Understanding quantitative genetic variation. (1) QTL analysis of model organisms and farm animals. (2)Twin studies.

Francis Galton, Karl Pearson, WFR Weldon, representatives

of ‘biometric school: - established at 19th century the bases of

quantitative genetics and statistical tools of correlation and

regression

‘biometric view’ placed emphasis on natural selection acting

on minor variants as opposite to Mendelian genetics

At the beginning of 20th century it was recognized that minor

Mendelian variants could account for inherited variation of

continuous traits

Quantitative traits: (1) morphological traits (height, body

mass, skeletal shape, (2) metabolic traits (hypertension, drug

response), (3) survival traits (longevity, immunity) etc.

Quantitative traits:

(1) a few loci with large effects or

(2) Many loci with small effects?

Infinitesimal model: Quantitative trait variation is based on very many genes of very small effect

Thus, selection does not cause appreciable changes in frequency of any particular allele and doe not erode variation, which allows the response to selection to continue

Alternative genetic models for long-term selection response. Simulations of artificial selection on an addictive trait with environmental variance Ve=1. 50 highest scoring individuals were chosen from 250 in each generation. Initial h2=30%

10 unlinked loci with major alleles 400 unlinked loci with minor effects, incl 2 major loci

100 unlinked loci, allelefrequencies as in (a)

2 major loci fixed

Time in generations

Two simulationreplicates

QTL analysis:*Localization of regions where loci responsible for quantitative trait variation lie by linkage analysis*this analysis is done in experimental organisms by crossing two lines that differ markedly in the quantitative trait and also differ in alleles at marker genes or loci*F1 between the two lines is then crossed with itsself to make a segragating F2, or it may be back-crossed to one of parental lines.

Recombinant inbred strain Consomic Congenic

Receiver’s chromosomes Donors’s chromosomesX

F1Repeated backcrossing of F1Animals to receiver strain

Intercrosses of F1 animalsBrother-sister inbreeding

Advantages of rodent models:

*numerous genetically well-defined lines that differ from each

other in phenotypic characteristics

*modest cost of mainenance

*short generation times

*can be kept under well defined environmental conditions

*can be manipulated experimentally (transgenic, knockout)

*interraction of genes and environment is expressed in

measurable phenotypes

*several naturally occurring models and genetic toolsline

congenic etc. strains

*rodent-human homology well understood

Other animal models:

Dogs (behaviour), Pigs (atherosclerosis), baboons (Parkinson

disease), zebrafish and Ciona intestinalis (developmental biology)

Cox and Brown, 2003

History of rat research:

*The first mammalian species to be domesticated for scientific work (19850ies)

*the first genetic studies were carried out 1877-1885 by Crampe and were focused on the inheritance of coat colour

*in 1903 William Bateson used the consepts of Mendel’s laws to show that a variant of a rat coat-colour gene was inherited in a Mendelian fashion.

*the first inbred strain was established by King 1909, the same year that inbreeding began for the first inbred strain mouse DBA.

*Mouse soon became the model of choise for mammalian geneticists, while rat became a model for physiologists, nutritionists, and other biomedical researchers

*234 inbred rat strains have been developed primarily by physiologists by selective breeding for disorders ranging from hypertension to urological defects

*1sr trangenic rat 1990

Integratingdata fromthe rat and mouse for studiesof human disease

Transgenic mouse: harbour large pieces of human genome

Knockout mouse: deletion of a syntetic locus to human disease in mouse genome using homologous recombination

NB! Rodent models do not always recapitulate the outcome of human disese, owing species specific differences

Nethertheless, the animal models can provide the entry points into clinically relevant pathways

e.g. Both, in mice and rats involvement of LEPTIN in obesity has been shown. There are conflicting result in involvement of leptin in human obesity

BUT elucidation of the leptin pathway has provided new insights into food intake and metabolism that before these studies were unknown both in human and rodents

QTL mapping in inbred rodent strains versus single gene knock-out or transgenic animal

+ can identify regions of the genomic that carry allelic variants that collectively contribute to certain phenotype+ quicker results+ closer to the human phenotype of a complex disease

-a QTL is genetically complex and large region-combinatory effect of several genes, difficult to decide what is primary and what is secondary effect-hitchhiking variation of linked genes, difficult to decide the causative variant

Application of congenic, recombinant congenic and consomic strais

GENOTYPE GENOTYPE

EFFECTEFFECT

PHENOTYPE PHENOTYPE

individual

In combination only

no individual effect

either combination only

1. Additive

2. Multipli-cative

3. Epistatic

4. MixedMultipli-cative

+

+

x

x

x

OR

x

Models for the interraction of loci in complex diseases (by Gabriel et al., 2002)

Recombinant congenic strain generation:

(a) Two parental strains are crossed(b) An offspring F1 is back-crossed to

one of the parents(c) Repeated back-crossing to the

blue strain accumulates recombination events, reducing the amount and length of green inherited DNA (results in CONGENIC strains)

(d) Finally the strains are inter-crossed several times, brother-sister mated, and the green DNA fragments fixed to homozygosity on a blue DNAa background (results in RECOMBINANT CONGENIC STRAIN)

QTL study from New Zealand Obese (NZO) and Nonobese

Nondiabetic (NON) mouse strain (Reifsnyder P et al, 2002):

Used Recombinant Congenic approach developing 10 interval

directed strains that carry QTL interval DNA from NZO on a

relatively lean NON background.

Important observations:

1.Computationally predicted epistatic interractions between QTLs

from studies of F2-intercrosses and backcrosses were confirmed

2.Obesity could be uncoupled from diabetes (but not vice verse)

3.Stepwise diabetes development with step-wise increase in

diabetogenic QTL was shown

4.Toxisity and vialibity effects were separated and investigated

5.The map position of QTL-containing loci were refined

Functional complementation by transgenesis:The role of a candidate gene in a quantitative trait locus (QTL) that is carried by a congenic rat strains on a reciprocal genetic background can be tested by transgenesis.The copy number control is required to rule out the likelihood that the phenotypic effects of the transgene have been brought about by introduction of an abnormal number of gene copies

Jacob and Kwitek, 2001

Mutagenesis screens in rodents

*New mutations can be generated in mice at relatively high frequencies using radiation, chemical mutagens and transgene insertion. *powerful germline mutagen ENU (N-ethyl-N-nitrosourea)*ENU is a point mutagen that is capable of inducing many different alleles*ENU can induce mutations in mouse spermatogonia at rate equivalent to isolating a mutation in a single gene of choise in 1 every 700 gametes screened*typical protocol includes the treatment of male mice with ENU, followed by mating with wild-type mice.

Comparative genomics

Questions: 1. Broad insite about types of genes can be gleaned by genomic comparisons at

very long phylogenetic distances, e.g. > 1 billion years since their separation e.g. by comparing genomes of yeast, worms and flies reveals that these

eukaryotes encode many of the same proteins2. At moderate phylogenetic distances (70-100 million years) both functional and

nonfunctional DNA is found within the conserved DNA e.g. comparison between mouse and human, among several species of yeast or

among enteric bacteria Here functional sequences show signal of puryfing (negative) selection. These comparisons assist to identify coding exons, noncoding RNAs, concerved

regulatory regios3. Comparison between close species as human and chimpanzee (separated

about 5 million years), are particularly apt for finding the key sequence differtences in the organisms.

Here the sequences have changed under positive selection.

Conserved syntety between human and mouse

Human and mouse comparison:

*Separated 75-80 million ya

*the large-scale gene organization and gene order have been preserved

*about 90% of human genome is in large blocks of homology with mouse

QTL associated with complex disease phenotypes that map to regions of conserved syntety in the human, rat and mouse genomes.Blue -obesity, red - hypertension, autoimmune/inflammatory phenotype

QTL associated with complex disease phenotypes that map to regions of conserved syntety in the human, rat and mouse genomes.Blue -obesity, red - hypertension, autoimmune/inflammatory phenotype

Farm animals as models of quantitative genetics:*large family sizes*Monitored long for thousands of years by human*large variety of different breeds, which have been adapted for different needs and climate conditions*rich collection of mutation that affects phenotypic traits*possible to dissect monogenetic traits as coat colour, but also qualtitative traits as fertility, growth, behaviour

a. An intercross between the european wild board (recedssive allele of KIT locus) and Large white Domestic pigs (dominant allele of the KIT locus. The segregation of white colour in F2.

b. The three KIT alleles in the pig. The tandem duplication present in Patch and Dominant White alleles is larger than 400 kb and it includes the entire KIT sequence

Splice mutation GtoA: Skipping of exon 17

KIT - mast/stem-cell growth factor receptor; crucial for the survival of migrating melanocytes during embryogenesis and for hematopoiesis and germ-cell development

Johansson Moller et al, 1996; Marklund et al, 1998

Farm animal breeds are expected to have large homozygous regions due to selective sweeps:Advantage in mapping genes responsible for the trait

Andersson and Georges, 2004

Identity by decent mapping (IBD) - determining the minimum shared haplotype among the animals carrying Q2 allele.

*Q1 to Q2 mutation at certain at generation 0: complete LD between the Q2 and alleles of other loci at mutated gamete

LD is decayed through generations by recombination events

Haplotype of closely linked loci has preserved around Q2

Andersson and Georges, 2004

Approaches to mapping and positional cloning of QTL in domestic animals (Andersson and Georges, 2004)

Andersson and Georges, 2004

Example: IGF2 quantitative trait locus in pigs

*Idenification of IGF2 by intercrosses between European wild board and Large White domestic pigs*QTL from domestic pig was associated with high muscularity, less backfat and a larger heart*Swedish Large White and Pietrain pigs shared haplotype IDB: high muscle growth (IGF*Q)*wild board and Belgian Large White: alternative haplotype with low muscle growth (IGF*q)*Belgian Large White actually as a hybrid between European and Asian breeds, thus possessing IGF*q*the causative variant of IGF*Q is G-to-A substitution at position 3072 in intron 3

Van Laere et al., 2003

silencer

mutated silencer

3 -fold upregulation of IGF2 expression in postnatal, but not prenatal scelectal and cardiac muscle

Galton F (1875) “The history of twins as a criterion of the relative powers of nature and nurture” JR Anthropol Inst Gt Br Ireland 5, 391-406.*the first classical twin paper

Siemens HW (1924) Die Zwillingpathologie:Ihre Bedeutung, ihre Methodik , ihre bisherigen Ergebnisse. Springer, Berlin*the twin rule of pathology: any heritable disease will be more CONCORDANT in identical twins than in non-identical twins, and concordance will be even lower in non-siblings.

Revival of twin studies

Classical twin studies:

*Compares phenotypic resemblance of monozygotic (MZ) and dizygotic (DZ) twins

*MZ twins derive from single fertilized egg and therefore inherit identical genetic material

*Hertitability of the trait h2 =2x difference in MZ and DZ correlations

e.g. for depression rMZ=0.4 and rDZ=0.2, h2 =40%

*Contribution due to shared environment is calculated

rMZ- h2 and rDZ- h2/2

e.g. for taking up smoking rMZ=0.9 and rDZ=0.7

Environmental role= 0.9-0.4 =0.7-0.2+= 50%

Percentages of variances explained by:Genetic factorsEnvironmental factorsDifferences in ageUnique environmental influence

EXAMPLES OF CLASSICAL TWIN STUDIES

X

X

X

X

X Differences betweenMales and females

age

Boomsma, 2002

Boomsma, 2002

Twin discordance:MZ twins - only one exhibits cleft lip and palateDifferent penetrance?

* Patients in father’s family

Twin registers:

*originate as spin-offs from specific research projects, usually in medicine or psychology

•GENOMEUTWIN - european community funded large integrated project involving 6 participating twin cohorts from Scandinavia, the Netherlands and Italy•More than 0.6 million pairs of twins•More than 30 000 DNA samples

Twin registers outside Europe: USA (13), Canada (2), Australia (3), Sri Lanka (1), China (1), Japan (1), S. Korea (2)