Tuesday 04/15/25 Genetics I

Phenotype vs. Genotype of an Organism 

• Gene: A sequence of DNA that encodes a protein 

• Trait: the physical manifestation of a gene or set of genes

• Depending on what version of this gene you have (the genotype), you might have the trait of green eyes, or the trait of blue eyes (the phenotype) 

• So the GENOTYPE (gene) gives rise to the PHENOTYPE (trait)

• Each gene often has several different variations (i.e., slight variations in its specific nucleotide sequence from one organism to the next)

  • These different variations are called “alleles”

    • (different versions of the same gene)

• Remember: diploid organisms inherit 2 homologs of each type of chromosome, this means they’re inheriting two versions of each gene (1 from mom, 1 from dad)

  • An organism can inherit 2 of the same allele for a particular gene, in which case the organism is said to be homozygous for that gene

• Organisms can have heterozygous alleles for one gene & homozygous alleles for another

  • Alternatively, an organism can inherit 2 different alleles for a gene, in which case the organism is heterozygous for that gene

  • In heterozygotes, what the associated trait ends up looking like (in other words, the phenotype) depends on which allele is dominant - more on that soon

Patterns of Inheritance

• Genetics and inheritance are random

  • Can be attributed to meiosis 

    • In meiosis I, which homolog ends up in each daughter cell is independent for each chromosome - based on random orientation of homologs during metaphase

    • (we also see this we recombinant/non-recombinant sister chromatids in metaphase II)

  • This is the basis of inheritance

    • We can predict the chances of offspring inheriting particular combinations of alleles using the mathematical rules of probability

• The basis of inheritance lies in two key principles 

1. The segregation of alleles of each gene in genome

   1. Individuals inherit two alleles of each gene, one from the mother & one from the father, & when that individual forms its own gametes, those two alleles separate equally into each gamete

2. The independent assortment of different genes on different chromosome 

   1. The two alleles of one gene on one chromosome segregate into gametes independently of the two alleles of another gene on a different chromosome

• These principles of inheritance were discovered in 1800’s by crossing pea plants 

  • Pea plants have 7 easily observed traits (phenotypes)

  • The probabilities of inheriting different phenotypes were determined by crossing (mating) hundreds of pea plants with different traits over many generations and seeing what phenotypes popped up

Experimental Footsteps of Gregor Mendel

• Mendel knew that crossing yellow seeded plant with itself always gives more yellow, same with green (“true breeding”) 

  • But what happens if we cross yellow x green ? 

• “F1” generation: All yellow seeds, no green

  • Where did the green go?

• Does green trait just disappear? 

  • To find out, Mendel allowed all yellow F1’s to self-fertilize 

  • Green seeds came back in “F2” generation 

  • Not only that, but when he calculated the number of yellow to green seeds in the F2 generation he always found a 3:1 ratio 

• Mendel’s conclusions about the 3:1 ratio in gen F2

1. F1 must inherit a dominant allele from one parent (in this case, yellow) & a recessive allele (green) from the other (heterozygous)

2. In the transmission of these alleles from F1 to F2 (i.e., when F1 forms gametes by meiosis), those dominant (yellow) and recessive (green) alleles from P1 must separate from each other, such that any given F2 can inherit either the dominant (yellow) or recessive (green) allele from EACH parent (Principle of Segregation) 

3. Explains why green reappears in ~ ¼ of F2’s: these inherit recessive alleles from BOTH heterozygous F1 parents, thus no dominant (yellow) allele to mask it

• How does Principle of Segregation explain why dominant : recessive phenotype in F2 is always 3:1*

  • Let’s call the alleles for seed color gene A and a:

    • CAPITAL LETTER denotes DOMINANT allele for a gene (in this case, A for yellow allele of seed color gene)

    • lower case letter denotes recessive allele for a gene (in this case, a for green allele of seed color gene)
      

      

  • So if we look at our P1 (parental) generation, the true-breeding yellow-seeded P1 is AA (“homozygous dominant”) and green-seeded P1 is aa (“homozygous recessive”) 

  • By Principle of Segregation, when each true-breeding (homozygous) parent makes gametes, the seed color allele on maternal homolog & paternal homolog will segregate (separate) during meiosis I

    • b/c these are homozygous (“true breeding”) plants, notice each produces only one type of gamete (with regards to seed color gene)

    • Yellow parent only produces gametes with A allele, green parent only produces gametes with a allele

    • When we cross the AA plant with the aa plant 

      • No matter which gametes end up coming together in this cross, the offspring (F1 generation) will always be heterozygous for seed color gene, having inherited an A from one parent and an a from the other

• Once again, by the Principle of Segregation, where heterozygous F1’s form their own gametes, A allele and a allele will get separated

  • So when meiosis II is complete, ½ the gametes will contain A and the other ½ a

  • This means each F1 can contribute a gamete carrying an A allele or a gamete carrying a allele to the next generation 

• Now, let’s cross the F1 heterozygous to each other 

  • (meaning F1 “brothers” are used to fertilize F1 “sisters” to give F2 generation) 

  • In the formation of the F2 generation, the gametes produced by the F1 parents (either containing A or a) combine at random

  • The probabilities of different allelic combos from this union can be determined in a “Punnett square” 

  • Probabilities of each phenotype in next gen is 3:1, Probability of each genotype in next generation is 1 (AA) : 2 (Aa) : 1 (aa) 

Independent Assortment of Different Genes on Different Chromosomes 

• Reflects the fact that nonhomologous chromosomes can orient in either of two ways at metaphase I that are equally likely & independent of one another

  • If we’re looking at gene A on one pair of chromosomes and gene B on another pair of chromosomes

    • This orientation (A and B on top) results in gametes with either AB or ab

    • This equally likely orientation (A and b on top) results in gametes with either Ab or aB

  • Remember that organisms have a large number of germ cells undergoing meiosis (not just 1 or 2), so all possible allelic combinations (AB, ab, Ab, aB) would be equally represented in the resulting pool of gametes 

A Dihybrid Cross by Tracking Traits of Seed Color & Seed Texture

• Seed color gene has alleles A (yellow), a (green)

• Seed texture gene has alleles B (smooth), b (wrinkled) 

  • *remember, CAPITAL LETTER = DOMINANT, lower case = recessive

• We will cross a yellow, wrinkly seeded-plant (AAbb) to a green, smooth-seeded plant (aaBB)

• F1’s will all be heterozygotes for both genes (Aa Bb)

• Each F1 will produce the following gametes…

  • Remember, each gamete will have an allele for both seed color (A or a) AND seed texture (B or b) & these two genes independently assort into the gametes (i.e., which gamete each seed COLOR allele goes to does not dictate which gamete seed TEXTURE allele goes to)

  • TIP: Remember FOIL from math? (First Outer Inner Last)

    • You can apply the same method to find gametes from an individual’s genotype

Summary

• Genotype describes the genetic makeup of an organism (e.g., which alleles it has)

• Phenotype describes an organism’s physical appearance 

• Genotype gives rise to phenotype

• Alleles are different versions of a gene; organisms can be homozygous for a particular gene (they have 2 of the same alleles for that gene) or heterozygous (they have 2 different alleles for that gene)

• The genotype (and thus phenotype) an organism inherits is based in two fundamental principles: 

  • Principle of Segregation (due to anaphase I of meiosis when homologous pairs are separated)

  • Principle of Independent Assortment (due to metaphase I when homologous pairs randomly orient independently of one another) 

• We can determine the probability of offspring genotypes and phenotypes by identifying all possible gametes each parent can make & using a Punnett Square to visualize possible outcomes of union between different gametes