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ECOLOGICAL GENOMICS lecture 10 Finding functionally important genetic variation part I

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Coat colour in several mammals such as horse, red fox and pocket mice (Mundy et al. 2004) ... MC1R in Arctic skua. Candidate gene approach. ECOLOGICAL GENOMICS ... – PowerPoint PPT presentation

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Title: ECOLOGICAL GENOMICS lecture 10 Finding functionally important genetic variation part I


1
ECOLOGICAL GENOMICSlecture 10 Finding
functionally important genetic variation part I
2
Outline
  • Quantitative trait locus (QTL) mapping
  • Association analysis (linkage disequilibrium
    mapping)
  • Candidate gene approach
  • Future developments
  • Technical advances
  • Challenges

3
Strategies for identifying functional DNA
variation
4
Basic requirements for quantitative trait locus
(QTL) mapping
- A genetic map of variable markers - A pedigree
(family) with which to follow the segregation of
those markers. - Phenotypic data (trait
measurements) on the individual members of that
pedigree.
5
Various pedigrees
6
Phenotypic variation expressed in F2 generation
in monkey flowers
F1
Mimulus lewisii
Mimulus cardinalis
F2
7
Quantitative trait locus (QTL) mapping
Parents
First generation hybrids (F1)
F2 and further
8
Quantitative trait locus (QTL) mapping
Parents
First generation hybrids (F1)
F2 and further
9
Factors affecting QTL mapping
-Marker number and type (e.g. dominant vs.
co-dominant markers) - Population sample size
(the prior estimates of 300 individuals should be
appropriate for 1015 cM marker intervals in most
experimental designs). - Experimental design
(inbreed vs. outbreed design, F2 vs. backcross
design, pedigree vs. sib-pair methods)
10
What can be realistically achieved using QTL
mapping in non-model species?
- The mapping of QTL effects down to the
nucleotide (QTN) will very difficult in most of
non-model systems. - QTL analyses can
efficiently identify candidate loci for further
fine scale analysis - For many interesting
evolutionary and ecological applications it is
not necessary to go down to the nucleotide (QTN)
level
11
Precision of initial QTL mapping
- Let one 1 bp equals 1 mm - The average size
of the genome in mammal 3X109 bp - The lenght
of the genome 3 000 km - After initial QTL
mapping in F2, the QTN that affects particular
triat is commonly identified within the region of
30-60 km
12
Publications on QTL mapping in natural populations
13
Association analysis (linkage
disequilibrium mapping)
tests if a certain genotype (or haplotype)
associates nonrandomly with the phenotypic trait
of interest within families or populations.
14
Association analysis (linkage
disequilibrium mapping)
tests if a certain genotype (or haplotype)
associates nonrandomly with the phenotypic trait
of interest within families or populations.
15
Association analysis (linkage
disequilibrium mapping)
The extent of LD depends on many biological and
demographic factors, including recombination
rate, population history, selection and mating
system characteristics. The extent of linkage
disequilibrium varies widely across species,
populations and genomic regions In humans, one
million random SNPs has been suggested to provide
reasonable wholegenome coverage for association
studies (Hirschhorn Daly 2005).
16
Mapping of the orange blotch colour pattern in
cichlid fish
QTL mapping
Association analysis
Streelman et al. 2003
17
Comparative mapping with Tiger puffer fish and
human genome
Pax7 is related closely to Pax3, which is
required for melanocyte development in human
Foxd3 is capable of repressing melanogenesis in
human
Transporter protein responsible for the
orange-red mutant in medaka fish
Streelman et al. 2003
18
Candidate gene approach
  • Candidate genes are selected by knowledge of how
    they influence similar traits in other organisms.
  • There is increasing evidence that some genes can
    control similar phenotypic traits even in
    distantly related species.
  • Easy to apply lets see if this primer set works
    on this particular species!

19
Candidate gene definitions
  • Candidate genes are genes of known biological
    action involved with the development or
    physiology of the trait - Biological candidates
  • They may be structural genes or genes in a
    regulatory or biochemical pathway affecting trait
    expression
  • Positional candidates lie within the QTL region
    that affect the trait

20
Traditional candidate genes and traits
  • MHC related genes for studying disease and
    parasite resistance, and mate choice
  • Heat shock proteins (HSP) for temperature and
    stress tolerance
  • Growth hormone and its receptors for growth, size
  • Candidate genes also available for many
    ecologically relevant traits incl. morphology,
    color, foraging, learning and memory, social
    interactions, alternative mating strategies

21
Success story Melanocortin-1 receptor gene
  • Coat colour variation in mice (Robbins et al.
    1993)
  • Hair and skin color in humans (Valverde et al.
    1995)
  • Feather coloration in chickens (Takeuchi et al.
    1996)
  • Coat colour in pigs (Kijas et al. 1998)
  • Feather coloration in several bird species
    (Theron et al. 2001 Mundy et al. 2004)
  • Coat colour in several mammals such as horse, red
    fox and pocket mice (Mundy et al. 2004)
  • Skin color in lizards (Rosenblum et al. 2004).

Candidate gene approach
22
Melanocortin-1 receptor gene (MC1R)
Candidate gene approach
Mundy 2005
23
MC1R in pocket mouse
Candidate gene approach
Nachman et al. 2003
24
MC1R in pocket mouse habitat differences
Nachman et al. 2003
25
MC1R in lesser snow goose
Candidate gene approach
Mundy et al. 2004
26
MC1R in Arctic skua
Candidate gene approach
Mundy et al. 2004
27
ECOLOGICAL GENOMICSlecture 10 Challenges and
future developments part II
28
Outline
  • Quantitative trait locus (QTL) mapping
  • Association analysis (linkage disequilibrium
    mapping)
  • Candidate gene approach
  • Future developments
  • Technical advances
  • Challenges

29
Technical advances
  • High troughput gene expression profiling is
    getting mainstream
  • The number of loci possible to genotype increases
    significally
  • The speed and costs of sequencing
  • decreases substantially
  • generating more and more data

30
Number of loci matters
Technical advances
  • The speed and efficiency of genetic analyses
    techniques has increased substantially
  • With the same amount of time one can analyze much
    higehr number of individuals and genes/markers
    than earlier

10000 loci
100s loci
10s loci
1-2 loci
31
Molecular inversion probes
32
Molecular inversion probes
http//www.affymetrix.com/technology/mip_technolog
y.affx
33
Molecular inversion probes
Genotyping up to 120,000 SNPs currently requires
a single assay and a single microarray!!!
34
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35
Frederick Sanger                           
B. 1918 - D.
  • Won Nobel Prize in 1958 for determining amino
    acid sequence of insulin
  • Won Nobel Prize in 1980 with Walter Gilbert and
    Paul Berg for their nucleic acid research

36
454 Life Sciences technology
Sequence more than 2 million bases within 3 days
37
454 Life Sciences technology
38
454 Life Sciences technology
39
Large-scale sequencing of Mammoth
  • DNA extracted from well-preserved wooly mammoth
    specimen (28000 year-old bone)
  • 13 million base pairs of the sequencing reads
    were identified as mammoth DNA.
  • Sequence identity between mammoth and African
    elephant was 98.55, consistent with divergence
    date of 5 to 6 million years.
  • The high percentage of recoverable DNA from would
    allow for completion of mammoths genome.

Poinar et al. 2006
40
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41
Only a tiny proportion of sequences are actually
from Neanderthal
42
When did we split?
43
Neanderthal genome project is on its way
To achieve one-fold coverage of the Neanderthal
genome (3 GB), about 20g of bone and 6,000 runs
on the current version of the 454 sequencing
platform would be necessary.
44
Challenges in Ecological Genomics... What was
the question in a first place?
45
Challenges in Ecological Genomics...
  • no data
  • too much data
  • not appropriate tools available (yet?)
  • too many tools to choose

46
From single genes to pathways and networks
  • GenBank and Gene Ontology (http//www.geneontology
    .org/) provide descriptions about the gene
    themselves
  • Kyoto Encyclopedia of Genes and Genomes (KEGG
    http//www.genome.jp/kegg/) and Alliance for Cell
    Signaling (http//signaling-gateway.org) provide
    information about biological interactions

47
The power of integration
- Combination of independent research approaches
at various functional (e.g. DNA, mRNA, protein)
and biological (e.g. individual, population,
species) levels provides MUCH DEEPER
UNDERSTANDING of the role of molecular variation
in ecological and evolutionary processes than any
single approach alone.
48
The future of Ecological Genomics as an approach
to understand adaptation speciation looks more
promising than ever beforeWelcome aboard!
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