Genetics

1. Genetics Mendel and beyond.

2. Sometimes we’d like to know what results occur when a plant reproduces with its own genetic content… Figure 13-1a Self-pollination SELF- POLLINATION Female organ (receives pollen) Male organs (produce pollen grains, which produce male gametes) Eggs

3. …and sometimes we just have to chop out some sexual structures, to see what happens when we cross individuals. CROSS- POLLINATION Figure 13-1b Cross-pollination 1. Remove male organs from one individual. 3. Transfer pollen to the female organs of the individual whose male organs have been removed. 2. Collect pollen from a different individual.

4. Trait Phenotypes Seed shape Mendel observed in his pea plants that each of these traits occurred in only two forms, what we would now call phenotypes. He concentrated on these, assuming that his crossing-results would make more sense if there were a limited number of outcomes possible. Round Wrinkled Seed color Yellow Green Pod shape Constricted Inflated Figure 13-2 Pod color Green Yellow Flower color Purple White Flower and   pod position Axial (on stem) Terminal (at tip) Stem length Tall Dwarf

5. Figure 13-3-reciprocal_cross

6. So what is necessary to make sense of the results that can occur in crosses? • crossing random individuals with unknown traits is a waste of time! • thus we must “manufacture” strains or types of individuals with a limited set of trait-values – “PURE STRAINS” – and cross individuals drawn from these strains • Mendel didn’t know why at first, but found that INBREEDING – self-crossing individuals repeatedly – eliminated unwanted variation in a strain • crossing pure-strain individuals thus permits the “cleanest” experimental designs

7. Trait Phenotypes Seed shape Mendel observed in his pea plants that for each of these traits, one form could be “masked” by another. As soon as he crossed pure round-seed plants with pure wrinkled-seed plants, for example, all the offspring were round. Thus he surmised that some traits were “stronger than”, or DOMINANT to, others. Round Wrinkled Seed color Yellow Green Pod shape Constricted Inflated Figure 13-2 Pod color Green Yellow Flower color Purple White Flower and   pod position Axial (on stem) Terminal (at tip) Stem length Tall Dwarf

8. A cross between two homozygotes Homozygous mother Mendel’s “pure strains”… the parental (P) types Figure 13-4a Meiosis Female gametes Homozygous father The offspring are referred to as the “first filial” (F1) generation Male gametes Meiosis Offspring genotypes: All Rr (heterozygous) Offspring phenotypes: All roundseeds

9. A cross between two homozygotes Homozygous mother Figure 13-4a Meiosis Female gametes Homozygous father Male gametes Meiosis We will now proceed to cross these F1s with each other… Offspring genotypes: All Rr (heterozygous) Offspring phenotypes: All roundseeds

10. A cross between two heterozygotes Heterozygous mother Figure 13-4b Female gametes The offspring of this F1 x F1 cross are referred to as the “second filial” (F2) generation Heterozygous father Male gametes Offspring genotypes: 1/4 RR :1/2 Rr : 1/4 rr Offspring phenotypes: 3/4 round:1/4 wrinkled

11. What happens with multiple traits? • assume you have created strains that are pure for more than one trait at the same time • you cross P individuals drawn from these strains • what sort of results might you expect to obtain? • The F1 generation will be obvious – heterozygote for both traits, so phenotypically “dominant, dominant”… but what about the F2 generation?

12.      Hypothesis of independent assortment: Alleles of different genes don’t stay together when gametes form. F1 PUNNET SQUARE Female parent Female gametes Male parent Male gametes F1 offspring all RrYy X F2 male parent Male gametes F2 offspring genotypes: 9/16 R–Y– : 3/16 R–yy : 3/16 rrY– : 1/16 rryy F2 offspring phenotypes: 9/16 : 3/16 : 3/16 : 1/16

13. What happens with multiple traits? (cont’d) • in the F2, there are two major possibilities: • the variant traits are inherited together, i.e. as a “package” of information… Or • the traits are inherited separately, i.e. one is passed along in a manner unrelated to the other… So which is it?

14. “Dependent assortment”: In the F1 individuals, the traits are linked on the strands inherited from each parental type, so are also passed along that way – together.      Hypothesis of dependent assortment: Alleles of different genes stay together when gametes form. Female parent F1 PUNNET SQUARE Female gametes Male parent Male gametes Figure 13-5b F1 offspring all RrYy F2 female parent F2 PUNNET SQUARE Female gametes F2 male parent Male gametes F2 offspring genotypes: 1/4 RRYY : 1/2 RrYy : 1/4 rryy F2 offspring phenotypes: 3/4 : 1/4

15. “Independent assortment”: in the F1 individuals, the traits are not constrained to stay in the parental combinations, and can be passed along separately.      Hypothesis of independent assortment: Alleles of different genes don’t stay together when gametes form. Female parent F1 PUNNET SQUARE Female gametes Male parent Male gametes Figure 13-5a F1 offspring all RrYy F2 female parent F2 PUNNET SQUARE Female gametes F2 male parent Male gametes F2 offspring genotypes: 9/16 R–Y– : 3/16 R–yy : 3/16 rrY– : 1/16 rryy F2 offspring phenotypes: 9/16 : 3/16 : 3/16 : 1/16

16. What happens with multiple traits? (cont’d) • in the F2, there are two major possibilities: • the variant traits are inherited together, i.e. as a “package” of information… this would yield only two phenotypes (the original P phenotypes, actually), in a ratio of 3:1 Or • the traits are inherited separately, i.e. one is passed along in a manner unrelated to the other…this would yield four phenotypes (not just the P types), in a ratio of 9:3:3:1 So which is it?

17. Mendel says the second option, as these data show: Figure 13-5c Mendel’s results 556 total fractions Mendel was “lucky”, since all of the traits he chose to study in detail turned out to be inherited by independent assortment… well, probably he wasn’t lucky, but instead smart enough to recognize that some traits were harder to work with than others!

18. What if you don’t know the genotype of a dominant-phenotype individual? • carry out a TEST-CROSS • if you have an individual of unknown genotype – “A_”, and you cross it with an individual with a homozygous-recessive genotype – “aa”… • if all the offspring are phenotypically “A”, it means…? • if the offspring are a mixture of “A” and “a” phenotypes, it means…?

19. You can also do test-crosses with multi-trait cases… F1 parent R_ Y_ Figure 13-6 Homozygous recessive parent All

20. You can also do test-crosses with multi-trait cases… F1 parent ? Figure 13-6 Homozygous recessive parent All

21. What if the genes (loci) are located on the same chromosome pair (dependent assortment)? Figure 13-15 Gene 1 Gene 1 Gene 2 Crossing over is rare between genes that are close together Crossing over occurs frequently between genes that are far apart Crossing over can occur anywhere along the length of a chromosome; pink arrows indicate just a few of the possible crossover sites Gene 3 The outcome depends on where the loci are located along the length of the chromosome; but crossovers occur by chance, NOT according to which loci are located where!

22. Frequency of recombinant offspring can be used to map genetic distance. Figure 13-16a Yellow body White eyes 1.4 21 19.6 Singed bristles The frequency of recombinant offspring is directly correlated with the distance between the two genes, so 19.6% recombinant offspring translates to 19.6 map units (centimorgans, cM)

23. What happens when there are multiple loci at stake, and you want to make predictions? • it depends on where they are (on the same, or on different, chromosome pairs) • it depends on what you wish to know (a specific case in the outcome, or classes of cases) • it depends on how the genes are expressed relative to one another (i.e. if the loci are in an epistatic interaction) We must work through these criteria, and others.

24. What happens when there are multiple loci at stake, and you want to make predictions? • Where they are: let’s assume they are on separate chromosome pairs (not always the case, but simplifies the math!) • What you wish to know: are you interested in highly specified outcomes, or just outcomes satisfying broader requirements? • How the genes are expressed: let’s start by looking at this one, using an example from Freeman

25. Crosses between chickens with different comb phenotypes give odd results  Rose comb Pea comb Parental generation Figure 13-18a All Walnut combs These F1s are then crossed with each other to make the F2 F1 9           :           3           :           3           :           1 Walnut combs Pea combs Single combs Rose combs F2

26. A genetic model to explain the results Parental generation Rose comb RRpp  Pea comb rrPP Figure 13-18b All Walnut combs ; intercross two of these RrPp F1 F2 R_P_ Walnut comb R_ppRose comb rrP_ Pea comb rrpp Single comb The expression of one locus depends completely on what is being expressed at the other locus – EPISTASIS.

27. Predictions for multiple loci (or, “beyond 9:3:3:1”) It will be much easier to calculate probabilities than to draw Punnett squares! Consider a simple case: how likely are you to get three “heads” in a row, if you flip a coin three times? Think about it…

28. Each flip of an ordinary coin has a “half-half”, or 50%-50%, outcome. The probability of a head is ½, and the probability of a tail is also ½. (The chance of any other outcome is vanishingly small, unless you have a really thick coin or a really soft surface!) Note that this is not a random outcome! Three heads in a row requires all three flips to go the right way… so the overall probability of three heads in a row is the product of three head-flips: ½ x ½ x ½ = ⅛

29. What is the likelihood of getting two heads in three flips of a coin? There are three different, independent ways of this happening: 1st/2nd, 2nd/3rd, or 1st/3rd. No other possibilities! 1st/2nd: you must have a head on the first, and a head on the second, and NOT a head on the third! The other ways, also. (Two heads, and NOT a third.) So the answer is… think about it…

30. For each of the three ways, the calculation will be: ½ x ½ x ½ = ⅛ And each of the ways is an independent sequence… so we must add the probabilities together: ⅛ + ⅛ + ⅛ = ⅜ Consider – “two tails” will be the same probability, and three tails (zero heads) will be like three heads… so all the outcomes add up to 1! (⅛ + ⅜ + ⅜ + ⅛)

31. Now consider a cross involving three loci (D, E, F): DDeeFf x DdEeff What fraction of the offspring will be heterozygote for all three loci (i.e. be DdEeFf)? First question – is this actually possible? (i.e. a non-zero case… the outcomes here are more complex than just a coin-flip) Second question – what is the answer?

32. Take it step by step: evaluate the loci separately – DDeeFf x DdEeff For the D: the chance of Dd will be… For the E: the chance of Ee will be… For the F: the chance of Ff will be…

33. Take it step by step: evaluate the loci separately – DDeeFf x DdEeFf For the D: the chance of Dd will be…½ For the E: the chance of Ee will be…½ For the F: the chance of Ff will be…½ So for the full outcome: ½ x ½ x ½ = ⅛

34. Now consider this cross: DDeeFfgg x DdEeffGg What fraction of the offspring will be (for instance): • of the genotype “D_E_F_G_”? • heterozygous for at least two loci? • homozygous at all loci? If you can answer these, you’ve got it!

35. Further extensions of basic Mendelian genetics… • first, SEX-LINKAGE – what effects are apparent when loci are found on chromosomes concerned with sex-determination? • take the example of eye-colour in Drosophila

36. The fruit fly Drosophila melanogaster Figure 13-9 Eye color is a variable trait. Red is wild-type, phenotype “w+” White is mutant, phenotype “w”

37. One half of reciprocal cross Male (“w”) eye Figure 13-11a X X X X Male gametes Female (“w+”) eye X X X X Female gametes Females Males all are “w+” in appearance

38. Male (“w+”) Other half of reciprocal cross eye Figure 13-11b X Male gametes Female (“w”) eye X Female gametes Females all “w+” Males all “w”

39. Why? Because sperm nuclei may or may not provide eye-colour information. Y chromosome X chromosome Figure 13-10 Meiosis I Meiosis II Gametes 50% of sperm (with an X chromosome) have “w” info… the other 50% of sperm (with a Y chromosome) lack “w” info.

40. One half of reciprocal cross Male Figure 13-11a Male gametes Female Female gametes Females Males

41. Male Other half of reciprocal cross Figure 13-11b Male gametes Female Female gametes Females Males

42. Further extensions of basic Mendelian genetics… CODOMINANCE – more than one allele can be expressed equally, at one time. e.g.: the human ABO blood-type system (see Chapter 44 in Freeman for further background, if you wish)

43. The “I” locus – alleles IA, IB, and i. Individuals of genotype ii(i.e. homozygous recessive) are phenotypically “O”. Individuals of genotype IAIA or IAi are phenotypically “A”. Individuals of genotype IBIB or IBi are phenotypically “B”. Individuals of genotype IAIB are phenotypically “AB”. Both traits are expressed equally.

44. Further extensions of basic Mendelian genetics… Flower color is variable in four-o’clocks. Figure 13-17a This demonstrates the phenomenon of INCOMPLETE DOMINANCE at a locus.

45. Incomplete dominance in flower color Parental generation Figure 13-17b F1 generation Self-fertilization F2 generation White Purple Lavender

46. Why does flower colour matter? Bee Remember: each flower “appeals to” (i.e. is recognized by) specific pollinators – so it matters how they look! Probably the white four o’clocks are pollinated by moths, at night.

47. Incomplete-dominance-like patterns can occur across multiple loci also… DOSE-DEPENDENT, or QUANTITATIVE, traits Wheat kernel color. Figure 13-20a Parental generation More phenotypes than you might expect in the F2 generation – why? F1 generation 20 15 15 F2 generation 6 6 1 1

48. Hypothesis to explain inheritance of kernel color aa bb cc (pure-line white) AA BB CC (pure-line red) What matters is the total number of dominant alleles present – the loci on which they occur is not a critical factor. 1 + 6 + 15 + 20 + 15 + 6 + 1 = 64 ; these represent the 64 squares in an 8x8 Punnett square! Figure 13-20b Aa Bb Cc (medium red) Self- fertilization

49. So how can we approach new situations? An example. • A cross involving yellow mice…

50. So how can we approach new situations? An example. • A cross involving yellow mice…