MAPPING GENOMES – genetic, physical & cytological maps Genetic distance (in cM) 1 centimorgan = 1 map unit, corresponding to recombination frequency of 1% 1 cM corresponds to ~ 1 Mbp DNA for human genome Gibson Fig. 1.3 Physical distance (in bp) - determined by DNA sequencing (or restriction fragment sizing)

- no absolute relationship between genetic & physical distances Fig Discrepancies (at times) between genetic & physical maps Genetic mapping data may have limited resolution or limited accuracy (eg recombinational “hotspots”) (eg if not enough progeny) Yeast chr III or “coldspots”

Powell, Science 336:1711, 2012 Nature May 31, 2012 Sl-GLK2 gene mutation improves uniformity of red colour… but less sugar & less tasty Ottawa Citizen September 15, 2012 Why don’t tomatoes taste as good as they used to?

STRATEGIES USED IN GENOMIC ANALYSIS Fig. 3.3 Markers used to anchor assembled sequences on map - because of recent advances in rapid sequencing technologies & powerful bioinformatics tools, “shotgun” approach is now usually used - except for genomes with high amounts of repetitive DNA

RFLPs – restriction fragment length polymorphisms SSLPs – simple sequence length polymorphisms SNPs – single nucleotide polymorphisms DNA MARKERS USED IN GENETIC MAPPING DNA marker must have (at least) two different alleles to be useful in monitoring inheritance patterns Alleles – alternative forms of a gene (or DNA sequence) at a particular locus (chromosomal site) Polymorphisms – occurrence of two or more variants (alleles, phenotypes, sequence variants) at significant frequencies in a population if present < 2% in population, called “mutation” or “mutant allele” Haplotype – set of alleles linked on a chromosome usually inherited together as a block, “haploid genotype”

1. RFLPs (Restriction Fragment Length Polymorphisms) Fig inherited pattern of restriction sites follows Mendelian rules

How to detect RFLPs? i. by Southern hybridization analysis Fig if “polymorphic” restriction site is present, detect two hybridizing fragments, vs. one if site is absent Length of large fragment = sum of two small ones

Fig. 3.5 ii. by PCR analysis Lane 1 = size markers Lane 2 = DNA homozygous for allele 1 Lane 3 = DNA homozygous for allele 2

Fig SSLPs (simple sequence length polymorphisms) Microsatellites - tandem repeats of short stretches ( < 5 bp or so) in clusters usually < 150 bp Different number of GA copies in tandem

Fig.3.5 Interpretation if lane A = DNA from person #1 and lane B = DNA from person #2 ? How to detect SSLPs by PCR The more copies in tandem, the larger the PCR product... and the slower it migrates electrophoretically Profile for lane A sample in blue & size markers in brown

Fig Differences in copy number in microsatellite array among individuals useful in genetic profiling Blue, Green: fluorescent tagged PCR products Red: DNA size markers - high heterozygosity of microsatellites (multiple alleles in population) homozygous vs. heterozygous state for a particular microsatellite locus? Each lane = DNA profile (with microsatellite length variants) from different individual - estimated that ~ 3 million differences between any two copies of human genome (natural sequence variation) DNA fingerprinting, forensic analysis

Fig SNPs (single nucleotide polymorphisms) SNPs usually exist as just two variants in population, because for a third allele to arise, mutation must occur at exactly the same position (see p.69)

“...found population-specific allele frequency changes.... one SNP in EPAS1 (transcription factor gene involved in response to hypoxia) showed a 78% frequency difference between Tibetan [high altitude] and Han [sea level] samples.” Yi et al. Science 329:75 (July 2 & August 13, 2010) “Thus, a population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude.” Exome = “coding sequences of 92% of human genes”

Fig. 3.8A - “stringency” of hybridization conditions (eg.temperature, salt…) influences stability of imperfect complementarity - reduced stability of hybrid between oligomer probe & test DNA if any mis-matches Oligomer-specific hybridization tests How to detect SNPs

(i) Detecting hybridization by “dye-quenching” - when oligomer probe forms stable hybrid with template DNA (vs. hairpin structure), generates fluorescent signal Fig.3.8B “molecular beacon” FRET (fluorescence resonance energy transfer) NB: your text just shows a figure for this type of hybridization probe, but others include tagged PCR products (ss), end-labelled oligomers, etc. see Topic 3

(ii) Detecting oligomer hybridization using DNA microarrays “Oligo chips” Tech.note for large scale analysis of SNPs (see later Topics for other applications) - grid of different oligomers synthesized in situ on glass wafer by photolithographic process - fluorescently labelled DNA (or cDNA…) allowed to hybridize - hybrids monitored by laser scanning - density ~ 10 6 oligos/cm 2 “~150,000 polymorphisms can be typed in a single experiment...” p.71 Affymetrix's GeneChip

World Array 1: Axiom® Genome-Wide EUR 1 Array Plate – European ancestry World Array 2: Axiom® Genome-Wide EAS 1 Array Plate – East Asian ancestry etc. “SNPs selected from disease and drug response GWAS databases [from Genome-Wide Association Studies] … saturated coverage in over 5,000 gene regions previously identified as disease-associated…. ” Applications for drug discovery:

Griffiths p.404 Note: microarray Fig.T3.2 (p.71) shows RNA expression data not SNP data Why might some signals be stronger than others in SNP analysis?

Advantages of DNA markers - easy to generate large number & easy to detect - codominant, can detect both alleles in heterozygote - SNPs & microsatellites rather evenly spread in genome Fig & 3.21 Fig.7.24 Microsatellite analysis by PCR Genetic markersDNA markers

PHYSICAL MAPPING APPROACHES 1. Restriction mapping - determine relative positions of restriction sites in DNA molecule by analyzing sizes of fragments generated by restriction enzymes Fig How many EcoRI sites are present? Where?...

2. FISH (fluorescence in situ hybridization) - intact metaphase chromosome (as ss DNA, denatured with formamide) hybridized with fluorescently labelled probe Fig ~ 1 Mbp resolution of markers 46 human chromosomes telomere-specific repetitive DNA probe Ottawa Citizen newspaper Sept. 6, 2012 (see Topic 1)

10 – 25 kb resolution Fig Fibre-FISH Probes: cosmid 1, cosmid 2, (overlap region in yellow) Nature Feb mechanically-stretched chromosomes or “molecular combing” of isolated DNA for higher resolution

3. STS (sequence tagged site) physical mapping What are STSs? - any short, known DNA sequence ( bp) which is unique in genome - wish to have many STSs along chromosome STSs A B C D E F G HI J K L MN O P Q R S T U V W BACs - if STS is present in two clones, can deduce that those clones are overlapping … so can be used as physical mapping marker

1.ESTs – expressed sequence tags (from cDNA clones, ie. representing mRNAs for various genes see Fig.3.36) 2. SSLPs (Microsatellites) 3. Random genomic sequences Examples of sequences that can serve as STSs - tandem simple sequence repeats with unique flanking sequences as long as single copy in genome eg. only one hybridization signal in Southern experiment

Distance between 2 STSs will determine whether they are: likely, sometimes or never located on same DNA fragment In genomic analysis, want overlapping set of DNA fragments spanning genome (or chromosome separated by flow cytometry, Fig.3.38) Fig (eg. clone library)

Fig Clone libraries Fig. 3.1

Potential problems in mapping genomes with repetitive DNA Fig.3.2A - omission of internal regions of tandem repeat array… (DNA sequences shown as single stranded, eg. from computer file) 1. Tandem repeats 2. Dispersed repeats Fig. 3.2B - omission of sequences located between two repeats or incorrect linking (eg from different chromosomes)