Methods of Genome Mapping

linkage maps, physical maps,QTL analysis

The focus of the course should be on analytical (bioinformatic) tools for genome mapping, i.e., relevant

background from (a) statistics,

(b) appl. math. (c) software

A few elementary genetic and molecular-genetic notions A few elementary genetic and molecular-genetic notions (subjects) you are supposed to know(subjects) you are supposed to know

General Genetics: meiosis, syngamy, gamete, zygote, DNA, genome, nucleus, chromosome, centromere, bivalent, hybrid, homozygote, F1, F2, heterozygote, inbred, haploid, diploid, mutant, gene, allele, locus, phenotype,Mendelian segregation (single-, two-, multilocus), dominant, co-dominant, recessive, additive, linkage, recombination, epistasis, quantitative variation, heritability, test-cross, backcross, intercross, linkage phase (coupling, repulsion), multiple crossovers, interference, polymorphism, linkage disequilibrium, haplotype

Molecular Genetics: restriction fragment, DNA hybridization, Southern blot analysis, PCR, tandem repeats, microsatellite, SNP, DNA cloning, BAC-clone, genomic library, DNA fingerprinting, overlapping clones, contig, radiation hybrid, candidate gene, microarray

Mendelian (qualitative) vs qualitative traitsMendelian (qualitative) vs qualitative traits

Simple Mendelian traits - discrete (discontinuous) traits - •   One gene = one trait •   Finite number of genotypes      •   One gene = 3 genotypes = 2 or 3 phenotypes (folding hands, blood type, fruit color, wing shape)

Complex non-Mendelian traits – continuous distribution•    Quantitative or continuous traits - controlled by several loci Each quantitative trait locus (QTL) contributes to phenotype QTL(s) + Environment (e.g., climate) + Culture = Phenotype  A fundamental question: Do QTLs represent the same Mendelian genes, or these are a specific class of elements ?

SEN (degree)

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0,40 0,69 0,98 1,27 1,56 1,85 2,14 2,43

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RWC (%)

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33,0 35,8 38,6 41,4 44,2 47,0 49,8 52,6 55,4

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RTH (mm)

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0,36 0,40 0,44 0,48 0,52 0,56 0,60 0,64 0,68

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WT (day)

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6,0 6,2 6,4 6,6 6,8 7,0 7,2 7,4 7,6 7,8

10-30 23-38

Complexity of segregation of quantitative traits

Distribution of “tolerance traits” of F4 means in a cross of mesic xeric ecotypes of wild barley

(the transgressive segregation is noteworthy)

Phenotypic distribution of quantitative traits

(A) single genetic locus

+ non genetic factors1:2:1

(B) two and more unlinked genetic loci

2 loci 4 loci many loci

Multiple loci & alleles, variable individual effects Variable intralocus relationships (additive, dominant, heterotic) Epistatic interactions Pleiotropy Environmental & developmental effects, canalization

Genetic Architecture of Quantitative TraitsGenetic Architecture of Quantitative Traitsand properties of QTLand properties of QTL

An old discussion: What is the nature of QTLs ?

Mendelian genes, but with smaller individual effects Specific modifiers, e.g., changes in the promoter regions Infinitesemal model (diffused effects of chromosomal regions, rather than a set of Mendelian loci)

Mendelian vs Biometrical schools in Quantitative Genetics

Genetic dissection of complex traitsGenetic dissection of complex traits

development genotype phenotype + markers environment observations (data)

“explaining” the phenotype

ApplicationsApplications

QTL of economic or medical importance Fitness-related QTL Gene expression as molecular phenotype

QTL analysis

GeneticsStatistics

Comp. Sci.Appl. Math.

• Multi-factorial, due to genetic and environmental precursors– migraine, cancer, hypertension

• Difficult to study many influences

• Do not exhibit “classic” Mendelian segregation

• No distinct relationship between genotype and phenotype

• Difficult to find a marker co-segregating with a complex trait

• Low penetrance (of individuals exhibiting phenotypic characteristics of a genotype for a trait) – missing heritability

• Phenocopy (environmentally induced phenotype that resembles the phenotype produced by a mutation – epigenetics)

Complex traits as applied to human/medical genetics

1. Genome mapping (family-based linkage analysis)2. Local analysis (population-based mapping -

association analysis, LD analysis)3. Candidate gene approach (guess-based analysis)

Quantitative Genetics: Mendelian vs Biometrical

Marker analysis vs Variance components Payne, 1918 Fisher, 1918 Sax, 1923 Lush, 1949

Marker-trait Broad- & narrow-sense association heritabilities

Strategies for finding QTLs

QTL mapping

• QTL detection– check if QTL is present

• QTL location– determine the position of the QTL on the chromosome

• QTL effect– estimate the allelic effect or trait variance due to QTL

• Diagnostics (risk factors in human genetics)• Marker assisted breeding• Positional cloning

Identify QTL based on association of trait phenotype with alleles at marker loci ( (anonymous or gene-based) or gene-based)

• Required components:Required components:

- - Molecular geneticsMolecular genetics - - identification and mapping identification and mapping of genes and of genetic markersof genes and of genetic markers

- - Suitable resource (mapping) populations, molecular markersSuitable resource (mapping) populations, molecular markers

- - Statistics – tools for detection and estimation of associations Statistics – tools for detection and estimation of associations

of identified genes or markers with economic traits of identified genes or markers with economic traits

Molecular Strategies for QTL detection

markers traits x,y,z, …

Analysis of the genetic composition of segregating recombinant genotypes

individual recombinant chromosomes

:

Segments from Parent A

Segments from Parent B

AB generations of selfing (RIL) generations of intercross (IRL)

Examination of the effect of a genetic segments (with different alleles) on a trait

Large values ? Small values

genotypes: 1 2 3 4 5 6 7 8 .... 1 2 3 4 5 6 7 8 ......

Chromo-some

Population structure at QTL

d

A B C D E Q F G H

a b c d e q f g h

The population contentat a quantitative trait locus(backcross, RIL, DH).

Can be deduced by observationof marker groups. In the figure,the observation using a markercoinciding with QTL.