syntenic genes
Genes located on the same chromosome
-so close together that alleles cannot assort independently
Genetic linkage
-can be quantified to map the positions of genes on chromosomes
Alleles of syntenic genes can be reshuffled when crossing over occurs between homologs to produce ______________
recombinant chromosomes
Homologs that do not reshuffle alleles under study are called-
parental chromosomes or nonrecombinant chromosomes
plots the positions of genes on chromosomes
Genetic linkage mapping
crossing over occurs during-
prophase I of meiosis
an organism that exhibits complete linkage [rare]
-drosophila males have no crossing over
true or false: The two parental types are approximately equal in frequency, as are the two recombinant types
TRUE
r [recombination frequency]=
r= # recombinant gametes / total # meioses
crossing over occurs at a ____ rate between genes that are further apart [lower/higher]
Crossing over occurs at a higher rate between genes that are farther apart, and a lower rate between genes that are closer together
-higher rate = higher frequency
______ suggested that nonparental allele combinations resulted from recombination between the X chromosomes of the heterozygous female parent
Morgan
-X linked gene for eye/wing in Drosophila
map units (m.u.) vs centiMorgan (cM) vs recombination frequency
1 m.u. = 1 cM = 1% recombination
three-point test-cross analysis
-allows you to map 3 linked genes simultaneously
-
what crossover event is least frequent in 3-point test-cross?
-double crossover
-both events must occur
_________ can be used to determine gene order
double recombinants, or double crossover
-only one allele is different; this is the middle gene
-list in each of 3 possible orders
when calculating recombination frequencies, for the larger distance, the double crossover progeny are-
-added twice because each represents 2 crossovers between them
interference [I]
I=1-c
-the double crossovers expected but not produced
-negative interference produces more double crossovers than expected
coefficient of coincidence [c]=
observed double crossovers/expected double crossovers
Creighton and McClintock
-obtained cytological evidence that recombination between the genes was accompanied by physical exchange between the homologs
-fragment on one end of chromosome knob on other
why are genes that are closer together less likely to recombine?
-the closer the genes are, the less likely a recombination nodule will form between them
upper limit to recombinant gametes-single crossovers
-single crossover produces 50% recombinant gametes and 50% parental
-all 4 possible single crossovers result in same recombinant gametes
upper limit: Two-strand double crossovers
produce ONLY PARENTAL gametes
upper limit: Three-strand double crossovers
produce 50% parental and 50% recombinant gametes
upper limit: Four-strand double crossovers
produce all recombinant gametes
-recombination LIMIT is 50%
what is recombination limit? why?
50%
-Once genes are far enough apart to produce recombination frequencies of 50%, the pattern of segregation is that expected of independent assortment
Intragenic recombination
infrequent event in which crossing over occurs within a gene
what can affect recombination frequency?
age, environment, and sex
-dietary levels of metal ions can affect crossover in flies
mapping function [based on Poisson distribution]
-does not account for interference
-can be used to correlate the frequency of crossover with the actual number of crossover events
allelic phase
-the arrangement of alleles of linked genes on parental chromosomes
-obstacle for mapping human genes
-can be determined when disease-causing allele segregates with known genetic marker
LOD score
-logarithm of the odds ratio
-determines theta value
-sum all lod scores for each theta value to get Zmax
-higher than 3.0=linkage at theta value
-less than -2.0=significant evidence against genetic linkage
-between -2.0 and 3.0 are inconclusive
odds ratio
-numerator=likelihood that distribution of genotypes and phenotypes in pedigree is produced by genetic linkage
-denominator=chance that it is produced by independent assortment
theta value
-range 0-.50
Zmax
-corresponds to the recombination frequency that is most likely to be correct
haplotype
-specific array of alleles in a set of linked genes on a single chromosome
-these alleles tend to be passed on together during meiosis
-may consist of any combination of linked genes with genetic variation
linkage equilibrium
genotype for a chromosome at one gene is expected to be independent of its genotype for other genes
linkage disequilibrium
certain haplotypes are maintained in a population, usually due to natural selection
The diploid cells undergo meiosis to produce four haploid ______ in a sac called an _____
four haploid ASCOSPORES in a sac called an ASCUS
tetrad
The four ascospores in an ascus
In lab studies, the ascospores can be removed from the ascus and cultured to determine their genotypes; this process is called-
tetrad analysis
parental ditypes (PD)
-Assuming no crossover between the homologs, ascospores produced by one of these arrangements contain the same alleles as the original parent strains
-also 2-strand double crossover [no recombination]
The ascospores produced by the second arrangement will contain alleles in different combinations from the original parent strains, called a ______
nonparental ditype (NPD)
-forming only when 4-strand double crossovers take place
If a single crossover occurs between either of the homolog pairs, a _______ is produced, containing two parental spores and two nonparental spores
tetratype (TT)
tetratypes are [more/less] frequent than PD
less frequent
-->NPD are even less frequent
recombination frequency=
r=[.5TT]+[NPD]/total tetrads
-only half TT spores are recombinant
arrangement of daughter spores reflects the orientation of alleles carried by each chromatid in metaphase I
ordered ascus
second-division segregation pattern
-In a heterozygous meiocyte, if a crossover occurs between the gene and the centromere, the alleles segregate at meiosis II when sister chromatids segregate
each ascus contains 4 parentals and 4 recombinant spores
true or false: homologous crossover occurs sometimes during mitosis
TRUE
the arrangement of alleles of linked genes on homologous parental chromosomes
allelic phase
ascus (ascospore)
sac-like structure containing haploid gametes (ascospore)
Why are double crossover progeny the least frequent of all progeny classes?
Both crossover events must occur simultaneously to produce double recombinants
Double recombinants =
double crossovers
[3 Patterns of double crossover btw two genes]
Produces no recombinants
Two-strand double crossover
[3 Patterns of double crossover btw two genes]
Half of all gametes are recombinant
Three-strand double crossover
[3 Patterns of double crossover btw two genes]
All gametes are recombinant
Four-strand double crossover
The smallest proportions of recombinant chromosomes are associated with
the most tightly linked genes
Recombination proportions increase as
the distance between genes becomes greater
Recombination frequencies between linked genes can increase up to ___% as the distance between genes gets larger
50
Recombination frequencies between linked genes can increase up to 50% as the distance between genes gets larger, and the corresponding frequency of parental chromosomes decreases to ___%
50
Most instances of genetic linkage produce substantially more than what percentage of parental and non-parental chromosomes
>50% parental chromosomes
<50% nonparental
First-division segregation
lack of recombination between a locus and its centromere
A linear pattern of spore phenotypes within an ordered ascus for a particular allele pair, produced when the alleles go into separate nuclei at the first meiotic division, showing that no crossover has occurred between that allele pair and the centromere.
First-division segregation
Number of spores in an ascus after meiosis 2 for Ascomycetes species
4 member unordered asucs
Number of spores in an ascus after mitosis for Neurospora crassa species
8 member ordered ascus
Mitotic crossing over is
rare
Mitotic crossing over produces
patches of tissues with unusual phenotype
Complete genetic linkage
Expect the F1 progeny to produce gametes like:
All gametes contain parental chromosomes
Incomplete genetic linkage (crossover in 20% of gametes)
Expect the F1 progeny to produce gametes like:
Parental gametes are 80%
Recombinant gametes are 20% for these genes
Incomplete genetic linkage (crossover in 40% of gametes)
Expect the F1 progeny to produce gametes like:
Parental gametes are 60%
Recombinant gametes are 40% for these genes
the random distribution into gametes of alleles of linked genes achieved by crossing over between the genes
linkage equilibrium
the nonrandom distribution into gametes of alleles of linked genes
linkage disequilibrium
Tetrad formation w/linked genes
No crossover
Parental ditype (PD)
4 parentals
Tetrad formation w/linked genes
Single crossover
Tetra type (TT)
2 parental, 2 recombinant
Tetrad formation w/linked genes
Double crossover (2 strand)
Parental ditype (PD)
4 parentals
Tetrad formation w/linked genes
Double crossover (3 strand)
Tetra type (TT)
2 parental, 2 recombinant
Tetrad formation w/linked genes
Double crossover (4 strand)
Nonparental ditype (NPD)
4 recombinants
Formula to determine recombination frequency in tetrad analysis
r = number of recombinants
What type of linkage?
-dihybrid cross produces two equally frequent gametes containing only parental allele combos with 0 recomb.
Complete linkage
syntenic genes
Genes located on the same chromosome
-so close together that alleles cannot assort independently
Genetic linkage
-can be quantified to map the positions of genes on chromosomes
Alleles of syntenic genes can be reshuffled when crossing over occurs between homologs to produce ______________
recombinant chromosomes
Homologs that do not reshuffle alleles under study are called-
parental chromosomes or nonrecombinant chromosomes
plots the positions of genes on chromosomes
Genetic linkage mapping
crossing over occurs during-
prophase I of meiosis
an organism that exhibits complete linkage [rare]
-drosophila males have no crossing over
true or false: The two parental types are approximately equal in frequency, as are the two recombinant types
TRUE
r [recombination frequency]=
r= # recombinant gametes / total # meioses
crossing over occurs at a ____ rate between genes that are further apart [lower/higher]
Crossing over occurs at a higher rate between genes that are farther apart, and a lower rate between genes that are closer together
-higher rate = higher frequency
______ suggested that nonparental allele combinations resulted from recombination between the X chromosomes of the heterozygous female parent
Morgan
-X linked gene for eye/wing in Drosophila
map units (m.u.) vs centiMorgan (cM) vs recombination frequency
1 m.u. = 1 cM = 1% recombination
three-point test-cross analysis
-allows you to map 3 linked genes simultaneously
-
what crossover event is least frequent in 3-point test-cross?
-double crossover
-both events must occur
_________ can be used to determine gene order
double recombinants, or double crossover
-only one allele is different; this is the middle gene
-list in each of 3 possible orders
when calculating recombination frequencies, for the larger distance, the double crossover progeny are-
-added twice because each represents 2 crossovers between them
interference [I]
I=1-c
-the double crossovers expected but not produced
-negative interference produces more double crossovers than expected
coefficient of coincidence [c]=
observed double crossovers/expected double crossovers
Creighton and McClintock
-obtained cytological evidence that recombination between the genes was accompanied by physical exchange between the homologs
-fragment on one end of chromosome knob on other
why are genes that are closer together less likely to recombine?
-the closer the genes are, the less likely a recombination nodule will form between them
upper limit to recombinant gametes-single crossovers
-single crossover produces 50% recombinant gametes and 50% parental
-all 4 possible single crossovers result in same recombinant gametes
upper limit: Two-strand double crossovers
produce ONLY PARENTAL gametes
upper limit: Three-strand double crossovers
produce 50% parental and 50% recombinant gametes
upper limit: Four-strand double crossovers
produce all recombinant gametes
-recombination LIMIT is 50%
what is recombination limit? why?
50%
-Once genes are far enough apart to produce recombination frequencies of 50%, the pattern of segregation is that expected of independent assortment
Intragenic recombination
infrequent event in which crossing over occurs within a gene
what can affect recombination frequency?
age, environment, and sex
-dietary levels of metal ions can affect crossover in flies
mapping function [based on Poisson distribution]
-does not account for interference
-can be used to correlate the frequency of crossover with the actual number of crossover events
allelic phase
-the arrangement of alleles of linked genes on parental chromosomes
-obstacle for mapping human genes
-can be determined when disease-causing allele segregates with known genetic marker
LOD score
-logarithm of the odds ratio
-determines theta value
-sum all lod scores for each theta value to get Zmax
-higher than 3.0=linkage at theta value
-less than -2.0=significant evidence against genetic linkage
-between -2.0 and 3.0 are inconclusive
odds ratio
-numerator=likelihood that distribution of genotypes and phenotypes in pedigree is produced by genetic linkage
-denominator=chance that it is produced by independent assortment
theta value
-range 0-.50
Zmax
-corresponds to the recombination frequency that is most likely to be correct
haplotype
-specific array of alleles in a set of linked genes on a single chromosome
-these alleles tend to be passed on together during meiosis
-may consist of any combination of linked genes with genetic variation
linkage equilibrium
genotype for a chromosome at one gene is expected to be independent of its genotype for other genes
linkage disequilibrium
certain haplotypes are maintained in a population, usually due to natural selection
The diploid cells undergo meiosis to produce four haploid ______ in a sac called an _____
four haploid ASCOSPORES in a sac called an ASCUS
tetrad
The four ascospores in an ascus
In lab studies, the ascospores can be removed from the ascus and cultured to determine their genotypes; this process is called-
tetrad analysis
parental ditypes (PD)
-Assuming no crossover between the homologs, ascospores produced by one of these arrangements contain the same alleles as the original parent strains
-also 2-strand double crossover [no recombination]
The ascospores produced by the second arrangement will contain alleles in different combinations from the original parent strains, called a ______
nonparental ditype (NPD)
-forming only when 4-strand double crossovers take place
If a single crossover occurs between either of the homolog pairs, a _______ is produced, containing two parental spores and two nonparental spores
tetratype (TT)
tetratypes are [more/less] frequent than PD
less frequent
-->NPD are even less frequent
recombination frequency=
r=[.5TT]+[NPD]/total tetrads
-only half TT spores are recombinant
arrangement of daughter spores reflects the orientation of alleles carried by each chromatid in metaphase I
ordered ascus
second-division segregation pattern
-In a heterozygous meiocyte, if a crossover occurs between the gene and the centromere, the alleles segregate at meiosis II when sister chromatids segregate
each ascus contains 4 parentals and 4 recombinant spores
true or false: homologous crossover occurs sometimes during mitosis
TRUE
the arrangement of alleles of linked genes on homologous parental chromosomes
allelic phase
ascus (ascospore)
sac-like structure containing haploid gametes (ascospore)
Why are double crossover progeny the least frequent of all progeny classes?
Both crossover events must occur simultaneously to produce double recombinants
Double recombinants =
double crossovers
[3 Patterns of double crossover btw two genes]
Produces no recombinants
Two-strand double crossover
[3 Patterns of double crossover btw two genes]
Half of all gametes are recombinant
Three-strand double crossover
[3 Patterns of double crossover btw two genes]
All gametes are recombinant
Four-strand double crossover
The smallest proportions of recombinant chromosomes are associated with
the most tightly linked genes
Recombination proportions increase as
the distance between genes becomes greater
Recombination frequencies between linked genes can increase up to ___% as the distance between genes gets larger
50
Recombination frequencies between linked genes can increase up to 50% as the distance between genes gets larger, and the corresponding frequency of parental chromosomes decreases to ___%
50
Most instances of genetic linkage produce substantially more than what percentage of parental and non-parental chromosomes
>50% parental chromosomes
<50% nonparental
First-division segregation
lack of recombination between a locus and its centromere
A linear pattern of spore phenotypes within an ordered ascus for a particular allele pair, produced when the alleles go into separate nuclei at the first meiotic division, showing that no crossover has occurred between that allele pair and the centromere.
First-division segregation
Number of spores in an ascus after meiosis 2 for Ascomycetes species
4 member unordered asucs
Number of spores in an ascus after mitosis for Neurospora crassa species
8 member ordered ascus
Mitotic crossing over is
rare
Mitotic crossing over produces
patches of tissues with unusual phenotype
Complete genetic linkage
Expect the F1 progeny to produce gametes like:
All gametes contain parental chromosomes
Incomplete genetic linkage (crossover in 20% of gametes)
Expect the F1 progeny to produce gametes like:
Parental gametes are 80%
Recombinant gametes are 20% for these genes
Incomplete genetic linkage (crossover in 40% of gametes)
Expect the F1 progeny to produce gametes like:
Parental gametes are 60%
Recombinant gametes are 40% for these genes
the random distribution into gametes of alleles of linked genes achieved by crossing over between the genes
linkage equilibrium
the nonrandom distribution into gametes of alleles of linked genes
linkage disequilibrium
Tetrad formation w/linked genes
No crossover
Parental ditype (PD)
4 parentals
Tetrad formation w/linked genes
Single crossover
Tetra type (TT)
2 parental, 2 recombinant
Tetrad formation w/linked genes
Double crossover (2 strand)
Parental ditype (PD)
4 parentals
Tetrad formation w/linked genes
Double crossover (3 strand)
Tetra type (TT)
2 parental, 2 recombinant
Tetrad formation w/linked genes
Double crossover (4 strand)
Nonparental ditype (NPD)
4 recombinants
Formula to determine recombination frequency in tetrad analysis
r = number of recombinants
What type of linkage?
-dihybrid cross produces two equally frequent gametes containing only parental allele combos with 0 recomb.
Complete linkage