Interaction and • In each of these problems you examine a single phenotypic trait that is determined by 2 . Each of the genes has a dominant and a recessive allele. • In each problem you start with a set of three true-breeding strains. For example, three plants with either red, purple or white flowers.

• In these problems two main goals are to: - determine the of each of the 3 true-breeding strains; - determine the genotype and of the 4th true-breeding strain. • You will determine the genotype of each of the true-breeding strains by (a) crossing pairs of the 3 given strains, then (b) performing an intercross on the first generation (F1) offspring in each cross, for example: Cross 1 red x purple ratio F1 all red F1 Intercross ratio F2 3 red 1 purple

______Review: Traits Controlled by One Gene In the simplest case genetic traits are controlled by a single gene with two and simple . The traits Mendel studied in peas are like this. For example, pea color was controlled by a dominant yellow allele and a recessive green allele.

In this situation there are four possible : There are only two functional genotype categories, since there are just two : 4 Total Genotypes 2 Functional Genotypes Genotype Phenotype GG yellow Genotype Phenotype Gg yellow G- yellow gG yellow gg green gg green

The three genotypes with at least one dominant allele are yellow all have yellow peas. We use the abbreviation “G-“ this functional genotype category. This notation represents all the genotypes with at least one dominant G allele; the “-“ indicates it doesn’t matter if the second allele is dominant or recessive.

True-breeding genotypes. Two of these genotypes are true-breeding (homozygous): GG yellow and gg green. If we cross these true-breeding strains: Yellow (GG) x Green (gg) all the first generation (F1) offspring will inherit a dominant allele from the 1st parent and a recessive allele from the other:

F1 100% Yellow (Gg)

If we perform an intercross on these first generation offspring:

Yellow (Gg) x Yellow (Gg) ¾ of the offspring will fall in the G- category, and ¼ will fall in the gg category, so we sill see yellow and green offspring in the ratio 3 to 1: Phenotype Ratio Genotype __Yellow______3______G-______Green______1______gg____ Traits Controlled By Two Genes As Mendel showed, when there are two genes with two alleles of each, there are 16 possible genotypes. If each gene controls a different phenotype, there are four different phenotype categories. For instance, yellow peas and smooth skin yellow peas and wrinkled skin green peas and smooth skin green peas and wrinkled skin and the 16 genotypes fall into 4 functional genotype classes:

At least one dominant A least one dominant A least one dominant No dominant alleles of of both genes allele of A, but not B allele of B, but not A either gene Genotypes AABB AAbb aaBB aabb AaBB Aabb aaBb aABB aAbb aabB AABb AaBb aABb AAbB AabB aAbB Ratio 9 3 3 1 Summary A-B- aaB- A-bb aabb Phenotype yellow, smooth yellow, wrinkled green, smooth green, wrinkled

In this situation there are four doubly homozygous, true-breeding genotypes:

True breeding AABB aaBB AAbb aabb

When two genes control a single phenotypic trait, we have the same four functional genotype classes, and can have as many as four phenotypes:

Two Genes and Two Traits: Two Genes and One Trait: Genotype Phenotype___ Genotype Phenotype___ A-B- yellow, smooth A-B- red flowers aaB- yellow, wrinkled __aaB- _ orange flowers A-bb green, smooth __A-bb yellow flowers aabb green, wrinkled __aabb white flowers

Epistasis. But different true-breeding genotypes can have the same phenotype, and the four true-breeding strains may only have 3 different phenotypes or even 2 different phenotypes, as described below.

Crossing Strains That are True-Breeding for Two Genes

One Gene Segregating If we cross these two true-breeding genotypes: AABB x AAbb Each offspring will inherit a dominant A allele from both parents, a dominant B allele from the first parent, and AABb a recessive b allele from the second parent:

In this cross, we say one gene segregated (B).

When we intercross these F1 offspring: AABb x AABb We will obtain four F2 offspring genotypes:

• All strains will have 2 dominant A alleles. AABB • Three strains will have at least one at least one AABb dominant B allele will have the same phenotype. AAbB AAbb • The fourth strain with two recessive bb alleles will

generally have a different phenotype. Since the four genotypes have equal frequencies, there will be a 3-1 ratio in the F2 offspring frequencies with the two phenotypes.

Two Genes Segregating If we cross these two true-breeding genotypes: AAbb x aaBB Each offspring will inherit a dominant A allele & recessive b allele from the first parent, and a recessive a allele & dominant B allele from the second parent: AaBb

In this cross, we say two genes segregated (both A and B).

When we intercross these F1 offspring: AaBb x AaBb This is like Mendel’s di-hybrid cross, and we will obtain 16 genotypes, as Mendel did:

• 9 will have at least one dominant allele of both genes AABB, AaBB, aABB, AABb, AaBb, AabB, aABB, aABb, aAbB

• 3 will have at least one dominant A allele and recessive bb alleles AAbb, Aabb, aAbb

• 3 will have recessive aa alleles and at least one dominant B allele aaBB, aaBb, aabB

• 1 will have recessive aa alleles and recessive bb alleles aabb

• If there is no epistasis, we will observe four phenotypes in the familiar 9-3-3-1 ratios.

Pathways that result in Genetic Epistasis Two genes can act together in many ways to create a phenotype. We use flower pigmentation as a phenotype examples to discuss these alternative pathways.

A. Two Genes have the Same Basic Effect. A1. Either gene alone yields the full phenotypic effect. A2. Either gene alone yields a partial phenotypic effect; together they yield an enhanced effect. A dominant allele of either gene yields full yellow pigment. A dominant allele of either gene yields lavender pigment, and a dominant allele of both genes yields darker, purple pigment. AABB AAbb aaBB aabb AABB AAbb aaBB aabb AaBB Aabb aaBb AaBB Aabb aaBb aABB aAbb aabB aABB aAbb aabB AABb AABb AaBb AaBb aABb aABb AAbB AAbB AabB AabB aAbB aAbB 9 3 3 1 9 3 3 1 A-B- aaB- A-bb aabb A-B- aaB- A-bb aabb 15 genotypes yield yellow flowers; 1 genotype yields white 9 genotypes yield purple flowers; 6 yield lavender; 1 yields white

B. Two Genes work in succession on a single path. B1. A dominant allele of 1 gene creates an intermediate product. B2. A dominant allele of 1 gene creates a phenotype. A dominant A dominant allele of the other creates the new phenotype. allele of the other acts on this product to create a phenotype. A dominant allele of A creates an intermediate product and a A dominant allele of A creates a product with orange pigment; a dominant allele of B acts on this product to create blue pigment. dominant allele of B acts on this product to create red pigment. AABB AAbb aaBB aabb AABB AAbb aaBB aabb AaBB Aabb aaBb AaBB Aabb aaBb aABB aAbb aabB aABB aAbb aabB AABb AABb AaBb AaBb aABb aABb AAbB AAbB AabB AabB aAbB aAbB 9 3 3 1 9 3 3 1 A-B- aaB- A-bb aabb A-B- aaB- A-bb aabb 9 genotypes yield blue flowers; 7 genotypes yields white 9 genotypes yield red flowers; 4 yield white; 3 yield orange

C. One Gene Blocks Expression of Another Gene. C1. One gene fully blocks expression of a second gene. C2. One gene acts on a precursor phenotype to create a new one. The other gene blocks formation of the precursor phenotype. A dominant allele of A yields pink pigment, but a dominant A dominant B allele acts on a yellow pigment to form orange. allele of B blocks all expression of A. A dominant A allele blocks formation of the yellow precursor. AABB AAbb aaBB aabb AABB AAbb aaBB aabb AaBB Aabb aaBb AaBB Aabb aaBb aABB aAbb aabB aABB aAbb aabB AABb AABb AaBb AaBb aABb aABb AAbB AAbB AabB AabB aAbB aAbB 9 3 3 1 9 3 3 1 A-B- aaB- A-bb aabb A-B- aaB- A-bb aabb 13 genotypes yield white flowers; 3 genotypes yields pink 12 genotypes yield white flowers; 3 yield yellow; 1 yellow