1. Patterns of Inheritance Chapter 9

2. Overview Definitions Patterns of Mendelian Inheritance Non-Mendelian Inheritance

3. Genes: Info in chromosomal DNA Heritable traits passed to offspring Diploid (2n): Pairs of genes on pairs of homologous chromosomes

4. Alleles: Alternative forms of a gene One form usually dominant over other If pair is identical over many generations = true-breeding lineage Hybrid: Cross between 2 true-breeding individuals that have non-identical alleles for trait e.g. AA x aa = hybrid offspring

5. Homozygous: Pair of identical alleles on pair of homologous chromosomes e.g. A & A Heterozygous: Pair of non-identical alleles on pair of homologous chromosomes e.g. A & a

6. M locus: leaf colour Both alleles are the same = homozygous D locus: plant height Both alleles are the same = homozygous Bk locus: fruit shape Alleles are different = heterozygous chromosome 1 from tomato pair of homologous chromosomes M D Bk

7. Dominant allele (e.g. A): Effect on trait masks effect of recessive allele (e.g. a) Note: dominant alleles are not necessarily more common or “better” Homozygous dominant genotype = AA Homozygous recessive genotype = aa Heterozygous genotype = Aa

8. Genotype: “Genes” Individual’s alleles e.g. Aa Phenotype: “How genes are expressed” Individual’s observable traits e.g. green eyes

9. P = true-breeding parents F 1 = 1 st -generation offspring F 2 = 2 nd -generation offspring of self-fertilized or crossed (mated) F 1 individuals

10. Old Inheritance Theory Hereditary material from both parents mixed at fertilization e.g. red flowers + white flowers = pink flower offspring Couldn’t explain obvious variation in traits +

11. Gregor Mendel & His Peas Viennese monk who studied botany & math Pisum sativum: garden pea Self-fertilizing (flowers produce male & female gametes that fuse to form new plant so that parent & offspring = same traits) Can also be cross-fertilized

12. Mendel tracked 7 traits over 2 generations

13. Mendel’s Theory of Segregation Monohybrid cross: 2 homozygous parents that differ in trait dictated by alleles of 1 gene P F 1 AA x aa  Aa

14. After Mendel tracked 7 traits for 2 generations, he found that: F 2 : ¼ recessive forms & ¾ dominant forms of trait

15. Fertilization is chance event with # of possible outcomes Can calculate probabilities of possible outcomes of genetic crosses Can determine all types of genetically different gametes that can be produced by male & female parents Genetics is a science of probability

16. homozygous parent AAAA gametes

17. heterozygous parent AaaA gametes

18. The Punnett Square Method Allows prediction of both genotypes & phenotypes of genetic crosses A a aA

19. Draw Punnett square with each row & column labelled with one of possible gametes of sperm & eggs respectively Fill in genotype of offspring in each box by combining male & female gametes A A A A a a a a AAAa aAaa

20. Count # offspring with each genotype & convert to fraction of total # offspring To determine phenotype proportions, add fractions of genotypes that would produce given phenotype Phenotype I (dominant; AA & Aa) = ¼ + 2/4 = ¾ Phenotype II (recessive; aa) = ¼ AA = ¼ Aa = aA = 2/4 = ½ aa = ¼ A A a a AAAa aAaa

21. So, for Mendel’s cross of F 1 offspring from monohybrid cross, he predicted: F 2 = ¼ AA, ½ Aa, ¼ aa Phenotypic ratio = 3:1 –¼ AA + ½ Aa = ¾ dominant phenotype –¼ aa = ¼ recessive phenotype A A a a AAAa aAaa

22. Since each gamete is equally likely, each of these offspring is equally likely Due to dominance we see a ratio of 3 purple:1 white

23. An Example Imagine you are crossing a true breeding plant with yellow peas & a true breeding plant with green peas. If yellow color is dominant: What would the F 1 generation look like? What would the F 2 look like?

24. PPPP PpPpPp These three all look the same! PP pPpP PpPp P ppp white spermeggs offspring genotypes genotypic ratio (1:2:1) phenotypic ratio (3:1) 1212 1212 1212 1212 1212 1212 1212 1212 1414 1414 1414 1414 1414 2424 1414 1414 Dominance creates some problems for scientists For example: How can I know which genotype I have if all I can see is phenotype?

25. Test cross: Individual shows dominance for trait but genotype is unknown Cross with homozygous recessive individual to see if homozygous dominant or heterozygous

26. If homozygous dominant:If heterozygous:

27. Test crosses supported Mendel’s predictions Mendel found that crossing F 1 purple flowers with true- breeding white flowers: ½ F 2 = purple (Aa), ½ F 2 = white (aa)  F 1 purple flowers were heterozygous sperm p p P pp PpPp all eggs PP or Pp sperm unknown if PP if Pp egg pollen p 1212 1212 1212 P p 1212 all Pp sperm

28. An Example Imagine you have a plant with yellow peas but you don’t know its genotype. Remember that yellow is dominant to green. What type of pea would you mate it with? Why? If the offspring are all yellow what does this tell you? Does it matter how many offspring there are?

29. Mendel’s Big Ideas Genes have alternate versions (alleles) Organisms have two “particles” for each gene = diploid Some alleles are “dominant” to others (in organisms with two different alleles (heterozygous), the dominant allele masks the recessive allele) Alleles separate during gamete formation = the law of segregation Heterozygotes produce two different types of gametes

30. Mendel’s Theory of Segregation 2n cells have pairs of genes on pairs of homologous chromosomes Members of each gene pair separate during meiosis & end up in different gametes

31. Applying Mendel’s Ideas Imagine you have mated a black guinea pig with an albino guinea pig. They have 12 offspring & all are black. What alleles are dominant in this case? How do you know? What are the parents’ phenotypes? Genotypes?

32. Now imagine a cross between a different pair of guinea pigs, one black & one albino. If they have 7 black & 5 albino offspring: What are the parents’ genotypes? How do you know?

33. Mendel performed a lot of crosses & sometimes he was tracking more than one trait at a time This let him develop one more “Big Idea”

34. Mendel’s Theory of Independent Assortment Dihybrid cross: True-breeding homozygous parents that differ in 2 traits dictated by alleles of 2 genes P F 1 AABB x aabb  AaBb F 1 heterozygous for alleles of both genes

35. ab AB F 1 = 100% AaBb AaBb For P (AABB), gametes = AB For P (aabb), gametes = ab

36. With independent assortment, alleles for one trait are independent of alleles for another e.g. if you have A you are equally likely to have B or b This means that each of the four gametes are equally likely

37. During meiosis of F 1 cells, there are 4 possible combos of alleles in sperm or eggs: 1/4 AB, Ab, aB, ab With 4 different sperm & egg types, F 2 offspring of hybrid cross = 16 possible combos of gametes

38. AABBAABbAaBBAaBb AABbAAbbAaBbAabb AaBBAaBbaaBBaaBb AaBbAabbaaBbaabb AB Ab aB ab aBAbAB

39. e.g. with A = purple, a = white B = tall, b = dwarf 9/16 tall, purple 3/16 dwarf, purple 3/16 tall, white 1/16 dwarf, white Phenotypic ratio = 9:3:3:1 abaBAbAB Ab aB ab AABBAABbAaBBAaBb AABbAAbbAaBbAabb AaBBAaBbaaBBaaBb AaBbAabbaaBbaabb

40. An Example A true breeding plant with wrinkled green seeds was mated to a true breeding plant with smooth yellow seeds. In the first generation all the plants had smooth yellow seeds. What alleles are dominant in this case? How do you know?

41. Taking these (dihybrid) F 1 plants, Mendel allowed them to self-fertilize We could write the F 1 genotypes like this: SsYy x SsYy What would their gametes look like? SY Sy sY sy What would the zygotes look like? Use a Punnett Square.

42. SY SSYY SsYY ssYY ssyY SsyY SSYy SsYySsYy SsYySsYy ssyy Ssyy SSyy sSyYsSyY sSyy sSYY sSYy SSyY sYsY sYsY sy SySy SySy eggs self-fertilize ssYy 1 4 1 4 1 4 1 4 1 4 1 4 1 4 1 4 sperm 1 16 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 9/16 smooth yellow 3/16 smooth green 3/16 wrinkled yellow 1/16 wrinkled green Phenotypic ratio: 9:3:3:1

43. P p PP P p pp PpPp eggs Pp self-fertilize pPpP 1212 1212 1212 1212 1414 sperm 1414 1414 1414 Remember that a monohybrid cross will give you a 3:1 ratio The 9:3:3:1 ratio is actually just two 3:1 ratios “stacked” on top of each other

44. seed shape (3:1) seed color (3:1) phenotypic ratio (9:3:3:1) smooth yellow smooth yellow smooth green wrinkled yellow wrinkled green yellow green smooth wrinkled 3 4 3 4 3 4 3 4 1 4 1 4 1 4 1 4 3 16 3 9 1 x x x x= = = =

45. Independent Assortment Alleles for one trait are independent of alleles for another This happens because of events in metaphase of meiosis I Remember that chromosomes line up independently of non-homologous chromosomes

46. S S ss s s Y S Y YY y yy S y Independent assortment produces four equally likely allele combinations during meiosis SYsySysY meiosis II meiosis I S S S S s s s s Y Y Y Y y y y y chromosomes replicate S S ss Y Y y y replicated homologues pair during metaphase of meiosis I, orienting like this or like this pairs of alleles on homologous chromosomes in diploid cells S s Y y

47. Mendel’s Big Ideas Genes have alternate versions (alleles) Organisms have two “particles” for each gene = diploid Some alleles are dominant to others (In organisms with two different alleles (heterozygous) the dominant allele masks the recessive allele) Alleles separate during gamete formation (the law of segregation) (heterozygotes produce two different types of gametes) Alleles for one trait are independent of alleles for another = the law of independent assortment

48. Mendel’s Theory of Independent Assortment After meiosis, genes on each pair of homologous chromosomes are sorted out, but independently of how genes on other pairs of homologous chromosomes are sorted out

49. Independent assortment + segregation = genetic variation # genotypes = 3 n where n = # gene pairs More pairs = more genotypes

50. AABBAABbAaBBAaBb AABbAAbbAaBbAabb AaBBAaBbaaBBaaBb AaBbAabbaaBbaabb AB Ab aB ab aBAbAB 3 n = 3 2 = 9 different genotypes

51. In horses grey coat colour is dominant to chestnut. Imagine you own a grey horse & a chestnut horse & over the years they have several offspring, 2 chestnut & 1 grey. Given what you know about genetics, what is the genotype of each parent & of each offspring? How do you know? Using Mendel’s Big Ideas

52. Applying Mendel’s Ideas Imagine you have mated a true-breeding tall plant with round seeds to a true-breeding dwarf plant with wrinkled seeds. In the F 1 generation, the plants are all tall with round seeds. What alleles are dominant in this case? Now imagine you have mistakenly mixed these F 1 plants with some true-breeding tall round plants. What kind of cross do you need to do to tell the plants apart?

53. A Test Cross! You need to do a test cross on your tall round plants. What kind of plant will you mate your tall round plants with? Genotype? Phenotype? Now predict the two possible outcomes of your cross using a Punnett square.

54. Crossing Over & Inheritance During meiosis, crossing-over occurs between non-sister chromatids on homologous chromosomes Get combos of alleles not seen in parents

55. Some genes stay together more often than others because closer together  chance that crossing over will separate ACDB

56. 2 genes are closely linked when distance between them is small = combos of alleles usually end up in same gamete When far apart, crossing over is very frequent = genes independently assort into different gametes ACDB

57. Dependent Assortment Genes on the same chromosome are linked Their alleles tend to assort dependently

58. flower color gene purple allele, P long allele, L red allele, p round allele, l pollen shape gene sister chromatids homologous chromosomes (duplicated) at meiosis I sister chromatids Copyright © 2005 Pearson Prentice Hall, Inc.

59. Alleles for genes on the same chromosome assort dependently = alleles tend to stay together during meiosis The 4 types of gametes are not equally likely: Two (called the parental type) are common Two (called the recombinant type) are rare

60. How can you ever get recombinant gametes? Remember the events of Prophase I? Crossing-over generates recombinant gametes Dependent Assortment

62. Detecting Linkage Imagine you have mated a true breeding black guinea pig with smooth hair to a true breeding white one with rough hair. All the offspring are black with rough hair. What are the dominant alleles here? What is the genotype of the F 1 ?

63. You now mate one of your black rough F 1 guinea pigs to a white smooth one. What are the four types of offspring that should be produced? What ratio would you expect them to be in if: There isn’t linkage? There is linkage?

64. What are the four types of offspring that should be produced? Black rough Black smooth White rough White smooth

65. Without linkage, all are equally likely: Black rough Black smooth White rough White smooth

66. With linkage: Black smooth: more common (>25%) White rough: more common (>25%) Why are these the parental types? White smooth: less common (<25%) Black rough: less common (<25%) Why are these the recombinant types?

67. Remember the lineage of the offspring: We mated a true-breeding black smooth guinea pig to a true-breeding white rough to get the F 1 so... Black smooth & white rough are together from the parents

68. The lineage of the offspring determines the parental type Linkage is between gene loci, not alleles Recombination constantly shuffles the alleles so that it is only if you know the lineage of an organism that you can predict the parental type But you can just observe the parental type...

69. An example from fruit flies A grey bodied, normal winged fly in a test cross produces all four offspring types but...

70. Four offspring are not in equal proportions: The rare offspring type represent the recombinant type The more common offspring represent the parental type You don’t really need to know lineage to figure out which is which

71. Genes have alternate versions (alleles) Organisms have two “particles” for each gene: diploid Some alleles are dominant to others (recessive) Alleles segregate during gamete formation Law of independent assortment = isn’t true for linked genes (on same chromosome) Mendel’s Big (Modified) Ideas

72. Exceptions to the Rule Mendel looked at traits that were either dominant or recessive Some traits do not follow these clear patterns

73. Codominance Pair of non-identical alleles expressed at same time in heterozygotes

74. e.g. The ABO Blood System RBCs have membrane glycolipid that differentiate between types Structure of glycolipid determined by enzyme 3 alleles code for enzyme: I A, I B, i = multiple allele system

75. I A & I B are codominant when paired i is recessive when paired with I A & I B

76. I A I A or I A i = 1 type of sugar = blood type A I B I B or I B i = other type of sugar = blood type B I A I B = both sugars = blood type AB ii = no sugar = blood type O I A & I B have different forms of enzyme that attaches last sugar to glycolipid

77. If a boy’s father has blood type AB & his mother has type O, what blood types could the boy have? How likely is each? Imagine a young woman has type B blood & her mother has type AB. What blood type can you rule out for her father? Using Multiple Alleles

78. Incomplete Dominance 1 allele not fully dominant, so both expressed in heterozygotes Phenotype is somewhere between 2 homozygotes

79. e.g. snapdragons True-breeding P red flowers & white flowers produce F 1 pink flowers +

80. Red flowers (AA) have 2 alleles & produce red pigment White flowers (aa) have 2 mutant alleles so produce no pigment Pink F1 (Aa) have 1 red & 1 white allele = enough red pigment to make pink colour, but red allele not dominant enough to make flowers red

81. Sometimes alleles are not dominant = heterozygote has a different phenotype In snapdragons heterozygotes for flower color are intermediate in phenotype (pink) to either parent This does not mean there is a pink allele! Modifying Mendel’s Big Ideas

82. Epistasis More than 1 gene affects 1 given trait e.g. coat colour in labs determined by 2 genes (E/e & B/b)

83. Pleiotropy 1 gene affects more than 1 trait Can have positive or negative effects e.g. many genetic disorders, aging e.g. SRY gene: codes for protein that activates other genes, that code for proteins that control male development

84. e.g. sickle cell anemia Normal RBCs

85. Phenotype is not just a result of genotype Environment plays a key role in many traits e.g. skin colour, body size, intelligence, personality For many traits, genes & environment play a roughly equal role in determining phenotype BUT: Effects of the environment are not heritable Environmental Influence

86. Genes & the Environment Environmental conditions can affect how genes are expressed (i.e. variation in traits) e.g. soil acidity (aluminum availability) & hydrangea colour

87. e.g. the Himalayan rabbit Gene for black fur expressed in cool areas of body (has genotype for black fur all over but pigment only produced if < 34°C)

88. What was the main idea about inheritance prior to Mendelian inheritance? Blending inheritance = offspring are a “blend” of parents = offspring phenotype is usually in between the phenotype of parents We now explain this in terms of polygenic inheritance

89. Polygenic Inheritance Individuals in population show range of small differences in most traits e.g. eye colour, human height, etc. Multiple genes influence a single trait

90. Polygenic inheritance mimics blending inheritance because of the large number of genes each with an additive effect (plus environmental effects)

91. Alleles for different genes act additively to build a phenotype Several genes influence phenotype each with a +1 or +0 allele So traits have a characteristic distribution pattern in a population & offspring are often intermediate between parents Polygenic Inheritance

92. An Example: Wheat Grain Colour 2 genes with incompletely dominant alleles determine wheat grain colour = R1 & R1’ & R2 & R2’ (R alleles = 1 unit of red pigment) (R’ alleles = no pigment) 2 heterozygous wheat plants will produce 5 colours of offspring Because 2 genes, are 5 possible combos of alleles: (4 R), (3 R & 1 R’), (2 R & 2 R’), (1 R & 3 R’), (4 R’)

93. R1R1R2R2R1R1R2R2 eggs R1R1R2R2R1R1R2R2 R1R1R2R2R1R1R2R2 R1R1R2R2R1R1R2R2 R1R1R2R2R1R1R2R2 R1R1R2R2R1R1R2R2 R1R1R2R2R1R1R2R2 R1R1R2R2R1R1R2R2 R1R1R2R2R1R1R2R2 R1R1R2R2 R1R1R2R2 R1R1R2R2R1R1R2R2 R1R1R2R2 R1R1R2R2 R1R1R2R2 R1R1R2R2 R1R1R2R2R1R1R2R2 R1R1R2R2R1R1R2R2 R1R1R1R2R1R1R1R2 R1R1R2R2R1R1R2R2 sperm R1R2R1R2 R1R2R1R2 R1R2R1R2 R1R2R1R2 R1R2R1R2 R1R2R1R2 R1R2R1R2 R1R2R1R2 R1R1R2R2R1R1R2R2 R alleles = +1 to colour R’ alleles = +0 to colour

94. Imagine a couple, one with very light skin, and one with very dark skin, have children. What will their children’s skin colour be? (remember this is a bit of an oversimplification of skin color inheritance)

95. In polygenic inheritance, alleles are influenced by environment so traits blend even more

96. Distribution of all forms of trait is more continuous when  genes & environmental factors are involved = bell curve Becomes harder to classify phenotypes reliably

97. Example A rooster with grey feathers is mated to a hen who also has grey feathers. Among their offspring 15 chicks are grey, 6 are black & 8 are white. What is the simplest explanation for this inheritance pattern? What phenotypes would you expect in the offspring resulting from a cross between a grey rooster & a black hen?

98. Example Imagine two organisms with the genotypes AABB & aabb are bred to make a heterozygous offspring (AaBb). What will the offsprings’ gametes look like? If these two genes (A & B) are linked, what would this do to the gametes that are produced? Why?