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Haixu Tang School of Informatics

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1 Haixu Tang School of Informatics
Basic genetics Haixu Tang School of Informatics

2 Mendel’s two innovations
Developed pure lines a population that breeds true for a particular trait Counted his results and kept statistical notes

3 Phenotypes of Mendel's pea plants
round or wrinkled seed phenotype yellow or green seed phenotype red or white flower phenotype tall or dwarf plant phenotype

4 Results from Mendel's Experiments
Parental Cross F1 Phenotype F2 Phenotypic Ratio F2 Ratio Round x Wrinkled Seed Round 5474 Round:1850 Wrinkled 2.96:1 Yellow x Green Seeds Yellow 6022 Yellow:2001 Green 3.01:1 Red x White Flowers Red 705 Red:224 White 3.15:1 Tall x Dwarf Plants Tall l787 Tall:227 Dwarf 2.84:1

5 Phenotypes Dominant - the allele that expresses itself at the expense of an alternate allele; the phenotype that is expressed in the F1 generation from the cross of two pure lines Recessive - an allele whose expression is suppressed in the presence of a dominant allele; the phenotype that disappears in the F1 generation from the cross of two pure lines and reappears in the F2 generation

6 Conclusion The hereditary determinants are of a particulate nature. These determinants are called genes. Each parent has a gene pair in each cell for each trait studied. The F1 from a cross of two pure lines contains one allele for the dominant phenotype and one for the recessive phenotype. These two alleles comprise the gene pair. One member of the gene pair segregates into a gamete, thus each gamete only carries one member of the gene pair. Gametes unite at random and irrespective of the other gene pairs involved.

7 Some terms Allele - one alternative form of a given allelic pair; tall and dwarf are the alleles for the height of a pea plant; more than two alleles can exist for any specific gene, but only two of them will be found within any individual Allelic pair - the combination of two alleles which comprise the gene pair Homozygote - an individual which contains only one allele at the allelic pair; for example DD is homozygous dominant and dd is homozygous recessive; pure lines are homozygous for the gene of interest Heterozygote - an individual which contains one of each member of the gene pair; for example the Dd heterozygote Genotype - the specific allelic combination for a certain gene or set of genes

8 F1: Symbol representation

9 F2: Punnett Square Union of Gametes At Random D d DD (Tall) Dd (Tall)
dd (Short)

10 Mendel's First Law The law of segregation: during gamete formation each member of the allelic pair separates from the other member to form the genetic constitution of the gamete

11 Test the hypothesis

12 Genotype of the F2 individuals
Phenotypes Genotypes Genetic Description F2 Tall Plants 1/3 DD 2/3 Dd Pure line homozygote dominant Heterozygotes F2 Dwarf Plants all dd Pure line homozygote recessive Thus the F2 is genotypically 1/4 Dd : 1/2 Dd : 1/4 dd

13 Backcross: Dd x dd The cross of an F1 hybrid to one of the homozygous parents; for pea plant height the cross would be Dd x DD or Dd x dd; most often, though a backcross is a cross to a fully recessive parent Backcross One or (BC1) Phenotypes: 1 Tall : 1 Dwarf BC1 Genotypes: 1 Dd : 1 dd

14 Monohybrid Monohybrid cross - a cross between parents that differ at a single gene pair (usually AA x aa) Monohybrid - the offspring of two parents that are homozygous for alternate alleles of a gene pair Remember --- a monohybrid cross is not the cross of two monohybrids.

15 Variations to Mendel's First Law of Genetics
Codominance - a relationship among alleles where both alleles contribute to the phenotype of the heterozygote Incomplete dominance - the F1 produces a phenotype quantitatively intermediate between the two homozygous parents;

16 Pedigree Analysis

17 Traits exhibiting dominant gene action
affected individuals have at least one affected parent the phenotype generally appears every generation two unaffected parents only have unaffected offspring


19 Traits exhibiting recessive gene action
unaffected parents can have affected offspring affected progeny are both male and female


21 Mendel's Law of Independent Assortment
We have followed the expression of only one gene. Mendel also performed crosses in which he followed the segregation of two genes. These experiments formed the basis of his discovery of his second law, the law of independent assortment.

22 Dihybrid cross Dihybrid cross - a cross between two parents that differ by two pairs of alleles (AABB x aabb) Dihybrid- an individual heterozygous for two pairs of alleles (AaBb)

23 Mendel’s experiment Parental Cross: Yellow, Round Seed x Green, Wrinkled Seed F1 Generation: All yellow, round F2 Generation: 9 Yellow, Round, 3 Yellow, Wrinkled, 3 Green, Round, 1 Green, Wrinkled Seed Color: Yellow = G; Green = g Seed Shape: Round = W; Wrinkled = w

24 Parental cross

25 GGww (Yellow, wrinkled) Ggww (Yellow, wrinkled)
Female Gametes GW Gw gW gw GGWW (Yellow, round) GGWw (Yellow, round) GgWW (Yellow, round) GgWw (Yellow, round) Male GGww (Yellow, wrinkled) Ggww (Yellow, wrinkled) Gametes ggWW (Green, round) ggWw (Green,ROUND) ggWw (Green, round) ggww (Green, wrinkled)

26 Phenotype General Genotype 9 Yellow, Round Seed G_W_ 3 Yellow, Wrinkled Seed G_ww 3 Green, Round Seed ggW_ 1 Green, Wrinkled Seed ggww

27 Mendel's Second Law - the law of independent assortment
During gamete formation the segregation of the alleles of one allelic pair is independent of the segregation of the alleles of another allelic pair.

28 backcross - F1 dihybrid x
Female Gametes GW Gw gW gw Male Gametes GgWw (Yellow, round) Ggww (Yellow, wrinkled) ggWw (Green, ggww (Green, The phenotypic ratio of the test cross is: 1 Yellow, Round Seed 1 Yellow, Wrinkled Seed 1 Green, Round Seed 1 Green, Wrinkled Seed

29 The Chi-Square Test An important question to answer in any genetic experiment is how can we decide if our data fits any of the Mendelian ratios we have discussed. A statistical test that can test out ratios is the Chi-Square or Goodness of Fit test. Degrees of freedom (df) = n-1, where n is the number of classes

30 An example Let's test the following data to determine if it fits a 9:3:3:1 ratio. Observed Values Expected Values 315 Round, Yellow Seed (9/16)(556) = Round, Yellow Seed 108 Round, Green Seed (3/16)(556) = Round, Green Seed 101 Wrinkled, Yellow Seed (3/16)(556) = Wrinkled, Yellow   32 Wrinkled, Green (1/16)(556) =   Wrinkled, Green 556 Total Seeds                         Total Seeds                                                   Number of classes (n) = 4 df = n = 3 Chi-square value = 0.47

31 A Chi-Square Table Probability Degrees of Freedom 0.9 0.5 0.1 0.05
0.01 1 0.02 0.46 2.71 3.84 6.64 2 0.21 1.39 4.61 5.99 9.21 3 0.58 2.37 6.25 7.82 11.35 4 1.06 3.36 7.78 9.49 13.28 5 1.61 4.35 9.24 11.07 15.09

32 Pleiotropic Effects and Lethal Genes
In 1904, a cross was made between a yellow-coated mouse and a mouse with a gray coat. The gray- coated mouse was extensively inbred and therefore was considered to be pure bred.

33 Next a cross was made between two yellow mice
Next a cross was made between two yellow mice. What genetic ratio would we expect to see? Yy x Yy should give a ratio of 3 yellow:1 gray. The result, though, was a ratio of 2 yellow to 1 gray mice. How can this result be explained? Let's first set up a Punnett Square.

34 Testcross All testcross data with the yellow mice give a 1:1 ratio. This ratio is typical of what is seen with heterozygous individuals. All of the yellow mice from the cross of two heterozygous yellow mice are genotypically Yy. Somehow the YY genotype is lethal. The 2:1 ratio is the typical ratio for a lethal gene.

35 Lethal gene Lethal Gene - a gene that leads to the death of an individual; these can be either dominant or recessive in nature. Pleiotropic gene - a gene that affects more than one phenotype

36 Gene Interactions Rose                                              Pea Single                                                Walnut

37 Phenotypes Genotypes Frequency Walnut R_P_ 9/16 Rose R_pp 3/16 Pea rrP_ Single rrpp 1/16

38 Epistasis The interaction between two or more genes to control a single phenotype

39 Modifier Genes Instead of masking the effects of another gene, a gene can modify the expression of a second gene. In mice, coat color is controlled by the B gene. The B allele conditions black coat color and is dominant to the b allele that produces a brown coat. The intensity of the color, either black or brown is controlled by another gene, the D gene. At this gene, the dominant D allele controls full color whereas the recessive d allele conditions a dilute or faded expression of the color expression at the B gene. Therefore, if a cross is made among mice that are BdDd, the following phenotypic distribution will be seen: 9 B_D_ (black) 3 B_dd (dilute black) 3 bbD_ (brown) 1 bbdd (dilute brown) The D gene does not mask the effect of the B gene, rather it modifies its expression.

40 Gene linkage One experiment was performed by Bateson and Punnett with sweet peas. They performed a typical dihybrid cross between one pure line with purple flowers and long pollen grains and a second pure line with red flowers and round pollen grains. Because they knew that purple flowers and long pollen grains were both dominant, they expected a typical 9:3:3:1 ratio when the F1 plants were crossed.

41 Observed Expected Purple, long (P_L_) 284 215 Purple, round (P_ll) 21 71 Red, long (ppL_) Red, round (ppll) 55 24 Total 381

42 Linked Genes On The Same Chromosome
F1 Gamete Testcross Distribution Gamete Type pr+ vg+ 1339 Parental pr+ vg 151 Recombinant pr vg+ 154 pr vg 1195

43 Coupling and repulsion
F1 Gamete Testcross Distribution Gamete Type pr+ vg+ 1339 Parental pr+ vg 151 Recombinant pr vg+ 154 pr vg 1195


45 Genotype Observed Type of Gamete ABC 390 Parental abc 374 AbC 27 Single-crossover between genes C and B aBc 30 ABc 5 Double-crossover abC 8 Abc 81 Single-crossover between genes A and C aBC 85 Total 1000


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