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Appendix 1.

A pool of examples to draw on in teaching within an integrated framework that can provide the “missing links” (Steps 2–3 in Figure 1) of how genes lead to traits. A balance of better-known examples (which are easier to incorporate) and lesser-known examples (which are attention-grabbing) is presented. The table, and all references, can be found at http://domin.dom.edu/faculty/skreher/.

Example of Trait with VariationOrganismGene/AllelesProteinTrait CategoryaUse in Framework: Linking Genes to Proteins to Traits & Explaining Trait Variation
I. Trait Variation due to Mutations in Coding Region (“Gene”) 
Round/wrinkled peasb Peas Rugosus gene Starch branching enzyme Physical See text for details. Example of classical trait that we understand molecularly. 
Fruit fly body axis development Fruit flies Toll Membrane receptor protein Physical Signaling through Toll communicates cell fate. Example of interesting D/R relationships.c 
The “waltzing” mouseb Mouse Snell’s waltzer deafness gene Myosin VI Behavior Not completely understood. Myosin VI is important for sensory hair cell development in the inner ear, which is linked to balance. 
C. elegans roller phenotypeb C. elegans worms rol-6 Collagen Behavior Mutations change interactions between collagen molecules in the cuticle, causing animals to roll. 
Bitter taste sensitivityb Humans TAS2R38 ≥5 alleles Taste Receptor Protein Biochemical/ Physiological Bitter substances such as PTC bind to this taste receptor. Different alleles linked to differential sensitivity to bitter compounds. 
Resistance to penicilin family antibiotics Various bacteria β-lactamase β-lactamase Biochemical/ Physiological The β-lactamase enzyme modifies β-lactam-containing antibiotics. Different alleles linked to differential activity and specificity (can disarm either some or many family members). 
Resistance to rifamycin family antibiotics Various bacteria rpoB RNA polymerase Biochemical/ Physiological Rifamycin antibiotics inhibit transcription by binding to RNA polymerase. Resistance mutations reduce binding to RNA polymerase. 
Organ transplant compatibility Humans HLA/MHC several genes 100s of alleles MHC proteins Biochemical/ Physiological Degree of match between MHC proteins in transplant vs. recipient determines immune response. MHC alleles are also linked to differential ability to respond to infections. 
Inherited breast cancer riskb Humans BRCA1 Many alleles DNA repair enzyme Disease/Risk Defective DNA repair increases chance of cancer mutations. Mutation is a dominant loss of function – example of haploinsufficiency. 
Inherited risk for Alzheimer’s disease Humans APOE-ε 4 ≥4 alleles Apolipoprotein E Disease/Risk Strong genetic association; but role of APOE, found in amyloid plagues in brain, is not completely understood. 
Sickle cell diseaseb Humans β-globin Many alleles Globin protein of hemoglobin Disease/Risk See text for details. Many alleles also cause different thalassemias, which range in severity. 
II. Trait Variation due to Mutations in Regulatory Regions 
Human eye-color variationb Humans OCA-2 Many alleles Membrane protein Physical Role of protein not completely understood. 
Dog size variation Dogs IGF-1 Insulin-like growth factor Physical IGF-1 induces cell mitosis. Alleles with higher growth-factor levels linked to larger dog size. 
Monogamy in voles Voles Interspecies V1aR Vasopressin receptor Behavior Vasopressin released during mating activates reward areas in brain in monogamous prairie voles, but not in montane or meadow voles. 
Human lactose intolerance Humans LCT Lactase enzyme Metabolism and Disease See text for details. 
Sickle cell diseaseb Humans β-globin Many alleles Globin protein of hemoglobin Disease/Risk Hereditary mutations related to the fetal hemoglobin (HbF) gene lead to continued HbF expression in adults, ameliorating SCD.d 
III. Trait Variation due to Epigenetics 
Agouti coat color in mice Mice Viable yellow Agouti allele Signaling protein Physical Epigenetic modification (DNA methylation) regulates deposition of color pigment. 
Flowering time in Arabidopsis Thale cress plants PCG and FLC Polycomb and flowering locus Physical Polycomb proteins regulate gene expression by regulating overall chromatin structure. 
Prader-Willi and Angleman Syndromes Humans Probably several genes Probably several proteins Disease/Risk Inherit epigenetically imprinted (differentially between the sexes) version from one parent and version with large deletion from the other. 
IV. Trait Variation due to Environmental Influences 
Sun tanning Humans Many genes  Physical UV light induces skin darkening. Also, example of mutations linked to evolutionary adaptation. 
Respiration capacity at high altitudes Humans Many genes  Biochemical/ Physiological Multiple physiological responses to high altitudes. Also example of mutations linked to evolutionary adaptation. 
Sickle cell diseaseb Humans β globin Globin protein of hemoglobin Disease/Risk High altitudes, exercise, level of hydration, and drugs (hydroxyurea) influence hemoglobin interactions or fetal hemoglobin gene expression, which affects symptom frequency and severity. 
Example of Trait with VariationOrganismGene/AllelesProteinTrait CategoryaUse in Framework: Linking Genes to Proteins to Traits & Explaining Trait Variation
I. Trait Variation due to Mutations in Coding Region (“Gene”) 
Round/wrinkled peasb Peas Rugosus gene Starch branching enzyme Physical See text for details. Example of classical trait that we understand molecularly. 
Fruit fly body axis development Fruit flies Toll Membrane receptor protein Physical Signaling through Toll communicates cell fate. Example of interesting D/R relationships.c 
The “waltzing” mouseb Mouse Snell’s waltzer deafness gene Myosin VI Behavior Not completely understood. Myosin VI is important for sensory hair cell development in the inner ear, which is linked to balance. 
C. elegans roller phenotypeb C. elegans worms rol-6 Collagen Behavior Mutations change interactions between collagen molecules in the cuticle, causing animals to roll. 
Bitter taste sensitivityb Humans TAS2R38 ≥5 alleles Taste Receptor Protein Biochemical/ Physiological Bitter substances such as PTC bind to this taste receptor. Different alleles linked to differential sensitivity to bitter compounds. 
Resistance to penicilin family antibiotics Various bacteria β-lactamase β-lactamase Biochemical/ Physiological The β-lactamase enzyme modifies β-lactam-containing antibiotics. Different alleles linked to differential activity and specificity (can disarm either some or many family members). 
Resistance to rifamycin family antibiotics Various bacteria rpoB RNA polymerase Biochemical/ Physiological Rifamycin antibiotics inhibit transcription by binding to RNA polymerase. Resistance mutations reduce binding to RNA polymerase. 
Organ transplant compatibility Humans HLA/MHC several genes 100s of alleles MHC proteins Biochemical/ Physiological Degree of match between MHC proteins in transplant vs. recipient determines immune response. MHC alleles are also linked to differential ability to respond to infections. 
Inherited breast cancer riskb Humans BRCA1 Many alleles DNA repair enzyme Disease/Risk Defective DNA repair increases chance of cancer mutations. Mutation is a dominant loss of function – example of haploinsufficiency. 
Inherited risk for Alzheimer’s disease Humans APOE-ε 4 ≥4 alleles Apolipoprotein E Disease/Risk Strong genetic association; but role of APOE, found in amyloid plagues in brain, is not completely understood. 
Sickle cell diseaseb Humans β-globin Many alleles Globin protein of hemoglobin Disease/Risk See text for details. Many alleles also cause different thalassemias, which range in severity. 
II. Trait Variation due to Mutations in Regulatory Regions 
Human eye-color variationb Humans OCA-2 Many alleles Membrane protein Physical Role of protein not completely understood. 
Dog size variation Dogs IGF-1 Insulin-like growth factor Physical IGF-1 induces cell mitosis. Alleles with higher growth-factor levels linked to larger dog size. 
Monogamy in voles Voles Interspecies V1aR Vasopressin receptor Behavior Vasopressin released during mating activates reward areas in brain in monogamous prairie voles, but not in montane or meadow voles. 
Human lactose intolerance Humans LCT Lactase enzyme Metabolism and Disease See text for details. 
Sickle cell diseaseb Humans β-globin Many alleles Globin protein of hemoglobin Disease/Risk Hereditary mutations related to the fetal hemoglobin (HbF) gene lead to continued HbF expression in adults, ameliorating SCD.d 
III. Trait Variation due to Epigenetics 
Agouti coat color in mice Mice Viable yellow Agouti allele Signaling protein Physical Epigenetic modification (DNA methylation) regulates deposition of color pigment. 
Flowering time in Arabidopsis Thale cress plants PCG and FLC Polycomb and flowering locus Physical Polycomb proteins regulate gene expression by regulating overall chromatin structure. 
Prader-Willi and Angleman Syndromes Humans Probably several genes Probably several proteins Disease/Risk Inherit epigenetically imprinted (differentially between the sexes) version from one parent and version with large deletion from the other. 
IV. Trait Variation due to Environmental Influences 
Sun tanning Humans Many genes  Physical UV light induces skin darkening. Also, example of mutations linked to evolutionary adaptation. 
Respiration capacity at high altitudes Humans Many genes  Biochemical/ Physiological Multiple physiological responses to high altitudes. Also example of mutations linked to evolutionary adaptation. 
Sickle cell diseaseb Humans β globin Globin protein of hemoglobin Disease/Risk High altitudes, exercise, level of hydration, and drugs (hydroxyurea) influence hemoglobin interactions or fetal hemoglobin gene expression, which affects symptom frequency and severity. 

aMany traits do not have official or popular names – and may rely on descriptions at the biochemical level such as metabolic abilities or physiological functions. Most of these are categorized in this table as “Biochemical/Physiological” traits; this does not mean that they do not affect organisms more widely (e.g., tasting ability affects behavior and antibiotic production and antibiotic resistance is critical for bacterial survival). Also, a trait can belong in more than one category; for example, bitter taste sensitivity may be linked to behaviors such as food choice and tobacco use.

bMarks classical traits – examples from classical genetics described at the phenotypic level. As we understand better their molecular basis, classical traits are important in making the link between molecular and classical genetics.

cD/R = dominant/recessive.

dSCD = sickle-cell disease.

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