Week 4
Ch 4
Genetics maps are useful for strain building, for interpreting evolutionary
mechanisms, and for discovering a gene’s unknown function.
Discovering a gene’s function is facilitated by integrating information on
recombination-based and physical maps
4.1 diagnostics of linkage
When two genes are close together on the same chromosome pair (that is, when they
are linked), they do not assort independently but produce a recombinant frequency of
less than 50 percent. Hence, a recombinant frequency of less than 50 percent is a
diagnostic for linkage
Two equally frequent nonrecombinant classes totaling in excess of 50 percent
Two equally frequent recombinant classes totaling less than 50 percent
For linked genes, recombinants are produced by crossovers between nonsister
chromatids during meiosis. (the two new combinations are called crossover products)
Chiasmata are the visible manifestations of crossovers (a cross-shaped structure
often formed between two nonsiters chromatids)
Crossovers produce recombinants for linked genes
o Homologous chromosomes pair at meiosis
o Chromosomes get ds DNA breaks
o Ds breaks are repaired by recombination between non-sister chromatids
o crossing over visible as a chiasma (chiasmata)
o Each chromosome pair has at least 1, often a few chiasmata
o Very precise process: recombination does not introduce mutations
Cis conformation: in a heterozygote having two mutant sites within a gene or within a
gene cluster, the arrangement AB/ab
Trans conformation: in a heterozygote with two mutant sites within a gene or gene
cluster, the arrangement Ab/aB
A crossover is the breakage of two DNA molecules at the same position and their
regioning in two reciprocal recombinant combinations
Non crossover: only parental type gametes
Single crossover: 2 parental and 2 recombinant type gametes
Reciprocal types are equally frequent: the proportion of recombinants correlates to
the distance separating two gene loci on a chromosome map
If 10% of meiosis there is crossing over between A-B, there will be 5% recombinant
meiotic products
Multiple (two or more) crossovers can produce both recombinant and parental
chromatids (so you can have crossing over between just two chromomes or three or
four making a difference in what new genotypes can be created)
If you cross ABC x abc (for example)
o Two: ABC, AbC, aBc and abc
o Three: ABc, abC, aBC, abc
o Four: ABc, Abc, aBC, abC
4.2 mapping by recombinant frequency
The farther apart the genes are, the more likely that a crossover will take place and
the higher the proportion of recombinant products will be
, Thus the proportion of recombinants is a clue to the distance separating two gene loci
on a chromosome map
Recombinant frequencies for different linked genes range from 0 to 50%, depending
on their closeness (farther apart closer to 50%)
Distance in m.u. based on recombinant fraction of markers ABC
o A-B: 2/16 = 0,125 12,5% rec = 12.5 cM
o B-C 6/16 = 0,375 37,5% rec = 37,5 cM
o A-C ong 50 cM (12,5 + 37,5)
Distance based on average chiasma frequency (better)
o A-B: ¼ chiasma/meiosis 1/4x50 cM = 12,5 cM
o B-C: 1 chiasma/meiosis 1x50cM = 50 cM
o A-C ong. 62,5 cM
A region with 1 crossover on average has a genetic distance of 50 cM, so 66 cM
results from 66/50 = 1,3 crossovers on average per meiosis 1 or 2 per meiosis
expected for this chromosome
Linkage map: a chromosome map; an abstract map of chromosomal loci that is
based on recombinant frequencies
The greater the chance of crossovers in the region between the genes the greater the
proportion of recombinants that would be produced
Thus by determining the frequency of recombinants, we can obtain a measure of the
map distance between the genes
Recombination between linked genes can be used to map their distance apart on a
chromosome. The unit of mapping (1 m.u.) is defined as a recombinant frequency of
1 percent. Map distances are roughly additive
Three-point (and higher) trestcrosses enable geneticist to
evaluate linkage between three (or more) genes and to
determine gene order, all in one cross
Single gene inheritance and two-gene inheritance (linked
and unlinked) can be inferred form diagnostic phenotypic
ratios in both selfing and testcrossing
4.3 mapping with molecular markers
Molecular markers: a DNA sequence variant that can be
used to map an interesting phenotype to a specific region
of DNA
Loci of any DNA heterozygosity can be mapped and used as molecular chromosome
markers or milestones
4.4 using the chi-square test to infer linkage
The chi-square test is useful in testing the significance of deviations form a 1:1:1:1
ratio in deducing linkage between two genes
Interference: are crossovers in adjacent regions independent evens, or does c.o. in
one region affect the likelihood of c.o. in the other region?
Generally, there is interference inhibition of nearby crossovers interference (I)
I = 1 – observes number of DCO/expected number of DCO
o Observed: 8
o Distance between v-ct = 13,2 and ct-cv = 6.4
o Total amount of gametes: 1448
o So I = 1- (8/(0,132x0,064x1448) = 1/3
Ch 4
Genetics maps are useful for strain building, for interpreting evolutionary
mechanisms, and for discovering a gene’s unknown function.
Discovering a gene’s function is facilitated by integrating information on
recombination-based and physical maps
4.1 diagnostics of linkage
When two genes are close together on the same chromosome pair (that is, when they
are linked), they do not assort independently but produce a recombinant frequency of
less than 50 percent. Hence, a recombinant frequency of less than 50 percent is a
diagnostic for linkage
Two equally frequent nonrecombinant classes totaling in excess of 50 percent
Two equally frequent recombinant classes totaling less than 50 percent
For linked genes, recombinants are produced by crossovers between nonsister
chromatids during meiosis. (the two new combinations are called crossover products)
Chiasmata are the visible manifestations of crossovers (a cross-shaped structure
often formed between two nonsiters chromatids)
Crossovers produce recombinants for linked genes
o Homologous chromosomes pair at meiosis
o Chromosomes get ds DNA breaks
o Ds breaks are repaired by recombination between non-sister chromatids
o crossing over visible as a chiasma (chiasmata)
o Each chromosome pair has at least 1, often a few chiasmata
o Very precise process: recombination does not introduce mutations
Cis conformation: in a heterozygote having two mutant sites within a gene or within a
gene cluster, the arrangement AB/ab
Trans conformation: in a heterozygote with two mutant sites within a gene or gene
cluster, the arrangement Ab/aB
A crossover is the breakage of two DNA molecules at the same position and their
regioning in two reciprocal recombinant combinations
Non crossover: only parental type gametes
Single crossover: 2 parental and 2 recombinant type gametes
Reciprocal types are equally frequent: the proportion of recombinants correlates to
the distance separating two gene loci on a chromosome map
If 10% of meiosis there is crossing over between A-B, there will be 5% recombinant
meiotic products
Multiple (two or more) crossovers can produce both recombinant and parental
chromatids (so you can have crossing over between just two chromomes or three or
four making a difference in what new genotypes can be created)
If you cross ABC x abc (for example)
o Two: ABC, AbC, aBc and abc
o Three: ABc, abC, aBC, abc
o Four: ABc, Abc, aBC, abC
4.2 mapping by recombinant frequency
The farther apart the genes are, the more likely that a crossover will take place and
the higher the proportion of recombinant products will be
, Thus the proportion of recombinants is a clue to the distance separating two gene loci
on a chromosome map
Recombinant frequencies for different linked genes range from 0 to 50%, depending
on their closeness (farther apart closer to 50%)
Distance in m.u. based on recombinant fraction of markers ABC
o A-B: 2/16 = 0,125 12,5% rec = 12.5 cM
o B-C 6/16 = 0,375 37,5% rec = 37,5 cM
o A-C ong 50 cM (12,5 + 37,5)
Distance based on average chiasma frequency (better)
o A-B: ¼ chiasma/meiosis 1/4x50 cM = 12,5 cM
o B-C: 1 chiasma/meiosis 1x50cM = 50 cM
o A-C ong. 62,5 cM
A region with 1 crossover on average has a genetic distance of 50 cM, so 66 cM
results from 66/50 = 1,3 crossovers on average per meiosis 1 or 2 per meiosis
expected for this chromosome
Linkage map: a chromosome map; an abstract map of chromosomal loci that is
based on recombinant frequencies
The greater the chance of crossovers in the region between the genes the greater the
proportion of recombinants that would be produced
Thus by determining the frequency of recombinants, we can obtain a measure of the
map distance between the genes
Recombination between linked genes can be used to map their distance apart on a
chromosome. The unit of mapping (1 m.u.) is defined as a recombinant frequency of
1 percent. Map distances are roughly additive
Three-point (and higher) trestcrosses enable geneticist to
evaluate linkage between three (or more) genes and to
determine gene order, all in one cross
Single gene inheritance and two-gene inheritance (linked
and unlinked) can be inferred form diagnostic phenotypic
ratios in both selfing and testcrossing
4.3 mapping with molecular markers
Molecular markers: a DNA sequence variant that can be
used to map an interesting phenotype to a specific region
of DNA
Loci of any DNA heterozygosity can be mapped and used as molecular chromosome
markers or milestones
4.4 using the chi-square test to infer linkage
The chi-square test is useful in testing the significance of deviations form a 1:1:1:1
ratio in deducing linkage between two genes
Interference: are crossovers in adjacent regions independent evens, or does c.o. in
one region affect the likelihood of c.o. in the other region?
Generally, there is interference inhibition of nearby crossovers interference (I)
I = 1 – observes number of DCO/expected number of DCO
o Observed: 8
o Distance between v-ct = 13,2 and ct-cv = 6.4
o Total amount of gametes: 1448
o So I = 1- (8/(0,132x0,064x1448) = 1/3
