Download Genetic Data I. Basics of genetic information A. Nuclear genetic

Genetic
Data
I. Basics
of
genetic
information
A. Nuclear
genetic
information
is
contained
on
chromosomes.
Chromosomes
composed
of
DNA:
Purines:
Adenine
and
Guanine
Pyrimidines:
Thymine
and
Cytosine
B. The
Central
Dogma
DNA

RNA

Proteins
Transcription
Translation
II. Other
forms
of
genetic
material
in
cells
Mitochondria
–
circular
DNA,
haploid,
non‐recombining
Chloroplasts
–
circular
DNA,
haploid,
non‐recombining
Table
1:
Comparison
of
the
genomes
in
plant
cells
Genome
size
(kbp)
Inheritance
Ploidy
Utility
Chloroplast
135‐160
Maternal
or
parental
Haploid
High
Mitochondrion
200‐2500
Maternal
or
parental
Haploid
Low*
1.1
x
106
–
1.1
x
Biparental
Diploid+
High
11
10 +
Could
be
polyploidy
*
Mitochondrial
markers
are
widely
used
in
animals,
but
the
mitochondrial
genome
in
plants
exhibits
rearrangements,
gene
duplications
and
gene
losses,
making
it
difficult
to
use
III. Coding
vs.
non‐coding
regions
A. Coding:
Exon
=
coding
part
of
a
gene;
transcribed
and
translated
B. Non‐coding:
Intron
=
non‐coding
part
of
a
gene;
transcribed
but
not
translated
Intergenic
spacers
=
regions
between
genes
C. We
target
non‐coding
regions
for
studies
of
population
structure
and
gene
flow.
IV. Exercise
on
selecting
an
appropriate
genetic
marker
–
see
associated
handouts
A. Studies
of
mating
systems
B. Studies
of
hybridization
C. Studies
of
adaptation
and
selection
V. Classes
of
genetic
data
A. What
makes
for
an
ideal
molecular
marker?
Nucleus
The
best
markers
are
highly
variable,
inexpensive
and
easy
to
use.
Co‐dominant
markers
contain
more
information.
B. Classes
of
genetic
markers
1. Protein
Allozymes
–
co‐dominant,
but
often
low
polymorphism
and
may
not
be
neutral
2. DNA
a. Fragments
vs.
sequences
b. RFLP
–
restriction
fragment
length
polymorphism;
coded
as
presence/absence
of
a
band
c. Polymerase
chain
reaction
–
a
molecular
Xerox
machine
d. RAPD/ISSR/AFLP
–
dominant
markers;
coded
as
presence/absence
of
a
band;
primers
are
not
species‐specific.
e. Microsatellites
–
co‐dominant
markers
representing
variation
in
the
number
of
repeats
(e.g.,
CACACACA);
alleles
are
identified
in
homozygous
and
heterozygous
individuals;
the
most
commonly
used
markers
currently;
must
be
isolated
and
developed
for
species.
f. SNP’s
–
single
nucleotide
polymorphisms;
considered
to
be
highly
polymorphic
but
can
be
difficult
to
develop
g. Sequences
–
nucleotide
sequence
for
a
gene
region;
high
information
content;
co‐dominant.
3. RNA
–
not
yet
used
extensively,
but
next‐generation
methods
are
making
RNA
studies
easier
to
do
VI. Measures
of
genetic
diversity
–
what
do
we
want
to
know?
A. Relative
levels
of
diversity
examples:
Genetically
depauperate
Inbreeding
Clonality
B. Genetic
structure
examples:
Genetic
drift
Bottlenecks
Cryptic
taxa
Gene
flow
C. Candidate
loci
example:
Local
adaptation
VII. Examples
from
the
literature
–
see
associated
handouts
A. Neostapfia
colusana
–
microsatellites
B. Astragalus
ampullarioides
–
AFLP’s