg
male

What do we expect?

pr = purple eyes pr+ = red eyes (wildtype)

vg = vestigal wings vg+ = wildtype wings

Testcross pr+/pr vg+/vg

female

pr/pr vg/vg
male

What do we expect? P(pr+/pr vg+/vg) P(pr+/pr vg/vg) P(pr/pr vg+/vg) P(pr/pr vg/vg) Final genotypes

pr = purple eyes pr+ = red eyes (wildtype)

vg = vestigal wings vg+ = wildtype wings

Testcross pr+/pr vg+/vg

female

pr/pr vg/vg
male

What do we expect? P(pr+/pr vg+/vg) = P(pr+) P(pr) P(vg+) P(vg) P(pr+/pr vg/vg) = P(pr+) P(pr) P(vg) P(vg) P(pr/pr vg+/vg) = P(pr) P(pr) P(vg+) P(vg) P(pr/pr vg/vg) = P(pr) P(pr) P(vg) P(vg) Final genotypes Probability of each allele

pr = purple eyes pr+ = red eyes (wildtype)

vg = vestigal wings vg+ = wildtype wings

Testcross pr+/pr vg+/vg

female

pr/pr vg/vg
male

What do we expect? P(pr+/pr vg+/vg) = P(pr+) P(pr) P(vg+) P(vg) P(pr+/pr vg/vg) = P(pr+) P(pr) P(vg) P(vg) P(pr/pr vg+/vg) = P(pr) P(pr) P(vg+) P(vg) P(pr/pr vg/vg) = P(pr) P(pr) P(vg) P(vg) Final genotypes Probability of each allele = 0.510.51 = 0.510.51 = 0.510.51 = 0.510.51 numbers

pr = purple eyes pr+ = red eyes (wildtype)

vg = vestigal wings vg+ = wildtype wings

Observed pr+/pr vg+/vg pr/pr vg/vg pr +/pr vg/vg pr /pr vg+/vg 1339 1195 151 154 2839

Expected 709.75 709.75 709.75 709.75 2839

Observed pr+/pr vg+/vg pr/pr vg/vg pr +/pr vg/vg pr /pr vg+/vg 1339 1195 151 154 2839

Expected 709.75 709.75 709.75 709.75 2839

2 = (O-E)2 / E = (1339 - 709.75)2 + (1195 - 709.75)2 + (151 - 709.5)2 + (154-709.75)2

709.75 709.75 709.75 709.75

=1764.29

Observed pr+/pr vg+/vg pr/pr vg/vg pr +/pr vg/vg pr /pr vg+/vg 1339 1195 151 154 2839

Expected 709.75 709.75 709.75 709.75 2839

Overrepresented pr+/pr vg+/vg pr/pr vg/vg pr +/pr vg/vg pr /pr vg+/vg

Observed 1339 1195 151 154 2839

Expected 709.75 709.75 709.75 709.75 2839

Overrepresented pr+/pr vg+/vg pr/pr vg/vg pr +/pr vg/vg pr /pr vg+/vg

Observed 1339 1195 151 154 2839

Expected 709.75 709.75 709.75 709.75 2839

pr+ and vg+ are physically linked because they are on the same chromosome pr and vg are physically linked because they are on the same chromosome

Overrepresented pr+/pr vg+/vg pr/pr vg/vg pr +/pr vg/vg pr /pr vg+/vg

Observed 1339 1195 151 154 2839

Expected 709.75 709.75 709.75 709.75 2839

pr+ and vg+ are physically linked because they are on the same chromosome pr and vg are physically linked because they are on the same chromosome

Number of Recombinants Total Number of Progeny

= distance in m.u.

m.u. = map unit or centimorgan

Observed pr+/pr vg+/vg pr/pr vg/vg pr +/pr vg/vg pr /pr vg+/vg Recombinants 151 + 154 2839 1339 1195 151 154 2839

Expected 709.75 709.75 709.75 709.75 2839

= 0.107 = ~11%

= 11 m.u. apart

Three point test cross Parents v+/v+ cv/cv ct/ct X v/v cv+/cv+ ct+/ct+ Gametes v+ cv ct F1 trihybrid v+/v cv+/cv ct+/ct Testcross v+/v cv+ /cv ct+ /ct X v/v cv/cv ct/ct v cv+ ct+

v+/v cv+ /cv ct+ /ct X v/v cv/cv ct/ct Gametes v cv+ ct+ v+ cv ct v cv ct+ v + cv+ ct v cv ct v + cv+ ct+ v cv+ ct v + cv ct+ Recombinant for loci v and cv v and ct cv and ct 580 592 45 40 89 94 3 5

v+/v cv+ /cv ct+ /ct X v/v cv/cv ct/ct Gametes v cv+ ct+ v+ cv ct v cv ct+ v + cv+ ct v cv ct v + cv+ ct+ v cv+ ct v + cv ct+ Recombinant for loci v and cv v and ct cv and ct 580 592 45 40 89 94 3 5 1448

R R R R

R R R R R R 191

R R 93

268

Map distance between v and cv 268 = .185 =18.5%=18.5map units 1448 v and ct 191 =.132 = 13.2% = 13.2 map units 1448 cv and ct 93 = .064 = 6.4% =6.4 map units 1448

Map distance between v and cv 18.5 map units v and ct 13.2 map units cv and ct 6.4 map units

What is the order?

Map distance between v and cv 18.5 map units v and ct 13.2 map units cv and ct 6.4 map units

What is the order? v and cv are the farthest apart because the most map units separate them ct sits between them and is 6.4 mu from cv and 13.2 mu from v and ct

Map distance between v and cv 18.5 map units v and ct 13.2 map units cv and ct 6.4 map units

What is the order? v and cv are the farthest apart because the most map units separate them ct sits between them and is 6.4 mu from cv and 13.2 mu from v and ct Why dont they add up? You have to count the double recombinants twice to compute the distance between the outer genes.

v+/v cv+ /cv ct+ /ct X v/v cv/cv ct/ct Gametes v cv+ ct+ v+ cv ct v cv ct+ v + cv+ ct v cv ct v + cv+ ct+ v cv+ ct v + cv ct+ Recombinant for loci v and cv v and ct cv and ct 580 592 45 40 89 94 3 5 1448

R R R R

R R R R R R 191

R R 93

268

Interference

Observed frequency of double recombinants I = 1Expected frequency of double recombinants

Mapping with Molecular Markers

Single Nucleotide Polymorph
Simple Sequence Length Polymorph

 Some bands of a DNA fingerprint show linkage

Figure 4-18

 A microsatellite locus can show linkage to a disease gene Figure 4-15b

Centromere Mapping
Species Specific
Why?

Homework 4:
Chapter 4:
Define: Cis formation, double-stranded break, genetic map unit, linked genes, null hypothesis, recombination frequency Basic Problems: 3, 12, 14, 17, 20, 28 Due July 9nd, 2013 at the beginning of class

Things to keep in mind when using the Chi-Square Test

The probability obtained from the Chi-Square test is the probability of observing a deviation from the expected results at least this large based on chance. The Chi-Square only allows us to reject hypotheses. It doesnt prove that they are true. The Chi-square test is heavily dependent on sample size. Therefore, you have to use actual numbers rather than fractions, ratios, or percentages