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Definitions • Locus • The position of a coding or non codinggeneticelement • Gene • All the nucleotideelementsrequired for the expression of a transcript • Promoter, ORF, introns, exons, etc.
GeneticDefinitions(Cont’d) • Allele • Version of a geneticelementat a given locus • Everyonenecessarily has twoalleles for eachgenomic locus • The twoallelesmaybe the same • Homozygotes • The twoallelesmaybedifferent • Heterozygote • A population of individualsmay have multiple alleles of a genomic locus
GeneticDefinitions(Cont’d) • Genotype: • Nucleicacidsequence responsable for the phenotype • Physicaldetection by molecular techniques • Phenotype: • Trait thatcanbedistinguishedresultingfrom a genotype • Severaldifferentgenotypesmay have the samephenotype
The Differences • Between individuals of the same sex • <0.5% • Between humans and chimpanzes • <2%
Molecular Markers • Characteristics of the nucleotide sequence • The phenotype often corressponds to a specific genotype • Restriction polymorphisms (RFLP) • Length polymorphisms (VNTR) • Variable number of tandem repeats • Single nucleotide polymorphisms (SNP)
Length Polymorphisms - RFLP • Based on the presence or absence of a restriction site at a givenpoistion • Ex. The enzyme EcoR1 recognizes and cleaves the sequence: • GAATTC • A single base mutation abolishes the site • GAGTTC
Polymorphism E E E E E A B * A+B 1 2 Genome 1 Genome 2 Detection of Genomic RFLP 2 possible phenotypes • 2 alleles can be distinguished • Several possible genotypes 8
Length Polymorphisms • Minisatellites and Microsatellites: • Sequencesrepeated in tandem • Highly variable number of repetitionsbetweenindividuals; thusseveralalleles • Lengthpolymorphisms • Molecularphenotype=Genotype • Minisatellites • Low distribution throughout the genomeMostlyfoundwithintelomeres • Microsatellites: • High distribution throughout the genome • VNTR
VNTRs • The number of repetitions • = different lengths • = different alleles • = different genotypes • = different molecular phénotypes
Exemples: DinucleotiderepeatGTGTGTGTGTGT…… TrinucléotiderepeatACGACGACGACG…… TetranucléotiderepeatTATCTATCTATC…… LengthPolymorphisms - VNTR • DNA Regionwhere tandem copies of di-, tri- or tetrarepeatedunits are located
Allele1 CA CA CA CA CA Allele2 CA CA CA CA CA CA CA CA Allele3 CA CA CA CA CA CA CA CA CA CA CA CA VNTR (Cont’d) Different fragment lengths would be generated by a digestion at the indicated positions • Highly variable number of repetitionsindividuals • Thusseveralalleleswithin a population
Individual 1 AGCTGCTTAATGCTGCTGCTGCTGCTGCTGCATAACATTGC Individual 2 AGCGGCTTAATGCTGCTGCATAACATTGC 1 2 Amplification & gel separation Detection of VNTR by PCR 14
VNTR Profile of NuclearGenome From whom does the blood come from? 16
Bob Marc Luc Paul Tom VNTR Profile of NuclearGenome Who is Bob’s father? 17