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Mendelian genetics, also known as classical genetics ✓ Dominant and Recessive Traits: revealed the concept of dominant and recessive traits. Dominant traits are expressed when an individual has at least one dominant allele, while recessive traits are only expressed when an individual has two recessive alleles. ✓ Alleles: Genes come in pairs, and these gene pairs are called alleles, one inherited from each parent. Alleles are variations of a gene that can code for different phenotype of a trait. ✓ Segregation: During gamete formation, the two alleles segregate, with each gamete receiving one allele. This explains how traits are passed from one generation to the next. Exceptions/Extensions to Mendelian Genetics ✓ Mendelian genetics, also known as classical genetics ✓ Dominant and Recessive Traits: revealed the concept of dominant and recessive traits. Dominant traits are expressed when an individual has at least one dominant allele, while recessive traits are only expressed when an individual has two recessive alleles. ✓ Alleles: Genes come in pairs, and these gene pairs are called alleles, one inherited from each parent. Alleles are variations of a gene that can code for different phenotype of a trait. ✓ Segregation: During gamete formation, the two alleles segregate, with each gamete receiving one allele. This explains how traits are passed from one generation to the next. Mendelian Inheritance ✓ Independent Assortment: Independent Assortment states that genes for different traits segregate independently during gamete formation. This process evolved for the creation of genetic diversity. ✓ Recombination: Mendelian genetics explains the recombination of genes that produces new combinations of genes, contributing to genetic diversity. ✓ Homozygous and Heterozygous: Individuals can be homozygous if they have two identical alleles for a particular gene (e.g., TT or tt) or heterozygous if they have two different alleles (e.g., Tt). Homozygous individuals will express the corresponding trait, while heterozygous individuals will express the dominant trait or both in case of codominance Mendelian Inheritance ✓ Phenotype and Genotype: Phenotype refers to the observable physical or biochemical characteristics of an organism (e.g., flower color or seed texture), while genotype refers to the genetic makeup of an organism, usually denoted by the combination of alleles (e.g., TT, Tt, tt). ✓ Punnett Squares: Punnett squares are graphical tool. They help to determine the probabilities of offspring inheriting specific traits based on the genotypes of the parents. ✓ Mendel's Contributions: Mendel's work laid the foundation for modern genetics. His discoveries revolutionized the understanding of how traits are passed from one generation to the next. Mendelian Inheritance Exceptions Exceptions to Mendelian inheritance refer to situations where the observed patterns of inheritance do not conform (obey) to the classical Mendelian principles outlined by Gregor Mendel. Exceptions ✓ Gregor Mendel's laws of inheritance provide a foundational understanding of genetic inheritance, they do not explain and account several genetic phenomena. There are several exceptions/extensions and complexities to Mendelian genetics, which include: 1. Incomplete Dominance 2. Co-Dominance 3. Multiple Alleles 4. Pleiotropy 5. Lethality 6. Penetrance 7. Expressivity 8. Phenocopies 9. Epistasis 10.Genetic Linkage 11.Polygenic Inheritance 12.Environmental Influence (Epigenetics) 13.Non-Nuclear Inheritance (Extrachromosomal Inheritance) Incomplete Dominance Incomplete dominance is an exception to the principle of complete dominance. In this case, neither allele is completely dominant, and the heterozygous (hybrid) individual displays an intermediate phenotype (usually in F1 generation) • When the alleles showed incomplete dominance then deviations in Mendelian (phenotypic and genotypic) ratios can be observed in various crosses. • Intercrossing (Inbreeding) of two F1 hybrids displays three phenotypes: • Two parental • One intermediate SO, in F2 generation: 1:2:1 ratios of Phenotypes and genotypes Unlike the 3:1 Phenotypic and 1:2:1 genotypic ratios observed by Mendel in F2 generation. Incomplete Dominance Incomplete dominance is an exception to the principle of complete dominance. In this case, neither allele is completely dominant, and the heterozygous (hybrid) individual displays an intermediate phenotype Rr Rr Rr Rr R R rr RR r r Pink Pink Pink Pink Incomplete Dominance (F2) Rr Rr R r RR Rr Rr rr R r Red Pink Pink White Phenotype Genotype Red: 1 Homozygous Red: 1 Pink: 2 Heterozygous Pink: 2 White:1 Homozygous white: 1 Incomplete Dominance Dihybrid Cross If a Red flower producing Tall Plant is crossed with White flower producing short plant. All plant in F1 generation were tall with pink flowers. What would be the phenotypic ratios in F2 generation, if you are asked to cross two F1 hybrids? Phenotype Tall Red TTRR Phenotype Tall Pink TTRr Phenotype Tall Red TtRR Phenotype Tall Pink TtRr Phenotype Tall Pink TTRr Phenotype Tall white TTrr Phenotype Tall Pink TtRr Phenotype Tall white Ttrr Phenotype Tall Red TtRR Phenotype Tall pink TtRr Phenotype Short Red ttRR Phenotype Short pink ttRr Phenotype Tall pink TtRr Phenotype Tall white Ttrr Phenotype Short pink ttRr Phenotype Short white ttrr TR Tr tR tr TR Tr tR tr TtRr x TtRr (F2) Phenotypic Ratios 6:3:3:2:1:1 Incomplete Dominance Dihybrid Cross If a Red flower producing Tall Plant is crossed with White flower producing short plant. All plant in F1 generation were with intermediate height of their parents and white flowers. What would be the Genotypic ratios in F2 generation, if you are asked to cross two F1 hybrids? Phenotype TTRR Phenotype TTRr Phenotype TtRR Phenotype TtRr Phenotype TTRr Phenotype TTrr Phenotype TtRr Phenotype Ttrr Phenotype TtRR Phenotype TtRr Phenotype ttRR Phenotype ttRr Phenotype TtRr Phenotype Ttrr Phenotype ttRr Phenotype ttrr TR Tr tR tr TR Tr tR tr TtRr x TtRr (F2) Phenotypic Ratios Incomplete Dominance Dihybrid Cross If a Red flower producing Tall Plant is crossed with White flower producing short plant. All plant in F1 generation were short with pink flowers. What would be the Genotypic ratios in F2 generation, if you are asked to cross two F1 hybrids? Incomplete Dominance Dihybrid Cross If a Red flower producing Tall Plant is crossed with White flower producing short plant. All plant in F1 generation were with intermediate height and pink flowers. What would be the Genotypic ratios in F2 generation, if you are asked to cross two F1 hybrids? Phenotype TTRR Phenotype TTRr Phenotype TtRR Phenotype TtRr Phenotype TTRr Phenotype TTrr Phenotype TtRr Phenotype Ttrr Phenotype TtRR Phenotype TtRr Phenotype ttRR Phenotype ttRr Phenotype TtRr Phenotype Ttrr Phenotype ttRr Phenotype ttrr TR Tr tR tr TR Tr tR tr TtRr x TtRr (F2) Co-Dominance In co-dominance, neither allele is dominant or recessive. The heterozygous (hybrid) individuals experience the full expression of both alleles A classic example is the blood type system, where individuals with the genotype IAI B have type AB blood, expressing both A and B antigens. Multiple Alleles While Mendel's experiments involved traits controlled by two alleles (e.g., dominant and recessive), many traits are controlled by multiple alleles at a single gene locus. The classic example is the ABO blood group system, which involves three alleles (IA, IB, and i) controlling blood type. Human blood types: A,B,O and AB A and B are codominant to each other. Both A and B are dominant over O. I AI A I AI B I Ai I AI B I BI B I Bi I Ai I Bi ii I A I B i I A I B i A A B B O AB 4 Phenotypes 6 Genotypes Modified Dihybrid Cross: First Consider Each Trait on its Own Ex. 2 humans heterozygous for albinism and are blood type AB Modified Dihybrid Cross: Next Consider Both Traits Together Multiple Alleles A man with type AB blood marries a woman with type B blood whose father has type O blood. What are the chances that they have a child with following types of blood type A? Type AB? Type B? Type O? Multiple Alleles Genotype of man with type AB blood: I AI B Genotype of woman with type B blood whose father has type O blood. I Bi What are the chances that they have a child with type A blood? Type AB? I AI B I BI B I Ai I B i I A I B I B i AB: 25% A: 25% B: 50% Pleiotropy Some genes have multiple effects on an organism's phenotype. A single gene can influence multiple traits or characteristics An example is the gene responsible for sickle cell anemia, which affects not only red blood cell shape but also overall health. Polygenic Inheritance Many traits are influenced by the interaction of multiple genes at different loci. Each gene contributes to the phenotype incrementally. The overall phenotype of an organism produce by an additive effect of all genes contributing/control that phenotype. Polygenic Inheritance Traits controlled by two or more genes. Examples: • Human height, • eye and skin • color Environmental Influence The expression of certain traits can be influenced by environmental factors. The environmental factors could be both external and internal. Separate discipline of genetics-Epigenetics. • Epigenetics is the study of changes in gene expression or cellular phenotype that do not involve alterations to the underlying DNA sequence. • These changes can be heritable and reversible and are often influenced by environmental factors. • Epigenetic modifications can affect how genes are turned on or off, leading to variations in traits and behaviors without changes in the DNA sequence itself. Genetic Linkage Genetic linkage occurs when genes located close to each other on the same chromosome tend to be inherited together, rather than assorting independently as predicted by Mendel's Law of Independent Assortment Non-Nuclear (Extra Chromosomal) Inheritance While Mendelian genetics primarily focuses on the inheritance of nuclear DNA, genetic material can also be inherited from other cellular structures, such as mitochondria and chloroplasts. These non-nuclear genes exhibit unique inheritance patterns. • Maternal Inheritance or • Cytoplasmic Inheritance Lethality (Lethal Genes) A condition in which the presence of certain genetic mutations (DNA Sequence alteration) or alterations in a specific gene leads to the death or non-viability of an organism. Typically, during its development or at some stage of its life cycle. A gene is considered lethal when its normal function is essential for the survival of the organism, and any significant disruption or loss of function of that gene results in severe harm (Genetic disorder) or death. Lethality (Lethal Genes) In some mouse species homozygous dominant genotype is lethal Lethality (Lethal Genes) In some mouse species homozygous recessive genotype is lethal Lethality (Lethal Genes) In some mouse species homozygous recessive genotype is lethal Lethality (Lethal Genes) In all cases shown in mouse species 2:1 ratios will be observed instead of 3:1 Penetrance (Genetic) Penetrance is a measure of the proportion of individuals carrying a specific genetic mutation or variant who express the associated phenotype. Consider a dominant genetic mutation that leads to a specific disease. If 80% of individuals with the mutation develop the disease, the penetrance of that mutation is 80%. Expressivity Expressivity refers to the degree or extent to which a genetic trait or mutation is expressed in individuals who carry it. The variability in the severity or range of phenotypes associated with a particular genetic mutation. Consider a genetic mutation that can lead to a specific congenital disorder. Some individuals with the mutation may exhibit mild symptoms, while others may have severe symptoms. The range of symptom severity represents the expressivity of that mutation. Phenocopies • A phenocopy is a phenomenon in which an individual displays a particular phenotype that is similar to what would be expected from a specific genetic mutation • But the phenotype is not actually caused by that genetic mutation. Instead, the observed phenotype results from environmental factors or other non-genetic influences. Intra-Allelic interaction ▪ When allele of a same gene interact to produce ➢ Dominant effect ➢ Incomplete dominant effect ➢ Co-dominant effect Gene 1: A or either a allele Gene 2: B or b Gene 3: IA, IB or I ✓ Consider any two gene in di-hybrid cross Intra-Allelic interaction X A a B b X X X X A a IA i X X X X A a IB i X X X X A a IA IB X X X can affect the phenotype X Can’t affect the phenotype Both Allele X A a B b X X X X B b IA i X X X X B b IB i X X X X B b IA IB X X X Inter-Allelic interaction A a B b This type of interaction is also known as Epistasis Epistasis Epistasis Epistasis Epistasis Epistasis Eepistasis ▪ Epistasis is a genetic phenomenon in which the expression of one gene (locus) masks or modifies the expression of another gene at a different locus. ▪ In other words, the effect of one gene is dependent on the presence or absences alleles of other genes. ▪ Epistasis can result in complex patterns of inheritance and is an imperative interactions where one gene dictates other gene to express and vice versa Hypostatic and Epistatic Gene ▪ Epistatic gene (dictator gene): The gene that mask or modify the expression of other gene. ▪ Hypostatic gene (to be dictated): The gene whose effects are being modified are referred to as hypostatic gene. Epistatic Interactions Several types are epistatic interactions have been proposed and got experimental validation. 1.Recessive Epistasis (9:3:4) 2.Dominant Epistasis (12:3:1) 3.Duplicate Recessive Epistasis (9:7) 4.Duplicate Dominant Epistasis (15:1) 5.Polymeric (Gene action) Epistasis (9:6:1) 6.Additive (Quantitative) Epistasis (9:3:3:1) 7.Inhibitory Gene action (13:3) Epistatic Interactions AABB AABb AaBB AaBb AABb AAbb AaBb Aabb AaBB AaBb aaBB aaBb AaBb Aabb aaBb aabb AB Ab aB ab AB Ab aB ab AaBb x AaBb Recessive Epistasis (9:3:4) Recessive epistasis occurs when the presence of two recessive alleles at one gene locus prevents the expression of another gene at a different locus, regardless of the alleles present at the second gene. The genotype A-/bb and aa/bb will produce same phenotype AABB AABb AaBB AaBb AABb AAbb AaBb Aabb AaBB AaBb aaBB aaBb AaBb Aabb aaBb aabb AB Ab aB ab AB Ab aB ab AaBb x AaBb (9:3:4) Dominant Epistasis (12:3:1) In this type, the presence of one dominant allele at one gene locus can mask the expression of another gene at a different locus, regardless of the alleles present at the second gene. This is also known as dominant epistasis. •The genotype A-/B- and A-/bb will produce same phenotype AABB AABb AaBB AaBb AABb AAbb AaBb Aabb AaBB AaBb aaBB aaBb AaBb Aabb aaBb aabb AB Ab aB ab AB Ab aB ab AaBb x AaBb (12:3:1) Duplicate Recessive Epistasis (9:7) In this type of epistasis, two different gene loci, when homozygous recessive, can independently inhibit the expression of a third gene (allele). The genotype A-/bb, aa/B- and aa/bb will produce same phenotype AABB AABb AaBB AaBb AABb AAbb AaBb Aabb AaBB AaBb aaBB aaBb AaBb Aabb aaBb aabb AB Ab aB ab AB Ab aB ab AaBb x AaBb (9:7) Duplicate Dominant Epistasis (15:1) Duplicate dominant epistasis happens when two different gene loci need to have at least one dominant allele each for a specific trait to be expressed The genotype A-/B-, A-/bb and aa/B- will produce same phenotype AABB AABb AaBB AaBb AABb AAbb AaBb Aabb AaBB AaBb aaBB aaBb AaBb Aabb aaBb aabb AB Ab aB ab AB Ab aB ab AaBb x AaBb (15:1) Polymeric Gene action (9:6:1) Two homozygous recessive alleles at either gene loci produce similar phenotype in the presences of Dominant allele from either gene loci. The genotype A-/bb, B-/aa will produce same phenotype AABB AABb AaBB AaBb AABb AAbb AaBb Aabb AaBB AaBb aaBB aaBb AaBb Aabb aaBb aabb AB Ab aB ab AB Ab aB ab AaBb x AaBb (9:6:1) II. Novel phenotypes and F2 ratios due to gene interaction F2 = A-B- disc A-bb sphere aaB- sphere aabb long Additive (Quantitative) Epistasis (9:3:3:1) In additive epistasis, the alleles at different gene loci have additive effects on a trait. The presence of each additional dominant allele increases the expression of the trait. This effect often mistaken as non-epistatic interaction Additive (Quantitative) Epistasis (9:3:3:1) A-/B- A-/bb aa/B- aa/bb Inhibitory Gene action (13:3) The dominant allele of both genes become epistatic either homozygous or heterozygous state. Additionally, one gene in homozygous recessive state act as epistatic gene The genotype A-/B-, aa/B- and aa/bb will produce same phenotype aa in homozygous is epistatic AABB AABb AaBB AaBb AABb AAbb AaBb Aabb AaBB AaBb aaBB aaBb AaBb Aabb aaBb aabb AB Ab aB ab AB Ab aB ab AaBb x AaBb (13:3) Inhibitory Gene action (13:3) The dominant allele of both genes become epistatic either homozygous or heterozygous state. Additionally, one gene in homozygous recessive state act as epistatic gene The genotype A-/B-, A-/bb and aa/bb will produce same phenotype bb in homozygous is epistatic AABB AABb AaBB AaBb AABb AAbb AaBb Aabb AaBB AaBb aaBB aaBb AaBb Aabb aaBb aabb AB Ab aB ab AB Ab aB ab AaBb x AaBb (13:3) FUT1 Gene Control the production of a substance call H HH, Hh Genotypes will produce H[1]Substance hh Genotypes will not produce H[1]Substance FUT1 Gene Modifier gene effect on another locus that control ABO blood group I A – Antigen-A Blood Group A I B – Antigen-B Blood Group B I A I B – Antigen-A & B Blood Group AB Formation of Antigen A & Antigen B only Possible in the presence of H substance Example 1: H/h and AB pathway Precursor H substance H Substance A antigen B antigen A allele B allele HH or Hh hh Example 1: H/h and AB pathway Example 1: H/h and AB pathway FUT1 Gene- Bombay Gene Bombay- Phenotype Persons has Genes for Blood group A, B or AB Due to Absence of H substance their blood group become O Example 1: H/h and AB pathway Summary of modified F2 ratios - was Mendel just wrong? No, none of these cases has violated the principles of segregation and independent assortment - just added complexity. Practice Problem In a plant, a tall variety was crossed with a dwarf variety. All F1 plants were tall. When two F1 plants were interbred, 9/16 of the F2 were tall and 7/16 were dwarf. Explain the inheritance of height by a) indicating the number of gene pairs involved and b) by designating which genotypes yield tall and which yield dwarf. 1. When studying a single character, a ratio expressed in 16 parts suggests that two gene pairs are “interacting” during the expression of the phenotype. 2. A 9:7 ratio implies a dihybrid condition with epistasis. A-B- 9/16 A-bb 3/16 aaB- 3/16 aabb 1/16 3. From any dihybrid cross of double heterozygotes, we see the following genotypic ratio: 4. In our problem, we see a 9:7 phenotypic ratio. If the 3:3:1 groups above were lumped together, a 9:7 ratio emerges. Assign tall to any plant with both A-B- and dwarf to any plant that is homozygous recessive for either or both the recessive alleles. tall dwarf dwarf dwarf AaBb x AaBb