DNA Polymorphisms: DNA markers

DNA Polymorphisms: DNA markers

Transmission Genetics Transmission genetics is the sub-field of genetics that is concerned with the study of inheritance in individuals. Individuals reproduce sexually (crosses) and the appearance of traits in the offspring is studied. Farmers since the dawn of agriculture used transmission genetics to improve varieties. Gregor Mendel used the scientific method to study inheritance. 1 Mendel and Transmission Genetics Gregor Mendel, monk, Czech Republic, 1856-1863

Studied 7 traits in pea plants, Pisum sativum Established basic rules of transmission genetics Good science, but ignored for >30 years Why peas? Many varieties w/ contrasting traits Self-pollinating, with true-breeding varieties easy to snip parts to cross pollinate Need little space, produce lots of offspring 2 Basics of Mendelian Genetics Terminology Traits: characteristic of appearance that can come in different forms, such as different flower colors.

Hybrid: offspring formed by crossing of parents that differ in a trait Monohybrid, dihybrid, etc: based on how many traits parents differ by. Reciprocal crosses: matings with traits swapped in parents 3 More definitions P1 generation: the parents F1: first generation of offspring F2: second

generation of offspring 4 5 6 Scientific and historical context Ideas about heredity Every organism carries all the traits to be found in its descendants Blending: when traits are inherited from 2 sources, they blend and lose their individual identities.

Mendel: sources of traits are discrete (particulate) http://giftaroo.com/Merchant2/graphics/00000002/RD105_lg.jpg http://www.edwardst50.freeserve.co.uk/Image11.jpg 7 First observations Mendel did many monohybrid crosses Multiple generations looking at seeds, pods, flowers, stems In each case, he crossed parents with contrasting traits, obtained seeds, and grew the F1 generation. Phenotype of the offspring was that of

one parent, not any blend of the two traits. (e.g. round x wrinkled = all round). 8 First observations-2 Crossing plants of the F1 generation: F2 generation Missing trait returned (e.g. wrinkled seeds) Missing trait always about of the offspring.

(3:1 ratio) 9 Mendels postulates 10 Genetic characters controlled by unit factors These exist in pairs in organisms Unit factors are genes; contrasting forms are alleles 3 combos possible (e.g. 2 factors for tall, 2 factors for dwarf, or 1 each for tall and dwarf). Terminology Homozygous: both alleles are the same.

Heterozygous: alleles are different (1 of each) Mendels postulates continued 11 When the 2 factors are different, one masks the other (is dominant; the other is recessive) In F1 generation, the recessive factor was hidden, e.g. the round seed allele masks the wrinkled one. Segregation: during formation of gametes, the paired unit factors separate (segregate) so that each gamete gets one of them (at random). For a plant with one allele each for round seeds and wrinkled seeds, a gamete has a 50% chance of

having either. Law of Segregation Punnett Square Two units for each trait; during meiosis, each gamete gets only one unit. Single gamete from each parent combines to produce diploid offspring. Law of Segregation: Each gamete equally likely to receive either unit. Nomenclature W & w Genotype: 1:2:1 ratio Phenotype: 3:1 ratio

12 When is dominant dominant? 13 Visual phenotype: Pea plants homozygous for the wrinkled seed allele make wrinkled seeds. Homozygous for round seed allele: round seeds Heterozygous plants also make round seeds. Molecular phenotype: What do alleles code for? The presence (or absence) of a starch-branching enzyme. The normal gene is disrupted by insertion of a

transposon, so enzyme is not made, resulting in the wrinkled trait . Molecular analysis of wrinkled When DNA fragments are separated, larger pieces move slower (are at top of gel). Seeds made by heterozygous plants show dominant visual phenotype, but the molecular phenotype shows co-dominance (neither allele masks the other).

DNA which includes gene for the enzyme. 14 Dominance 15 Dominance is a situation in a diploid organism in which one allele masks another. Dominant does NOT mean most common Dominance can be co-dominance (neither trait masks the other) or partial dominance (both traits are partially seen, neither completely

masks the other). Crosses Mendel did to confirm his predictions 16 When the F1 generation was selfed, a 3:1 ratio of round to wrinkled seeds was produced (3/4 round). Of that , 2 were heterozygous, 1 homozygous dominant Therefore, when all the round-seeded plants were selfed, 1/3 would produce only round seed, but the other 2/3 would produce round and wrinkled seeds (in a 3:1 ratio) Crosses Mendel did to confirm his predictions

17 Testcross: kind of backcross in which the parent has a known genotype (homozygous recessive!) Backcross: any cross between offspring and parent Problem: individuals with the dominant phenotype could be either homozygous or heterozygous. By crossing with the homozygous recessive, offspring will either all have the dominant phenotype or will be 50:50 dominant and recessive. Possible results of testcross 18

19 The Dihybrid Cross G (dominant) = yellow W (dominant) = round (recessive) = wrinkled g (recessive) = green WW GG x gg W Gg (all heterozygous) W Gg x W Gg (self the F1 generation) W G W

g G g WG WW GG WW Gg W GG W Gg

Wg WW Gg WW gg W Gg W gg G W GG W Gg

GG Gg g W Gg W gg Gg gg Dihybrid cross (continued)

20 Phenotypic classes: 9:3:3:1 Genotypic classes: 1:2:1:2:4:2:1:2:1 Actual data (phenotypic) Round, yellow 315 Round green 108 Wrinkled, yellow 101 Wrinkled, green 32 Independent Assortment During gamete formation, segregating pairs of alleles assort independently of each other

Because 2 traits are inherited independently, the product law can be use to calculate probabilities. Events in Meiosis I provide the cytological basis for Mendels Independent Assortment 21 Disjunction (separation of chromosomes) of homologues is a random event, that is, any combination of maternal and paternal chromosomes can separate together. Alleles present on these chromosomes can likewise be expressed in different combinations. This is what Mendel saw when the F2 generation of peas produced

seeds that showed a 3:1 ratio for both the yellow/green trait and for the round/ wrinkled trait. Neither affected the other. Trihybrid cross 22 Mendel also crossed peas and looked at inheritance of 3 traits simultaneously. These showed independent assortment also. A Punnett square to determine the phenotypic ratios would be unwieldy It would require an 8 x 8 matrix: 64 squares

Because independent events are involved, one can use the product law Multiply each probability. Simplest way: forked-line method = branch diagram Branch diagram for figuring trihybrid cross 23 Crossing 2 individuals heterozygous for all 3 traits: Ww Gg Pp x Ww Gg Pp What proportion of the offspring are expected to have round, green peas and purple flowers, where W is

round, w is wrinkled; G is yellow, g is green; and P is purple and p is white? W_ gg P_ x x = 9/64

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