Lecture 4 Dominance relationships

1. Lecture 4 Dominance relationships

2. What is the biochemical explanation for dominance? The genetic definition of dominance is when an allele expresses its phenotype in the heterozygous condition. By saying A is dominant over a, we are saying AA and Aa have the same phenotype. Conversely the genetic definition of recessive is when allele does not express its phenotype in the heterozygous condition. For example a gene responsible for height in the pea plant has a dominant allele, T. T/T= 6ft T/t= 6ft t/t=2ft By definition 6ft is dominant to 2ft. And t is recessive to T. Now if the short phenotype is observed in the heterozygote, then T/T= 6ft T/t= 2ft t/t=2ft short is dominant to tall. Dominant and recessive are operational definitions.

3. Some genes make enzymes Genes are responsible for the production of specific proteins/enzymes. ***** Remember enzymes catalyze biochemical reactions. Substrate ---------> product EnzymeA ^ | GeneA Wild-type= phenotype observed most of the time in nature Phenotype characteristic of the majority of individuals of a species under “natural” conditions

4. For example here is the biochemical reaction responsible for producing the red pigment in flowers: Substrate ---------> Red pigment EnzymeA ^ | GeneA GeneA has two alleles: A= which is normal and makes functional enzyme a = which is mutant and produces nonfunctional enzyme Genotype Enzyme amount Phenotype (pigment) AA 2 enzyme units Red Aa 1 enzyme unit Red aa 0 enzyme unit white So for genes that code for an enzyme, Dominant = functional enzyme Recessive = nonfunctional enzyme

5. Incomplete dominance- Now lets look at something different: Although straightforward dominance/recessive relationships are the rule, there are a number of variations on this pattern of inheritance of PHENOTYPES One of these variations is called Incomplete dominance Incomplete dominance is the occurrence of an intermediate phenotype in the heterozygote. The heterozygote exhibits a phenotype intermediate between the two homozygotes A good example of this is in four o'clock plants:

6. Incomplete dominance- Although straightforward dominance/recessive relationships are the rule, there are a number of variations on this pattern of inheritance. One of these variations is called Incomplete dominance Incomplete dominance is the occurrence of an intermediate phenotype in the heterozygote. The heterozygote exhibits a phenotype intermediate between the two homozygotes A good example of this is in four o'clock plants: P: Pure white x Pure red F1: All Pink F2: 1/4Red 1/2Pink 1/4White How are these results explained? How do we relate genotype to phenotype

7. The following explanation readily explains the phenotypic outcome: P: Pure white x Pure red F1: All Pink F2: 1/4Red 1/2Pink 1/4White Do not use C and c to denote the two alleles- Use C1 and C2 C1= white C2= red C1/C2= pink In practice incomplete dominance can lie anywhere on the phenotypic scale Height: A1A1= 2ft A2A2= 6ft A1A2= 2ft -6ft The phenotype of the heterozygous individual is the key towards determining whether an allele behaves as a recessive, dominant, or incomplete dominance In incomplete dominance, Phenotype ratio= Genotype ratio

8. Another classic example of this is the colors of carnations. R1R2 x R1R2 R1 R2 R1 R1R1 R1R2 R2 R1R2 R2R2 R1 is the allele for red pigment. R2 is the allele for no pigment. Thus, R1R1 offspring make a lot of red pigment and appear red. R2R2 offspring make no red pigment and appear white. R1R2 and R2R1 offspring make a little bit of red pigment and therefore appear pink. Often in biological systems, substrate/product is limiting leading to incomplete dominance phenotypes.

9. Co-dominance: Another variation on the classical pattern of inheritance of phenotype is co-dominance The biochemical basis of co-dominance is understood for the blood groups M and N The surface of a red blood cell carries molecules known as antigens. More than 20 different blood group antigen systems are recognized. ABO system Rh system …….. The MN blood group system is of little medical importance. In this system there are two antigens, M and N. The L gene in humans codes for a protein present on the surface of the red blood cells. There exist two allelic forms of this gene LM and LN These two alleles represent two different forms of the protein on the cell surface.

10. So with respect to the red blood cells, the genotype and phenotype relationships are as follows: Genotype Phenotype LM LM LN LN LM LN At the protein level most phenotypes are Codominant!!! Both proteins are being expressed in the heterozygote. We are used to phenotypes as flower color, height, hair length, shape etc. The blood group phenotype is at a much finer level- that of the cell and is harder to observe. ***** Remember the phenotype chosen is what the geneticists happens to notice. In this respect it can be somewhat subjective and depend on how observant the geneticists happens to be.

11. Question: How do you study these phenotypes? To determine the phenotype of the LM and LN blood cells a very specific set of antibodies is required. The anti- LM antibodies specifically recognize the LM blood-cell surface proteins and the anti LN antibodies specifically recognize the LN surface proteins. In practice, specific recognition by each antibody results in precipitation of the red-blood cells. The antibody allows us to determine if the cell surface markers are LM or LN So with the anti- LM and anti- LN antibodies, one can determine which form of the L gene (LM or LN) is being expressed in each individual

12. Genotype Assay Phenotype Precipitation by - LN- LM antigen on RBC surface LM LM No Yes LM LN LN Yes No LN LN LM Yes Yes LM and LN In this case, the heterozygote is expressing both proteins. Therefore, with regards to expression of LM and LN protein on the RBC surface these alleles are co-dominant P: LM LM x LN LN F1: LM LN (self cross) F2: LM LM:LM LN : LN LN 1 2 1 Once again phenotype ratios are the same as genotype ratios. Co-dominant phenotype is different from incomplete phenotype

13. Paternity issues: Paternity issues: The M and N blood typing can be used to disprove that an individual was the biological father of a child. For example if the mother expressed only the M antigen, she could be only of one genotype- LMLM. If the child was of the genotype LMLN, we know the biological father must possess at least one LN allele. Mother's genotype Father's genotype LMLM x LMLN or LNLN This technique only rules out potential fathers (LmLm). It cannot prove that an individual is the father. As you will learn later in the course, DNA fingerprints can actually be used to identify the individual father.

14. Phenotypes When examining a dominance relationship between two alleles, we analyze phenotype in a heterozygote. Genotype phenotype Tt tall? Short? In between? With respect to blood in a LN LM individual and a LM LM individual Looking at RBC by the naked eye- the heterozygote will be like the homozygote. With regards to the M and N blood groups (by Immunoprecipitation) the phenotype is different in the two individuals. We have discussed pea shape, flower and eye color, Morphology as phenotypes. These are all properties that are easily visualized. However with specialized tools, microscopes and specific probes such as antibodies we can detect less easily visualized phenotypes.

15. Phenotypes Wild-type Mutant We have discussed pea shape, flower and eye color, Morphology as phenotypes. These are all properties that are easily visualized. However with specialized tools, microscopes and specific probes such as antibodies we can detect less easily visualized phenotypes. This indicates that the phenotype has subjective nature to it. It depends on the way the observer chooses to define it. This in turn depends on the individual's powers of observation and the tools available. For example, shown below are a normal and a mutant Drosophila wing. What is the difference?

16. Sickle cell anemia Sickle cell anemia is a good example of the variance in dominance relationships. Sickle cell is an inherited disorder that results from a mutation in the gene coding for the protein globin. Hemoglobin is a major constituent of the red blood cells and is involved in O2 transport. HbA: an allele that codes for the normal beta globin protein HbS: an allele that codes for an abnormal form of beta globin We will examine the phenotype of the two homozygotes and the heterozygote at three levels: the individual, the cell the protein. Remember, the phenotype of the heterozygote is the key to understanding whether a gene behaves as a dominant or recessive.

17. Normal O2 levels Sealevel Normal Normal Anemic Low O2 levels High altitude Normal Anemic Anemic HbA/HbA HbA/HbS HbS/HbS Depending on the O2 levels, the HBS allele (and the HBA allele) behaves as a dominant or recessive.

18. Genes and their products What is the cellular phenotype with respect to these genotypes The HBS allelic form of the protein causes the red blood cells to sickle. Cell shape HbA/HbA Normal shape HbS/HbS Sickled HBS/HbA Partially sickled *** At this level the alleles HbA and HBs are incompletely dominant

19. Phenotype at the level of the protein. With respect to the presence or absence of the proteins - + HbS/HbS HbA/HbS HbA/HbA HbS and HbA are co-dominant So the HbS allele is classified differently depending on the level the phenotype is analyzed: Individual Cell Protein Recessive &/or incomplete co-dominant Dominant dominant

20. Fitness Individuals homozygous for HbS/HbS often die in childhood. Yet, the frequency of the HbS allele is quite high in some regions of the world. In parts of Africa frequencies of 20% to 40% are often found for the HbS allele. It was found however that in areas in which there was a high HbS allelic frequency, that there was also a corresponding high frequency of mosquitoes infected with the protozoan parasite, plasmodium. This parasite causes Malaria in humans. It was proposed and later proven that heterozygous HbA/HbS individuals are more resistant to the mosquito born parasite. Consequently this allele in maintained in the population in spite of its deleterious consequences in the homozygous state. This condition in which the heterozygote is more fit than either of the two homozygotes is known as a balanced polymorphism (over dominance, heterozygote advantage) HbA/HbA HbA/HbS HbS/HbS Malaria sensitive resistant dead resistance

21. Lethal alleles- Most of the mutations that we have discussed do not affect the viability of the individual. For example the mutations that produce white eyes in Drosophila or wrinkled yellow cotyledons in the plant do not disrupt viability. This means that the mutated gene is specifically involved in determining eye color and is not involved in processes central to viability of the fly. What would be the genetic consequences if we isolated a mutation that disrupted an enzyme that was critical for the viability of the organism? In a plant RPN1/rpn1 x RPN1/rpn1 seeds produced You Plant seeds 75% produce plants 25% do not produce plants (lethal) RPN1 is a essential enzyme (proteosome)

22. In animals lethal mutations are difficult to follow You detect them by a distortion in the normal segregation ratio For example in Drosophila, Cy Cy+/Cy+ is normal wings (flies are alive) Cy+/Cy is curly wings (flies are alive) Cy/Cy is (curly wings) (flies are dead) WHEN YOU LOOK AT WING SHAPE- The Curly mutation is a dominant mutation that produces Cy wings in the heterozygous condition Flat wings (wild type) is recessive WHEN YOU LOOK AT LIFE, The curly mutation behaves as a recessive- recessive lethal.

23. Curly When a heterozygous Cy male is crossed to a heterozygous Cy female, look at LIVE PROGENY Cy to non-Cy progeny are produced in a 2:1 rather than the Mendelian 3:1 ratio + = normal or wild type gene cy= dominant Cy mutation

24. Curly When a heterozygous Cy male is crossed to a heterozygous Cy female, Cy to non-Cy progeny are produced in a 2:1___ rather than the Mendelian 3:1___ ratio + = normal or wild type gene cy= dominant Cy mutation cy/+ x cy/+ cy/cy cy/+ +/+ All Flies Lethal Curly Normal 1 2 1 Live Flies Curly: Non curly 2 : 1 Phenotype of survival 3alive (75%) : 1 dead (25%) Phenotype of curly 2 curly (66%) : 1 not curly (33%) The explanation for the _2:1__ rather than the expected _3:1__ ratio is that Cy behaves as a recessive lethal mutation and cy/cy individuals die prior to reaching adulthood. So you cannot score the wing phenotype.

25. How would you test this hypothesis? Take the progeny of the previous cross and perform a test cross with the homozygous recessive parent (+/+ wild-type fly)- Test cross +/+ x +/+ all normal flies cy/+ x +/+ 1:1 curly:normal cy/cy x +/+ all curly (not found) All curly flies from the previous cross only give a 1:1 ratio. There are no cy/cy flies!!!

26. Lethal mutations arise in many different genes. These mutations remain “silent” except in rare cases of homozygosity. A mutation produces an allele that prevents production of a crucial molecule Homozygous individuals would not make any of this molecule and would not survive. Heterozygotes with one normal allele and one mutant allele would produce 50% of wild-type molecule which is sufficient to sustain normal cellular processes- life goes on. Unlike cy, most recessive lethal alleles do not have an additional dominant visible phenotype. Mutations in enzymes required for DNA replication are lethal. Cells lacking this enzyme cannot replicate their DNA and die. For example let say a gene codes for an essential enzyme. GeneA (normal enzyme) Genea (mutant enzyme) The expected genotypes and phenotypes are as follows: genotype: A/A A/a a/A a/a phenotype: alive alive alive die Phenotype of survival is 3:1

27. Side bar-Lethal stocks It is difficult to keep a stock that is a recessive lethal and has no other phenotype. In each generation some of the lethal alleles are eliminated Gene A encodes an essential enzyme: · A = normal allele that encodes functional enzyme · a = mutant allele that encodes a non-functional enzyme and is recessive lethal (lethal when homozygous) Genetics helps solve this: In order to maintain a lethal allele geneticists use "marker" mutations such as cy

28. Lethal stocks It is difficult to keep a stock that is a recessive lethal and has no other phenotype. In each generation some of the lethal alleles are eliminated Gene A encodes an essential enzyme: · A = normal allele that encodes functional enzyme · a = mutant allele that encodes a non-functional enzyme and is recessive lethal (lethal when homozygous) A/a x A/a You get a/a A/a and A/A a/a die (some of the lethal alleles are eliminated) A/a and A/A cannot be distinguished!!!! Genetics helps solve this: In order to maintain a lethal allele geneticists use "marker" mutations such as cy cy+ wild-type allele cy is an allele that is dominant for curly wings and recessive for lethality.

29. Take a heterozygous fly for both the A gene and curly P:

30. Take a heterozygous fly for both the lethal A gene and the lethal curly gene P: a-CY+ X a-CY+ A-cy A-cy A-cy a-CY+ a-CY+ a-CY+ dead a-CY+ A-cy Alive a-CY+ a-cy A-CY+ Alive A-cy A-cy dead A-cy Notice only those classes identical to the parents survive and therefore the lethal allele can be kept in the heterozygous condition indefinitely

31. Multiple alleles We have described a gene as exiting in one of two states: normal or mutant. Each of these states is called an allele of that gene. Normal (wild-type) -----> Mutant Red eye white eye Smooth peas wrinkled peas However it is possible and common for a gene to have more than two forms. Many genes exist in three or more forms (we say there exists three or more alleles of that gene) Such a gene is said to have multiple alleles ****** It is important to remember that even though a given gene may have many forms, each individual possesses only two forms of that gene. Diploids contain two copies of each gene.

32. For example in Drosophila, many alleles exist for the white gene: 1) The normal (wild-type) allele W or w+ gives red eyes 2) white allele w has white eyes 3) white apricot wa gives apricot colored eyes As of 1996, there exist over 150 alleles of the white gene But in an individual fly there are only two alleles- e.g. W & wa or w & wa How many genotypes are possible given three alleles at the white gene? With 3 alleles, there are six possible pair-wise combinations W+/w W+/W+ W+/wa w/w wa/wa wa/w WT

33. WT -- Brown WT -- Vermilion WT -- White Enz V+ Precursor -----Brown pigment \ \ transporter W+ --------- Red / Precursor ----- Vermilion pigment / Enz B+

34. The C gene in rabbits · C- full color · cch- chinchilla (light gray) · ch- Himalayan (albino, black extremities) · c- albino These represent different alleles of the c locus with the following dominance relationship: Dominant ---------------> Recessive C ---> Cch ---> Ch ---->c The dominance relationship is relative to alleles being tested. You can only test TWO alleles at a time in a diploid (because there are only two alleles in any one individual) CC Ccch Cch Cc full color cchcch cchch cchcchinchila chch chc Himalayan cc albino

35. The C enzyme is a tyrosinase involved in melanin production Tyrosinase breaks down tyrosine Wildtype produces dark brown rabbits Ch allele has 20% of the activity of normal. Therefore Chinchilla is light brown h is a Ts mutant. Therefore Himalayan rabbits have black feet and ears but white body. C is albino. No enzyme made.

36. ABO blood groups The Human A,B,O blood group is the result of multiple allelism They were discovered in 1900 by Dr. Landsteiner. The 4 blood types were defined on the basis of a clumping reaction. Serum (the liquid part of the blood-Ab) from one individual is mixed with red blood cells (erythrocytes) from another individual. If they belong to different groups they will clump. This reaction is similar to the M and N groups discussed earlier. The clumping is due to the presence of antibodies in the serum. Blood group Genotype Ant on RBC Ab in blood A IAIA AB IAi B IBIB BA IBi AB IAIB AB -- O ii - AB A B

37. The ABO gene has three alleles IA synthesizes an enzyme that adds sugar A to RBC surface IB synthesizes an enzyme that adds sugar B to RBC surface i does not produce an enzyme The A phenotypes arises from two genotypes B blood type is due to two genotypes AB blood type is due to a single genotype O Blood type is due to a single genotype Three alleles give you six genotypes but only four phenotypes Each phenotype is determined by two alleles

38. The ABO gene has three alleles IA IB i IA synthesizes an enzyme that adds sugar A to RBC surface IB synthesizes an enzyme that adds sugar B to RBC surface i does not produce an enzyme A phenotype arises from two genotypes IAIA and Iai B blood type is due to two genotypes IBIB and Ibi AB blood type is due to a single genotype IAIB O Blood type is due to a single genotype ii Three alleles give you six genotypes but only four phenotypes Each phenotype is determined by two alleles IA is dominant to i but is co-dominant to IB

39. Blood transfusions B A B A There is a reciprocal relationship between antigens in the RBC surface and antibodies present in the serum. If an individual has A antigens in their RBCs, they will have B antibodies in their sera. The biological significance of this reciprocal relationship and the presence of the antibodies are not clear. This relationship has important implications for blood transfusions: A B B A A B B A AB O A B Cannot get blood from anyone except O individuals but can donate RBC to anyone UNIVERSAL DONOR Can get blood from anybody UNIVERSAL ACCEPTOR

40. Blood transfusions A B B A A B B A A B B A AB O A B If O individuals are transfused with A blood, the anti-A antibodies will react with the A cells resulting in clumping. · If O individuals are transfused with B or AB blood, clumping also occurs · O individuals can only receive O blood, but they can donate Red blood cells to A,B, AB, and O individuals- they are universal donors. · Since AB individuals have no antibodies they can receive RBC from A,B,AB, or O individuals. They are universal recipients · With respect to dominant relationships we say IA and IB are dominant to i and that IA and IB are co-dominant Cannot get blood from anyone except O individuals but can donate RBC to anyone (universal donor) Can get blood from anybody (Universal acceptor)

41. Evolutionary significance The evolutionary significance of these blood groups is obscure as there is no obvious advantage to possessing one blood group over another Blood group frequencies vary dramatically throughout the world and are invaluable in population genetic and anthropological studies Study in the Soloman Islands: One Island was 130 miles long and 40 miles wide. This island is home to over 17 major languages and most of these distinct languages are spoken in a range of less than 10 miles. Local populations appeared to have limited contact with one another suggesting that the island consisted of 17 socially and culturally isolated populations. That is there was little inbreeding among between the individual populations. Genetics were able to confirm this by identifying 17 distinct frequencies of ABO blood groups. This indicated that each population has been genetically isolated for a long time. If there were a significant frequency of marriages between the populations the frequencies would have equalized. This provided genetic evidence for the theory that they were culturally isolated.

42. Multiple alleles at the human HLA loci The HLA locus is the basis of tissue incompatibility in humans. That is, when an organ transplant or tissue graft is required, the success of the procedure depends on host donor genotypes. If the two are mismatched, graft rejection occurs. Whether a tissue is rejected depends primarily on the genotypes at two important loci known as the HLA loci: HLA-A------------ 23 recognized alleles HLA-B------------ 47 recognized alleles The HLA and HLB genes code for proteins that are located on the surface of the cells. For a successful transplant, the donor and recipient must have matching alleles at the HLA-A and HLA-B genes or risk graft rejection. If the alleles are different however, graft rejection will occur in some but not all of the transplant combinations Why this multiple allele system evolved at the HLA locus in unclear. It probably involved the tagging of the system as self or non-self (foreign). Cancer cells often express foreign antigens and are recognized by the immune system as foreign and destroyed.

43. Polymorphism Polymorphism is the existence of two or more allelic forms of a gene segregating in a population. Often these allelic forms have different phenotypic consequences.

44. Left-handedness: The inheritance of left-handedness in humans: 9% of the human population is left-handed Surprisingly no cultural group has been discovered that deviates substantially from this 9% value Population in remote area of Westerns Highlands 21/188 individuals statistically compatible with an 9 % value. Handedness and language- Most individuals have language functions located to their left hemisphere In 30% of left-handers and less than 5% of right-handers language functions are localized to right hemisphere

45. Handedness is human Rats, mice cats, dogs all show handedness- however there is no population preference 50% left-pawed 50% right-pawed Chimpanzee are 2/3 right handed and 1/3 left handed Humans are 90% right handed and 9% left handed A mutation may have produced a "dextral" (D) allele, strongly biasing handedness in favor of the right hand and control of speech toward the left cerebral hemisphere. Why study handedness? The laterization in the brain of language and handedness, indicates that studying handedness should illuminate the biology of language. Handedness much easier to measure and study than is language.

46. Is there a genetic basis for handedness? Family studies: Left-handedness runs in families Adoption studies- In contrast to that of biological children, the handedness of adapted children showed no relationship to that of their adoptive parents. The family trends reflect genetic rather than environmental effects. Modeling the genetics of handedness has always been difficult because of twin studies:The same Handedness is seen in Monozygotic twins (identical) only 82 % of the time.

47. iv gene in the mouse An important clue towards developing a model came from studying the inheritance of situs inversus encoded by the iv gene in the mouse Vertebrates are externally bilaterally symmetrical, but internal there is extensive left/right asymmetry with respect to the placement of internal organs. Researchers identified a mutation that caused the placement of the organs to be inverted with respect to the left/right axis. This mutation was named inversus viscerum (iv). Researchers identified a mutation that caused the placement of the organs to be inverted with respect to the left/right axis. This mutation was named inversus viscerum (iv). Heterozygous individuals exhibit normal positioning while homozygous individuals exhibit randomization: 50% of the homozygotes show a normal positioning and 50% an inverted positioning. The notion that a mutation may result in randomizing a process was new and readily applied to modeling the genetics of left-handedness in humans. The McNanus model- single gene at an autosomal locus has two alleles segregating in the population showing incomplete dominance