Chapter 4 Genetics Asano-Shrick KSU

What does a slash, dot, and semicolon mean for gene linkage?

1. No punctuation between alleles of genes on same homolog 2. Slash separates two homologs 3. Alleles always written in same order 4. Alleles of genes on different chromosomes separated by semicolon 5. Dot means unknown linkage.

You can score a molecular marker directly by a molecular test. Here are the three steps for a molecular test.

1. PCR (Polymerase Chain Reaction) 2. Restriction enzyme digestion 3. DNA sequencing Slide 34

In a trihybrid testcross, what are the three possible progeny from most to least common?

1. parental (noncrossover) (NCO); most abundant- 2. single crossovers (SCO); intermediate abundance 3. double crossovers (DCO); least abundant Slide 29

The chi-square test is useful in testing the significance of deviations from a ______ ratio in deducing linkage between two genes.

1:1:1:1

When two genes are close together on the same chromosome pair (i.e, when they are linked), they do not assort independently but produce a recombinant frequency of less than ___(#)__%. Hence, a recombinant frequency of less than __(#)__% is a diagnostic for linkage.

50%; 50%

Write the definition of a molecular marker and explain why it is neither dominant nor recessive.

A DNA sequence variant that can be used to map an interesting phenotype to a specific region of DNA. Many molecular markers can be present on one gene, so it cannot predict the dominance of the phenotype.

Why do today's geneticists use recombination maps together with physical maps?

A geneticist can use a recombination frequencies to map the positions of certain loci. He can then compare this to a physical map where the genes are presented on chromosome to get a better picture of how certain genes correspond to certain areas of the chromosome.

What is a physical map and how is it different from a recombination map?

A physical map is an ordered sequence of DNA and genes. It is different from a recombination map in that recombination maps don't show the genes on a chromosome.

Which statement explains why the recombination frequency between two genes is always less than 50%? A. Genes with a recombination frequency near 50% are unlinked and have an equal likelihood of being inherited together or separately. B. The genotype of the F1 gametes will always be 50% parental gametes and 50% recombinant gametes. C. Recombination cannot be more than 50% because chromosomes are only 50 map units in length. D. F1 gametes always have 50% of their alleles from each parental gamete.

A. Genes with a recombination frequency near 50% are unlinked and have an equal likelihood of being inherited together or separately.

How does a linkage analysis contribute to recombination mapping? A. It demonstrates whether two genes are on the same chromosome. B. It demonstrates which alleles are involved in crossing over. C. It demonstrates the Poisson distribution of genes. D. It demonstrates which alleles are on separate chromosomes.

A. It demonstrates whether two genes are on the same chromosome.

What is the key to chromosome mapping? A. Recombination frequency is correlated to the distance between genes. B. Chromosomal crossovers can inhibit nearby crossovers. C. Crossing over occurs between sister chromatids. D. Wild‑type genes are passed down through single inheritance.

A. Recombination frequency is correlated to the distance between genes.

Which test helps geneticists determine linkage between two genes? A. chi‑square B. Poisson distribution C. coefficient of coincidence D. interference

A. chi‑square

Explain why a test cross is not necessarily required to map molecular markers.

Any DNA heterozygosity can be mapped and used as a molecular chromosome marker. Molecular markers can also be found by a molecular test.

At what stage does crossing over occur? A. anaphase B. prophase C. interphase D. metaphase

B. prophase

If two genes are tightly linked, such that no crossing over occurs between them: A. Progeny will be 50% parental, 50% recombinants. B. All progeny will be recombinants. C. All progeny will be parentals. D. Progeny will be 25% nonrecombinant, 75% recombinant.

C. All progeny will be parentals.

What is the molecular mechanism of chromosome exchange in a crossing over event? A. Chiasmata form and are visible. B. Centromeres attach to the spindle randomly. C. DNA breaks and rejoins in a precise manner. D. Genes become linked together.

C. DNA breaks and rejoins in a precise manner.

Why is it important to know the position of a gene on a chromosome? A. Geneticists can visualize the formation of chiasmata. B. Geneticists can determine the recombination frequency. C. Geneticists can isolate and discover the structure and function of a gene. D. Geneticists can study the crossing over of sister chromatids.

C. Geneticists can isolate and discover the structure and function of a gene.

What is the result of multiple crossovers? A. only recombinants B. over 50 percent parental chromatids C. both recombinants and parental chromatids D. only parental chromatids

C. both recombinants and parental chromatids

For linked genes, recombinants are produced by crossovers between nonsister chromatids during meiosis. _______ are the visible manifestations of crossovers.

Chiasmata

Sites of crossover during Prophase I. They occur at random along chromosomes.

Chiasmata Slide 14

A representation of all chromosomes in the genome as lines, marked with the positions of genes known from their mutant phenotypes, plus molecular markers. Based on analysis of recombinant frequency.

Chromosome map

In a heterozygote having two mutant sites within a gene or within a gene cluster, the arrangement A1A2/a1a2.

Cis conformation

Define cis and trans conformations.

Cis conformation is when two alleles are on the same homolog and trans conformation is when two alleles are on different homologs.

The exchange of corresponding chromosome parts between homologs by breakage and reunion.

Crossing over

Meiotic product cell with chromosomes that have engaged in a crossover.

Crossover product

What is the difference between recombination based maps and physical maps? A. Recombination maps show the genes as both segments and loci of mutant genes. B. Physical maps show the loci of genes that have been identified as mutant phenotypes. C. Physical maps show the genes as both segments and loci of mutant genes. D. Recombination based maps do not show genes as segments on the chromosome.

D. Recombination based maps do not show genes as segments on the chromosome.

What would be the result of a crossover between two sister chromatids? A. There would be no interference with adjacent regions. B. The recombination frequency would be 50 percent. C. The recombination frequency would be less than 50 percent. D. There would be no new allele combinations.

D. There would be no new allele combinations.

Consider the experiment in Drosophila performed by Morgan that studied two autosomal genes affecting eye color and wing length. Write out the notation for two alleles given for each gene, as well as the phenotype of each allele. Note which allele of each gene is dominant.

Eye color: pr (purple) or pr+ (red) Wings: vg (vestigial) or vg+ (normal) pr+ (red) and vg+ (normal wings) are dominant

True or False: Crossing over occurs between chromosomes.

False, it occurs between chromatid Slide 15

True or False: Molecular markers always lead to a change in phenotype.

False; do not always lead to a change in phenotype. They are highly polymorphic (numerous markers could affect one phenotype) Slide 31

Given the results of a dihybrid testcross, once a probability value has been found, be able to determine what that means for the hypothesis being tested.

If the p value is greater than .05, do not reject the hypothesis. If the p value is less than .05, reject the hypothesis.

Where do we see evidence of crossing over?

In progeny ratios Slide 20

Consider the experiment in Drosophila performed by Morgan that studied two autosomal genes affecting eye color and wing length. Explain why the F1 are referred to as dihybrid.

It is a hybrid that is heterozygous for two different genes (eye color and wing length)

In your own words, describe what the chi-square test is.

It is a test that determines if the experimental result is significantly different from an expected result.

Set of linked genes

Linkage group

A chromosome map; an abstract map of chromosomal loci that is based on recombinant frequencies.

Linkage map

The situation in which two genes are on the same chromosome as deduced by recombinant frequencies less than 50 percent.

Linked

The specific place on a chromosome where a gene is located.

Locus

The "distance" between two linked gene pairs where 1 percent of the products of meiosis are recombinant; a unit of distance in a linkage map.

Map unit (mu) or centimorgan (cM)

A DNA sequence variant that can be used to map an interesting phenotype to a specific region of DNA.

Molecular marker

Do humans have more genes or chromosomes?

More genes, so there must be more than one gene on some chromosomes Slide 5

Do molecular markers show dominance or recessiveness?

No Slide 34

Explain what parental meiotic products are, what recombinant meiotic products are, and how recombinants arise.

Parental meiotic products - When the progeny has the same genotype as one of the parents Recombinant meiotic products - When the progeny has a genotype that isn't identical to one of the parents Recombinants arise due to crossing over

Consider the experiment in Drosophila performed by Morgan that studied two autosomal genes affecting eye color and wing length. Identify the parental types and the recombinant types in the testcross progeny and calculate the recombinant frequency.

Parental: pr+ * vg+ = 1339 Parental: pr * vg = 1195 Recombinant: pr+ * vg = 151 Recombinant: pr * vg+ = 154 (154+151)/2839 = 10.74%

Consider the experiment in Drosophila performed by Morgan that studied two autosomal genes affecting eye color and wing length. Diagram the cross between two pure parental lines, one with both recessive alleles and the other with both dominant alleles. Identify the gametes contributed by each parent, and write the genotype of the F1 progeny.

Parents were homozygous. One was recessive (pr/pr and vg/vg) while the other was dominant (pr+/pr+ and vg+/vg+) F1 was all pr+/pr and vg+/vg

Visibly different phenotypes

Phenotypic markers Slide 31

The ordered and oriented map of cloned DNA fragments on the genome.

Physical map

Ordered and oriented map of genomic DNA (a very long DNA sequence).

Physical map Slide 43

_______ is roughly proportional to physical distance between loci.

Recombinant frequency Slide 22

The proportion (or percentage) of recombinant cells or individuals.

Recombinant frequency (RF)

Revisiting Morgan's data, determine the distance between the two genes by using their recombinant frequency.

Recombinant frequency = % Change the percentage to centiMorgan. 2% RF = 2 cM apart

A chromosome map in which the positions of loci (genes) are based on recombinant frequencies, usually from mapping mutant alleles.

Recombinant map Slide 43

Describe the proposed hypothesis of how recombinants can be formed.

Recombinants are formed when crossing over occurs. Crossing over must be between nonsister chromatid. It can be between 2 chromatids or more.

_______ 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%. Map distances are roughly additive.

Recombination

A chromosome map in which the positions of loci shown are based on recombinant frequencies.

Recombination map

Explain why recombinant frequencies are never greater than 50%, and why recombinant frequencies are less than 50% for linked genes.

Since a single crossover involves 2 chromatid out of the 4 chromatid stage, the recombinant frequency can never be greater than 50%. Crossing over doesn't occur in each meiocyte.

Consider the experiment in Drosophila performed by Morgan that studied two autosomal genes affecting eye color and wing length. Understand the significance of a recombinant frequency of less than 50%.

Since crossing over doesn't occur at each meiocyte (a recombinant isn't created at each meiocyte) the recombinant frequency must be less than 50%.

Show how crossover occurs during the four-chromatid stage and identify the parental and recombinant tetrad types that result.

Slide 15

Consider the experiment in Drosophila performed by Morgan that studied two autosomal genes affecting eye color and wing length. Analyze the results of Morgan's testcross, and describe how they deviate from the Mendelian ratio that is expected from independent assortment.

The F2 generations consisted of lots of homozygous offspring (both dominant and recessive) and very little heterozygosity. This was very different from the 1:1:1:1 Mendelian ratio. This means purple eyes and short wings (recessive) are linked while red eyes and regular wings (dominant) are linked.

Recount the logic behind the relationship between map units and recombinant frequency that was developed by Sturtevant.

The farther apart two genes are, the greater the chance of crossing over and recombination.

Explain why higher recombinant frequencies translate to longer map distances between genes.

The farther apart two genes are, the greater the chance they will cross over and form a recombinant.

Be able to state a null hypothesis (for non-linkage) and set up a chi-square test for it.

The null hypothesis with regards to linkage is always the absence of linkage (no linkage occurs). This is because we know the expected ratio when no linkage is present.

How do we know if genes are linked?

There is deviation from expected independent assortment progeny ratios. Alleles of linked genes ALWAYS segregate together. Slide 6

Describe what it means for two genes to be linked.

They do not assort independently. They are often found together in genotypes.

In a heterozygote with two mutant sites within a gene or gene cluster, the arrangement a1 +/+ a2.

Trans conformation

Consider the experiment in Drosophila performed by Morgan that studied two autosomal genes affecting eye color and wing length. Explain why a tester used in a testcross is always a pure-bred individual carrying only recessive alleles (consider what this means for the genotype and phenotype of the progeny of a testcross).

We can predict phenotypic ratios in the progeny if one of the parents is homozygous recessive.

For linked genes, recombinants are produced by crossovers between nonsister _______ during meiosis. Chiasmata are the visible manifestations of crossovers.

chromatids

Alleles on the same homolog are in _______ conformation.

cis Slide 8

When two genes are [close together/far apart] on the same chromosome pair (i.e, when they are linked), they do not assort independently but produce a recombinant frequency of less than 50%. Hence, a recombinant frequency of less than 50% is a diagnostic for linkage.

close together

Compare order of genes in humans, primates, other vertebrates. Understand the evolution of human chromosomes. This is called...

comparative genomics Slide 6

A _______ is the breakage of two DNA molecules at the same position and their rejoining in two reciprocal recombinant combinations.

crossover

Greater physical distance between two loci, [greater/lesser] chance of recombination by crossing-over.

greater Slide 22

Any DNA ________ can be mapped and used as a molecular chromosome marker.

heterozygosity Slide 34

There is one linkage group for each ______.

homologous pair of chromosomes Slide 45

A slash separates two...

homologs Slide 7

Because crossing over does not occur in each meiocyte, frequency of recombinants must be ____%

less than 50% Slide 18

When two genes are close together on the same chromosome pair (i.e, when they are linked), they do not assort independently but produce a recombinant frequency of less than 50%. Hence, a recombinant frequency of less than 50% is a diagnostic for ______.

linkage

For linked genes, recombinants are produced by crossovers between nonsister chromatids during ______. Chiasmata are the visible manifestations of crossovers.

meiosis

Recombination between linked genes occurs by crossing over between non-sister chromatids during ______.

meiosis Slide 13

Recombination between linked genes occurs by crossing over between _______ during meiosis.

non-sister chromatids Slide 13

For linked genes, recombinants are produced by crossovers between ________ chromatids during meiosis. Chiasmata are the visible manifestations of crossovers.

nonsister

Recombination frequency =

number recombinants / total number of progeny Slide 24

If there is no punctuation between alleles, then their genes are...

on the same homolog Slide 7

Crossing over results in deviation from 1:1:1:1 in test crosses. The _______ combination is most frequent while the ______ combination is rarest

parental; recombinant Slide 21

Consider the experiment in Drosophila performed by Morgan that studied two autosomal genes affecting eye color and wing length. Use the testcross data to determine the conformation of the alleles on the chromosomes of the F1 dihybrid.

pr+ and vg+ must have been in cis conformation (on the same homolog) while pr and vg would also be in cis conformation.

Consider the experiment in Drosophila performed by Morgan that studied two autosomal genes affecting eye color and wing length. Write out the cross between an F1 dihybrid female and a tester male.

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

Chiasmata are sites of crossover during ______. They occur at random along chromosomes.

prophase I Slide 14

Multiple (two or more) crossovers can produce both ______ and ______ chromatids.

recombinant and parental chromatids

Crossing over produces ________.

recombinants Slide 12

Linked genes don't follow Mendel's ________ law.

second law (law of independent assortment) Slide 12

Alleles of genes on different chromosomes are separated by a ________.

semicolon Slide 7

Molecular markers don't require a ______ to assess recombinants.

test cross Slide 34

In the chi square test for linkage, the hypothesis is always testing for...

the absence of linkage (we know the expected ratios for unlinked genes) Slide 37

Alleles on different homologs are in ______ conformation.

trans Slide 8

A dot means...

unknown linkage Slide 7

Alleles of genes that are more than 50 cM apart on same linkage group behave as if they are _______.

unlinked Slide 45