Title: ECOLOGICAL GENOMICS lecture 10 Finding functionally important genetic variation part I
1ECOLOGICAL GENOMICSlecture 10 Finding
functionally important genetic variation part I
2Outline
- Quantitative trait locus (QTL) mapping
- Association analysis (linkage disequilibrium
mapping) - Candidate gene approach
- Future developments
- Technical advances
- Challenges
3Strategies for identifying functional DNA
variation
4Basic 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.
5Various pedigrees
6Phenotypic variation expressed in F2 generation
in monkey flowers
F1
Mimulus lewisii
Mimulus cardinalis
F2
7Quantitative trait locus (QTL) mapping
Parents
First generation hybrids (F1)
F2 and further
8Quantitative trait locus (QTL) mapping
Parents
First generation hybrids (F1)
F2 and further
9Factors 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)
10What 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
11Precision 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
12Publications on QTL mapping in natural populations
13Association analysis (linkage
disequilibrium mapping)
tests if a certain genotype (or haplotype)
associates nonrandomly with the phenotypic trait
of interest within families or populations.
14Association analysis (linkage
disequilibrium mapping)
tests if a certain genotype (or haplotype)
associates nonrandomly with the phenotypic trait
of interest within families or populations.
15Association 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).
16Mapping of the orange blotch colour pattern in
cichlid fish
QTL mapping
Association analysis
Streelman et al. 2003
17Comparative 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
18Candidate 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!
19Candidate 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
20Traditional 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
21Success 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
22Melanocortin-1 receptor gene (MC1R)
Candidate gene approach
Mundy 2005
23MC1R in pocket mouse
Candidate gene approach
Nachman et al. 2003
24MC1R in pocket mouse habitat differences
Nachman et al. 2003
25MC1R in lesser snow goose
Candidate gene approach
Mundy et al. 2004
26MC1R in Arctic skua
Candidate gene approach
Mundy et al. 2004
27ECOLOGICAL GENOMICSlecture 10 Challenges and
future developments part II
28Outline
- Quantitative trait locus (QTL) mapping
- Association analysis (linkage disequilibrium
mapping) - Candidate gene approach
- Future developments
- Technical advances
- Challenges
29Technical 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
30Number 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
31Molecular inversion probes
32Molecular inversion probes
http//www.affymetrix.com/technology/mip_technolog
y.affx
33Molecular inversion probes
Genotyping up to 120,000 SNPs currently requires
a single assay and a single microarray!!!
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35Frederick 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
36454 Life Sciences technology
Sequence more than 2 million bases within 3 days
37454 Life Sciences technology
38454 Life Sciences technology
39Large-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
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41Only a tiny proportion of sequences are actually
from Neanderthal
42When did we split?
43Neanderthal 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.
44Challenges in Ecological Genomics... What was
the question in a first place?
45Challenges in Ecological Genomics...
- no data
- too much data
- not appropriate tools available (yet?)
- too many tools to choose
46From 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
47The 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.
48The future of Ecological Genomics as an approach
to understand adaptation speciation looks more
promising than ever beforeWelcome aboard!