Extra Credit

Are the b and vg genes on the

same chromosome?

If so, how far apart are they?

A B C—•—————————

—•————————— a b c

Multiple crossovers can be useful for mapping three

genes at a time!

A B Ca b c

A B C—•—————————

—•————————— a b c

A b Ca B c

3 recessive phenotypes in maize (corn), coded by three

linked genes

l l lazy or prostrate growthg g glossy leavess s sugary endosperm

To map the genes, mate a triple heterozygote to triple

recessive homozygote

Ll Gg Ss x ll gg ss

Gene order is not known,so the order shown here is arbitrary.

Linkage phase is not know

How many different kinds of gametes do you get from triple

heterozygote?

L or l G or g S or s 2 * 2 * 2

Ll Gg Ss

L G S / l g s x l g s / l g sRecomb.Wildtpe for all lazy, gloss, sugary

Where to begin?

Parental types will constitute ≥ 50% of all progeny, so…

Rule 1

Two most-frequent gametes types are the parental types

Tells us the linkage phase of heterozygous parent:

L G S or L g S or l g S or L g s

l g s l G s L G s l G S

L G S // l g s x l g s // l g s

Linkage phase in heterozygous parent?

L G S or L g S or l g S or L g sl g s l G s L G s l G

S

Rule 2

The double-recombinant gametes will be the two least frequent types

A B C

a b c

L G S / l g s x l g s / l g s

Rule 3

Effect of double crossovers is to interchange the members of the middle pair of alleles between the chromosomes

A B C

a b c

A b C

a B c

Double-crossover types:L G s and l g S

Which gene is in the middle?

L s G

l S g

Parental types:L G S and l g s

L S G

l s g

Now you know linkage phase of heterozygous parent and

gene order

L S Gl s g

How far apart are the genes?

Count the crossovers between adjacent genes

• In parents, L allele on same homolog as S and l on same homolog as s. So if these get broken up ---> crossover between L and S loci

• In parents, S on same homolog as G and s on same homolog as g. If these get broken up --> recombination between S and G loci

L S Gl s g

ProgenyPhenotype

ProgenyGenotype #

Crossover or Non-Crossover?

wildtype L G S / l g s 286 Parental (NCO)

lazy l G S / l g s 33 si ngle CO be twee n L and S

gloss y L g S / l g s 59 si ngle CO be twee n S and G

s uga ry L G s / l g s 4 double CO

lazy,gl ossy l g S / l g s 2 double CO

lazy,su gary l G s / l g s 44 si ngle CO be twee n S and G

gloss y,s uga ry L g s / l g s 40 si ngle CO be twee n L and S

lazy,gl ossy ,su gary l g s / l g s 272 Parental (NCO)

Total 740

L S Gl s g

Rule 4: Reciprocal products expected to occur in approximately equal numbers

LGS ≈ lgs (286 ≈ 272) LgS ≈ lGs (59 ≈ 44) Lgs ≈ lGS (40 ≈ 33)LGs ≈ lgS (4 ≈ 2)

Rule 5

Don't forget to include the double recombinants when calculating

recombination frequency!

l G S 33L g s 40

L G s 4l g S 2

79

Rec Freq L-S Rec Freq S-GL g S 59l G s 44L G s 4l g S 2

109

ProgenyPhenotype

ProgenyGenotype #

Crossover or Non-Crossover?

wildtype L G S / l g s 286 Parental (NCO)

lazy l G S / l g s 33 si ngle CO be twee n L and S

gloss y L g S / l g s 59 si ngle CO be twee n S and G

s uga ry L G s / l g s 4 double CO

lazy,gl ossy l g S / l g s 2 double CO

lazy,su gary l G s / l g s 44 si ngle CO be twee n S and G

gloss y,s uga ry L g s / l g s 40 si ngle CO be twee n L and S

lazy,gl ossy ,su gary l g s / l g s 272 Parental (NCO)

Total 740

79/740 or 10.7% of gametes recombinant between L & S. So,

map distance between L & S = 10.7 map units

109/740 or 14.8 % of gametes recombinant between S & G. So, map distance between S & G=14.8 map units

l G S 33L g s 40

L G s 4l g S 2

79

Rec Freq L-S

Rec Freq S-GL g S 59l G s 44L G s 4l g S 2

109

Genetic Map

10.7 mu 14.8 mu_____________________________

L S G

Interference

Assuming independence, expected probability of double crossovers is the probability of recombination in one region times the probability of recombination in other (product rule).

Maize exampleProbability of recombination between L and S is 10.7% Probability of recombination between S and G is 14.8%

If crossovers independent, probability of double crossover should then be

0.107 * 0.148 = 0.0158

In 740 events, the double crossover class should occur

0.0158 * 740 = 12 times

Expected DCO = 12Observed DCO = 6

Typical Result: O < E

Conclusion: Crossing over in one region reduces probability of crossing over in adjacent regions

This is Interference

Why?

Physical constraints that prevent two chiasmata in close proximity during meiosis?

Quantifying Interference

Coefficient of coincidence = Obs DCOExp DCO

cc = 6/12

Interference = (1 - cc) = 1 - 0.5 = 0.5

Recombination is not independent at small distancesIf distance between genes is small (<10

map units in Drosophila) no double crossovers occur (interference is complete, I=1)

At large distances (> 45 map units, Interference disappears, Obs = Exp and I=0

In Drosophila, the allele b gives black body (wild type is tan); at a separate gene, the allele wx gives waxy wings (nonwaxy is wild type); and at a third gene, the allele cn gives cinnabar eyes (red is wild type). A female that is heterozygous for these three genes is testcrossed, and 980 progeny are classified as follows for body color, wing phenotype, and eye color:

Extra Credit Question for Next Time

PhenotypeHaploid

Genotype Numberbrown, nonwaxy, red + + + 6black, waxy, cinnabar b wx cn 6brown, waxy, cinnabar + wx cn 79black, nonwaxy, red b + + 77brown, nonwaxy, cinnabar + + cn 369black, waxy, red b wx + 369brown, waxy, red + wx + 38black, nonwaxy, cinnabar b + cn 36

a) What is the linkage phase of the heterozygous female parent?

b) What is the order of the three genes?

c) Construct a linkage map with the genes in their correct order and indicate the map distances between the genes.

d) Calculate the Interference.

Where to begin?Recombinant genotypes of all sorts will

constitute <= 50% of all progeny

0% Rec

50% Rec 100% Rec

50% Rec

50% Rec

Three-locus

mapping

To map the genes, mate a triple heterozygote to triple

recessive homozygoteL G S x l g s

l g s l g s

Gene order is not known, so the order shown here is arbitrary

Multiple crossovers can lead to inaccuracy

A C—•—————————

—•————————— a c

B

b