1. Plant Meiosis

3. Animals vs. Plants Plant ReproductionAnimal Reproduction Life cycle Alternation of generations No alternation of generations GametesHaploid gametes SporesHaploid sporesNo spores Gametes made by Haploid gametophyte, by mitosis Diploid organism, by meiosis Spores made by Diploid sporophyte, by meiosis No spores

4. Alternation of Generations Plants have a double life cycle with two distinct forms: Sporophyte: diploid, produce haploid cells by meiosis. Gametophyte: haploid, produce gametes by mitosis.

5. Non-flowering plants Mosses, ferns, and related plants have motile, swimming sperm.

6. Moss Life Cycle

7. Fern Life Cycle

8. Flower Higher Plant

9. Angiosperm Life Cycle

10. Gametogenesis: Male

11. G ametogenesis: Female

12. Double Fertilization

13. Flower to Fruit

14. Ovule to Seed

15. Unique events in Meiosis Homologous ( matching ) chromosomes pair up before 1 st cell division Homologous chromosomes: -look alike -code for same traits -receive one from each parent

16. During 1 st division, homologous chromosomes exchange genes during process called “crossing over” Unique events in Meiosis

17. These homologous chromosomes separate during 2 nd division of meiosis – so chromosomes in gametes are different from each other due to crossing over Crossing over increases genetic variation and is the reason why siblings look different Unique events in Meiosis

18. Crossing Over Sometimes in meiosis, homologous chromosomes exchange parts in a process called crossing-over, or recombination.

19. Process of Recombination Genes are on chromosomes. Meiosis is a mechanism for re-shuffling the chromosomes: each gamete gets a mixture of paternal and maternal chromosomes. However, chromosomes are long and contain many genes. To get individual genes re- shuffled, there needs to be a mechanism of recombining genes that are on the same chromosome. This mechanism is called “crossing over.

20. More Recombination Crossing over occurs in prophase of meiosis 1, when the homologous chromosomes “synapse”, which means to pair closely with each other. DNA strands from the two chromosomes are matched with each other. During synapsis, an enzyme, “recombinase”, attaches to each chromosome at several randomly chosen points. The recombinase breaks both DNA molecules at the same point, and re-attaches them to opposite partners. The result of crossing over can be seen in the microscope as prophase continues, as X-shaped structures linking the homologues. The genetic consequence of crossing over is that each chromosome that goes into a gamete is a combination of maternal and paternal chromosomes.

21. Recombination Process

22. Linkage. Linkage occurs when two genes are close to each other on the same chromosome. Two genes are syntenic, when they are on the same chromosome. Linked genes are syntenic, but syntenic genes are not always linked. Genes far apart on the same chromosome assort independently: they are not linked. Linkage is based on the frequency of crossing over between the two genes. Crossing over occurs in prophase of meiosis I, where homologous chromosomes break at identical locations and rejoin with each other. The failure of two genes to assort independently

23. Discovery of Linkage In 1900, Mendel’s work was re-discovered, and scientists were testing his theories with as many different genes and organisms as possible. William Bateson and R.C. Punnett were working with several traits in sweet peas, notably a gene for purple (P) vs. red (p) flowers, and a gene for long pollen grains (L) vs. round pollen grains (l).

24. Bateson and Punnett’s Results PP LL x pp ll selfed F1: Pp Ll F2 results in table Very significant deviation from expected Mendelian ratio: chi- square = 97.4, with 3 d.f. Critical chi square value = 7.815. The null hypothesis for chi square test with 2 genes is that the genes assort independently. These genes do not assort independently. phenot ype obsexp ratio exp num P_ L_2849/16215 P_ ll213/1671 pp L_213/1671 pp ll551/1624

25. Linkage Mapping Each gene is found at a fixed position on a particular chromosome. Making a map of their locations allows us to identify and study them better. In modern times, we can use the locations to clone the genes so we can better understand what they do and why they cause genetic diseases when mutated. The basis of linkage mapping is that since crossing over occurs at random locations, the closer two genes are to each other, the less likely it is that a crossover will occur between them. Thus, the percentage of gametes that had a crossover between two genes is a measure of how far apart those two genes are. As pointed out by T. H. Morgan and Alfred Sturtevant, who produced the first Drosophila gene map in 1913. Morgan was the founder of Drosophila genetics, and in his honor a recombination map unit is called a centiMorgan (cM). A map unit, or centiMorgan, is equal to crossing over between 2 genes in 1% of the gametes.

26. Gene Mapping Gene mapping determines the order of genes and the relative distances between them in map units 1 map unit = 1 cM (centimorgan) In double heterozyote: Cis configuration = mutant alleles of both genes are on the same chromosome = ab/AB Trans configuration = mutant alleles are on different homologues of the same chromosome = Ab/aB

27. Gene Mapping Gene mapping methods use recombination frequencies between alleles in order to determine the relative distances between them Recombination frequencies between genes are inversely proportional to their distance apart Distance measurement: 1 map unit = 1 percent recombination (true for short distances)

28. Recombination

29. 29 Gene Mapping Genes with recombination frequencies less than 50 percent are on the same chromosome = linked) Linkage group = all known genes on a chromosome Two genes that undergo independent assortment have recombination frequency of 50 percent and are located on nonhomologous chromosomes or far apart on the same chromosome = unlinked Recombination

30. Recombination between linked genes occurs at the same frequency whether alleles are in cis or trans configuration Recombination frequency is specific for a particular pair of genes Recombination frequency increases with increasing distances between genes No matter how far apart two genes may be, the maximum frequency of recombination between any two genes is 50 percent. Recombination

31. 31 Gene Mapping Recombination results from crossing-over between linked alleles. Recombination changes the allelic arrangement on homologous chromosomes Recombination

32. Genetic Mapping The map distance (cM) between two genes equals one half the average number of crossovers in that region per meiotic cell The recombination frequency between two genes indicates how much recombination is actually observed in a particular experiment; it is a measure of recombination Over an interval so short that multiple crossovers are precluded (~ 10 percent recombination or less), the map distance equals the recombination frequency because all crossovers result in recombinant gametes. Genetic map = linkage map = chromosome map Recombination

33. Gene Mapping: Crossing Over Two exchanges taking place between genes, and both involving the same pair of chromatids, result in a nonrecombinant chromosomes

34. Gene Mapping: Crossing Over Crossovers which occur outside the region between two genes will not alter their arrangement The result of double crossovers between two genes is indistinguishable from independent assortment of the genes Crossovers involving three pairs of alleles specify gene order = linear sequence of genes

35. 35 Gene Mapping: Crossing Over

36. Genetic vs. Physical Distance Map distances based on recombination frequencies are not a direct measurement of physical distance along a chromosome Recombination “hot spots” overestimate physical length Low rates in heterochromatin and centromeres underestimate actual physical length

37. Genetic vs. Physical Distance

38. Discovery of Genetic Linkage Classical genetics analyzes the frequency of allele recombination in progeny of genetic crosses New associations of parental alleles are recombinants, produced by genetic recombination. Tests crosses determine which genes are linked, and a linkage map (genetic map) is constructed for each chromosome.

39. MORGAN’s EXPERIMENTS Both the white eye gene (w) and a gene for miniature wings (m) are on the X chromosome. Morgan (1911) crossed a female white miniature (w m/w m) with a wild-type male (w+ m+/ Y). In the F1, all males were white-eyed with miniature wings (w m/Y), and all females were wild-type for eye color and wing size (w+ m+/w m).

40. MORGAN’s EXPERIMENTS F1 interbreeding is the equivalent of a test cross for these X-linked genes, since the male is hemizygous recessive, passing on recessive alleles to daughters and no X-linked alleles at all to sons. What is the expected ratio of phenotypes in F2, if white and miniature are on different chromosomes? In F2, the most frequent phenotypes for both sexes were the phenotypes of the parents in the original cross (white eyes with miniature wings, and red eyes with normal wings). Non-parental phenotypes (white eyes with normal wings or red eyes with miniature wings) occurred in about 37% of the F2 flies. Well below the 50% predicted for independent assortment, this indicates that non-parental flies result from recombination of linked genes.

41. Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings. Morgan’s experimental crosses of white-eye and miniature-wing variants of Fruit fly

42. MORGAN’S PROPOSAL During meiosis alleles of some genes assort together because they are near each other on the same chromosome. Recombination occurs when genes are exchanged between X chromosomes of the F1 females Parental phenotypes occur most frequently, while recombinants less. Terminology Chiasma: site of crossover Crossing over: reciprocal exchange of homologous chromatid segments Crossing-over occurs at prophase I in meiosis; each event involves two of the four chromatids. Any chromatids may be involved in crossing over.

43. Mechanism of crossing-over

44. Detecting Linkage through Testcrosses Linked genes are used for mapping. They are found by looking for deviation from the frequencies expected from independent assortment. A testcross (one parent is homozygous recessive) works well for analyzing linkage If the alleles are not linked, and the second parent is heterozygous, all four possible combinations of traits will be present in equal numbers in the progeny. A significant deviation in this ratio (more parental and fewer recombinant types) indicates linkage.

45. Testcross to show that two genes are linked

47. Chi-square for analysis of linkage A null hypothesis (‘the genes independently assort’) is used because it is not possible to predict the phenotype frequencies produced by linked genes. If two genes are not linked, a testcross should yield a 1:1 ratio of parentals: recombinants. Formula is X2 = sum (Obs-Exp)^2/Exp If P>0.05, deviation between Obs and Exp is not significant If P<=0.05, deviation is statistically significant; such that genes may be linked.

48. Concept of Genetic Map In an individual heterozygous at two loci, there are two arrangements of alleles: Cis (coupling) arrangement: has both wild type alleles on one homologous chromosome, and both mutants on the other (e.g., w+ m+ and w m). Trans (repulsion) arrangement: has one mutant and one wild-type on each chromosome (e.g., w+ m and w m+) A crossover between homologs in cis arrangement results in a homologous pair with the trans arrangement. A crossover between homologs in the trans arrangement results in cis homologs.

49. Drosophila Crosses They showed that cross over frequency for linked genes (measured by recombinants) is characteristics for each gene pair. The frequency stays the same, whether the genes are in coupling or in repulsion. Morgan and Sturtevant (1913) used recombination frequencies to make a genetic map. A 1% crossover rate is a genetic distance of 1 map unit (mu). A map unit is also called a centimorgan (cM). Geneticists use recombination frequency as a way to estimate crossover frequency. The farther apart the two genes are on the chromosome, the more likely it is that crossover will occur between them, and therefore the greater their crossover frequency.

50. Drosophila Crosses

51. First Genetic Map Three X-linked genes White (w): white eyes Miniature (m): miniature wings Yellow (y): yellow body Crosses gave the following recombination frequencies: White x miniature was 32.6 White x yellow was 1.3 Miniature x yellow was 33.9 MAP: m-----------------------------------w---y

52. Gene Mapping Using Two-Point Testcrosses With autosomal recessive alleles, when a double heterozygote is testcrossed, four phenotypic classes are expected. If the genes are linked, the two parental phenotypes will be about equally frequent and more abundant than the two recombinant phenotypes.

53. For autosomal dominants, a double heterozygotes (A B/A+B+) is testcrossed with a homozygous wildtype (recessive) individual (A+B+/A+B+) For X-linked recessives, a female double heterozygote (a+ b+/a b) is crossed with a hemizygous recessive male (a b/Y). For X-linked dominants, a female double heterozygote (A B/A+ B+) is crossed with a male hemizygous for the wild- type (A+ B+). Phenotypes obtained in these crosses will depend on whether the alleles are in cis or trans position.

54. GENETIC MAP Recombination frequency is used directly as an estimate of map units. The measure is more accurate when alleles are close together. Scoring large numbers of progeny increases accuracy.

55. GENERATING A LINKAGE MAP Genetic map is generated from estimating the crossover rate in a particular segment of a the chromosome. It may not exactly match the physical map because crossover is not equally probable at all sites on the chromosome. Recombination frequency is also used to predict progeny in genetic crosses. For example, a 20% crossover rate between two pairs of alleles in a heterozygote (a+ b+/a b) will give 10% gametes of each recombinant type (a+ b and a b+).

56. MULTIPLE CROSSOVERS If the genes are on the same chromosome, multiple crossovers can occur. The further apart two loci are, the more likely they are to have crossover events take place between them. The chromatid pairing is not always the same in crossover, so that 2,3, or 4 chromatids may participate in multiple crossover.

57. Demonstration that the recombination frequency between two genes located far apart on the same chromosome cannot exceed 50 percent

58. Demonstration that the recombination frequency between two genes located far apart on the same chromosome

59. Demonstration that the recombination frequency between two genes located far apart on the same chromosome cannot exceed 50 percent

60. Three-point mapping, showing the testcross used and the resultant progeny

61. Mapping using three- point testcrosses Geneticists design experiments to gather data on several traits in 1 testcross. An example of a three-point testcross would be p+r+j+/p r j X p r j / p r j In the progeny, each gene has two possible phenotypes. For three genes there are (2)^3=8 expected phenotypic classes in the progeny.

62. Establishing the order of genes The order of genes on the chromosome can be deduced from results of the cross. Of the eight expected progeny phenotypes: Two classes are parental (p+ r+ j+/ p r j and p r j / p r j) and will be the most abundant. Of the six remaining phenotypic classes, two will be present at the lowest frequency, resulting from apparent double crossover (p+ r+ j / p r j and p r j+ / p r j). This establishes the gene order as p j r.

63. Consequences of a double crossover in a triple heterozygote for three linked genes

64. Rearrangement of the three genesr

65. Rewritten form of the testcross and testcross progeny based on the actual gene order p j r

66. Calculating the recombination frequencies Cross data is organized to reflect the gene order, and this example the region between genes p and j is called region I, and that between j and r is region II.

67. Calculating recombination frequencies Recombination frequencies are now calculated for two genes at a time. It includes single crossovers in the region under study, and double crossovers, since they occur in both regions. Recombination frequencies are used to position genes on the genetic map (each 1% recombination frequency = 1 map unit) for the chromosomal region. Recombination frequencies are not identical to crossover frequencies, and typically underestimate the true map distance.

68. Genetic map of the p-j-r region of the chromosome

69. Calculating accurate map distances Recombination frequency generally underestimates the true map distance: Double crossovers between two loci will restore the parental genotype, as will any even number of crossovers. These will not be counted as recombinants, even though crossovers take place. A single crossover will produce recombinant chromosomes, as will any odd number of crossovers. Progeny analysis assumes that every recombinant was produced by a single crossover. Map distances for genes that are less than 7 mu apart are very accurate. As distance increases, accuracy declines because more crosses go uncounted.

70. Progeny of single and double crossover s