POLIMORFISMI MOLECOLARI
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POLIMORFISMI MOLECOLARI
POLIMORFISMI MOLECOLARI Questo documento è pubblicato sotto licenza Creative Commons Attribuzione – Non commerciale – Condividi allo stesso modo http://creativecommons.org/licenses/by-nc-sa/2.5/deed.it Genetica delle popolazioni a.a. 11-12 prof. S. Presciuttini Polimorfismi genetici prima del 1960 ● ● ● Per più di metà del 1900 la variazione genetica osservabile in natura che poteva essere interpretata a livello di singolo locus era molto limitata Il repertorio includeva il gruppo AB0 e le varianti emoglobiniche nell'uomo, le variazioni del colore del mantello nei vertebrati e delle colorazioni nelle chiocciole e nelle farfalle, oltre alle rare mutazioni morfologiche osservabili nell'uomo e in Drosophila Although they provided individual model systems for the study of evolution in action, it was not clear how general a picture of genetic variation they represented. Genetica delle popolazioni a.a. 11-12 prof. S. Presciuttini Polimorfismi cromosomici in Drosophila ● ● ● There were also extensive studies by Dobzhansky and his school of inversion polymorphism in Drosophila There was universal agreement that genomes totally homozygous for one or more chromosomes were on the average lower in viability and fecundity than were random heterozygotes The problem was that the observations could not be interpreted at the gene level ● Was the inbreeding effect the consequence of a few nearly recessive deleterious alleles carried by each genome as a consequence of the constant rain of mutations, or was it the consequence of homozygosity at very large numbers of loci that were normally heterozygous, held in heterozygous state in natural populations by some form of balancing selection? Genetica delle popolazioni a.a. 11-12 prof. S. Presciuttini Due scuole di pensiero ● Evolutionary geneticists were divided into opposing schools with more or less uncompromising views of the truth ● ● ● Dobzhansky and his followers belonged to what he called the “balance” school, holding that every individual in a sexually reproducing population was heterozygous at most or all of its loci. Dobzhansky opponents were derogatorily called by him the “classical” school, whose most influential spokesman was H. J. Muller, a school that believed nearly all loci to be essentially homozygous, with rare deleterious mutations segregating to produce a “genetic load” Population genetics seemed doomed to a perpetual struggle between alternative interpretations of great masses of inevitably ambiguous data Genetica delle popolazioni a.a. 11-12 prof. S. Presciuttini L'avvento dell'elettroforesi ● ● ● In 1966 two laboratories, one in Chicago (Lewontin) and one in London (Harris), independently published experimental results that apparently solved the problem, initiating 20 years of intensive investigation of protein variation in natural populations by hundreds of laboratories They applied electrophoresis of proteins to measure allozyme variation in natural populations of Drosophila and humans, and identified some 30% of the studied proteins highly variable among individuals There was a virtual explosion of electrophoretic investigations. A comprehensive literature search made 18 years after the first experiments were published, found studies of intraspecific variation in 1111 species, with an average of 23 loci and 200 individuals per species examined Genetica delle popolazioni a.a. 11-12 prof. S. Presciuttini Varianti allozimiche: un esempio ● ● Electrophoresis of tissue extracts from 15 different green treefrogs (Hyla cinerea) reveals 4 allelic versions of the enzyme aconitase (one of the enzymes of the citric acid cycle). The 4 alleles can be distinguished by the speed with which their protein product migrates: Fast (F), moderately fast (E), medium (M), and slow (S) The results: Eight frogs (#2, 3, 4, 6, 7, 9, 12, and 14) are homozygous for allele M. Frog #8 was homozygous for allele E. Three frogs (#1, 11, 15) are heterozygous for the M and S alleles. Two (#5, 13) are heterozygous for M and E.Frog #10 is heterozygous for M and F. Genetica delle popolazioni a.a. 11-12 prof. S. Presciuttini Generalità della tecnica elettroforetica ● ● Electrophoresis is a technique that could be learned easily by any moderately competent person, that is relatively cheap as compared with most physiological and biochemical methods, that gives instant gratification by revealing before one’s eyes the heritable variation in unambiguously scoreable characters, and most important, can be applied to any organism whether or not the organism could be genetically manipulated, artificially crossed, or even cultivated in the laboratory or greenhouse A typical species population for most organisms is polymorphic for about 1/3 of its loci that code for enzymes and other soluble proteins Genetica delle popolazioni a.a. 11-12 prof. S. Presciuttini The meaning of genetic variation ● From the publication of the first results of electrophoretic surveys of variation in 1966, the problem of the explanation of the variation became primary ● ● is the large amount of standing genetic variation in populations a consequence of some form of variation-preserving natural selection, such as overdominance or frequency dependent selection or is the variation simply what one would expect from the random accumulation of selectively neutral mutations reaching intermediate frequencies by genetic drift in finite populations accompanied by some small migration between populations? Genetica delle popolazioni a.a. 11-12 prof. S. Presciuttini Neutralism vs selectionism ● ● ● The struggle between these two views of genetic variation was evident from the beginning of electrophoretic studies Lewontin and Hubby, already in 1966, pointed out the immense genetic load that would exist in a population with 10% heterozygosity if it were maintained by simple overdominant selection, even very weak selection. Various more complex selective schemes were immediately proposed to meet the difficulty On the other hand, a theory of selectively neutral evolution of protein differences between species was proposed by Kimura (1968) and King and Jukes (1 969), and it was Kimura’s view that electrophoretic polymorphism was simply a stage in this neutral evolution of species differences. Genetica delle popolazioni a.a. 11-12 prof. S. Presciuttini Indecidibilità fra opposte teorie ● ● The old struggle between those who saw natural selection as the preserver of variation and those who saw it as essentially a purifying process, was transferred to the domain of electrophoretic polymorphism Although no one could now deny that there was indeed a great deal of genetic variation in natural populations, the assumption that this variation was unselected made the observations perfectly compatible with a view that when selection did occur, it was purifying in nature. Genetica delle popolazioni a.a. 11-12 prof. S. Presciuttini Inizio dell'era del DNA ● ● ● In 1970, Hamilton Smith discovered the first restriction enzyme that cuts DNA at specific sites In 1978, Yuet Wai Kan and Andrée-Marie Dozy were studying patients with sickle-cell anemia. They noticed, after they used a restriction enzyme to cut the DNA of affected subjects, that most of the patients had a DNA fragment containing the beta-hemoglobin gene that was 13 kb long, whereas normal subjects often lacked this particular DNA fragment Because the fragment produced was different in size from that normally seen, it was called a restriction-fragment-length polymorphism (RFLP). Genetica delle popolazioni a.a. 11-12 prof. S. Presciuttini PCR-RFLP ● ● ● A restriction fragment length polymorphism is defined by the existence of alternative alleles associated with restriction fragments that differ in size from each other RFLPs are visualized by digesting DNA from different individuals with a restriction enzyme, followed by gel electrophoresis to separate fragments according to size Coupled with PCR, restriction site polymorphisms can now easily and efficiently typed; it is commonly applied to mitochondrial DNA analysis Genetica delle popolazioni a.a. 11-12 prof. S. Presciuttini RFLP analysis: example of a nuclear gene ● ● ● A 244-bp fragment of the apoE gene covering the codons for amino acids 112 and 158 was amplified by polymerase chain reaction using the primer pair F4 and F6 After amplification, 8 µl of the PCR product were directly digested with 12 units of the restriction enzyme HhaI (Promega, Madison, WI) for 4 hrs at 37 °C Gene fragments were separated using 8% polyacrylamide nondenaturing gel electrophoresis (3 hrs, 45 mA) and detected by ethidium bromide staining under ultraviolet illumination (0.2 mg/l, 30 mins), using a known DNA size marker Genotyping of apoE using polymerase chain reaction and restriction fragment length polymorphism (PCRRFLP). Lane M, marker ladder; lane 1 to 6, e2/e2, e2/e3, e2/e4, e3/e3, e3/e4, and e4/e4 genotypes, respectively. Genetica delle popolazioni a.a. 11-12 prof. S. Presciuttini