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 (subjects) you are supposed to know General Genetics: meiosis, syngamy, gamete, zygote, DNA, genome, nucleus, chromosome, centromere, bivalent, hybrid, homozygote, F 1, F 2, 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 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 ?

Complexity of segregation of quantitative traits Distribution of “tolerance traits” of F 4 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 factors 1:2:1 (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 Traits and 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 traits development genotype phenotype + markers environment observations (data) “ explaining” the phenotype Applications QTL of economic or medical importance Fitness-related QTL Gene expression as molecular phenotype QTL analysis Genetics Statistics 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

( or gene-based) Identify QTL based on association of trait phenotype with alleles at marker loci (anonymous or gene-based) Required components: Required components: - Molecular genetics - identification and mapping - Molecular genetics - identification and mapping of genes and of genetic markers of genes and of genetic markers - Suitable resource (mapping) populations, molecular markers - Suitable resource (mapping) populations, molecular markers - Statistics – tools for detection and estimation of associations of identified genes or markers with economic traits - Statistics – tools for detection and estimation of associations 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 ABAB 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: 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 content at a quantitative trait locus (backcross, RIL, DH). Can be deduced by observation of marker groups. In the figure, the observation using a marker coinciding with QTL.