GENETIC LINKAGE

Exam 2 Lecture 4

UIC BioS 101 Nyberg

GENETIC LINKAGE

Genes are connected together in a linear order on chromosomes.

The connectedness means all possible gametic genotypes are not produced EQUALLY frequently.

Speaker Notes:

While many loci are linked together, linkage is measured between a PAIR of loci.

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UIC BioS 101 Nyberg

Independent Assortment

In a double heterozygote, AaBb, which includes both Ab/aB and AB/ab, independent assortment means that the segregation of A and a is independent of the segregation of B and b, i.e., the AB, Ab, aB & ab arrangements in the gametes are expected to be equally frequent.

Speaker Notes:

All the pairs of loci Mendel studied assorted independently.

Exam 2 Lecture 4

UIC BioS 101 Nyberg

LINKAGE

Two (or more) loci have to be heterozygous to ‘see’ linkage (in transmission genetics).
Linkage is non-independent assortment of alleles at separate loci during meiosis.
Linkage is a reflection of the fact that loci occupy specific places on the DNA of chromosomes.

Speaker Notes:

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UIC BioS 101 Nyberg

LINKAGE & parental types

An individual produces more gametes that have its parental configuration than it produces gametes with one allele from the father and one from the mother.

An Ab/aB individual will produce more Ab and aB gametes (the arrangement in the gametes that united to form it, and therefore called parental) than AB and ab gametes (which are called recombinants).

Speaker Notes:

In an AB/ab individual which two gametic types are parental?

Meiosis with no crossover

Exam 2 Lecture 4

UIC BioS 101 Nyberg

Speaker Notes:

Figure 13.12 p 278

Exam 2 Lecture 4

UIC BioS 101 Nyberg

Recombination fraction, r, is a variable with a different value for each pair of loci.

The closer together two loci are the less the proportion of recombinant types.
r takes values between 0 and ½.

Speaker Notes:

You must estimate r separately for each pair of loci. The loci proved to be in a linear order.

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UIC BioS 101 Nyberg

Estimating r & map distance

For a pair of loci, the expected proportion of the two parental types is 1 – r, and the expected proportion of two recombinant types will sum to r.
Each parental type is expected to be equally frequent, so each type =(1-r)/2.
Each recombinant type has the expected frequency of r/2.

Speaker Notes:

The following slides show how to estimate r. The two parental types are expected to be equal in frequency. Both recombinant types are expected to be equally frequent.

r = (86+44)/(86+44+4292+4605)= 0.014, so 1.4 map units

Exam 2 Lecture 4

UIC BioS 101 Nyberg

Speaker Notes:

Fig. 13.13 p279

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UIC BioS 101 Nyberg

Gamete production in a double heterozygote.

We will use H and Q as symbols for the loci.

Hq/hQ is diploid genotype

Possible gametes Hq HQ hq hQ

Parental YES NO NO YES

Recombinant YES YES

Expected proportions (1-r)/2 r/2 r/2 (1-r)/2

Complete Linkage ½ 0 0 ½

(r = 0.000…)

Independent (r = ½) ¼ ¼ ¼ ¼

Assortment

Speaker Notes:

What is the sum of the two parental types?

Exam 2 Lecture 4

UIC BioS 101 Nyberg

An Example of Linkage

We will look at an example from the pea.
To look at linkage we have to have two loci, so normally we have variation in two different characters.
Variety K TALL PUBESCENT leaves
Variety L SHORT GLABROUS leaves
F1 is TALL PUBESCENT

Speaker Notes:

All capital letters means a PHENOTYPE. As these are peas they are expected to be homozygous at all loci.

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Linkage of height and hairiness

Variety K TALL PUBESCENT
- SSGG
Variety L SHORT GLABROUS
- ssgg
The F1 genotype SG/sg slash notation
Possible gametic genotypes of F1:
- SG Sg sG sg
Expected proportions:
- ¼ ¼ ¼ ¼

Speaker Notes:

These are the expected values given the assumption of independent assortment.

Exam 2 Lecture 4

UIC BioS 101 Nyberg

EVALUATING GAMETIC PROPORTIONS with test cross

The most efficient way to determine the proportions of the F1 gametes that are of each type is to cross the F1 to the double recessive, ssgg, in this case.

F1 gametic genotypes

SG Sg sG sg

TALL

PUBESCENT

TALL

GLABROUS

SHORT

PUBESCENT

SHORT

GLABROUS

Speaker Notes:

The homozygous recessive produces only one type of gamete, sg, thus there is a single row.

Exam 2 Lecture 4

UIC BioS 101 Nyberg

Observed proportions are not compatible with equal amounts of each gametic genotype.

TALL

PUBESCENT

TALL

GLABROUS

SHORT

PUBESCENT

SHORT

GLABROUS

OBS

EXP

100

178

182

100

χ2 = (78)2/100 + (-82)2/100 + (-78)2/100 + (82)2/100

χ2 = 256, df = 3, Critical Value = 7.82 (α =0.05), so hypothesis of independent assortment is rejected.

N =400

Speaker Notes:

It is clear there is a great deficiency of TALL GLABROUS and SHORT PUBESCENT progeny.

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UIC BioS 101 Nyberg

Expected equalities

Two parental gametes about equally frequent and two recombinant types are also about equally frequent.
If that equality is not true, then one should suspect differential viability of the types or some other process.

Speaker Notes:

Check to see if the 2 parental types are equal and if the two recombinant types are equal.

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UIC BioS 101 Nyberg

Getting a Value for r

r = the proportion of the gametes that have recombinant genotypes.

r = # recombinant gametes/total # of gametes

r = (18 +22)/(178 + 18 + 22 + 182)

r = (40)/(400) = 0.10

Value of map units is 100 times r. In this case, the height locus and leaf hairiness locus are 10 map units apart.

Speaker Notes:

Add the two recombinant classes and divide by the total number observed.

Exam 2 Lecture 4

UIC BioS 101 Nyberg

If the F1 had Sg/sG genotype then the following is a typical result.

TALL

PUBESCENT

TALL

GLABROUS

SHORT

PUBESCENT

SHORT

GLABROUS

OBS

EXP

136

130

N =300

In this case, the parental gametes are Sg & sG and the recombinant gametes are SG & sg. In this example r is estimated to be 0.113 = 34/300, a small amount larger than the 10 map unit estimate of the original data.

Speaker Notes:

The two reciprocal types are either parental or recombinant.

Exam 2 Lecture 4

UIC BioS 101 Nyberg

Speaker Notes:

Fig. 13.15 p 280

Exam 2 Lecture 4

UIC BioS 101 Nyberg

Crossing over in 3 linked loci

Consider the genotype Hqr/hQR
Eight possible gametic genotypes can be produced
- HQR, HQr, HqR, Hqr, hQR, hQr, hqR & hqr
There are only two parental types no matter how many loci are considered, in this case the parental types are Hqr & hQR

Speaker Notes:

For each heterozygous locus two types can be produced. To get the total number of different types multiply the types possible at each locus. For 3 heterozygous loci there are 8 possible gametic genotypes.

3 linked loci (ordered HQR)

If a single crossover occurs between the H locus and the Q locus the resulting gametes will be HQR & hqr.
If a single crossover occurs between the R locus and the Q locus the resulting gametes will be HqR & hQr.
The only way to get HQr & hqR (the remaining 2) is to have crossovers between H & Q and between Q and R.

Exam 2 Lecture 4

UIC BioS 101 Nyberg

Speaker Notes:

Exam 2 Lecture 4

UIC BioS 101 Nyberg

Ordering loci on a chromosome

The recombination fraction, r, has been estimated for 5 pairs of 4 loci.
ED = 6 map units
IT = 2 map units
DT = 6 map units
DI = 4 map units
EI = 10 map units

Speaker Notes:

An r value of 0.01 is equal to one map unit.

Exam 2 Lecture 4

UIC BioS 101 Nyberg

CONSTRUCTING THE MAP

Start with the closest pair, {IT}. Use either the order TI or IT. The D locus could be to the right or the left, i.e., DIT or ITD. The distance information indicates that D is closer to I than to T, so correct order is DIT or TID.

Where does the E locus fit in?

E is closer to D than it is to I so the order must be EDIT, or TIDE as we have no “anchor” to establish left to right.

E D I T

6 4 2

| 10 |

| 6 |

Speaker Notes:

Go thru this in lecture.

Exam 2 Lecture 4

UIC BioS 101 Nyberg

Bacterial GENES

In bacteria the genes are all linked together into a single large circle.

Speaker Notes:

While the bacterial DNA is often called a chromosome, this term is not really approriate.

Exam 2 Lecture 4

UIC BioS 101 Nyberg

Bacterial SEX

In bacteria sex does not involve the union of two equal (more or less) genomes. Instead, one cell serves as a donor and the other cell functions as a recipient. Typically only part of the genome is transferred.

Speaker Notes:

The transfer is normally done in a particular order.

Exam 2 Lecture 4

UIC BioS 101 Nyberg

LINKAGE RECAPITULATION

Among gametes there is always an excess of the two parental arrangements of genes when the loci are linked.
Studies of many pairs of loci lead to the realization that all genes were arranged in a linear order.
The order of the loci is the same in all individuals in a species.

Speaker Notes:

Exam 2 Lecture 4

UIC BioS 101 Nyberg

Vocabulary

Recombination fraction
Parental gametic type
Recombinant gametic type
Double heterozygote
chromosome

Slash notation
Meiosis
Map unit
Sex linkage
Sex determination
mapping

Speaker Notes:

Knowing how to estimate r is important.