GENETIC PRINCIPLES The birth and evolution of modern genetics

Dana King 1-22-14

Genetic Principles • Part I: Readings & Questions

• Chapter 2: Mendel • Chapter 11: Mutation •  The Chromosomes in Heredity (Sutton)

• Part II: Genetics Refresher • Definitions • Meiosis • Pea crosses

Why are we talking about these guys?

q  I’ve taken one or two genetics courses. I’m down with the chromosomes but I don’t expect my research to involve much “classical” genetics.

q  My research has already involved some genetics. I like cloning genes or knocking things out or knocking things down. Genetics is cool.

q  I could do forward/reverse screens in my sleep… with one hand tied behind my back. Genetics is the BEST.

Part I: Mendel, Mutations, & Heredity • Mendel: The father of genetics

•  Model organism: Pisum et al. •  Principles of segregation and recombination •  Fisher’s criticisms: too good to be statistically true?

• Muller: Mutation •  Model organism: Drosophila •  Determination of mutation rates using sex-linked lethals •  A “one-hit” phenomenon

• Sulston: Chromosomal theory of inheritance •  Meiosis: unifying inheritance and chromosomes since 1903 •  Principle of independent assortment

Chapter 2: Mendel • Goal: To understand the principles of segregation and

independent assortment, as they were discovered by Mendel.

• Key points:

•  The scientific process isn’t perfect; Mendel tried several model systems before defining heredity in Pisum.

•  Mendel’s insights were likely in part due to his excellent record keeping.

•  Understanding the assumptions made in analyses is important (and so is thinking about statistics)

1. Other model systems: the good, the bad, & the ugly

A.  Hieracium: a poor choice because the seed is purely maternal in origin so impossible to study segregation or recombination

Mom x Dad = Kid always looks like mom A.  Mirabilis: a poor choice because the flowers had too

many shades of color to separate (likely a complex trait) For complex traits like human height, still don’t know all the genes/loci that contribute to height.

2. Mendel: The groundbreaker A.  Mendel employed three new procedures:

A.  Determined the number of forms of hybrid progeny B.  Arranged these forms according to their generations C.  Determined their statistical relations

B.  His approach was effective because: A.  Developed a simple interpretation of the ratios obtained B.  Carried out direct experiments to test this interpretation

3. Fisher’s criticisms A.  Fisher criticizes Mendel’s ratios for being too close to

expectation.

B.  Fisher calculates that, according to sampling theory, the chance of getting as close of a fit as reported by Mendel for all of the data is only 1 out of 14,000 (.00007).

4. Future scientists to the rescue! A.  Replications of Mendel’s experiments are in agreement with

expectation. B.  The overall impression is that the results fit neither too well

nor too too poorly with expectation.

QUESTIONS? Before we move on to the next sub-section…

Chapter 11: Mutation • Goal: To understand the contributions of early geneticists

to developing key genetic tools. • Key points:

•  One source of novel genetic variability are mutations. •  Experimental design is key, especially for screens. •  Early researchers demonstrate the power of quantitation. •  Also: Muller à Muller’s morphs.

5. The origins of genes A.  The first question in regards to the origins of genes was

if new genes arise (de novo mutations) or if all genetic variability is pre-existing.

B.  The “presence & absence” hypothesis explained newly arisen forms (phenotypes) as merely the result of gene loss.

6. Pedigree and “class” A.  The two classes of mutations that can be most easily

studied in diploid organisms are Dominant & Sex-linked.

B.  The detailed analysis of pedigreed material revealed that mutation occurs in one gene, in one cell, and it can occur at any stage of development.

7. Muller’s experimental design A.  Muller’s experimental design established a quantitative

study of mutation with 1) an objective index and 2) a class of mutations frequent enough to give statistically significant values.

B.  The “ClB” chromosome made it possible to detect new sex-linked lethals without counting or anesthetizing flies, which meant more chromosomes could be tested and adequate data on the frequency of the lethal phenotypes could be collected.

Balancer Chromosomes

From Kile et al. 2003

8. Ionization vs. mutation rates A.  The relationship between ionization and mutation rates

were determined to be direct and simple due to the superimposability of the rate curves.

B.  This conclusion was reached by using lead shields of different thicknesses and recording the ionization in each treatment in the induction of lethal mutations in Drosophila.

QUESTIONS? Before we move on…

The Chromosomes in Heredity (1903) • Goal: To understand the connection between heritable

traits (ie: Mendel) and the physical vectors of these traits, the chromosome, as discussed by Sutton himself.

• Key points: •  Physically of inheritance: connecting Mendel with meiosis •  Logical deduction can get you a long way •  Meiosis explains independent assortment and segregation, even

without defining a gene.

Remember Meiosis? • Synapsis: close pairing of homologous chromosomes to form a bivalent; during prophase I when crossing over occurs.

• Meiosis I: reduction division… separation of…

• Meiosis II: separation of…

9. Sutton’s thesis statement A.  The stated purpose of the manuscript is devoted to the

detailed discussion of the relationship between study of chromosomes in Brachystola and the conclusions drawn from observations of plant hybrids by Mendel.

Brachystola spermatocytes Pisum flower position

10. Parental purity & alternatives A.  Parental purity is the concept that all maternal

chromosomes are passed to one pole and all paternal chromosomes are passed to the other during meiosis, such that all germ cells are either maternal or paternal in origin.

B.  It predicts that no amount of cross breeding can accomplish more than the first cross, that there can be only four combinations in the offspring of a single set of parents, and offspring cannot inherit chromosomes (traits) from both paternal or both maternal grandparents.

C.  The term is independent assortment; the position of the chromosomes in the reducing division is purely a matter of chance.

11. Chromosomes & Allelomorphs A.  Sutton raises the possibility that allelomorphs

correspond to a part of a chromosome.

B.  He supports his hypothesis by arguing that this must be true since otherwise the number of distinct characteristics of an organism could not exceed the number of chromosomes.

12. Non-Mendelian cases! A.  The fourth class of non-Mendelian cases is Mosaics.

B.  Sutton hypothesizes that the underlying cause of mosaicism is that one body of chromatin is active in one group of cells while its homologue is active in another.

C.  We know that X-inactivation through epigenetic silencing causes the mosaic fur patterns of calico cats.

QUESTIONS? Then on to the genetics refresher!!

Part II: Genetics Refresher • Key areas covered:

• Alleles and ploidy •  Linkage • Comparative Genetics • Phenotyping • Epigenetics • Population Genetics

• Plus: • Pea crosses • Meiosis

Allele Status & Ploidy: A.  Homozygous- an

individual with two identical alleles at a locus

B.  Heterozygous- an individual with two different alleles at a locus

C.  Aneuploidy- having an abnormal number of chromosomes

Genetic Linkage D.  Linkage: the close

physical proximity of two or more genes.

E.  Linkage disequilibrium: the tendency for two (or more) alleles to be inherited together.

Genetic Linkage D.  Linkage: the close

physical proximity of two or more genes.

E.  Linkage disequilibrium: the tendency for two (or more) alleles to be inherited together.

Comparative Genetics/Genomics F.  Synteny: conservation of

blocks of order within two chromosomes that are being compared, usually between species.

Characteristics of Phenotypes Phenotype: a measurable trait.

G.  Expressivity: the degree to which a phenotype is displayed in individuals of a given genotype.

•  “Hemingway cat”: Polydactyly in cats has variable expressivity.

H.  Penetrance: the percentage of individuals of a given genotype that display a phenotype.

•  BRCA1/BRCA2 and breast cancer risk

Characteristics of Phenotypes I.  Pleiotrophy-

contribution by a single gene to more than one phenotype.

J.  Epistasis- interaction/modification of a gene by a gene at another locus.

Epigenetic Inheritance K.  Epigenetics: changes in gene production or regulation

produced through mechanisms acting independently of changes in DNA sequence that are heritable (mitotically and/or meiotically) and whose effects persist even after the environmental stimulus is removed.

Imprinting: DNA methylation marks preserved across generations.

Templating: DNA methylation and histone marks preserved across cell division.

Population Genetics • Study of variation in reproductive success

• Gametic • Environmentally induced

From Novembre et al. 2008

Population Genetics L.  Inheritance- the

way in which genes are passed to the next generation

M.  Heritablity- proportion of parental phenotypic variance passed on genetically to the offspring

Hardy-Weinberg Equilibrium •  In a large population with random mating and no

disruptive circumstances, genotype and allele frequencies will remain constant since they will remain in equilibrium.

•  Disruptive forces include: non-random mating, mutations, natural selection, genetic drift, and gene flow between two population.

•  Described mathematically as:

p2  +  2pq  +  q2  =  1  

Population Genetics O.  Evolution: changes

in frequency of alleles/characters in a population over time.

14. Monogenetic pea crosses •  If (R) has a dominant “WT” red phenotype then ratios would be: •  F1: all red flowers, (Rr)

genotype •  F2: phenotypes are 3:1,

red:white flowers with genotypes of 1(RR):2(Rr): 1(rr)

RR rr

Rr

R r

R

r

14. Monogenetic pea crosses

•  If (R) has an incomplete dominant red phenotype then ratios would be: •  F1: all pink flowers, (Rr)

genotype •  F2: phenotypes are

1:2:1, red:pink:white flowers

RR rr

Rr

R r

R

r

QUESTIONS?

Mendelian inheritance & complex phenotypes •  Incomplete/semi-dominance: when the phenotype of the heterozygote is intermediate to the phenotypes of each homozygote •  Snapdragon petal color

• Codominance: contributions from both alleles visible in the phenotype. •  E.g. blood type alleles in

human.