Genetics Unit 2

principle of segregation

each diploid organism has two alleles for each gene (locus)

these alleles separate during meiosis, so each gamete receives only one allele

this explains why offspring inherit one allele from each parent

principle of independent assortment

alleles at different loci (different genes) assort independently during gamete formation

separation of one pair of alleles does not affect how another pair separates

leads to genetic recombination

genetic recombination

new combinations of traits

F1 Ab or aB in addition to parental gametes A B or a b

recombination

process of sorting alleles into new combinations

in F1 (Aa Bb) individuals:

parental gametes: AB and ab

recombinant gametes: Ab and aB

recombination occurs when crossing over happens between homologous chromosomes

result: new combinations of alleles that differ from those found in either parent

recombination frequency helps geneticists measure the distance between genes on a chromosome

recombinant

gamete with new combinations of alleles

non-recombinant

gamete that contains only the original combinations of alleles that were present in the parents

connecting Mendel to chromosomes

Walter Sutton proposed genes are located on chromosomes

acts as physical basis for Mendel’s principles:

segregation: homologous chromosomes separate during meiosis I - each gamete gets one chromosome (and one allele per gene)

independent assortment: each pair of homologous chromosomes align and separate independently of others during meiosis

however most organisms have fewer chromosomes than genes, so some genes must share the same chromosome

if genes are on the same chromosome, they can violate independent assortment and tend to be inherited together

linked genes

genes located close together on the same chromosome

tend to be inherited together

these genes form a linkage group and do not assort independently

meiosis linked genes

usually travel together into same gamete

only crossing over can separate them and create recombinant gametes

degree of linkage

close together - strong linkage, few recombinants

far apart - weak linkage, more recombinants

notation for linkage

/ or fraction

linkage in sweet peas

experiment in sweet peas

parental cross: parent with purple flowers and long pollen and another parent with red flowers and round pollen

F1: all purple and long (dominant traits)

F2: ratios did not match expected 9:3:3:1 Mendelian ration

purple/long and red/round were more common than expected

genes for flower color and pollen shape are linked on same chromosome

they do not assort independently

recombination between them was limited

complete linkage

genes vey close together on same chromosome that do not cross over

only parental (nonrecombinant) gametes are produced

parent 1: mm dd parent 2: MD md

F1 inherited M and D together from one parent and m and d from the other

MD and md are on same chromosome showing complete linkage

crossing over and linked genes

crossing over occurs in prophase I of meiosis - an exchange of genetic material between nonsister chromatids of homologous chromosomes

produces new combinations of alleles - recombinant gametes

with single crossover

two chromatids remain unchanged - nonrecombinant

two chromatids exchange segments - recombinant

result 50/50 of each

single crossover affects only two of four chromatids in a homologous pair

calculating recombination frequency

RF = number of recombinant progeny/total number of progeny x 100

CMT2 family clues from DNA

two families with CMT2 - genetic neurological disorder

square = males; circles = females

filled shapes = affected individuals

arrows = first diagnosed (probands)

numbers = age when symptoms started

3 markers on chromosome 1 - everyone with inherited disorder at same region - likely causing the disease

helps researchers narrow down where to look for the CMT2 gene - bringing us closer to diagnosis and treatment

visual map of autosomes

each vertical bar represents one of 22 autosomes

dark - father; light - mother

real example of genetic recombination - the process that shuffles DNA during meiosis

shows that each sperm cell carries a unique mix of DNA from both of the man’s parents

how genetic diversity is created in offspring

coupling and repulsion

arrangement of alleles on homologous chromosomes affects which phenotypes appear most often in offspring

ex. austrailian blowfly

p+ p b+b = heterozygote;; p p b b = homozygous recessive

green is dominant over purple and brown is dominant over black

coupling (cis) configuration

arrangment of linked genes in which wild-type alleles of two or more genes are found on one chromosome, and mutant alleles are on the homologous chromosome

each chromosome carries the same type of alleles - normal and mutant 1 of each

most gametes will contain the original nonrecombinant parental because crossing over is rare between linked genes

when gamete is produced without crossing over, it will inherit either all wild-type alleles or all mutant alleles - no mixed combinations

nonrecombinant progeny

no crossing over

alleles are coupled together in blocks: wild with wild and mutant with mutant

repulsion trans configuration

arrangement of two linked genes in which each of a homologous pair of chromosomes contains one wild type dominant allele and one mutant recessive allele

p+b/pb+

mainly green p+b and pb+

differ from parental phenotypes

allele arrangement is different, not genotype

predicting outcomes of crosses with linked genes

knowing allele arrangement on a chromosome + recombination frequency allows prediction of progeny types and proportions

ex. cucumbers

smooth t is recessive to warty T

glossly d is recessive to dull D

frequency is 16%

cross homozygous warty/dull x homozygous smooth/glossy

F1: TD/td

test F1 with td/td

nonrecombinant parental: TD and td. - 42% each

recombinant Td and t D - 8% each

only t d - 100%

predicting progeny: multiply gamete probabilities to get offspring proportions

0.42 × 1 = 0.42 (42%)

method works for any linked genes when the recombination frequency is known

testing for independent assortment

genes may appear linked or independent depending on proportion of nonrecombinant vs recombinant progenty

deviations from 1:1:1:1 ration could be due to chance or linkage with crossing over

A a B b x a a b b

54 A B, 56 a b, 42 A b, 48 a B

close to ratio but not exact - unclear if independent assortment or partial linkage

calculate expected probabilities assuming independent assortment

use chi-square goodness-of-fit to compare observed vs. expected

chi-square goodness-of-fit test

to see if observed matches predicted

state hypothesis and calculate expected numbers

E = total x expected proportion

x² = sigm (O-E)²/E

df = number of categories -1

compare to critical value - significant deviation?

ex. 290 round, 110 wrinkled

expect 3:1

x² = 3.67; df = 1 - not significant and consistent with prediction

genes are assorting independetly

use table

problem with chi-square

can’t tell you the reason for deviation

could occur because of linkage (not independent, violating assumption2)

expected single-locus ratios are incorrect if lower survival and incomplete penetrance

chi-square test of independence

tests whether two traits or loci assort independently

no assumption about single-locus probabilites

contingency table

E = row total x column total / grand total

chi-square

df = #rows - 1 x #columns - 1

x² = 30.73, df = 1, p<0.005 - traits not independent and are linked

genetic maps

Morgan and students discovered that recombinantion frequencies reflect the physical distances between genes on chromosome

far apart are more likely to recombine than close together

maps of relative distances between loci, markers, or other chromosome regions determined by rates of recombination; measured in recombination frequencies or map units

relative positions of genes based on how often they recombine during meiosis

distances between markers based on crossing over not physical length

physical maps

map of physical distances in between loci, genetic markers, or other chromosome segments, measured in base pairs

Mb actual DNA length

map units

m.u. or cM

unit of measure for distances on a genetic map; also called a centiMorgan

1 map unit = 1% recombination rate

constructing genetic maps

end genes and middle genes

largest frequency = ends

remain gene = somewhere in between

use map units

more genes = comparison to multiple points = refine positions of all genes

highest = farther apart

limits and considerations in genetic mapping

50% recombination means we can’t tell if same yet far or different chromosomes

genes far apart on same behave as unlinked because crossing over occurs so frequently that parent and recombinant gametes are produced in equal numbers

double crossovers

two crossover events occur between same two genes

second crossover reverses effects of first, restoring original parental combination of allleles

some reombinant events may not be detected, leading to underestimation of true distance between genes

rare, but double crossovers more likely when genes are far apart

two point testcross

genetic maps are built using series of testcrosses

each test cross involves one heterozygous parent for a pair of genes

cross between individual heterozygous at 2 loci and individual homozygous for recessive alleles at those loci

recombination frequencies are calculated for each gene pair to determine relative distances

50% = allele segregate independetly; different or same on far

<50% = crossing over happens sometimes but not always; linked on same chromosome

distance

identify linked genes

compare possible positions

mapping

pairwise recombination frequencies and gene order

when mapping genes on a chromosome, we often only have pairwise recombination frequencies (RFs) - the percentage of offspring showing recombination between two genes

smaller RF - genes close together

larger RF - genes are farther apart

cytogenetic map

visual representation of the chromosomes under a microscope

p arm (short arm) and q arm (long arm)

bands (dark and light regions) created by staining technique 

labels correspond to band positions used in karyotyping

null hypothesis

two traits assort independently according to Mendel’s second law

no association between Trait 1 and Trait 2

knowing the genotype for one trait does not change the probability of the other trait

X has no effect of Y - assort independently

alternative hypothesis

two traits do not assort independently

association between Trait 1 and Trait 2

knowing the genotype for one trait changes the probability of the other trait

contingency table

rows and columns

why deviation might occur with chi square

genes are linked

two loci are not independent

violates the assumption of independent assortment

expected single-locus ratios are incorrect

some genotypes may have lower survival

incomplete penetrance: not all individuals with the genotype show the phenotype

environmnetal factors or sampling errors can also affect ratios

significant vs. unsignificant

does not match vs. matches

crossover types - genotype: Aa Bb Cc (heterozygous at 3 loci)

genotype: Aa Bb Cc (heterozygous at 3 loci)

coupling configuration:

chromosome 1: ABC (all dominant alleles)

chromosome 2: abc (all recessive alleles)

single crossover between A and B

produces 2 recombinants + 2 nonrecombinants

single crossover between B and C

produces 2 recombinants + 2 nonrecombinants

double crossover

crossovers between A and B and B and C —> produces 2 recombinants + 2 nonrecombinants

in double crossovers, only the middle gene changes compared to nonrecombinants

limitations of two point crosses

mapping pairs of genes is inefficient

many crosses are needed to determine gene order

double crossovers often go undetected —> inaccurate map distances

three point testcross advantages

maps three linked genes at once

detects double crossovers, providing more accurate distances

determines gene order from a single progeny set

2 vs 3 point test cross # of genes

2 vs 3

2 vs 3 point test cross detects linkage

both yes

2 vs 3 point test cross detects double crossovers

no vs. yes

2 vs 3 point test cross determines gene order

no vs. yes

2 vs 3 point test cross accuracy of map

lower vs. higher

three point test cross

determine gene order and genetic distances for linked loci

example: drosophilia (fruit fly)

3 recessive mutations on chromosome 3

st - scarlet eyes recessive

e - ebony body color recessive

ss - spineless bristles recessive

dominat: st+, e+, ss+

map genes based on recombination frequencies from 3 point testcross

steps of 3 point cross

1. create F1 heterozygotes (cross wild-type x recessive homozygotes to get heterozygote and coupling configuration)

2. perform test cross (F1 x homozygous recessive; F1 females x recessive males for all three - crossing over only occurs in females for fruit flies - 8 possible phenotypic classes for the progeny 2³ = 8)

3. interpreting testcross progeny (all progeny express alleles from the heterozygous parent, only recessive alleles contribute, recombination events in heterozygous parent determine genetic map - rare phenotypes - indicate double crossovers and gene order)

mapping principle

analyze which traits appear together most frequently - nonrecombinant types

rare phenotypes - double crossovers reveal middle gene

use recombination frequencies to calculate map distances

summary of 3 pont testcross

three-point testcross efficiently establishes gene order and distances

provides more accurate genetic maps than multiple two-point crosses

crossing over in heterozygous parent is essential

determining gene order steps

1. identify nonrecombinant and recombinant types

2. test possible gene orders

3. determining locations of crossovers

4. calculating recombination frequencies as map distances

nonrecombinant progeny

most frequent phenotypes (no crossover betweenn genes)

most gametes have no crossover

ex. wild type 283 and triple recessive 278

single crossover progeny

intermediate frequency phenotypes

one rare event

ex. ebony, spineless 50, scarlet 52, ebony 43, scarlet, spineless 41

double crossover progeny

rarest phenotypes

two rare events in one gamete

ex. spinless 5, scarlet, ebony 3

3 possible orders on chromosome

eye color in the middle (e-st-ss)

body color in the middle (st-e-ss)

bristle in the middle (st-ss-e)

draw heterozygous chromosomes for each other

stimulate double crossover - see which produces the observed double-crossover progeny

only the order with bristle locus in middle produces progeny

st+ e+ ss

st e ss+

middle gene is ss

correct order is st-ss-e

middle gene changes relative to nonrecombinants

st+e+ss+ (nonrecombinant) to st+e+ss (double crossover)

st+ = same

e+ = same

ss+ = changed to ss

nonrecombinant vs. st e ss+ (double crossover)

st = same

e = same

ss = changed to ss+

determining locations of crossovers

once gene order is known, we can analyze testcross progeny to determine where crossovers occurred

rewriting progeny genotypes in the correct order (st-ss-e) allows identification of recombination events

calculating recombination frequencies as map distances

include all recombinants single and double crossovers

st and ss: 50 spineless, ebony and 52 scarlet = 102

double crossovers: 5+3 = 8

total recombinats st-ss = 102+8 = 110

total progeny = 755

110/755 × 100 = 14.6 so map distance of 14.6 mu

effects of multiple crossovers

double crossovers can involve different numbers of chromatides

2 strand double crossover - only 2 of 4 chromatids swap - 0% recombinant gametes

3 strand double crossover - 3 chromatids swap - 50% recombinant gametes

4 strand double crossover. -all 4 chromatids swap - 100% recombinant gametes

not all double crossovers create new allele combinations

average effect of all double crossovers - 50% recombinant gametes

limits of genetic mapping accuracy

undetected crossovers: some multiple crossovers produce the same gametes as single crossovers; these go unnoticed in progeny - map distances appear shorter than actual physical distances

effect of gene distance: genes close together: few multiple crossovers - genetic map = phyiscal maps; genes far apart - more multiple crossovers - genetic map underestimates true distance

correction: use mathematical mapping functions (based on poisson distribution); estimate actual distances more accurately

undetected crossovers

when we measure recombination frequency, we assume each crossover creates a detectable recombinant gamete

problem: multiple crossovers (ex. 2 crossovers between the same two genes) can restore the original allele arrangement) - ex. double crossover between A and B can look like no crossover because the alleles return to their parental configuration

result: these events go unnoticed in progeny - we underestimate the recombination frequency

effect on map distances

genes close together - few multiple crossovers occur because there’s little space for 2 events; the genetic map (based on recombination frequency) = physical map

genes far apart: more multiple crossovers occur; many of these are undetected - recombination frequency plateaus at 50 % even if the physical distance is much larger; underestimation

underestimation

genetic map shows a shorter distance than the actual physical distance

observed vs. actual map distance

recombination frequency does not increase linearly with distance

starts proportional at short distances; flattens near 50% because multiple crossovers restore original arrangment

genes gar apart - recombination frequency maxes out at 50%; cannot distinguish very distant genes from genes on different chromosomes

result: genetic map understimates true physical distance

solution: use mapping functions to correct for undetected crossovers

mapping function

mathematical function that relates recombination frequencies to actual physical distances between genes

we use mapping functions to adjust for undetected crossovers; these functions assume crossovers occur randomly along the chromosome

haldanes and kosambis function

haldane’s function

assumes no interference (crossovers occur independently and randomly along the chromosome)

kosambi’s function

account for intereference (one crossover reductes the change of another nearby)

molecular markers

developed in 1980s to examine DNA sequence variations

ex. RFLPS - DNA cut by enzymes reveals differences; microsatellites - variable numbers of repeated DNA sequences; DNA sequencing - detects single-nucleotide differences

traditional genetic markers

genes withe easily observable traits (phenotypies)

examples: flower color, seed shaped, blood type, enzyme differences

limitation: many organisms have few observable traits - mapping was difficult

traditional gene mapping (linkage analysis)

studies inheritance in crosses or pedigrees

tracks association between a trait and specific markers

based on physical linkage and recombination frequency

used in many organisms like fruit flies, corn, mice, and humans

genome-wide association studies (GWAS)

looks for nonrandom associates between traits and many loci across the genome

does not require crosses or family pedigrees

compares allele patterns in populations

useful for traits and diseases with complex inheritance

SNPs

site in genome where individual members of a species differ in a single base pair

millions of SNPs have been mapped in humans and other organisms

SNPs serve as genetic markers for mapping traits

GWAS (genome-wide association studies)

compare SNP patterns between people with a trait/disease and healthy controls

SNPs usually don’t cause the disease themselves, but indicate nearby genes

GWAS applications and impact

indentifies chromosomal regions linked to traits or disease

after GWAS, researchers examine the region for possible causative genes

ex. height, skin pigmentation, eye color, body weight

coronary artery disease, diabetes, heart attacks, blood-lipid levels

bond density, glaucome

GWAS of 400,000 people found 64 regions associated with bipolar disorder (64 genes don’t cause but contain variants that correlate with the condition)

haplotype

set of linked alleles

A2, B2, C4, D-

inherited together more often than by chance

linkage disequilibrium (LD)

nonrandom association of alleles in a haplotype

D- and haplotype tend to be inherited together

crossing over effect

recombination can break up haplotypes and reduces LD

LD persistence

close loci - LD lasts longer

distant loci - LD breaks down quickly

GWAS detection LD

reseachers don’t usually see D- directly (it might not be genotyped)

but they detect that A2, B2, or C4 occur more often in bipolar cases than in controls

statistical signal tells us that something near those markers (like D-) likely contributes to the disorder

role of bacteria and viruses in our world

everywhere

viruses infect all organisms and are the most abundant biological entities on Earth

global impact: ocean bacteria produce 50% of Earth’s oxygen and remove 50% of atmospheric CO2

agriculture: pathogens of crops and animals, provide nutrients like nitrogen and phosphorus to plants

human health: natural bacteria live in the mouth, gut, and skin, aiding digestion, immunity, and disease prevention; many infectious diseases are caused by bacteria or viruses but can be controlled with antibiotics and vaccines

bacteria and viruses in medicine and genetics

medical and industrial importance: bacteria produce drugs, hormones, food additives, and chemicals; viruses are used in gene therapy to deliver healthy genes

genetic significance: simple genetic systems = ideal for studying heredity and gene functions; share core genetic features with humans and other organisms

studies of bacterial and viral genetics have led to

discovery of DNA as genetic material

gene regulation models (ex. lac operon in E. coli that allows the cell to digest lactose)

tools for biotechnology and molecular biology

advantages of using bacteria and viruses for genetic studies

reproduction is rapid

many progeny can be produced

haploid genome allows all mutations to be expressed directly

asexual reproduction simplifies the isolation of genetically pure strains

growth in the laboratory is easy and requires little space

genomes are small

techniques are available for isolating and manipulating their genes

they have medical importance

they can be genetically engineered to produce substances of commercial value

prokaryotes

unicellular organism with a relatively simple cell structure

bacteria (eubacteria) and archaea

DNA sequencing of uncultured bacteria has transformed our understanding of microbial diversity; bacteria and archaea are as genetically distinct from each other as bacteria are from eukaryotes

archaea

unicellular organisms with prokaryotic cell structure

found in all environments, including extreme conditions like hot springs and deep oceans

eubacteria

most familiar bacterial species

bacterial shape

size and shape - wide variety

cocci (spherical)

bacilli (rod-shaped)

spirilla (helical)

cocci

spherical

bacilli

rod-shaped

spirilla

helical

bacterial structures

functional diversity

photosynthetic bacteria capture sunlight and produce oxygen

spore-forming bacteria survive extreme conditions - resistant to heat, cold, radiation, drought, chemicals, etc.

stalks or filaments, superficially resembling fungi - stalks allow bacteria to anchor to surfaces, like rocks, plant roots, or sediments in aquatic environments allow to stay in nutrient rich environments

bacterial complexity

proteins like FtsZ help in bacterial cell division, similar to eukaryotic tubulin in mitosis

proteins

chromosome replication is coordinated with cell division, ensuring each daughter cell receives one copy of the genome

bacteria have proteins that

condense DNA (like histones in eukaryotes)

maintain cell shape and cytoskeletal support

studying bacteria genetically

bacterial heredity is similar to other organisms but they are haploid (only one copy of each gene) and cells are tiny, making phenotypes hard to observe directily