Genetic Variation - Molecular Genetics (PDF)

G E N E T I C VA R I AT I O N M O L E C U L A R G E N E T I C S ( G E N E 1 0 0 0 ) D R M E L I S S A K C O R B E T T  OUTLINE What is genetic variation? Applications of genetic variation Mechanisms of Genetic Variation Sources of genetic variation Types of DNA variation...

G E N E T I C VA R I AT I O N M O L E C U L A R G E N E T I C S ( G E N E 1 0 0 0 ) D R M E L I S S A K C O R B E T T  OUTLINE What is genetic variation? Applications of genetic variation Mechanisms of Genetic Variation Sources of genetic variation Types of DNA variation Effects of DNA variation Summary  W H AT I S G E N E T I C VA R I AT I O N ? Differences in the DNA sequence Can be; One gene with two or more variants (alleles) Two identical genes affected by variation in controlling genes Can be; Visible (i.e. affect the phenotype) Non-visible (i.e. no effect on phenotype) A mutation that persists in a population becomes a polymorphism Each allele of the polymorphism is a variant  W H AT I S G E N E T I C VA R I AT I O N ? C O N T. Variation is what allows evolution Variation gradient: Unrelated species > related species > related individuals Diploid genome more “forgiving” of variation Another copy present to compensate Haplosufficient Not all genetic variation is good e.g. genetic disease, physical deformity, spontaneous abortion Genetic variation can be continuous or discontinuous Continuous: controlled by multiple genes e.g. height, fibre diameter Discontinuous: controlled by one or very few genes e.g. drosophila vestigial wing mutant, coat colour A P P L I C AT I O N S O F G E N E T I C VA R I AT I O N : FORENSICS e.g. crime scene, ID, paternity testing A P P L I C AT I O N S O F G E N E T I C VA R I AT I O N : E V O L U T I O N A RY R E L AT I O N S H I P S e.g. Comparative Genomics e.g. Phylogenetic Trees Image adapted from Strachan & Read: Human Molecular Genetics 3 A P P L I C AT I O N S O F G E N E T I C VA R I AT I O N : PRODUCTION Commercially valuable traits e.g. selective breeding for better production  Molecular Tools Vaccines http://www.sanidadanimal.info/cursos/inmun/noveno1.htm A P P L I C AT I O N S O F G E N E T I C VA R I AT I O N : BIOTECHNOLOGY SOURCES OF GENETIC VA R I AT I O N Natural or Induced Induced Selective breeding S O U R C E S O F G E N E T I C VA R I AT I O N C O N T. Experimentally Induced Mutagens Cloning  S O U R C E S O F G E N E T I C VA R I AT I O N C O N T. Natural Errors in DNA replication Natural mutagens Natural selection Sexual reproduction  M E C H A N I S M S O F P O P U L AT I O N VA R I AT I O N Mutation A mutation could cause parents with genes for bright green coloration to have offspring with a gene for brown coloration. That would make the genes for brown beetles more frequent in the population.  M E C H A N I S M S O F P O P U L AT I O N V A R I A T I O N C O N T. Migration Some individuals from a population of brown beetles might have joined a population of green beetles. That would make the genes for brown beetles more frequent in the green beetle population.  M E C H A N I S M S O F P O P U L AT I O N V A R I A T I O N C O N T. Genetic Drift Imagine that in one generation, two brown beetles happened to have four offspring survive to reproduce. Several green beetles were killed when someone stepped on them and had no offspring. The next generation would have a few more brown beetles than the previous generation — but just by chance. These chance changes from generation to generation are known as genetic drift. M E C H A N I S M S O F P O P U L AT I O N V A R I A T I O N C O N T. Natural Selection Imagine that green beetles are easier for birds to spot (and hence, eat). Brown beetles are a little more likely to survive to produce offspring. They pass their genes for brown coloration on to their offspring. So in the next generation, brown beetles are more common than in the previous generation.  https://www.researchgate.net/figure/Evolutionary-mechanisms-mutation- MECHANISMS OF and-migration-to-induce-variation-as-well-as-natural_fig1_330314237 VA R I AT I O N HARDY WEINBERG PRINCIPLE Genotype frequencies (and therefore also allele frequencies) remain constant over succeeding generations Provided Members of the population mate randomly Selection is unbiased and does not favor or disfavor an individual carrying a particular allele or genotype Mutation does not change allele frequencies Migration does not occur and change allele frequencies A large population is studied In a small population sampling anomalies occur which cause change in allele frequencies (genetic drift)  ALLELE (OR GENE) FREQUENCY HWE is an ideal model which can be used to determine allele frequencies in current populations and predict future allele frequencies Allele frequencies can be calculated directly from genotype frequencies Genotype frequencies can’t always be calculated from allele frequencies (due to dominant or recessive alleles)  M E C H A N I S M S O F P O P U L AT I O N VA R I AT I O N C O N T. All of these mechanisms can cause changes in the frequencies of genes in populations, and so all of them are mechanisms of evolutionary change. However, natural selection and genetic drift cannot operate unless there is genetic variation — that is, unless some individuals are genetically different from others. If the population of anything was 100% the same, selection and drift would not have any effect because their genetic make-up could not change. So, what are the sources of genetic variation? G E N E T I C VA R I A N C E AT T H E DNA LEVEL Chromosomal Different types of change Small segment can lead to genetic variation Single Nucleotide (Point mutations) For diploid organisms a single organism can have a max. of two alleles Populations can have multiple alleles at a single locus  C H R O M O S O M A L VA R I A N C E Changes in chromosome Structure Number E.g. Cri du chat Structure syndrome Deletions Deletion of end of chromosome 5 Duplications Inversions Recombination C H R O M O S O M A L V A R I A N C E C O N T. Autotetraploidy in Extra chromosomes e.g. Number Some organisms (e.g. plants can lead to Klinefelters, Down’s-, Missing chromosomes wheat) are polyploid larger plants, fruits, Patan-, Edwards e.g. Turners syndrome flowers etc e.g. tobacco syndrome Monoploid = one copy of each chromosome K L I N E F E LT E R ’ S K A RY O T Y P E : XXY PATA U S Y N D R O M E KARYOTYPE: TRISOMY 13 TURNER’S KARYOTYPE: X0  SMALL SEGMENT VA R I AT I O N Size varies: “small” in relation to chromosome-scale variation Insertions Deletions Inversions Duplications Repetitive elements Minisatellites (VNTR) Microsatellites (STR, SSR)  E F F E C T S O F P O I N T M U TAT I O N S ON PROTEINS Many proteins are conserved or have conserved regions Deleterious mutations will not persist Mutations in these regions can affect the protein Coding region Non-coding region Regulatory regions Intergenic region Outcomes Incorrect protein No protein Incorrect splicing Incorrect sorting &/or stability of RNA  THALASSEMIA A variety of different types of mutation occur in the α or β–globin genes Transitions Transversion Deletions Insertions These cause; Frameshift Nonsense Missense Leading to problems with; RNA splicing RNA cleavage Transcription  SUMMARY Genetic variation is any difference in DNA, mutations become polymorphisms when they persist in the gene pool It can be “good”, “bad”, or “otherwise” It can be used for a variety of purposes It can be caused by natural or unnatural causes The size of the variation ranges from several Mb to 1bp Point mutations are the most common type of change STUDY QUESTIONS 1. Understand that genetic variation affects the genotype, but not always the phenotype. 2. How does variation change between related individuals? Related species? Unrelated species? 3. What is the difference between continuous variation and discontinuous variation? 4. What are some of the applications of genetic variation? 5. Understand the difference between natural and induced sources of genetic variation. 6. Understand the mechanisms which cause genetic variation (Mutation, migration, genetic drift, natural selection). 7. Understand that populations can have multiple alleles at a single locus. 8. Understand we can have changes at both the DNA and chromosome level. 9. Changes in chromosomes can affect the structure or number of chromosomes. Give an example of a syndrome resulting in an extra chromosome, and a missing chromosome. 10. Appreciate that depending on the type of mutation, and the location this mutation can occur can have different affects, resulting in different outcomes. MOLECULAR MARKERS MOLECULAR GENETICS GENE1000 OVERVIEW MOLECULAR MARKERS What are molecular markers? Why are they used? Applications Types of markers  A measurable attribute in the DNA that is exhibiting Mendelian inheritance W H AT A R E Different to morphological and MOLECULAR biochemical markers MARKERS? Morphological: colour, size, shape Biochemical: isozymes, proteins Molecular: DNA  10 CHARACTERISTICS OF AN IDEAL MARKER 1. Polymorphic Variable between individuals 2. Discriminating Allows differentiation between related individuals 3. Multi-allelic Has several alleles at a single locus 4. Co-dominant a heterozygote displays characteristics intermediate between its homozygous parents 5. Non-epistatic Genotype can be determined regardless of the genotype at other loci  10 CHARACTERISTICS OF AN I D E A L M A R K E R ( C O N T. ) 6. Independent of the environment Fixed regardless of the environment during development 7. Neutral No selective advantage of any allele or combination of alleles 8. Uniformly distributed Spread throughout the entire genome 9. Reproducible Across time and place of analysis 10. Economical Cost effective and able to be handled at high-throughput rates MORPHOLOGICAL MARKERS Poor level of polymorphism Affected by environment Dominant Not always neutral May be epistatic BIOCHEMICAL MARKERS Few loci Not neutral Not evenly distributed Can be expensive MOLECULAR MARKERS Thousands Evenly Independent available distributed of environment Cheap and Highly able to be Co-dominant polymorphic automated HOW DO THEY HELP? 25 Kb DNA per page; 1000 pages per volume Virus Bacteria Yeast Worm Fruit fly 2 pages 200 pages 500 pages 4.5 Volumes 7.5 Volumes Mammal 120 Volumes 1000 pages per volume 25Kb per page  Chimp Cow Human & Dog Rat Mouse Chicken Fugu MOLECULAR MARKERS ARE POWERFUL 3 possible genotypes 30 loci, each with two at each locus (AA, AB, alleles (A & B) BB) 200 trillion possible