Phenotypic Variations Notes PDF

SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology Molecular Genetics Module 3: Unit 2...

SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology Molecular Genetics Module 3: Unit 2 Variations in Gene Expression The Traits that we have learned from the previous units are considered qualitative traits. It means that the expression of the genes involved is pretty straightforward. For example, the gene for seed color has alleles for green or yellow color. So, when the gene is expressed, the phenotype of the seed would either be green or yellow. The traits are clearly defined into two categories, green or yellow. For some traits, however, their phenotypic differences are not that obvious. These traits are controlled by genes with a cumulative effect such that the phenotypes show small, gradual differences. For example, in height, a 6 ft individual is phenotypically different from a 6’1” or a 5’9” individual. But the difference is not that obvious. For these traits, phenotypic differences are measurable, thus they are called quantitative traits. Figure 3.1.1. Discontinuous vs Continuous Traits (Hassan, 2018) So, looking at these differences, we can say that variations in gene expressions or phenotypic variations are influenced by the type, number, and inheritance pattern of the gene/s. However, we still have to take into consideration the effects of the environment on phenotype, which could contribute also to the variations that we observe. For example, the gene for skin color has alleles for fair skin. But for a fair-skinned individual to work the farm and be exposed to the sun every day for several years, the skin would be darker than it usually is. Phenotypic variance, therefore, is an interplay between genetic makeup and environmental factors. mjmbuenaventura’24-25 1  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology A. Concepts in Gene Expression 1. Penetrance / Quantitative Concept - penetrance refers to the proportion of a population that will exhibit a particular trait if the allele is found in their genotype. a. Complete Penetrance - 100% of all individuals with the same allele in their genotype expresses the trait Example: In complete dominance, brown eyes (B) are dominant over blue (b) eyes. So, individuals with BB or Bb will have brown eyes while those with bb will have blue eyes. Let’s say, in a population of 100, 70 people have the allele B in their genotype. If all of the 70 people will have brown eyes, then the penetrance of the gene is 100%. It would then follow that the 30 remaining individuals with bb in their genotype will have blue eyes because the gene is completely penetrant. b. Incomplete / Reduced Penetrance - Not all individuals with the same allele in their genotype expresses the trait - This is the type of penetrance exhibited by incomplete dominance, codominance, gene interaction, and epistasis Example: In incomplete dominance, flower color is governed by two alleles, IW for white and IR for red. However, having both IW and IR will neither produce white nor red but will produce pink. In short, the gene for flower color exhibits incomplete penetrance because the allele IW does not always give rise to white, and allele IR does not always give rise to red. 2. Expressivity / Qualitative Concept - Expressivity refers to the degree of expression of a penetrant gene - Expressivity, therefore, is dependent on penetrance - A trait must be penetrant for expressivity to be assessed. Example: Polydactyly is a dominant trait that is 100% penetrant. Individuals with the dominant allele exhibit extra fingers. However, the expressivity of the extra finger varies, such that some may be long, others short, or others may even look like a small stump. 3. Phenocopy - Phenotypic traits are genetic expressions while a phenocopy is a trait that is non- genetic - A phenocopy is due to an environmental factor but mimics a phenotype mjmbuenaventura’24-25 2  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology Example: Deafness : if it is due to a mutant gene, then it is a phenotype : if it is due to a viral infection, then it is a phenocopy Albinism : if it is due to a mutant gene, then it is a phenotype : if it is due to the absence of a required amino acid for melanin synthesis, then it is a phenocopy 4. Concordance and Discordance - These two terms refer to the expression of traits by members of monozygotic twins Concordance - If a trait is exhibited by both monozygotic twins, the trait is called concordant - It means that the trait has a genetic basis - Since monozygotic twins have exactly the same genetic composition, a genetic trait present in one member is also present in the other Discordance - if a trait is exhibited by one member of a monozygotic twin but is not exhibited by the other member, the trait is discordant - it has no genetic basis - the trait is due to an environmental factor Example: Deafness : if both members of a monozygotic twin were born deaf, then the trait most likely has a genetic basis, thus concordant : if only one member of the monozygotic twin is deaf, the condition cannot be genetic, thus considered discordant B. Inheritance of Quantitative Traits 1. Multiple Genes / Polygenes - quantitative traits are governed by multiple genes/polygenes thus referred to as polygenic traits - each allele of each gene interact additively and contribute to the expression of that particular trait - some polygenic traits include height, eye color, skin color, weight, and intelligence Example: Plant height is governed by four genes (hypothetical) Each allele contributes a particular quantitative value Assuming: A = 10” a = 5” (chromosome 1) B = 8” b = 4” (chromosome 2) C = 6” c = 3” (chromosome 3) D = 4” d = 2” (chromosome 4) mjmbuenaventura’24-25 3  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology then a plant with a genotype AaBbCcDd has a height of 42 inches - the more the dominant allele, the taller the plant - the more the recessive allele, the shorter the plant What would be the genotype and height of the tallest plant? What would be the genotype and height of the shortest plant? 2. Analysis of Quantitative Characteristics Regions of the DNA that contribute to a quantitative trait are collectively referred to as quantitative trait loci (QTL) and located in different chromosomes - most regions are protein-coding regions called genes, while some are regulatory regions (thus not called genes) but still contribute to the trait quantitative traits are affected by both the DNA and the environment, thus called multifactorial - phenotypic ranges tend to overlap because of the effect of the environment - makes inferring of genotype from phenotype difficult A polygenic trait is considerably variable because of the small continuous differences - They can have any value between the extremes - For example, in humans, the shortest person ever recorded is 21/2 inches tall and the tallest man was 8 ft 3 inches tall. Between these two extremes are variable heights. The distribution of quantitative traits in a population can be analyzed by statistical methods that compute for the mean, variance, and standard deviation, which you will encounter in your laboratory activity C. Components of Phenotypic Variance 1. Phenotypic variance - is determined by the genes of an individual and the environment VP = VG + VE Where: VP = phenotypic variance = differences in the phenotype observed in a population VG = genotypic variance = differences observed in a population that is due ONLY to the genotype VE = environmental variance = differences observed in a population that is due ONLY to environmental factors mjmbuenaventura’24-25 4  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology 2. Genotypic variance - is determined by incomplete dominance, complete dominance, and gene interactions and epistasis VG = VA + VD + VI Where: VA = additive genetic variance (aka breeding value) = a polygene is made up of several genes, each of which has a pair of alleles, and each allele contributes quantitatively to the phenotype = thus, VA refers to the variance due to the total quantitative effects of each allele in a polygene = the example on plant height in the previous page represents VA = it is also known as the breeding value because it represents the worth of the genes to the next generation; how much would the genes contribute to the phenotype of the offspring VD = dominance variance = Some genes that act on the same characteristic exhibit complete dominance = thus, VD refers to the variance due to the effect of a dominant allele VI = interaction variance = some genes that act on the same characteristic exhibit gene interactions = thus, VI refers to the variance due to the interaction between genes at different loci 3. Heritability - refers to the percentage of phenotypic variation that is due to genotypic variations - in other words, how much of the phenotypic differences in a population is a result of the differences in the genotypes of the individuals in that population - For example, when we say that height in a population has a heritability of 80%, we mean that 80% of the variation in height results from differences in the genotype of the individuals Example: In a family of 5 biological siblings who, despite being raised in the same environment, fed with the same food, and did the same activities, exhibit slight variations in skin color. (I know our example is not realistic but work with me here, to simplify the explanation). We can say that their phenotypic variations are due to their genetic makeup. The heritability of the trait is approximately 100% (0.99%). Another example: Let’s consider monozygotic twins. For whatever reason, they were separated at birth. One was raised on a tropical island, the other was raised in an icy country. When they grew up, one had darker skin than the other. In this example, we can say that their phenotypic variation is due to the mjmbuenaventura’24-25 5  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology environment and not their genetic makeup. The heritability of the trait is 0. - although heritability does not include the effects of the environment on phenotypic variations, the result of heritability studies is used to interpret the influences of nature (genetics) and nurture (environment) on quantitative traits. Example: Milk production in cows is a quantitative characteristic. Let’s say for example, on a farm, more cows have been producing more milk than the others. If the differences are due to the genetic makeup of the cows, then choosing and breeding those with “good genes” can increase milk production on the farm. However, if the difference is environmental, providing a better environment for the cows that have been producing less milk may improve their milk production. There are two types of heritability: a. Broad Sense Heritability (H2) - the proportion of the phenotypic variation due to ALL the genetic factors - includes all genetic effects combined (VA + VD + VI) H2 = VG X 100 Where: H2 = broad-sense heritability VG = genotypic variance VP VP = phenotypic variance b. Narrow Sense Heritability (h2) - proportion of the phenotypic variation based on the additive genetic variance - It is a measure of how likely an offspring will resemble its parents - it is important in determining how a trait will respond to selection - extremely important for breeding because it deals with traits that are of value for the next generation h2 = VA X 100 Where: h2 = narrow sense heritability VP VA = additive variance VP = phenotypic variance NOTE: If H2 = 0, the phenotypic variance is due to environmental factors only If H2 = 100%, the phenotypic variance is due to the genotype only If H2> 0 the phenotypic variance is partly due to genotype If h2 = 0, the phenotypic variance is due to environmental factors only If h2 =100%, the phenotypic variance is due to the additive genetic variance If h2> 0 the phenotypic variance is partly due to genotype mjmbuenaventura’24-25 6  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology SAMPLE PROBLEM SOLVING 1. Astyanax eye diameter has a genetic variance of 0.506 a phenotypic variance of 0.563. What is the broad-sense heritability? Interpret the heritability value. (Hartl,2020) Given: VG = 0.506 Required: H2 = ? VP = 0.563 interpret result Solution: H2 = VG X 100 H2 = 0.506 X 100 = 89.88% or 90% VP 0.563 Interpretation: 90% of the variation in eye diameter is due to the differences in the genotype of the fishes. 2. In a certain species of plant, stem length has a breeding value of 40 cm, a dominance variance of 18 cm, an epistatic variance of 5 cm, and an environmental variance of 25 cm. Determine the broad sense and narrow sense heritability. Given: VA = 40 cm Required: (a) H2 = ? VD = 18 cm (b) h2= ? VI = 5 cm VE = 25 cm Solution: (a) H2 = VG X 100 H2 = 63 cm X 100 H2 = 71.59% or 72% VP 88 cm VP = VG + VE VP = 63 cm + 25 cm VP = 88 cm VG = VA + VD + VI VG = 40 cm + 18 cm + 5 cm VG = 63 cm (b) h2 = VA X 100 h2 = 40 cm X 100 h2 = 45.45% or 46% VP 88 cm Interpretation for H2: 72% of the variation in plant height is due to the differences in the genotype of the plants. Interpretation for h2: 46% of the variation in plant height is due to the breeding value of the genotype of the plant and will be the same value that will contribute to the height of the next generation mjmbuenaventura’24-25 7  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology D. Epigenetic Inheritance Epigenetics comes from the word “epi” which means outside and “genetics” referring to the genes, thus epigenetics refers to the study of factors that alter gene expression without changing the DNA nucleotide sequence. In short, the phenotype is altered without altering the genotype (Aboud, et. Al., 2020). Molecules that alter gene expression either promote or prevent the transcription of genes. All these “gene expression-altering” molecules taken together make up the entire Epigenome. Most epigenetic changes are irreversible. All mitotic daughter cells inherit the change, thus remain throughout the lifetime of the organism. For example, an epigenetic change occurs in a stem cell so that it differentiates into a muscle cell. Once the cell has undergone the epigenetic change, the muscle cell will remain a muscle cell for the rest of the life of the organism. Another type of epigenetic change can occur in another stem cell and this time produces a connective tissue cell, which, under normal circumstances, will also remain a connective tissue cell for the rest of the life of the organism. This is differentiation. However, most epigenetic changes are reset or reprogrammed during gametogenesis or fertilization, thus the next generation does not inherit the epigenetic change. Everything goes back to zero so that the new organism formed will be the one to create its own epigenetic changes. And the cycle of epigenetics in the organism continues. There are always exceptions to a rule. Transgenerational epigenetic inheritance can occur if the epigenetic change is retained during gametogenesis, that is, the gametes still have the epigenetic change (Heard & Marteinssen 2014). So, when the sperm fertilizes the egg, the epigenetic change is transferred to or inherited by the offspring. This concept will be the concentration of our discussion later. 1. Mechanisms of Epigenetics a. DNA methylation - Functions to turn off gene expression - Methyltransferase adds a methyl group to the cytosine of the cytosine-guanine sequence in promoter regions - It prevents gene transcription, thus involved in gene silencing b. Histone modification - Histone proteins have tails that stick out of the nucleosome - These tails are easily accessible for epigenetic modifications that alter the packaging of the DNA, to either promote or prevent transcription - acetylation, methylation, phosphorylation, and ubiquitylation are some processes that alter gene expression via histone modification mjmbuenaventura’24-25 8  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology c. Gene Silencing by ncRNA - Non-coding RNAs (ncRNAs) are transcribed by the DNA but not translated to proteins - There are several different types of ncRNAs including microRNA (miRNA), small interfering RNA (siRNA), Piwi-interacting RNA (piRNA), and long non-coding RNA (IncRNA) - These ncRNAs regulate gene expression during and after transcription by participating in heterochromatin formation, histone modification, DNA methylation, and gene silencing. Figure 3.1.2. Mechanisms of Epigenetics (Khalil, 2014) 2. Epigenetic Factors Aside from differentiation, epigenetic processes may also occur due to environmental factors (fig 3.1.3) that could trigger DNA methylation, histone modifications, and miRNA post-translational modification (Alegria-Torres, et. Al., 2011). mjmbuenaventura’24-25 9  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology Figure 3.1.3. Epigenetic Factors (Alegria-Torres, et. Al., 2011) 3. Transgenerational Epigenetic Inheritance a. Paramutation - one allele (paramutagenic) will prevent the expression of another allele (paramutable) Example: In maize, allele A is responsible for dark color while allele a is for light color and is paramutagenic. Parent phenotype dark light Parent genotype AA X aa Gamete types A a R F1 genotype Aa Genotypic ratio 100% F1 phenotype light (because allele a is paramutagenic) Phenotypic ratio 100% mjmbuenaventura’24-25 10  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology Parent phenotype light light Parent genotype Aa X Aa Gamete types A a A a R R R F1 genotype AA Aa Aa aa Genotypic ratio 25% 50% 25% (or may also be written as) 1 : 2 : 1 F1 phenotype dark light light Phenotypic ratio 25% 75% (or may also be written as) 1 : 3 As long as the paramutagenic a is present in the genotype, the paramutable A is not expressed, thus the color of the corn kernel becomes light b. Genomic Imprinting - one allele is marked via DNA methylation for silencing, while the other allele is expressed (Smith & Bourc’his, 2018) This becomes a problem if the silenced allele is normal and the expressed allele is damaged or mutated - the expression of the trait of the offspring is dependent on the sex of the parent where the allele came from Example: In mice, if the insulin-like growth factor 2 (IgF2) is present (IgF2+), normal growth occurs. However, if it is absent (IgF2-), the mouse develops as a dwarf. The allele inherited from the father will be expressed while the allele inherited from the mother will be silenced. Mother Father Parent Genotype IgF2- IgF2- IgF2+ IgF2+ F1 Genotype IgF2- IgF2+ F1 Phenotype normal mjmbuenaventura’24-25 11  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology NOTE: We cannot identify the phenotypes of the parent since we do not know where their alleles came from (maternal or paternal) Reciprocal Cross: (exchange the genotype of parents) Mother Father Parent Genotype IgF2+ IgF2+ IgF2- IgF2- F1 Genotype IgF2+ IgF2- F1 Phenotype dwarf Example: In humans, a deletion in chromosome #15 leads to two types of syndromes, depending on the parental source of the chromosome. If the chromosome is inherited from the father, the offspring will have Prader-Willi Syndrome (PWS), whereas if the chromosome is inherited from the mother, the offspring will have Angelman Syndrome (AS). Assume: A+ represents the normal chromosome #15 A- Represents the chromosome #15 with deletion Mother Father Parent Genotype A+A+ A-A- F1 Genotype A+ A- F1 Phenotype Prader-Willi Syndrome Reciprocal Cross: (exchange the genotype of parents) Mother Father Parent Genotype A-A- A+A+ F1 Genotype A-A+ F1 Phenotype Angelman Syndrome mjmbuenaventura’24-25 12  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology c. Dosage Compensation - balances the expression of the X-linked genes in males and females Human - females are homozygous XX: one paternal in origin and the other maternal in origin - males are hemizygous XY - to balance the expression of X-linked genes in males and females, one of the X chromosomes of the female undergoes X-inactivation and forms a Barr body - X-inactivation occurs during early embryonic development, specifically during the formation of the embryonic epiblast (Van den Berg, et al., 2020) - It occurs randomly such that either the paternal X-chromosome or maternal X- chromosome is inactivated in the different epiblast cells - When the epiblast cells divide, the X-inactivation is passed on to daughter cells - Soon, the female body ends up having clusters of cells expressing X-linked genes from either the paternal X-chromosome or the maternal X-chromosome - Normally, 50% of cells inactivate a paternal X-chromosome and the other 50% inactivate a maternal X-chromosome. - But in some instances, there is a skewed X-inactivation (Minks, Robinson, & Brown, 2007) - Events like this are significant if an X-chromosome contains a recessive allele for a disorder - X-linked recessive is usually expressed only if they are in pairs, but a skewed inactivation can express a single X-linked recessive allele (fig 3.1.3) Figure 3.1.3. Skewed X-inactivation (Bouchard,2020) mjmbuenaventura’24-25 13  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology Drosophila - Females are homozygous XX, but both X chromosomes remain expressed - Males are hemizygous XY - To balance the expression of X-linked genes between the male and female drosophila, the X-linked genes of the male are expressed twice, or the expression is doubled Worms - Females are homozygous XX and males are hemizygous with only one X- chromosome, no Y chromosome (written as XO) - To balance the expression of X-linked genes, the expression of the X-linked genes in both X chromosomes of the female is reduced to 50% each Example: Female Calico Cats undergo random X-inactivation XO – orange Coat Xo – black coat Parent phenotype Orange black Parent genotype XOXO X XoY Gamete types XO Xo Y F1 genotype XOXo XOY F1 phenotype cells with inactivated XO black coat gives rise to black coat cells with inactivated Xo gives rise to orange coat orange and black combined mjmbuenaventura’24-25 14  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology Figure 3.1.4. X-inactivation in Female Calico Cats (Banna, 2018) References: BOOKS Brooker, R. (2015). Concepts of Genetics. 2nd ed. McGraw-Hill Education. Griffiths, AJF, Miller, JH, Suzuki, DT, et al. (2000). An introduction to Genetic Analysis. 7th ed. W.H. Freeman. Klug., WS, Cummings, M., Spencer, CA, et al. (2020). Essentials of Genetics. 10th ed. Pearson. INTERNET Alegrai-Torres, JA, Baccarelli, A, & Bollati, V. (2011). Epigenetics and Lifestyle. Epigenomics. Vol 3. No. 3. https://www.futuremedicine.com/doi/10.2217/epi.11.22 Al Aboud, NM, Tupper, C, Ishwarlal, J. (2020). Genetics, Epigenetic Mechanism. https://www.ncbi.nlm.nih.gov/books/NBK532999/ Banna, LK. (2018). X-chromosome inactivation in female “calico” cats. https://www.slideshare.net/LamaKBanna/genetics- dentistry-inheritance-patterns-or-modes-of-inheritance Bouchard, E. (2020). Skewed X-inactivation. https://genetics.thetech.org/ask-a-geneticist/x-inactivation-and-color- blindness Handy, DE, Castro, R, & Loscalzo, J. (2011). Epigenetic Modifications: Basic Mechanisms and Role in Cardiovascular Disease. Circulation, 123 (10), 2145-2156. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107542/ Hassan, MI. (2018). Qualitative vs Quantitative Traits [image]. https://www.slideshare.net/AhmedSallam1/quantitative-trait- mjmbuenaventura’24-25 15  SAINT LOUIS UNIVERSITY SCHOOL OF NURSING, ALLIED HEALTH, AND BIOLOGICAL SCIENCES Department of Biology loci-qtl-analysis-and-its-applications-in-plant-breeding Hill, W.G. (2010). Understanding and using quantitative genetic variation. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 365 (1537), 73-85. ttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842708/ Khalil, CA. (2014). Histone modification [image]. The emerging role of epigenetics. Therapeitic advances in Chronic Disease 5(4): 178-87. https://www.researchgate.net/publication/263585631_The_emerging_role_of_epigenetics_in_cardiovascular_disease /figures?lo=1 McClean, P. (1997). Quantitative Genetics. https://www.ndsu.edu/pubweb/~mcclean/plsc431/quantgen/qgen1.htm mjmbuenaventura’24-25 16