genetics 320 eehh understanding genetics for life sciences

Genetics 320Understanding Genetics for Life SciencesMohsen Mohammadi, Assistant Professor of Wheat Breeding and Quantitative Genetics

Department of Agronomy, Purdue University, West Lafayette, Indiana, USA Email: mohamm20@purdue.edu

Introduction Quantitative genetics

Contemporary genetics - Reverse genetics

Genetics is fun and plays role in almost every discipline. Along with physiology of production, genetics is the foundation of modern agricultural economy.

Which one?

or

or

Which one? Which one?

or or

oror

Punnett square makes it easier

25% AB 25% Ab 25% aB 25% ab

25% AB AABB AABb AaBB AaBb

25% Ab AABb AAbb AaBb Aabb

25% aB AaBB AaBb aaBB aaBb

25% ab AaBb Aabb aaBb aabb

Hypostatic gene

EE

Ee

ee

HH

Hh

hh

HH

Hh

hh

HH

Hh

hh

EEHH

EEHh

EEhh

EeHH

EeHh

Eehh

eeHH

eeHh

eehh

Progeny genotypes

1/16

Epistatic gene

Hypostatic gene

EE

Ee

ee

HH

Hh

hh

HH

Hh

hh

HH

Hh

hh

EEHH

EEHh

EEhh

EeHH

EeHh

Eehh

eeHH

eeHh

eehh

Progeny genotypes

FrequencyEpistatic gene

2/16

1/16

2/16

4/16

2/16

1/16

2/16

1/16

1/16

2/16

1/16

2/16

4/16

2/16

1/16

2/16

1/16

12/16 – 3/16 – 1/16 | 12:3:1 9/16 – 3/16 – 4/16 | 9:3:4

3E

1 e (3

H: 1

h)

3E

(3H

: 1h

1 e

Dominant E does not let H to play a role Recessive e does not let H to play a role

Dominant epistasis Recessive epistasis

2200 bp

796 bp702 bp

DNA ladder

120 bp

1 2 3 4 4 6 7 8 9 10

Number of favorable allele (A2)

A1A1 A1A2 A2A2

0 1 2

Ph

eno

typ

e

Relationship: AdditiveAllele A2 is dominant

P = G + EVP = VG + VE

p= ? q = ?

Classical genetics

Transmission genetics Punnett square

Chi-squared procedure

Determination of sex

Pedigree analysis

Mitosis and Meiosis

Molecular genetics

Epistasis

Griffith Hershey-Chase Meselson–StahlWatson-Crick

Franklin

DNA structure

DNA replication

DNA packing

PCR

The Central Dogma

Prokaryotic control of transcription Eukaryotic gene model

The genetic code

Genetics of linked genes

Haldane correction

Kosambi correction

Population genetics

Crossing over and recombination fraction

Gene ordering

Map distance

Gene pool Migration Mutation Genetic drift Bottlenecking Selection

Founder effectInbreeding

q1q1q2q2q3q3 x q1q1Q2Q2Q3Q3

µ, σ2

Offspring-parent regression

poor x poor

good x poor

good x good

Pro

ge

ny

pe

rform

an

ce

HeritabilityTransgressive

segregation

Change of genetic material

Contemporary genetics Forward genetics

QTL mapping GWASMutants

Contemporary genetics Sequencing

Sanger sequencing Chromosome walking

Next-generation sequencingSequence

homology

Cloning site directed mutagenesis

TALEN

Zinc Finger Nucleases

CRISPR-Cas

Contemporary genetics – Gene expression

Microarrays RNA seq qRT-PCR

Final Notes:

Mutation at partial chromosome levels

Nondisjunction in meiosis

Genetic syndromes Polyploidy

Expression patterns

Gene and sample clustering

Read alignment and quantification

Comparison of relative expression

Genetics 320Understanding Genetics for Life SciencesMohsen Mohammadi, Assistant Professor of Wheat Breeding and Quantitative Genetics

Department of Agronomy, Purdue University West Lafayette, Indiana, USA Email: mohamm20@purdue.edu