Genetics Exam 1

In cucumbers, orange fruit color (R) is dominant over cream fruit color (r). A cucumber plant homozygous for orange fruit is crossed with a plant homozygous for cream fruits. Give the genotypes and phenotypes of the offspring of a backcross between the F1 and the orange parent

½ RR orange, ½ Rr orange

In C. elegans unc-205 homozygotes cannot move. You mate unc-205 homozygotes to wild-type animals. The F1s move, but very slowly. You mate the F1s back to unc-205 homozygotes. Of the 100 progeny, which of the following proportions should you expect?

½ cannot move, ½ move slowly

Two parents are heterozygous for albinism, a recessive condition. Suppose we want to know the probability of these parents having 3 children, none of whom have albinism. What is the probability of this couple having one child with albinism and two with normal pigmentation?

- 27/64 (multiplication rule) - 27/64 (multiplication and addition rule)

What are different strategies by which sex is determined across different organisms?

- XX (females) & XY (males): mammals, some plants, insects and reptiles. - XX (females) & XO (males): default is female. Males only have 1 chromosome, the X (O means there is an absence chromosome). grasshoppers, C. Elegans, etc. - ZZ (males) & ZW (females): default is male. Birds, butterflies, snakes, etc. - environment: no sex chromosomes involved. Temperature can affect (alligators, turtles), social structure/hormones/size/etc. can affect (parrot fish).

Both parents are heterozygous for a dominant allele that results in a treatable blood disorder. If the couple has four children, what is the probability that two will have the disorder? Assume that individuals that are homozygous for the dominant allele are viable (i.e. they do not die) and have the blood disorder. (Hint: round to two decimal places)

0.21

What rations of offspring would you expect for an incompletely dominant trait compared with a completely dominant trait?

1 AA : 2 Aa : 1 aa. 1 completely dominant for every 2 incomplete dominant.

You are studying hearing in mice. You find that the majority of mice have normal hearing. However, you find some that cannot hear high pitches. You mate these animals that cannot hear high pitches to true-breeding mice with normal hearing. All five of the F1 progeny in the litter have normal hearing, so you hypothesize that normal hearing is dominant to a defect in hearing high pitches. You mate an F1 male to another female you find with a defect in hearing high pitches. Over the course of several litters, the mice have 30 progeny. 18 with normal hearing and 12 with a defect in hearing high pitches. To determine if the difference between the observed and expected phenotypes of the F2s is significant, calculate the Chi-square value. The Chi-square value is [_____] (round to 1 decimal point).

1.2

A Tortoiseshell (orange and black) female cat mates with a black male cat. One of their female progeny, who has all black fur, mates with an orange male cat. What fraction of their progeny will be Tortoiseshell?

1/2

Assume that the wild-type S allele encodes normal fly size, and the s allele encodes small fly size, and s is recessive to S. You mate a homozygous normal-sized fly to a heterozygous normal-sized fly. What genotypes and phenotypes would you expect in the F1 generation?

1/2 normal sized SS, 1/2 normal-sized Ss

Two parents are heterozygous for albinism, a recessive condition. What is the probability that they will have a child with albinism?

1/4

You are studying heart development in Drosophila and get two animals with a faulty heart valve from a true-breeding line from a collaborator. Your collaborator has found that the faulty valve phenotype is recessive to normally functioning valves in wild-type animals, and is 60% penetrant. You mate the two females with faulty valves to two wild-type males from your lab. In the F1, all of the progeny have normal valves. You mate some F1 males and females. What percentage of the progeny would you expect to have faulty valves?

15%

Two parents are heterozygous for albinism, a recessive condition. What is the probability that they will have a child with normal skin pigmentation?

3/4

Two parents are heterozygous for albinism, a recessive condition. What is the probability that they will have one child with albinism and one child with normal skin pigmentation?

3/8

C. elegans is a species of nematode that is a common genetic model organism used in modern genetics. There are two sexes: males and hermaphrodites. Their mating is, therefore, much like pea plants - hermaphrodites can either mate with males or fertilize their own eggs (generated through meiosis) with their own sperm (also generated by meiosis). A true-breeding short and wide "Dumpy" hermaphrodite mates with a normal male and their male and female progeny all have an intermediate phenotype: they are a little Dumpy. When an intermediate Dumpy male mates with a normal hermaphrodite, what percentage of their progeny will be a little Dumpy?

50%

C. elegans is a species of nematodes that are a common genetic model organism used in contemporary genetics. There are two sexes: males and hermaphrodites. Their mating is therefore much like pea plants - hermaphrodites can either mate with males, or fertilize their own eggs (generated through meiosis) with their own sperm (also generated by meiosis). You have two true-breeding C. elegans strains: one that is Dumpy (dpy) and Uncoordinated (Unc) movement, and one that has normal length and normal movement. The genes that encode these two phenotypes are on different chromosomes. You mate normal males to Dpy Unc hermaphrodites. You find in the F1 that all 1000 animals have normal length and movement. You allow the F1s to self-fertilize to generate F2s. What types of F2 progeny should you predict, and in what proportions?

9 normal: 3 Dpy: 3 Unc: 1 Dpy Unc

You are studying two loci - one that controls pea color and one that controls pea size. r+ homozygotes are purple, r homozygotes are red, and r+ is dominant to r. s+ homozygotes are large, s homozygotes are small, and s+ is dominant to s. You mate plants that are heterozygous at both loci to each other. What are the phenotypic proportions of the progeny? (I.e. what proportion of the progeny are: purple large, purple small, red large, red small?).

9 purple and large 3 purple and small 3 red and large 1 red and small

Why is there incomplete penetrance and variable expressivity?

Because there are other factors responsible such as other genes and/or environmental factors.

You are studying heart development in zebrafish. You isolate mutants that have defects in pumping but are still viable. You generate a true-breeding line of these mutants with pumping defects. You mate a true-breeding heart defect mutant with a true-breeding normal fish. The F1s all have normal pumping. You mate two F1s. In the F2 generation, you find that 140 of the fish have normal hearts and 34 have defective pumping. To test your hypothesis that the allele encoding pumping defects is recessive calculate the Chi-Square value and p-value using the table below. What do you conclude based on your results?

Chi square value is 2.77, the allele encoding defective heart pumping is likely recessive, the difference between the observed and expected values is likely due to chance, the null hypothesis is likely to be true, and we can accept it

What is cytoplasmic inheritance

Cytoplasmic inheritance is the transmission of genetic information through the cytoplasm of cells. This mechanism involves the transmission of cytoplasmic components, such as mitochondria or chloroplasts, from the mother cell to the offspring. Because these components contain their own genetic information, cytoplasmic inheritance can have a significant impact on the traits of the offspring. This genetic information is usually passed down by the mother because the egg cell contains more cytoplasm.

What are the differences between cytoplasmic inheritance and maternal effect inheritance? How are these different than the inheritance of nuclear genes?

Cytoplasmic inheritance is when non-nuclear DNA determines phenotype, and involves the mitochondria and chloroplasts. (mom's phenotype determines progeny's phenotype) Maternal effect is when maternal nuclear DNA determines phenotype, and involves maternal mRNA and maternal protein. (mom's genotype determines progeny's phenotype). This is different from inheritance of nuclear genes because those genes have an equal chance of being passed down from mom and dad.

In cucumbers, orange fruit color (R) is dominant over cream fruit color (r). A cucumber plant homozygous for orange fruit is crossed with a plant homozygous for cream fruits. The F1 are intercrossed to produce the F2. Give the genotype and phenotype of the F1.

F1: Rr orange

In cucumbers, orange fruit color (R) is dominant over cream fruit color (r). A cucumber plant homozygous for orange fruit is crossed with a plant homozygous for cream fruits. The F1 are intercrossed to produce the F2. Give the genotype and phenotype of the F2.

F2: ¼ RR orange, ½ Rr orange, ¼ rr cream

Describe how Thomas Hunt used eye color in Drosophila to study sex-linkage.

Hunt used a reciprocal cross. Hunt crossed white eyed (recessive) female flies with red eyed (dominant) male flies. He observed half of the females had red eyes and half had white eyes, and that all of the males had white eyes. He learned that the trait is not autosomal, but are located on the X chromosome. Because the allele for white eyes is recessive, when paired with another X chromosome that has the red eye trait, the female has red eyes. When the X with the recessive allele is paired with a Y chromosome, the resulting trait is white eyes because there is not dominant allele present. General rule for reciprocal cross: if you switch the genotype of male and female, if the phenotype of F1 and F2 are different, most likely sex linked.

How do multiple alleles at a single gene locus affect the possible observed phenotypes?

If there are multiple alleles, they are arranged in order of dominance. Therefore, because there are more than just 2 alleles, there are more phenotype outcomes.

How are phenotypes affected when two genes at different loci are both involved in affecting a trait?

If two genes at different loci are involved in affecting a trait, then the offspring will display more than just two phenotypes. In the pepper example, the parental generation was a red pepper and a cream pepper. In the F2 generation, we see red, orange, peach, and cream colored peppers. Therefore, we know that there are more than just one pair of alleles involved in determining this trait.

How does polydactyly demonstrate both incomplete penetrance and expressivity?

In a population of 42 individuals who have the genotype for this condition, 38 have have polydactyly and 4 have normal fingers. Penetrance is 38/42 which equals a 90% penetrance (aka incomplete penetrance). Polydactyly shows variable expressivity because some people can just have an extra little nub, while others can have a while extra finger!

Do epistatic genes tend to be upstream or downstream in biosynthetic pathways? Do epistatic genes tend to be upstream or downstream in signaling pathways?

In signaling pathways, the epistatic gene tends to be downstream while in biosynthetic pathways, the epistatic gene tends to be upstream.

Albinism displays several different genetics concepts. Match the trait with the concept demonstrated: Incomplete penetrance Variable expressivity Pleiotropy Recessive inheritance match with: carrying 2 loss of function alleles of oca2 affects hair color, skin color, and eye color individuals with 1 functional cope of oca2 make enough pigment that they do not display albinism some people with albinism will have a little pigmentation (eg. blonde hair), while others will lack all pigmentation (white hair) not everyone with two mutant alleles of a gene that can result in albinism, will have albinism

Incomplete penetrance: not everyone with two mutant alleles of a gene that can result in albinism, will have albinism Variable expressivity: some people with albinism will have a little pigmentation (eg. blonde hair), while others will lack all pigmentation (white hair) Pleiotropy: carrying 2 loss of function alleles of oca2 affects hair color, skin color, and eye color Recessive inheritance: individuals with 1 functional cope of oca2 make enough pigment that they do not display albinism

What is dosage compensation? how is it achieved? How does it affect phenotypes in offspring? In male offspring?

It is a genetic mechanisms that equalize the expression of X-linked genes in males and females by inactivating (silencing) genes on one X.

What is a lethal allele? How does it affect the ratio of phenotypes observed from a cross between two heterozygous individuals?

Lethal allele is an allele combination (homozygous) that prompts birth failure of an individual. With a cross between two heterozygous individuals, the ratio is then 3 (dominant): 1 (recessive). That is because the extra 1 is dead

The father of a certain family has the blood type MN and the mother has the blood type M. What is the probability that they will have a child with the bloodtype MN? What is the probability that they will have a child with the bloodtype M? What is the probability that they will have a child with the bloodtype N?

MN: 50%, M: 50%, N: 0%

What is maternal effect.

Maternal effect refers to the influence of the mother's phenotype on the development of her offspring, independent of the genetic information passed on through the nucleus. This can occur when the mother provides specific molecules, hormones, or environmental conditions that influence the development of the offspring. For example, the egg cell of a mother fruit fly can contain specific RNAs or proteins that determine the development of the offspring, regardless of the genetic information passed on through the sperm.

Explain the principal of independent assortment. What cross lead Mendel to establish this principal?

Mendel did a dihybrid cross of two pea plants. One had round, yellow peas while the other had green, wrinkled peas. The F1 generation had all yellow, round peas but the F2 generation had multiple combinations (yellow round, yellow wrinkled, green round, etc.) This result reveals that the allele for color separated independently from the allele for shape. Therefore, Mendel came up with this principal. When 2 alleles separate, their separation is independent of the separation of alleles at other loci (does not apply to loci on the same chromosome).

Explain principal of segregation (Mendel's first law). Explain what kind of cross lead Mendel to this principal.

Mendel did a monohybrid cross of pea plants with two different traits. In the F1 generation, Mendel observed that there were no blended traits. Although, the F1 plants display the phenotype of each parent, the both traits are passed down to the F2 plants in a 3:1 ratio. Therefore, Mendel concluded that the recessive trait did not disappear. Mendel learned that the two inherited alleles of a locus separated into different gametes with equal probability. The gametes then fused to form a zygote and bring together two randomly paired alleles per gene.

In cucumbers, orange fruit color (R) is dominant over cream fruit color (r). A cucumber plant homozygous for orange fruit is crossed with a plant homozygous for cream fruits. The F1 are intercrossed to produce the F2. Give the genotypes and phenotypes of the parents.

P0: RR orange and rr cream

What is pleiotropy?

The ability of a single gene to have multiple effects.

You find a zebrafish that has magenta stripes, instead of the usual black stripes. These are the only stripe patterns you ever observe. You want to sell a true-breeding magenta stripe line. Every time you cross two magenta-striped fish together, they always produce a mix of black-striped offspring and magenta-striped offspring. Choose all the possible explanations that can explain this phenotype.

The magenta stripe trait shows incomplete penetrance, The magenta-striped fish are heterozygous for a mutation that is lethal when homozygous

The B and E loci in the Labrador Retrievers above demonstrate epistasis. Which locus is epistatic and which is hypostatic? How do you know? Is this an example of dominant or recessive epistasis and how do you know? (Choose all the possible correct answers.)

This is an example of recessive epistasis because the masking only occurs when both alleles at the E/e locus are e (the recessive allele) The E/e locus is epistatic because the ee genotype masks the B locus phenotype The B/b locus is hypostatic because the phenotype it would produce is masked by the ee genotype

Imagine that you are studying C. elegans. You isolate a homozygous mutant that is Dumpy (i.e. shorter than other worms). Most C. elegans are hermaphrodites, producing both sperm and eggs through meiosis (like pea plants). You allow this homozygous dpy, mutant worm to self-fertilize, producing about 200 homozygous mutant dpy worms. Interestingly, some are very short, some are almost as long as normal worms, and there are a range of different lengths in between siblings all growing on the same plate with the same access to food and the same environmental conditions. What best explains this range of phenotypes?

Variable expressivity

What is epistasis?

When the genotype of one gene determines whether another is expressed. Remember the puppy example. One pair of alleles makes the enzyme that produces melanin while another pair of alleles makes the enzyme that transports the melanin into the hair. If the genotype for the transporting enzyme is homozygous recessive, it does not matter the genotype for the enzyme that produces melanin, the hair color will always be blonde. Think of the epistatic gene as the gene that MASKS the other gene.

You visit a farm that breeds pigs, and a farmer tells you that when a black female pig and a pink male pig mate, all of the female piglets show a patchy pattern, with pink patches and black patches of skin, and all of the male piglets are black. What is most likely causing the patchy skin color in female pigs?

X-inactivation

Assume that the blue eye color and green eye color are encoded by different alleles of the same gene. You mate a male mouse from a true-breeding green-eyed line to a female mouse from a true-breeding blue-eyed line. The male progeny are all blue-eyed. However, some females have green eyes, some have blue eyes, and two have one green eye and one blue eye. Which of the following statements is true?

X-inactivation could explain the phenotypes of the female progeny

Explain what a test cross is

an individual of unknown genotype is crossed with a homozygous recessive individual for the trait in question to reveal the unknown genotype. note: you need to cross with recessive to reveal!

Most Drosophila within the population you study have normal wings. However, you find some females with short wings. You mate these short-winged females to normal true-breeding long-winged males and find that their male and female progeny are all long-winged. You cross F1 males and females. In the F2, you find 75 long-winged females, 75 long-winged males, 25 short-winged females and 25 short-winged males. You correctly deduce that the allele encoding short wings is:

autosomal, recessive

In graduate school, you study genes involved in cell differentiation. In the strain of C. elegans that you study, the worms develop one neuron that senses an odorant called butanone. Complete loss-of-function mutations in gene b cause worms to develop two neurons that sense butanone. Complete loss-of-function mutations in gene c cause worms to develop no neurons that sense butanone. When you generate a double-mutant that is homozygous for complete loss-of-function mutations in both gene b and gene c, the animals have two neurons that sense butanone. If these genes act in a signaling pathway, which gene is epistatic, and which gene is likely to function downstream in the signaling pathway?

b is epistatic and functions downstream

How did Mendel know that each of his pea plants carried two alleles encoding a characteristic?

because the trait for both alleles appeared in the F2 generation

The MN locus that encodes antigens on red blood cells demonstrate ____________________ because both the M and N antigens are expressed on the red blood cells of individuals with the genotype LM LN.

codominance

The principle of segregation states that ___________ organisms have two ___________ for a particular characteristic, which segregate when gametes are formed so that one goes into each gamete.

diploid, alleles

What are the differences between dominance, incomplete dominance, and codominance? How would you be able to tell if an allele was dominant, incompletely dominant or codominant?

dominance: only the dominant allele is seen in the phenotype. incompletely dominant: if a genotype is heterozygous, there would be an intermediate phenotype (eggplant) codominant: both alleles are seen in the phenotype.

How does the environment affect the expression of genes?

ex. temperature sensitive alleles: product is functional only at certain temperatures

incomplete dominance

heterozygote has an intermediate phenotype. The dominant allele on its own doesn't produce enough purple pigment, it needs two of them.

Polydactyly, characterized by extra fingers and/or toes, is caused by a dominant mutation in humans. Three siblings inherit the polydactyly allele, but only two of them have extra digits. This is an example of:

incomplete penetrance

How does albinism demonstrate incomplete penetrance, variable expressivity, and pleiotropy?

incomplete penetrance: some individuals with the alleles for albinism don't have albinism variable expressivity: some individuals with albinism have more pigmentation in their hair, eyes, and skin than others pleiotropy: hair, eye, and skin color are 3 different traits all caused by mutation in one gene

Zebrafish are a common model organism. Most zebrafish in the population you study see all colors of light and are true-breeding for this phenotype. However, one day you discover a male and a female fish that fail to see the color red. You mate these two fish and find that 1/2 of their progeny fail to see the color red, 1/4 of their progeny are completely blind, and 1/4 of their progeny have normal vision. The non-wild-type allele is most likely to be:

incompletely dominant

The Notch signaling pathway is essential for development of all animals, from nematodes to humans. You have three mutants in the Notch pathway. Normal worms make one anchor cell (AC). lag-2(0) and lag-1(0) mutants have 2 ACs. lin-12(gf) mutants have 0 ACs. You make a lag-2(0); lin-12(gf) double mutant and observe that all of the double mutant worms have 0 ACs. Which gene is epistatic and which one is hypostatic?

lin-12(gf) is epistatic and lag-2 is hypostatic

You are a researcher in a lab studying zebrafish. The majority of the population are large, and you have isolated a true-breeding line of large zebrafish. You find some small zebrafish in the population, and generate a true-breeding line of small zebrafish. Both large and small fish have equal numbers of progeny and equal viability. To determine the inheritance pattern, you cross a large zebrafish male from your true-breeding line to a small zebrafish female from your other true-breeding line. The F1 progeny are all small. You then cross and F1 male to an F1 female. All of the F2 progeny are large. What is the most likely inheritance pattern?

maternal affect inheritance

Two parents are heterozygous for albinism, a recessive condition. What is the probability that they will have 3 children with albinism and 4 children with normal skin pigmentation?

p = 0.17

You hypothesize that the T allele, which controls Drosophila size, is incompletely dominant, with tt homozygotes being normal sized, Tt heterozygotes being large, and TT homozygotes being enormous. To test this hypothesis, you cross heterozygous (Tt) males and females. You find that of 100 progeny, 15 are enormous, 30 are large, and 55 are normal. Calculate the Chi-square value to compare the observed and expected number of progeny. What is the p-value (Chi-square table on next page)? Do you accept or reject the null hypothesis?

p = 48. we reject the null hypothesis, there is a significant difference between observed and expected that is not due to random chance

When calculating chi square, what does it mean when p > or equal to 0.5? what about if p < 0.5?

p > or equal to 0.5: accept the null hypothesis (due to chance) p < 0.5: reject the null hypothesis (another factor is involved)

What is penetrance? Describe the difference between incomplete vs. full penetrance.

penetrance is the percentage of individuals with a particular genotype that express the expected phenotype. Full penetrance means that 100% of the population showed the expected trait based on their alleles. Incomplete penetrance means that less than 100% of the population showed the expected trait based on their alleles.

You cross together a female duck with the genotype MR M with a male duck with the genotype mdmd. What are the expected proportions of offspring with each of the following phenotypes? Proportion restricted proportion mallard proportion dusky

restricted: 1/2 mallard: 1/2 dusky: 0

What is the difference between autosomes and sex chromosomes?

sex chromosomes differ from males and females (XX and XY). Autosomes are non-sex chromosomes that are the same between males and females (aka they have the same genes).

How does the ABO blood type demonstrate how multiple alleles at a single gene locus affect phenotype? How does the ABO blood type show dominance and codominance?

the ABO blood type shows how there are more than just two phenotype outcomes. For example, if you cross a parent with blood type A and a parent with blood type B, the possible blood types for the children include: A, B, AB, and O. ABO shows dominance because when the A allele is paired with the O allele, the A allele is dominant and the person with have blood type A. ABO shows codominance because blood type A and B are both dominant, so if a person has both alleles, they will have AB blood type.

You are a geneticist studying a disease that results in severe defects in the immune system that you call ISD (for immune system defect). You find after studying many families, that when women with no history of immunological defects and men with ISD have children, their children never have ISD. However, when women with ISD and men with no history of immunological defects have children, their female children never have ISD and their male children always have ISD. From this information, you correctly determine that the gene that is affected in people with ISD is on ____________.

the X chromosome

What is expressivity?

the degree in which a genotype is phenotypically expressed. Aka, how "dramatic" the phenotype is".

What is codominance?

when both alleles contribute to the phenotype (ex: blood type)

principal of independent assortment

when two alleles separate, their separation is independent of the separation of alleles at other loci. (this applies only to loci on different chromosomes due to independent segregation of homologous chromosomes during anaphase I of meiosis.)

Concept of Dominance

when two different alleles are present in a genotype, only the trait encoded by one of them (the dominant allele) is observed in the phenotype

In Labrador Retrievers, coat color is determined by both the B locus and the E locus. The B locus encodes an enzyme involved in the production of melanin (pigment) while the E locus encodes an enzyme involved in the transport of melanin into the hairs. The B allele is dominant and produces more pigment than the b allele, so animals with the B_ genotypes have black pigmentation while animals with the bb genotype have brown pigmentation. In animals with at least one functional E allele, pigment is transported into the hair shaft and animals will appear black or brown depending on their genotype at the B locus. However, in animals with the genotype ee no pigment can be transported into the hair and and animals appear pale yellow. You cross a female dog with the genotype BbEe with a male dog with the genotype BbEe. What are the expected proportions of phenotypes in the puppies?

yellow: 1/4 brown: 3/16 black: 9/16