Information

Difference between null and recessive allele?

Difference between null and recessive allele?


We are searching data for your request:

Forums and discussions:
Manuals and reference books:
Data from registers:
Wait the end of the search in all databases.
Upon completion, a link will appear to access the found materials.

I get that in a single gene locus, an individual can haveRR,Rr, orrras the two alleles for that gene.Ris "wild type" because it is the allele occurring most frequently.ris the allele that is not WT.

RRandRrshow dominant phenotypes, whereasrrshows the recessive phenotype.

But what's the difference betweenrand a null allele (allele generated by a loss of function mutation outputting the complete loss of the WT phenotype)? Where_is a null allele, my questions are below:

  • R _would produce the same asRr, correct or not?
  • r _would produce the same asrr, correct or not?
  • _ _would produce the same asrr, correct or not?

Good question +1. Unfortunately, the mechanisms by which dominance work is relatively poorly understood and it is likely that the mechanism differs from one locus to another.

You might want to have a look at the posts

or some papers such as

I don't think one can make any general prediction about the phenotype of R_, r_ or __ without having a priori knowledge of the biological pathway (incl. allele interaction (see Llaurens et al. (2009)) and gene interaction network) by which this particular locus is affecting the phenotype. It is tempting to say thatR_is alikeRrorRR, andr_is alikerrbut this is not necessarily true.


To add to Remi b's answer - this question is confusing because 'null' and 'recessive' are terms emerging from two very different levels of analysis. The concept of 'recessive' existed before we knew what genes were, or how they worked. It just describes the patterns of inheritance you see in a gene's effects.

The concept of a 'null' allele however came later, and explicitly describes how an allele works - by destroying gene activity. So 'null' is molecular concept, 'recessive' is an abstract genetic concept. It so happens that null alleles are very often recessive, because usually one working copy of a gene is fine. But the two terms are describing genetics at very different levels.


Basically, a recessive allele leads to formation of a product that has a low activity or no activity, which is complemented in the presence of the dominant allele (there can be effects related to dosage, in some cases). This can be easily understood in terms of an enzyme; a dominant allele would code for an enzyme with full activity whereas the recessive allele codes for one with a reduced activity. There are further complexities but this is a simple example.

A null allele however results in zero activity of the gene. This may be because of many reasons:

  • The allele may produce a non-functional protein (for e.g. an enzyme with mutated active site such that it cannot carry out the catalysis)
  • The geneic region of the allele may be transcribed but not translated (loss of ORF)
  • There may be no transcription at all (deletion of DNA sequences critical for transcription)

In cases where there is no dosage effect, a null allele is always recessive but the converse is not true.

  • R _would produce the same asRr, correct or not?
  • r _would produce the same asrr, correct or not?
  • _ _would produce the same asrr, correct or not?

The first two these assumptions are true for a simplistic case (no dosage effects). Since,ris a hypomorphic allele (by assumption) i.e. it has a reduced activity whereas_has zero activity,_ _may not have the same phenotype asrr. Only in cases where there is a threshold on the activity leading to phenotype, can a low activity allele/genotype (activity below threshold) lead to same phenotype as the null allele.

If we add further complexities,R _orr _may not be functionally equivalent toRrorrrrespectively. EvenRRmay behave functionally different thanRr. This would happen because of altered gene dosage (expression level) and reduced expression level of the functional product can cause a change in the net activity. (Also see: Can difference in the expression potential of alleles lead to dominance?)


What are the different types of epistasis?

Epistasis occurrs when one allele of a gene masks the expression of alleles of another gene.

When there is no epistasis a dihybrid cross (two characteristics) of two heterozygote individuals(each individual has one of each allele) results in a phenotypic ratio or 9:3:3:1 (both dominant:first dominant, second recessive:second dominant, first recessive:both recessive).

here are the different types:

1. Recessive epistasis, i.e. the epistatic allele is recessive so for it to mask the other gene two copies are needed. To illustrate this carry out a dihybrid cross with a homozygous dominant individual and a homozygous recessive individual and you will see a ratio of 9:3:4 (dominant both: dominant epistatic, recessive other:recessive epistatic).

2. Dominant epistasis, i.e. the epistatic allele is dominant so only one copy is needed to mask the other gene. If you carry out the same cross as for recessive you will see a ratio of 12:3:1 (dominant epistatic: recessive epistatic, dominant other: recessive both).

3. Complementary epistasis, i.e. the genes work together in a complementary fashion so you need at least one dominant allele of both genes to get one phenotype and all other combinations give another phenotype. The ratio you get is 9:7 (dominant both: recessive either or both).


Carrier (Genetics)

In genetics, the term carrier describes an organism that carries two different forms (alleles) of a recessive gene (alleles of a gene linked to a recessive trait) and is thus heterozygous for that the recessive gene. Although carriers may act to convey and maintain recessive genes within a population by passing them on to offspring, the carriers themselves are not affected by the recessive trait associated with the recessive gene.

Although a carrier's genome contains a particular mutant allele, another gene (e.g., a dominant gene), or series of genetic mechanisms act to prevent the observable expression of that mutant allele (phenotypic expression). If, for example, at the genetic level an organism had a genotype (T, t), with the capital letter "T" designating a completely dominant allele and the lowercase letter "t" representing the recessive allele, that organism would express the observed trait associated with "T" and be a carrier for the recessive gene designated by "t." In contrast, the human blood type AB presents an example of allele codominance because the allele IA and IA allele are both expressed and contribute to the phenotype (blood group AB).

Because heterozygous organisms carry contain different forms (alleles) of a particular gene, diploid carriers produce sex cells (gametes) by the process of cell meiosis. Accordingly, heterozygous organisms produce gametes that contain different copies of the genes for which they are heterozygous. With regard to a (T, t) genotype, such an diploid organism would produce equal numbers of gametes that carried a single "T" allele or a single "t" allele.

At the observable level, an individual may, for example, act to convey the sickle cell gene but remain unaffected by sickle cell disease that strikes those who are homozygous for the sickle cell gene (i.e., carry two copies of the recessive sickle cell allele).

Under some conditions, a carrier may actually be more fit for a particular environment. Carriers who benefit from this heterozygote superiority or advantage are able to pass on and maintain a particular recessive allele within a population. In the case of sickle cell, the heterzygote carrier has a greater resistance to some forms of malaria. Accordingly, in malaria stricken areas, carriers of sickle cell disease avoid (in greater numbers) the selective disadvantages of malaria.

Studies of patients of Ashkenazi Jewish heritage (Jews of Eastern European descent), indicate that as many as one in seven individuals acts as a carrier of at least one of several different genetic diseases. Although some of these diseases are potentially fatal, the carriers of these diseases remain observably healthy individuals and show no signs of being affected with the disease related to the particular gene they carry.

Geneticists and physicians have developed a number of screening tests (carrier screening) to identify individuals who may be carriers for a particular gene.


See also

An allele is one of two, or more, forms of a given gene variant. For example, the ABO blood grouping is controlled by the ABO gene, which has six common alleles. Nearly every living human's phenotype for the ABO gene is some combination of just these six alleles. An allele is one of two, or more, versions of the same gene at the same place on a chromosome. It can also refer to different sequence variations for several-hundred base-pair or more region of the genome that codes for a protein. Alleles can come in different extremes of size. At the lowest possible size an allele can be a single nucleotide polymorphism (SNP). At the higher end, it can be up to several thousand base-pairs long. Most alleles result in little or no observable change in the function of the protein the gene codes for.

A genotype is an organism’s complete set of genetic material. Often though, genotype is used to refer to a single gene or set of genes, such as the genotype for eye color. The genes take part in determining the characteristics that are observable (phenotype) in an organism, such as hair color, height, etc. An example of a characteristic determined by a genotype is the petal color in a pea plant. The collection of all genetic possibilities for a single trait are called alleles two alleles for petal color are purple and white.

A microsatellite is a tract of repetitive DNA in which certain DNA motifs are repeated, typically 5󈞞 times. Microsatellites occur at thousands of locations within an organism's genome. They have a higher mutation rate than other areas of DNA leading to high genetic diversity. Microsatellites are often referred to as short tandem repeats (STRs) by forensic geneticists and in genetic genealogy, or as simple sequence repeats (SSRs) by plant geneticists.

In genetics, dominance is the phenomenon of one variant (allele) of a gene on a chromosome masking or overriding the effect of a different variant of the same gene on the other copy of the chromosome. The first variant is termed dominant and the second recessive. This state of having two different variants of the same gene on each chromosome is originally caused by a mutation in one of the genes, either new or inherited. The terms autosomal dominant or autosomal recessive are used to describe gene variants on non-sex chromosomes (autosomes) and their associated traits, while those on sex chromosomes (allosomes) are termed X-linked dominant, X-linked recessive or Y-linked these have an inheritance and presentation pattern that depends on the sex of both the parent and the child. Since there is only one copy of the Y chromosome, Y-linked traits cannot be dominant nor recessive. Additionally, there are other forms of dominance such as incomplete dominance, in which a gene variant has a partial effect compared to when it is present on both chromosomes, and co-dominance, in which different variants on each chromosome both show their associated traits.

A gene knockout is a genetic technique in which one of an organism's genes is made inoperative. However, KO can also refer to the gene that is knocked out or the organism that carries the gene knockout. Knockout organisms or simply knockouts are used to study gene function, usually by investigating the effect of gene loss. Researchers draw inferences from the difference between the knockout organism and normal individuals.

The human leukocyte antigen (HLA) system or complex is a group of related proteins that are encoded by the major histocompatibility complex (MHC) gene complex in humans. These cell-surface proteins are responsible for the regulation of the immune system. The HLA gene complex resides on a 3 Mbp stretch within chromosome 6p21. HLA genes are highly polymorphic, which means that they have many different alleles, allowing them to fine-tune the adaptive immune system. The proteins encoded by certain genes are also known as antigens, as a result of their historic discovery as factors in organ transplants. Different classes have different functions:

Genetic variation is the difference in DNA among individuals or the differences between populations. There are multiple sources of genetic variation, including mutation and genetic recombination. The mutation is the ultimate source of genetic variation, but mechanisms such as sexual reproduction and genetic drift contribute to it as well.

A heterozygote advantage describes the case in which the heterozygous genotype has a higher relative fitness than either the homozygous dominant or homozygous recessive genotype. The specific case of heterozygote advantage due to a single locus is known as overdominance. Overdominance is a condition in genetics where the phenotype of the heterozygote lies outside of the phenotypical range of both homozygote parents, and heterozygous individuals have a higher fitness than homozygous individuals.

Equine coat color genetics determine a horse's coat color. Many colors are possible, but all variations are produced by changes in only a few genes. Extension and agouti are particularly well-known genes with dramatic effects. Differences at the agouti gene determine whether a horse is bay or black, and a change to the extension gene can make a horse chestnut instead. Most domestic horses have a variant of the dun gene which saturates the coat with color so that they are bay, black, or chestnut instead of dun, grullo, or red dun. A mutation called cream is responsible for palomino, buckskin, and cremello horses. Pearl, champagne and silver dapple also lighten the coat, and sometimes the skin and eyes as well. Genes that affect the distribution of melanocytes create patterns of white such as in roan, pinto, leopard, white, and even white markings. Finally, the gray gene causes premature graying, slowly adding white hairs over the course of several years until the horse looks white. Some of these patterns have complex interactions.

Non-Mendelian inheritance is any pattern of inheritance in which traits do not segregate in accordance with Mendel's laws. These laws describe the inheritance of traits linked to single genes on chromosomes in the nucleus. In Mendelian inheritance, each parent contributes one of two possible alleles for a trait. If the genotypes of both parents in a genetic cross are known, Mendel's laws can be used to determine the distribution of phenotypes expected for the population of offspring. There are several situations in which the proportions of phenotypes observed in the progeny do not match the predicted values.

Pleiotropy occurs when one gene influences two or more seemingly unrelated phenotypic traits. Such a gene that exhibits multiple phenotypic expression is called a pleiotropic gene. Mutation in a pleiotropic gene may have an effect on several traits simultaneously, due to the gene coding for a product used by a myriad of cells or different targets that have the same signaling function.

Conservation genetics is an interdisciplinary subfield of population genetics that aims to understand the dynamics of genes in populations principally to avoid extinction. Therefore, it applies genetic methods to the conservation and restoration of biodiversity. Researchers involved in conservation genetics come from a variety of fields including population genetics, molecular ecology, biology, evolutionary biology, and systematics. Genetic diversity is one of the three fundamental levels of biodiversity, so it is directly important in conservation. Genetic variability influences both the health and long-term survival of populations because decreased genetic diversity has been associated with reduced fitness, such as high juvenile mortality, diminished population growth, reduced immunity, and ultimately, higher extinction risk.

The ABO blood group system is used to denote the presence of one, both, or neither of the A and B antigens on erythrocytes. In human blood transfusions it is the most important of the 38 different blood type classification systems currently recognized. A mismatch in this, or any other serotype, can cause a potentially fatal adverse reaction after a transfusion, or an unwanted immune response to an organ transplant. The associated anti-A and anti-B antibodies are usually IgM antibodies, produced in the first years of life by sensitization to environmental substances such as food, bacteria, and viruses.

In genetics, a locus is a specific, fixed position on a chromosome where a particular gene or genetic marker is located. Each chromosome carries many genes, with each gene occupying a different position or locus in humans, the total number of protein-coding genes in a complete haploid set of 23 chromosomes is estimated at 19,000󈞀,000.

The Kell antigen system is a human blood group system, that is, group of antigens on the human red blood cell surface which are important determinants of blood type and are targets for autoimmune or alloimmune diseases which destroy red blood cells. The Kell antigens are K, k, Kp a , Kp b , Js a and Js b . The Kell antigens are peptides found within the Kell protein, a 93-kilodalton transmembrane zinc-dependent endopeptidase which is responsible for cleaving endothelin-3.

The Kidd antigen system are proteins found in the Kidd's blood group, which act as antigens, i.e., they have the ability to produce antibodies under certain circumstances. The Jk antigen is found on a protein responsible for urea transport in the red blood cells and the kidney. They are important in transfusion medicine. People with two Jk(a) antigens, for instance, may form antibodies against donated blood containing two Jk(b) antigens. This can lead to hemolytic anemia, in which the body destroys the transfused blood, leading to low red blood cell counts. Another disease associated with the Jk antigen is hemolytic disease of the newborn, in which a pregnant woman's body creates antibodies against the blood of her fetus, leading to destruction of the fetal blood cells. Hemolytic disease of the newborn associated with Jk antibodies is typically mild, though fatal cases have been reported.

In medical genetics, compound heterozygosity is the condition of having two or more heterogeneous recessive alleles at a particular locus that can cause genetic disease in a heterozygous state that is, an organism is a compound heterozygote when it has two recessive alleles for the same gene, but with those two alleles being different from each other. Compound heterozygosity reflects the diversity of the mutation base for many autosomal recessive genetic disorders mutations in most disease-causing genes have arisen many times. This means that many cases of disease arise in individuals who have two unrelated alleles, who technically are heterozygotes, but both the alleles are defective.

Zygosity is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism.

A gene is said to be polymorphic if more than one allele occupies that gene's locus within a population. In addition to having more than one allele at a specific locus, each allele must also occur in the population at a rate of at least 1% to generally be considered polymorphic.

The agouti gene (ASIP) is responsible for variations in color in many species. Agouti works with extension to regulate the color of melanin which is produced in hairs. The agouti protein causes red to yellow pheomelanin to be produced, while the competing molecule α-MSH signals production of brown to black eumelanin. In wildtype mice, alternating cycles of agouti and α-MSH production cause agouti coloration. Each hair has bands of yellow which grew during agouti production, and black which grew during α-MSH production. Wildtype mice also have light-colored bellies. The hairs there are a creamy color the whole length because the agouti protein was produced the whole time the hairs were growing.


Genetics Questions

1. A floriculturist is interested in generating roses with larger petals. He measures the following components for petal radius in a population of plants from his farm.

Additive genetic variance (VA): 5.1
Dominance genetic variance (VD): 1.1
Interaction genetic variance (VI): 0.5
Environmental variance (VE): 3.0
Genetic-environmental variance (VGE): 0.1

Based on your estimations of heritability, if this floriculturist starts a breeding program to generate flowers with larger petals, do you think he will succeed?

2. Why do you use model organisms (mouse, fruit flies, and so on) instead of humans to study genetics?

3. The CFTR gene codes for a specific transport protein found in cell membranes. Cystic fibrosis is an inherited illness, where a mutation in the CFTR gene causes chloride ions to build up inside the cells, which causes them to absorb more water by osmosis. In the lungs and pancreas, this occurrence leads to the production of thick, sticky mucus that can affect breathing and the production of digestive enzymes.

a. From the pedigree diagram, what can you say about how cystic fibrosis is inherited? Explain your answer.

b. Write out possible genotypes for individuals 1 and 2. Use CF to represent the normal allele and cf to represent the disease allele.

c. What is the probability that individual number 3 is heterozygous? What is the probability that they are homozygous for the normal allele? Use a Punnett square to help you. How will this affect their chances of having a child with cystic fibrosis?

4. Coat color in rabbits is controlled by four alleles: C is the agouti allele, which is dominant to all others c ch is the allele for the chinchilla color (grey) c h is the allele for the Himalayan coat color, which is white with brown ears, nose and paws and c is the albino allele, which is recessive to all the other alleles.

A rabbit breeder wants to buy a female chinchilla rabbit, but he needs it to be homozygous for the c ch allele. How could he find out if the rabbit he has his eye on is true-breeding for the chinchilla coat color? Explain your answer.

5. In a mythical dragon species, the pretend gene "glittery" determines if the dragon's scales are sparkly or drab. However, sparkly individuals vary greatly in how much they glisten: some are blinding in the Sun, while others barely reflect the light. What are some possible explanations for this observation?

6. You scratch the inside of your ear, and you discover you have dry earwax. You know from carefully reading the "To Pea or Not to Pea" section of this genetics unit that "dry" earwax is recessive, while "wet" earwax is dominant. You ask your mom, and she also has dry earwax, but your dad is not into checking his earwax's consistency. However, what can you deduce about your father's genotype for earwax?

7. A coat color gene in cats, located on the X chromosome, has two alleles: X B (black) and X b (ginger).

a. Complete the diagram above by filling in the missing female genotypes.

b. Are the following statements true or false?

i. A cross between a male black cat and a female ginger cat would give female tortoiseshell kittens.
ii. The same cross would give male tortoiseshell kittens.
iii. A tortoiseshell female can have tortoiseshell kittens by whatever colored male she mates with.

c. A cat breeder wants to produce a pure-breeding strain of tortoiseshell cat. Is this possible?

8. You are writing a plot for a forensics show. The story involves the alleged kidnapping of a baby, named Clara, many years ago after the death of her mother. A couple, the Stuarts, raised the girl and claimed that she is their biological daughter. The parents of the deceased woman, the Sullivans, appeal to a court to try to get custody of the girl they believe is their granddaughter.

a. Could mitochondrial DNA testing be useful for this case? In what way?

b. Whose mitochondrial DNA would need to be tested? Why?

c Assume the relevant people were tested. If the Stuarts are telling the truth and Clara is their biological daughter, what are the results of the test? If, on the contrary, the Sullivans are Clara's grandparents what are the results of the test?

9. Often, the F2 generation resulting from crossing two pure-breeding strains for a quantitative trait present phenotypes that were not present in either the parentals or the F1 generation. Often, these phenotypes are extreme, for example, lighter color than the lightest or taller than the tallest. Can you explain why this might happen?

10. Two true breeding strains of maize plants, one with yellow round seeds and the other with white shrunken seeds, were crossed. The F1 was found to have yellow round seeds. A test cross was then carried out and the numbers of seeds with different phenotypes was counted. In this F2, there were 332 yellow round seeds, 340 white shrunken seeds, 14 yellow shrunken seeds, and 11 white round seeds.

a. From the information given, what can you say about the relationship between the alleles for yellow and white seed color, and the alleles for round and wrinkled seeds? Explain your answer.

b. The recombination frequency, or crossover value, between genes can be used as an indicator as to whether or not two genes are linked. The lower the crossover value, the closer the two genes are to each other. It can be calculated using the following equation:

Cross-over value (%) = Number of recombinant phenotypes x 100
Total number of offspring

Calculate the recombination frequency for the F2 cross using the above equation.

c. What does this tell you about the genes controlling seed color and shape in maize?

d. What phenotypic ratio would you have expected to see in the F2 if the genes had not been linked?

11. A plant breeder crosses 2 pink snapdragon plants and obtains 780 plants: 197 red, 182 white, and 401 pink. His daughter has been studying plant genetics and decides to use her Dad's results to revise the &chi 2 -test.

a. What phenotypic ratio would the student be expecting from this cross and why?

b. What would the student's null hypothesis be?

c. Carry out a &chi 2 analysis of this cross. Present your calculations in a table.

d. How many degrees of freedom are there for this cross?

e. Compare the &chi 2 result to the &chi 2 probability table here at a significance level of 0.05. Can the student accept her null hypothesis? Explain your answer.

Answers

1. Not necessarily. Because the heritability ranges from 52% to 68%, this range suggests that there are large environmental factors also acting on petal size, not just what genes the plants have.

2. Model organisms tend to produce lots of offspring, which is necessary to clearly see any patterns in inheritance. They also breed more quickly than humans, who produce only small numbers of offspring and have a nine-month gestation period. Some model organisms, such as fruit flies, are also comparatively cheap to work with. Experimenting on humans could also be considered unethical, particularly in an enforced breeding program.

3a. Cystic fibrosis is a recessive disease because unaffected parents can have affected children. It is not sex-linked because it affects both males and females, and men can be carriers as well as women.

3b. Individuals 1 and 2 are both heterozygote carriers, so their genotypes will both be CFcf.

3c. There is a 50% probability that they will be heterozygous and therefore a carrier for cystic fibrosis and a 25% probability that they will be homozygous for the normal allele. If they are carriers and have a child with another carrier, then the child could have cystic fibrosis. If they are homozygous for the normal allele, then there is virtually no chance that they will have a child with cystic fibrosis.

4. He could carry out a test cross with an albino rabbit. Because the albino allele c is recessive to all the other coat color alleles, it will reveal what the exact genotype of the other parent is. If the chinchilla rabbit is true-breeding, then all of the offspring would be chinchilla if there are any other alleles present, such as the Himalayan or albino allele, then there will be other-colored offspring in the phenotypic ratio of 1 chinchilla : 1 Himalayan/albino.

5. Some possibilities are a second, epistatic gene, variable expressivity, and possibly a quantitative trait.

6. He must be either homozygous for dry earwax, or be heterozygous. If he were homozygous for wet earwax, or the dominant condition, you'd have wet earwax, too.

7a. Row II: ginger female &ndash X b X b , tortoiseshell female &ndash X B X b Row III: black female &ndash X B X B , tortoiseshell female X B X b

7c. No. A tortoiseshell female will produce tortoiseshell kittens whether she mates with a black or a ginger male, but there is no such thing as a male tortoiseshell cat, as you need both an X B and an X b allele to get the tortoiseshell coloring.

8a. Yes. It would allow Clara's mother to be identified because Clara will have inherited all of her mtDNA from her mom.

8b. The DNA of Clara, Mrs. Stuart, and Mrs Sullivan would need to be tested. Mrs Sullivan is the dead woman's mother, so she would have passed her mtDNA onto her daughter, who would have passed it on to Clara&mdashif Clara is her daughter!

8c. If the Stuarts are telling the truth, then Clara and Mrs. Stuart will have the same mtDNA, and Mrs. Sullivan's will be different. If the Stuart's aren't telling the truth, then Clara and Mrs. Stuart will have different DNA, and Clara's mtDNA will match that of Mrs. Sullivan.

9. There could be multiple loci involved, there could be an environmental effect on gene expression, there could be an epistatic effect, or there could be any combination of the above!

10a. Yellow is dominant to white, and round is dominant to wrinkled because when the two true-breeding parental strains were crossed, the F1 generation, or the heterozygotes, all had round yellow seeds.

10b. 25/697 = 0.036 x 100 = 3.6%.

10c. They are linked because the recombination frequency is very low.

10d. 1:1:1:1 because independent assortment of the alleles for both genes would give roughly equal numbers of all four possible phenotypes. Remember: a test cross is between an organism with the dominant phenotype and a homozygous recessive organism.

11a. 1 red : 2 pink : 1 white&mdashincomplete dominance

11b. The null hypothesis would be that there is no difference between the observed numbers of flowers and the expected numbers of flowers from this cross

Phenotype Observed Expected (O-E) (O-E)2 (O-E)2/E
Red 197 195 2 4 0.02
Pink 401 390 11 121 0.31
White 182 195 -13 169 0.87
Total 780 780 1.20

Calculated &chi 2 value = 1.20.

11d. 2. There are three phenotypes, so df = 3 - 1 = 2.

11e. Yes, she can, because the calculated &chi 2 value is less than the value in the &chi 2 probability table for 2 degrees of freedom and a confidence level of 0.05. There is no statistically significant difference between the number of flowers her father bred and the number that were expected theoretically.


What is Sun Sneezing?

The scientific term for sun sneezing is Photic Sneeze Reflex, or PSR.

Believe it or not, people have been wondering what causes PSR since the fourth century B.C. In his Book of Problems, the Greek philosopher Aristotle wondered, “Why does the heat of the sun provoke sneezing?”. While scientists still aren’t sure exactly what causes the phenomenon, they are sure it has nothing to do with the heat of the sun. Instead, current models predict that PSR is due to the arrangement of the nerves in the eyes and nose and the way that those nerves are triggered in some people upon looking at a bright light.

This video does a great job at explaining what scientists believe happens to cause a sun sneeze.


Examiners report

A usual guideline for examiners is to have 50% more points on the mark scheme than raw marks in Section B questions. There were fewer points than that for part (a) of this question and only the strongest candidates found enough to say to reach a total of four. A point that was almost always missed was that males and females do not differ in the autosomes that they possess. This is a significant distinction between the sex chromosomes and autosomes.

For part (b), a small proportion of candidates forgot or did not know that hemophilia is a sex linked condition and so scored few marks here. Most candidates who did know that sex-linkage is involved used the expected notation of an upper case X to represent the X chromosome with superscript upper case and lower case letters to show the alleles. If an upper case Y is also shown, even though it does not carry a copy of the gene, it makes mistakes much less likely when working out possible outcomes from a cross between two parents. The most significant cross is one between an unaffected male and a carrier female as this is how almost all cases of hemophilia are derived. Most candidates showed this. Parental genotypes were often missing and gametes on the Punnett grid were usually shown but not labelled as gametes. The best answers showed the phenotypes of each possible type of offspring, together with the genotype on the Punnett grid. It was also useful to add a ratio or percentages below the grid. Candidates who showed a series of different crosses rarely scored any more marks after the first cross.

Part (c) is a standard question but even so, answers were very variable, probably because meiosis is complicated and there are multiple causes of genetic variety, which some candidates struggle to understand. Terminology was sometimes used rather loosely. The best candidates distinguished between random orientation of bivalents in metaphase I and independent assortment of genes due to random orientation or crossing over, depending on whether pairs of genes are on different or the same type of chromosome.


Using Signatures of Directional Selection to Guide Discovery

Genetic and Genomic Consequences of Selection: Beyond Gene Lists

Recent studies have used the strong genetic differences produced by directional selection as starting material. They have applied what might be thought of as informatics-driven filters to try to focus on individual genes whose manipulation will affect the selected trait. A clear example comes from Zhifeng Zhou and David Goldman's work with P and nonpreferring (NP) rats. 36 P rats have been bred for many generations to have high preference for 10% alcohol versus water, and the NP rat line was bred for low preference. They first sequenced the exomes of six individual rats from each selected line, finding >120,000 single nucleotide polymorphisms (SNPs). About 20% of these SNPs were homozygous and consistently different between P and NP rats, suggesting that they represented the signature of response to selection pressure for high versus low drinking. Alternatively, given the relatively small population sizes necessarily involved in producing the selected lines, these SNPs could represent accidental inbreeding. To distinguish between these alternatives, they mapped the differential SNPs and found numerous relatively large haplotype blocks. About 1000 such blocks of SNPs could be mapped to known functional genes.

Clearly, it was necessary to further reduce the number of potential targets. Two of the segregating SNPs revealed stop codons in known genes, and 31 others showed exomic sequence differences predicted to adversely affect protein function. At this point, Zhou and Goldman turned back to behavior. They used an F2 segregating population of P and NP rats obtained by intercrossing inbred variants of P and NP lines. They tested hundreds of F2 rats for alcohol preference and performed a standard QTL linkage analysis to identify four variants in three genomic regions linked to preference variation. Comparing the QTL results to the exome sequencing SNP patterns consistently identified a stop codon in the Grm2 gene (Grm2 ∗407) (see Fig. 11.2 ): this gene encodes the metabotropic glutamate receptor 2, and the stop codon variant in P rats leads to widely deficient receptor function. With a clear target gene of interest, these investigators amassed a wealth of evidence that consistently implicated the mGluR2 receptor in P rats, including absence of receptor expression and impaired mGluR-mediated synaptic depression. They demonstrated elevated alcohol consumption in mice with a null mutation for Grm2. Overall, this paper shows how the power of directional selection to influence the genome can yield fruitful results. Three additional possible genes of interest were discussed in the paper, but these have not yet been validated.

Figure 11.2 . Exome sequencing of preferring (P) and nonpreferring (NP) rats identified the mGluR2 gene as important for ethanol preference drinking. SNPs are shown for chromosomes 8, 9, 10, and 11.

From Zhou Z, Karlsson C, Liang T, et al. Loss of metabotropic glutamate receptor 2 escalates alcohol consumption. Proc Natl Acad Sci USA. 2013110:16963–16968 with permission.

A similar conceptual approach was also applied to ethanol preference drinking, also in rats. These investigators took advantage of the other rat preference lines selected at Indiana University, the High Alcohol Drinking and Low Alcohol Drinking rats. 37 HAD and LAD rats were bred for high versus low preference in the same way P and NP rats were. 38 This population offered three major advantages from a genetic perspective. First, the lines were derived from a genetically heterogeneous intercross of eight inbred rat strains and thus presented high genetic diversity at the outset. 39 Rats from this segregating population were also available to serve as controls. Second, two independent populations of HAD rats, and two of LAD rats, were developed. Because laboratory populations are always relatively small (from a population genetic perspective), many differences between divergently selected lines emerge during the course of selection due to accidental fixation of gene variants (i.e., loss of genetic variation, or inbreeding). The occurrence of identical gene or chromosomal regional fixation during selection in two completely independent pairs of lines, but not in the nonselected controls, is thus relatively unlikely this improves the detection of signatures of selection versus noise. 1,2,29

Many details of the genomics analyses in this experiment differed from the analysis of P versus NP rats. Signatures of selection in the HAD/LAD populations were found for nearly 1000 genes, and most were located within a single gene. Within those genes, very few (four) were found in exonic regions: most were in promoter or intronic regions (see Fig. 11.3 ). Functional overrepresentation analyses suggested an important role for genes involved with synaptic transmission, memory, and reward pathways and included those coding for several ion channels and excitatory neurotransmitter receptors. 37 Unlike the NIAAA group, these investigators did not pursue individual candidate genes and attempt to provide further confirmatory evidence.

Figure 11.3 . Signatures of selective breeding in genome of High and Low Alcohol Drinking rat lines. Chromosome 7 is depicted for Slc17a8, a vesicular glutamate transporter (see inset). Allele frequencies for HAD (red) and LAD (green) are plotted versus chromosomal position. Excessive differentiation in genomic architecture between lines across both replicates, termed signatures of selection (SS), are plotted in red based on intraclass correlation values (θ), plotted in blue.

Adapted from Lo CL, Lossie AC, Liang T, et al. High resolution genomic scans reveal genetic architecture controlling alcohol preference in bidirectionally selected rat model. PLoS Genet. 201612:e1006178 with permission.

Our group has also taken advantage of the existence of replicated selectively bred lines. 40 A binge has been defined by the National Institute on Alcohol Abuse and Alcoholism of the US National Institutes of Health as a period of temporally focused drinking that leads to a blood ethanol concentration (BEC) > 80 mg%, or 0.8 mg/mL. 41 Binge drinking is a risk for development of an alcohol use disorder, and most alcohol abusers binge drink. Binge drinking is also a strong predictor of medical diagnosis and has deleterious health consequences. 42 Prevalence of binge drinking is increasing in the United States, 43,44 and it is highly prevalent in both veterans and active military duty personnel. Alcohol use disorder is comorbid with many other psychiatric conditions: in these populations, posttraumatic stress disorder is also a frequent diagnosis. 45 To develop an animal model of binge-like drinking, we explored several alternatives with the goal of achieving a simple behavioral assay for binge-like drinking in the mouse. Following earlier work in the area, 46 we developed the drinking in the dark (DID) assay, where mice consume enough alcohol in 2–4 h to reach intoxicating BECs. 47 The basic paradigm we used was to substitute 20% ethanol for water for a limited period each day, during the early hours of the circadian dark cycle, as this is when rodents consume much of their daily food and fluid. We have determined the optimal time after “lights off” to start access, 47 and the optimal duration of access to result in elevated blood alcohol levels. 48 Consumption of the ethanol solutions remains relatively consistent across 12 days. When we examined panels of multiple inbred strains in the DID procedure, we found that the trait was reliable upon retest and significantly heritable. 49,50

We subsequently selectively bred high DID (High Drinking in the Dark [HDID]-1 and HDID-2) mouse lines for high BECs after a 4-h DID session these mice drink to the point of behavioral intoxication and reach blood levels that average about 200 mg/mL [Refs. 48,51 see Fig. 11.4 ]. Behavioral characterization of HDID mice has revealed that HDID mice exhibit behavioral impairment after drinking, withdrawal after a single binge drinking session, and escalate their intake in response to induction of successive cycles of dependence. 48,50 Notably, HDID mice do not exhibit altered tastant preference or alcohol clearance rates. 52,53 One clear limitation of the DID model is that ethanol is not offered as a choice versus water, and when it is, ethanol intake and blood alcohol levels are somewhat lower. 48,53 This selection has one or two unusual features. The first is that we bred for a pharmacological endpoint (blood alcohol level after drinking) rather than for increased intake. As Fig. 11.4 shows, animals did nonetheless show elevated drinking across generations, which was expected. However, they achieve higher blood levels by patterning their drinking differently. HDID-1 mice show larger (longer) bouts of sustained drinking, while HDID-2 mice show more frequent, smaller bouts. 54 Second, given that the HS/Npt foundation population shows very low blood levels (and intake: see data at Generations S0 and S14 in Fig. 11.4 ), we elected not to develop parallel lines for low blood levels after DID.

Figure 11.4 . Upper panel: Response to unidirectional selective breeding for blood ethanol concentration (BEC) in mice. High Drinking in the Dark (HDID) mice were offered 20% ethanol in place of water for 4 h starting 3 h into their circadian dark session. Each data point represents the mean ± standard error BEC at the end of drinking for that generation's population of about 100–150 mice (approximately half males and half females). HDID-1 mice (closed symbols) have been selected for 37 generations. The gap between S28 and S29 for HDID-1 represents 2 generations where selection was relaxed. Selection of HDID-2 mice (open symbols) was initiated 2 years later and is at the 31st selected generation. Response lines are plotted versus selected generation. Lower panel: Consumption in g ethanol/kg body weight is also shown, although selection was based entirely on BEC. HS/Npt data are shown at the outset (generation S0) and for 14th generations later. This genetically segregating population served as the foundation population for both lines and has never been directionally selected. For details, see Refs. 48,51 .

In an initial attempt to explore the genomic structure of response to intense selection, we compared patterns of gene expression in ventral striatum tissue from 48 naïve, male mice from all three genotypes. 40 We compared HDID-1 mice from the 22nd selected generation, HDID-2 mice from the 15th selected generation, and HS/Npt unselected controls. Using Illumina WG 8.2 arrays, we analyzed SNP variation in 3683 markers: analyses were carried out marker by marker and with Weighted Gene Coexpression Network Analysis [WGCNA: Refs. 55,56 ]. For both QTL analyses and network analyses, we predicted that genetic variability across animals would be greatest in the unselected HS mice, which we found to be true. We predicted that the HDID-2 mice would show differences from HS, and that the HDID-1 mice would show even larger changes given their greater response to selection at that point. Of the more than 9000 transcripts (more than 7000 unique genes) surveyed, there were more genes differentially expressed between HDID-1 and HS than HDID-2 and HS, and 94 transcripts differed from HS in both lines, with the same directionality.

One interesting finding from this study is shown in Fig. 11.5 . The WGCNA identified 21 modules, each representing a number of coexpressed genes. Of these, four modules were strikingly and consistently affected by selection. In some instances, the coherence of the module was increased by increased selection (i.e., HDID-1 > HDID-2 > HS), while for others, the opposite was true (see Fig. 11.5 ). The overall signature of selection indicated that intramodule coherence was more meaningfully responsive to selection (i.e., consistent across the two replicates) than the specific differences in expression of individual genes. 40

Figure 11.5 . Multidimensional scaling plots of the coexpression networks in (A) heterogeneous stock (HS/Npt), (B) High Drinking in the Dark (HDID)-2, and (C) HDID-1 datasets. For visual clarity, only the four modules most consistently affected by selection (“black,” “magenta,” “dark red,” and “green”) are depicted. Each dot represents a transcript, with colors corresponding to module assignments. The distances between points correspond to network adjacency. The figure illustrates (1) the modularity of the networks, with similar colors clustered together, and (2) the effect of selection on the network structure, with HDID-2 and HDID-1 successively diverging more from the original HS/Npt network structure. In particular, the “dark-red” module appears have become more dispersed, while the “magenta” module appears to have become more compacted in the selection networks.

From Iancu OD, Overbeck D, Darakjian P, et al. High Drinking in the Dark selected lines and brain gene coexpression networks. Alcohol Clin Exp Res. 201337:1295–1303 with permission.


What is the molecular biology behind an allele being recessive or dominant?

The dominance of different alleles of a gene is largely determined by the nature of the protein that it encodes. For example, defects in structural proteins generally manifest as dominant traits because being heterozygous results in defective protein synthesis, which disrupts the native healthy protein. On the other hand, defects in enzymes tend to be recessive because there is a certain amount of compensation, such that heterozygotes may be asymptomatic (aka gene dosage effect). These rules do not always hold (eg haploinsufficiency with familial hypercholesteremia), but are useful generalizations.

Here's my attempt to simplify the above via analogy:

So think of structural proteins (very simplistically) as bricks. The allele (B) codes for a normal brick, while the allele (b) codes for a brick that is spherical instead of rectangular. You can have BB, which makes the wall all rectangular and normal, or you can have bb, which is just a pile of spheres. What about the heterozygote? Bb will lead to half normal bricks and half spheres, which ultimately does your wall no good. In this scenario, the heterozygote still has a loss of function, so we think of that trait as ɽominant'.

Now think of enzymes (very simplistically) as trucks carrying cargo from point A to point B. Again, you can have working trucks (T) or broken trucks (t). Having only working trucks (TT) is great - everything gets delivered on time. Having only broken trucks (tt) is bad. What about the heterozygote (Tt)? Well it depends on how much cargo you need to deliver! If you have a low cargo day, then the number of working trucks you have may be sufficient. In this case, the heterozygote is not affected, so we think of the trait of 'recessive'.

Excellent explanation, I particularly like the truck analogy.

Thank you for this excellent explanation, and thanks to the OP for asking the question. I didn't realize I was never taught this, and it's such a simple concept to understand. I'm glad to have that hole in my understanding of the world filled.

Just a follow up question: Does the expression levels of an allel maybe also contribute whether an allele is recessive or dominant? For example, what if you've got a allele with a strong promotor, compared to it recessive homologue with a weaker one? For example, one gene encodes for a protein which produces a yellow pigment, another homologue of said gene encodes for a protein producing a red pigment. Assuming identical expression levels of the gene and identical synthesis rates of the proteins, the resulting colour would be orange. I'm just wondering if an altering of the colour (or the dominance of a gene) really just entirely depends upon the proteins structure (and thus its efficency) or also up its expression levels.

You should be more explicit in your explanations.

In this scenario, the heterozygote still has a loss of function, so we think of that trait as ɽominant'.

The dominant allele was the little b and the the recessive allele was the big B. This confused me for a minute since the common notation is that the large B for dominant and little b for recessive.

In this case, the heterozygote is not affected, so we think of the trait as "recessive."

I don't know if I'm misunderstanding the way you wrote this or if you made a mistake. If a heterozygote is unaffected, then the heterozygote's expression would be a dominant trait. The only thing recessive in this situation would be the little t (broken truck) allele.

When an organism is heterozygous for some trait I always thought all the proteins expressed were going to be identical to someone with homozygous dominant. By your analogy it seems I was totally wrong about that. I think I got that impression from learning about Mendel's peas where heterozygous with a dominant green allele manifested as the same phenotype as the homozygous dominant for green color. Would the color of the peas be determined by a structural protein in this case? Would the dominant allele be expressed more in the heterozygote? I guess I'm still a little confused how the color ends up the same with heterozygous with a green phenotype and homozygous dominant green phenotype

This was a great explanation!

There's an important point that should be emphasized here. The dominant vs recessive nature of an allele tells you very little about the actual molecular nature of the mutation on its own. All it says is: do you see an observable effect (phenotype) with one copy of the mutant allele (dominant) or two (recessive)? What is actually happening on the molecular level requires further experiments, especially if it's dominant.

So let's say you have an egg factory with an assembly line, two workers, one on each side at each stage (those are our alleles). One day the supervisor comes in and notices a bunch of broken eggs and scattered boxes at the end of the line. Well what happened? So the supervisor switches workers around and narrows it down to a problem with one of the egg sorters determining it's a ɽominant' problem (this would be the equivalent of getting a family history and genotyping). Well, why is this one worker a problem? Maybe he just isn't working hard enough and the other guy can't pick up the slack, causing the quality control guy at the end of the line to get angry and throw half filled boxes on the floor (loss of function, haploinsufficient). Maybe he's a little overzealous and loads too many eggs into a box causing them to stack wrong and fall on the floor (gain of function, hypermorph). Maybe he's a joker and distracts the other sorter who would normally be able to pick up the slack, again pissing off the QC guy (gain of function, antimorph). Or maybe he's just a dick and throws a few eggs down the line on occasion to piss off the boss (gain of function, neomorph).

My point is that all of these are possibilities already knowing it's a dominant mutation (the same goes for recessive, although its a bit simpler). There are some neat genetic tricks to figure out which of these is the case, but it takes some legwork to go from phenotype to molecular mechanism.

Sorry, but using your brick and sphere analogy, wouldn't the spheres be the "dominant" trait since the heterozygotes would have the same phenotype as the ones with the genotype homozygous for spheres?

To add to this, mutations can also affect the regulation of gene expression in addition to the gene products themselves.

Of the thousands of genes a typical organism, only some will be active at any given time. Some only turn on for brief periods in response to a signal. Some are only present in particular tissues (like photopigments in your retina, digestive enzymes in your digestive epithelium, neurotransmitters in your brain, etc.). In fact, most will cycle throughout the day as part of your circadian rhythm.

A gene that's OFF is just like youɽ imagine there's little or no transcription of the DNA, so no RNA or protein products are made. ON can be a little more complicated. Sometimes ON means hundreds of transcripts being made in a day, or perhaps thousands. It varies a lot, and the degree to which a gene is ON is also part of this regulation.

Back to alleles: an allele is just a different version of DNA sequence. Sometimes that change (mutation) will lie in the part of a gene that codes for a protein. Other times, that change will occur in the sequence before, after, or within a gene that is responsible for that gene's regulation. (yes, the within part is weird to think about, but it's true!)

This happens when special proteins called transcription factors (TFs) bind to particular sequences of DNA and affect transcription. This can happen when TFs recruit transcriptional machinery to the gene, or conversely, make it harder to access. Effectively, this means turning the gene ON or OFF.

If you mutate the sequence that's normally responsible for turning the gene ON, what happens? The gene never turns on, so it's like a null allele. Usually one copy is enough, so it usually only has an effect if both copies are null in this way (recessive). You can imagine similar problems happening when genes are turned too far ON. In this case, only one copy is needed to mess things up with extra gene product (dominant).

There's more than just OFF and ON, though. Some mutations will make it so that a gene no longer turns ON when it should, or perhaps it doesn't turn OFF when it should. The gene product can still be made, it just happens at the wrong time. Depending on the specifics of when and where this happens, it might not affect anything, or it could be lethal, or you get weird developmental abnormalities, etc.

That's the key insight, I think. The sky is the limit when it comes to mutant phenotypes. There's a lot more at play than just OFF and ON, dominant or recessive.


Frozen Evolution. Or, that’s not the way it is, Mr. Darwin. A Farewell to Selfish Gene.

Dominant and recessive relationships are the best known forms of gene interaction between alleles within a single locus. (See also Gene interactions). Diploid organisms have two alleles from each gene. If both alleles at a given locus are the same, then (from the standpoint of the particular gene) this is termed a homozygote individual, a homozygote. If the two alleles differ, then this is a heterozygote individual, a heterozygote. The manifestation of each allele can depend on the second allele in the given locus for the particular individual. It very often happens that a particular allele is recessive, i.e. it is manifested in the phenotype only when present in two copies in the given individual, i.e. in a recessive homozygote. A dominant allele is the opposite of a recessive allele. Its presence is manifested in the same way both in a carrier of two copies of the given allele, i.e. in a dominant homozygote, and in a heterozygote, i.e. in an individual in which it is present in only one copy. The degree to which semi-dominant alleles, i.e. alleles with partial dominance, are manifested in the phenotype of an individual depends on whether they occur in the genotype of the given individual in one or both copies. In co-dominance, the two alleles present are manifested to the same degree to which they would be manifested in the relevant homozygotes. While, in partial dominance, the degree of manifestation of the two alleles in a heterozygote is less than for one or the other homozygote, in super-dominance, the expression of the given trait is greater in a heterozygote than in either of the two homozygotes. Interactions between alleles of a single locus can be divided schematically only if these alleles are manifested in the degree of the phenotype expression of a simple quantitative trait. For traits of qualitative character, it is mostly possible to differentiate only between dominant and recessive alleles mutual differentiation of alleles with partial dominance, super-dominance and co-dominance is usually rather difficult or even impossible.

The picture is further complicated by the fact that that there are usually more than two alleles of a single gene and also by the fact that dominance is a relative matter, i.e. the matter of the relationship between two specific alleles of a given gene, rather than an absolute property of a particular allele. Allele a1 can act as dominant in relation to allele a2, allele a2 as dominant in relation to allele a3 and simultaneously allele a3 as dominant in relation to allele a1. So that the subject of dominance and recessivity is even more complicated, it is necessary to point out the fact that a particular relationship between two particular alleles can also depend on the context, i.e. the effects of genes present at other loci can also be important. In the presence of a particular allele at locus B, allele a1of locus A can be dominant in relation to allele a2 in the context of a different allele at locus B, allele a1can, on the other hand, act as recessive towards allele a2

A certain amount of direct and indirect evidence demonstrates that the dominance of alleles is actually a more complex phenomenon that is, itself, the subject of biological evolution (Bourguet 2001). For example, it was repeatedly found that, in the natural population, the most common alleles are usually dominant and, on the other hand, minority alleles are frequently recessive. If, on the other hand, we isolate individuals in the laboratory that bear two newly formed mutated alleles, or if we obtain individuals bearing minority alleles in mutually isolated natural populations, then the relationship of partial dominance is mostly found between their alleles. For different explanation of the phenomenon see also Haldane&rsquos sieve.



Comments:

  1. Dailmaran

    I think you are not right. I can defend my position.

  2. Donahue

    Thanks for the help in this matter, I also think that the simpler the better ...

  3. Goltikora

    I wanted to see for a long time thanks

  4. Gardarg

    From worse to worse.

  5. Corby

    Please, explain more in detail



Write a message