September 30th, 2013 Biology 2C03: Genetics Quantitative Genetics ...
Biology 2C03: Genetics Quantitative Genetics
September 30th, 2013
Quantitative Genetics - Thus far we have learned about Mendelian inheritance and population genetics, where we see that many traits are determined by 1 or 2 genes with a large effect - What about human height, crop yields, running speed, behaviour, etc. many genes and the environment play a role in these phenotypes - The genetic analysis of complex characteristics is known as quantitative genetics - Many interesting traits do not show simple patterns of inheritance - How do we study the genetics of these traits? - NOTE: each gene or locus still follows the rules of Mendelian inheritance
Qualitative (Discontinuous) Characteristic - Qualitative characteristics: exhibits only a few distinct phenotypes - May be determined by one gene with many alleles or multiple genes - Phenotype: tall or dwarf - Phenotype: dwarf, short, medium, tall, very tall
Quantitative Characteristics - Quantitative characteristics: continuous variation within a range of phenotypes 1) Many are polygenic
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2) Often affected by variation in the environment, even one gene can display this 3) Often both play a role (multifactorial) Phenotype: a quantitative measurement (number) of height such as 21cm, 22.5cm, 28cm, etc.
Types of Quantitative Traits 1) Continuous variation: can assume any value between two values (boundaries) – the number of phenotypes is limited by the resolution of the measurement tool E.g. human height, seed weight, milk production 2) Meristic characteristics: not continuous, but determined by multiple genetic and environmental factors E.g. dog litter size – measurements are discrete, 1 pup, 2 pups, 3 pups, but underlying mechanism quantitative 3) Threshold characteristics: not continuous, trait is simply present or absent, but determined by multiple factors E.g. human cancer – present or absent, but many factors (genetic, environmental) contribute to susceptibility Sickle cell: one genotype guaranteed to have disease
How Might Multiple Genes Lead to a Quantitative Characteristic? - Simplest scenario – multiple genes that do the same, so that different genotypes can lead to a range of variation
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Gene A: A+ functional allele that codes for a hormone; A-, non-functional alleles, no hormone Gene B: B+ functional allele that codes for a hormone; B-, non-functional alleles, no hormone Gene C: C+ functional allele that codes for a hormone; C-, non-functional alleles, no hormone Looking at potential genotypes: 6 different alleles that contribute Assume that all alleles are producing hormone will increase height More loci = more variation
Polygenic Inheritance in Wheat (Nilsson=Ehle) - One of the first demonstrations polygenic inheritance - Looks like incomplete dominance - If one gene is involved, what ratio would you expect? 1purple:2 red:1 white - Actual observation: 1 purple:4 dark red:6 red:4 light red:1 white
Interpretation of Nilsson-Ehle’s Cross - Let’s assign genes as if it were a dihybrid cross - Assign alleles as contributing or non-contributing (like incomplete dominance at each gene) - A+, B+ contribute pigment - A-, B- do not contribute pigment - AABB: purple - AaBB or AABb: dark red - AaBb: red - aaBb or Aabb: light red - aabb: white - In fact, Nilsson-Ehle identified three genes, making colouration appear as continuous variation between white and purple - Although this is a quantitative (continuous) trait, the underlying mechanism is Mendelian inheritance
Conclusion of Nilsson-Ehle’s Cross - The difference between quantitative characteristics and qualitative characteristics is the number of loci influencing the trait - When multiple loci affect a character, more genotypes are possible; so the relation between genotype and phenotype is less obvious - As we start to increase the number of loci involved we see more phenotypic classes and it makes it harder to determine which genotype gives which phenotype
Determining Gene Number for Polygenic Characteristic - Monohybrid: ¼ resemble a true-breeding parent - Dihybrid: 1/16 resemble a true-breeding parent - Trihybrid: ¼ resemble a true-breeding parent - General rule for genes that are contributing to a polygenetic inheritance: (¼)n of the F2 are similar to one of the original parents. N= number of participating genes - This is limited by several caveats Genes influencing characteristic have equal effects
Example colour in corn, two genes contributing to the same phenotype Effects are additive Loci are unlinked Limited environmental effects
Statistical Study of a Polygenic Characteristic - Case study: flower length in tobacco case study (Edward East) - How is flower length in tobacco plant determined? - Two strains of tobacco plant - Each inbred for many generations – this has the effect of making them homozygous for most genes (true-breeding) - Mean or average flower length is different in each strain - Within a strain there is no genetic variation for genes contributing flower length - Variation within each strain is due to environment - Strain A and strain B have the same genotype - Crossed two strains: 1) What is the mean flower length? ~67mm, halfway between two parental strains 2) What is the degree of genetic variation in F1? All F1 have the same genotype – heterozygotes so there was no genetic variation 3) How much variance do you see in F1 relative to the parents? About the same 4) What is the source of variance in F1? Environment - Interbred F1 1) What is the mean flower length About 67mm (same as F1) 2) What is the degree of variance in F2 Greater than F1 3) What is the degree of genetic variation in F2? Greater than F1, since F2 do not all have same genotype - Increased genetic variation due to different genotypes in F2 - Selected some F2 plants and interbred them to produce F3 progeny - Flower length in F3 was dependent upon phenotype of F2 parents Shorter flowers in F2 Longer flowers in F3
Statistical Study of a Polygenic Characteristic: Conclusions - Flower length differences were in part dependent upon genotype and therefore heritable - In F2, of 444 plants, none were similar in phenotype to the original parents - For 4 genes, (¼)4 = 1/256 would have been expected to have one of the parental phenotypes - This suggests that more than 4 genes are involved - Flower length is determined by several genes and their effects are additive October 1st, 2013
Environment Can Lead to Variation in Phenotype - Same genotype can produce different phenotypes under different conditions - The range is the norm of the reaction - Gene: vestigial - Phenotype: wing size - Mutant allele: vg - Mutant phenotype: reduced wings - One genotype, a range of phenotypes under different temperatures - Another example we touched on in lecture 9L the Himalayan phenotype in rabbits - Genotype did not chance, completely dependent on the temperature (environment)
Genetic and Environmental Factors Affecting Phenotypes - There may be a norm of reaction for each genotype, phenotypes may now overlap - Norm of reaction - If there is a higher environmental effect the norms of reactions begin to overlap
More Genes Plus Environmental Factors Equals a Large Range for Phenotype - Three genes - More genes responsible, more genotypic combinations - Vary in degrees of overlap depending on the environmental effect
Heritability - Heritability: the amount of phenotypic variation within a population that is due to genetic variation - Heritability is describing how much of a phenotype is due to a genetic contribution - Phenotypic variation may be: 1) Entirely due to genetic variation (heritability = 1) 2) Entirely due to environmental variation (heritability = 0) 3) Due to a combination of genetic and environmental variation (heritability = 0
September 30th, 2013
Quantitative Genetics - Thus far we have learned about Mendelian inheritance and population genetics, where we see that many traits are determined by 1 or 2 genes with a large effect - What about human height, crop yields, running speed, behaviour, etc. many genes and the environment play a role in these phenotypes - The genetic analysis of complex characteristics is known as quantitative genetics - Many interesting traits do not show simple patterns of inheritance - How do we study the genetics of these traits? - NOTE: each gene or locus still follows the rules of Mendelian inheritance
Qualitative (Discontinuous) Characteristic - Qualitative characteristics: exhibits only a few distinct phenotypes - May be determined by one gene with many alleles or multiple genes - Phenotype: tall or dwarf - Phenotype: dwarf, short, medium, tall, very tall
Quantitative Characteristics - Quantitative characteristics: continuous variation within a range of phenotypes 1) Many are polygenic
-
2) Often affected by variation in the environment, even one gene can display this 3) Often both play a role (multifactorial) Phenotype: a quantitative measurement (number) of height such as 21cm, 22.5cm, 28cm, etc.
Types of Quantitative Traits 1) Continuous variation: can assume any value between two values (boundaries) – the number of phenotypes is limited by the resolution of the measurement tool E.g. human height, seed weight, milk production 2) Meristic characteristics: not continuous, but determined by multiple genetic and environmental factors E.g. dog litter size – measurements are discrete, 1 pup, 2 pups, 3 pups, but underlying mechanism quantitative 3) Threshold characteristics: not continuous, trait is simply present or absent, but determined by multiple factors E.g. human cancer – present or absent, but many factors (genetic, environmental) contribute to susceptibility Sickle cell: one genotype guaranteed to have disease
How Might Multiple Genes Lead to a Quantitative Characteristic? - Simplest scenario – multiple genes that do the same, so that different genotypes can lead to a range of variation
-
Gene A: A+ functional allele that codes for a hormone; A-, non-functional alleles, no hormone Gene B: B+ functional allele that codes for a hormone; B-, non-functional alleles, no hormone Gene C: C+ functional allele that codes for a hormone; C-, non-functional alleles, no hormone Looking at potential genotypes: 6 different alleles that contribute Assume that all alleles are producing hormone will increase height More loci = more variation
Polygenic Inheritance in Wheat (Nilsson=Ehle) - One of the first demonstrations polygenic inheritance - Looks like incomplete dominance - If one gene is involved, what ratio would you expect? 1purple:2 red:1 white - Actual observation: 1 purple:4 dark red:6 red:4 light red:1 white
Interpretation of Nilsson-Ehle’s Cross - Let’s assign genes as if it were a dihybrid cross - Assign alleles as contributing or non-contributing (like incomplete dominance at each gene) - A+, B+ contribute pigment - A-, B- do not contribute pigment - AABB: purple - AaBB or AABb: dark red - AaBb: red - aaBb or Aabb: light red - aabb: white - In fact, Nilsson-Ehle identified three genes, making colouration appear as continuous variation between white and purple - Although this is a quantitative (continuous) trait, the underlying mechanism is Mendelian inheritance
Conclusion of Nilsson-Ehle’s Cross - The difference between quantitative characteristics and qualitative characteristics is the number of loci influencing the trait - When multiple loci affect a character, more genotypes are possible; so the relation between genotype and phenotype is less obvious - As we start to increase the number of loci involved we see more phenotypic classes and it makes it harder to determine which genotype gives which phenotype
Determining Gene Number for Polygenic Characteristic - Monohybrid: ¼ resemble a true-breeding parent - Dihybrid: 1/16 resemble a true-breeding parent - Trihybrid: ¼ resemble a true-breeding parent - General rule for genes that are contributing to a polygenetic inheritance: (¼)n of the F2 are similar to one of the original parents. N= number of participating genes - This is limited by several caveats Genes influencing characteristic have equal effects
Example colour in corn, two genes contributing to the same phenotype Effects are additive Loci are unlinked Limited environmental effects
Statistical Study of a Polygenic Characteristic - Case study: flower length in tobacco case study (Edward East) - How is flower length in tobacco plant determined? - Two strains of tobacco plant - Each inbred for many generations – this has the effect of making them homozygous for most genes (true-breeding) - Mean or average flower length is different in each strain - Within a strain there is no genetic variation for genes contributing flower length - Variation within each strain is due to environment - Strain A and strain B have the same genotype - Crossed two strains: 1) What is the mean flower length? ~67mm, halfway between two parental strains 2) What is the degree of genetic variation in F1? All F1 have the same genotype – heterozygotes so there was no genetic variation 3) How much variance do you see in F1 relative to the parents? About the same 4) What is the source of variance in F1? Environment - Interbred F1 1) What is the mean flower length About 67mm (same as F1) 2) What is the degree of variance in F2 Greater than F1 3) What is the degree of genetic variation in F2? Greater than F1, since F2 do not all have same genotype - Increased genetic variation due to different genotypes in F2 - Selected some F2 plants and interbred them to produce F3 progeny - Flower length in F3 was dependent upon phenotype of F2 parents Shorter flowers in F2 Longer flowers in F3
Statistical Study of a Polygenic Characteristic: Conclusions - Flower length differences were in part dependent upon genotype and therefore heritable - In F2, of 444 plants, none were similar in phenotype to the original parents - For 4 genes, (¼)4 = 1/256 would have been expected to have one of the parental phenotypes - This suggests that more than 4 genes are involved - Flower length is determined by several genes and their effects are additive October 1st, 2013
Environment Can Lead to Variation in Phenotype - Same genotype can produce different phenotypes under different conditions - The range is the norm of the reaction - Gene: vestigial - Phenotype: wing size - Mutant allele: vg - Mutant phenotype: reduced wings - One genotype, a range of phenotypes under different temperatures - Another example we touched on in lecture 9L the Himalayan phenotype in rabbits - Genotype did not chance, completely dependent on the temperature (environment)
Genetic and Environmental Factors Affecting Phenotypes - There may be a norm of reaction for each genotype, phenotypes may now overlap - Norm of reaction - If there is a higher environmental effect the norms of reactions begin to overlap
More Genes Plus Environmental Factors Equals a Large Range for Phenotype - Three genes - More genes responsible, more genotypic combinations - Vary in degrees of overlap depending on the environmental effect
Heritability - Heritability: the amount of phenotypic variation within a population that is due to genetic variation - Heritability is describing how much of a phenotype is due to a genetic contribution - Phenotypic variation may be: 1) Entirely due to genetic variation (heritability = 1) 2) Entirely due to environmental variation (heritability = 0) 3) Due to a combination of genetic and environmental variation (heritability = 0
