Genetics Study Guide #4
Genetics Study Guide #4 Bios 206
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This 15 page Study Guide was uploaded by Becca Sehnert on Tuesday April 26, 2016. The Study Guide belongs to Bios 206 at University of Nebraska Lincoln taught by Dr. Christensen in Fall 2016. Since its upload, it has received 84 views. For similar materials see Genetics in Biological Sciences at University of Nebraska Lincoln.
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Date Created: 04/26/16
BIOS 206 –General Genetics Dr. Alan Christensen Chapter 23 Notes “Quantitative genetics and multifactorial traits ” • Continuous variation –described in quantitative terms (quantitative inheritance) o i.e. Human height • Polygenic –more than one gene/loci influencing a trait • Multifactorial or complex traits –influenced by genes and environment 23.1 Not all polygenic traits show continuous variation • Meristic traits –phenotypes described by whole numbers o Number of seeds/eggs • Threshold traits –polygenic, multifactorial, continuous, small number of phenotypic classes o i.e. Type II diabetes 23.2 Quantitative traits can be explained in Mendelian terms Multiple-Gene Hypothesis for quantitative inheritance • Many genes contribute cumulatively • Cross of Red and White gr ain o F1 was all pink –suggesting incomplete dominance o F2 –most had some sort of red, 1/16 were all white o 4 shades of red o Suggests independent assortment • One potential additive gene (contributes to color gene) and one potential nonadditive gene (fails to make pigment) o F2 has 4,3,2,1,0 additive genes giving color • Nilsson-Ehle Additive alleles: the basis of continuous variation 1. Phenotypic traits with continuous variation can be quantified by measuring, weighing counting and so on 2. 2+ loci, throughout genome, account for hereditary influence on phenotype in additive way –called polygenic 3. Each locus has additive allele or nonadditive 4. Contribution of additive allele to phenotype is equal. Not always true 5. Additive alleles contributing to single qu antitative character produce substantial phenotypic variation Calculating the number of polygenes • Polygene –contribute to quantitative trait • Number of polygenes in phenotype for extremes calculated using 1/4 • (2n+1) =number of distinct phenotypic categories (smaller numbers) o Assuming all contribute equally and no environmental interaction 23.3 Study of polygenic traits relies on statistical analysis • Normal distribution –normal bell-shaped curve Mean • Where center is • Central point • Denoted • o is sum of all individual values in sample o n is number of individual values • Doesn’t tell you anything about the cluster and how far they are from the center point Variance • Denoted • • Sum of squared differences between measured and mean divided by one less than the total sample size • Determine degree of genetic control 2 2 • Unit is squared (m , g ) Standard deviation • Denoted s • • Shows percent of individuals within different multiples of standard deviation • Can be a form of probability • Standard error of the mean • Used to measure the accuracy of the sample mean • o s is standard deviation o sqrt(n) is square root of sample size • Always smaller than the standard deviation Covariance and correlation coefficient • Often have to measure 2 traits at a time. • This shows how much variation is common to both traits • Take deviations from mean for each then multiplied together. See below • • Correlation coefficient (r) o o is standard deviation of ? set of measurements o Can range from -1 (opposite ways) to +1 (go same way) • Does not show cause-effect relationship Analysis of quantitative character • Tomato varieties • Weight of F1 described as 12.04 +/ - 1.13, etc. 23.4 Heritability values estimate the genetic contribution to phenotypic variability • Low heritability estimate = mostly enviro nmental influence • Heritability is not fixed for a trait • Heritability estimate shows how much of phenotypic variation is due to genetic variation within a certain population in an environment • % values don’t mean phenotype is due to genes xx% of the time but that xx% of total variation is due to genotypic differences • Phenotypic variance à VP=V +G +V E GxE • Homogeneous individuals are mated with homozygous individuals and genotypic and environmental factors are assessed Broad-Sense Heritability • H 2 -measures the contribution of genotype variance to total phenotypic variance 2 V G • H = V P • Scale from 0-1. Close to 1 = environmental conditions don’t impact phenotypic variation • Doesn’t distinguish quantitative trait loci with alleles acting additive opposed to epistatic/dominance effects • Assume no interaction between genes-environment • Not good for breeding Narrow-Sense Heritability 2 • H –proportion of phenotypic variance due to additive genotypic variance alone • Divided into different modes of action o Additive variance –additive genes o Dominance variance –deviation from additive when heterozygous is not an intermediate o Interactive variance –deviation from additive components when 2+ loci behave epistatically (often excluded) • V =V +V +V G A D I 2 VA • Only due to additive genes à h = VP • h = VA V +V +V E A D • Used by breeders cuz more precise Artificial selection • Choose specific individuals for future breeding • Fast for trait with only 1 or 2 genes • NSH used to predict impact of selection o Higher value is more likely breeder will observe phenotypic range change • h = M2−M is the mean score of offspringh = R M1−M S o M2-M is selection response (R) –degree of response to mating selected parents o M1-M is selection differential (S) –difference between mean for whole population and mean for selected population • Realized heritability –NSH value from selective breeding and meas ure response of offspring o Corn kernels o Longest artificial selec tion = corn and increased oil content (gain additive alleles and decrease NSH) • Heritability low for traits essential to survival (Natural Selection has optimized traits) 23.5 Twin studies allow an estimation of heritability in humans • Identical twins (MZ) and fraternal twins (DZ) differences • MZ phenotypic differences completely environmental • Concordant –twins either both express or don’t express trait o Compare between MZ and DZ o If high in MZ, genetic component determining trait • Discordant –different expression between twins Twin Studies have several limitations • Treated differently if MZ compared to DZ –change environment • Same genes and same enviro nment mask values • Discoveries about twins o MZ twins differ in genomes by time born § Somatic mosaics –milder disease phenotype § Different CNV o Gene-expression patterns in MZ change with age à Phenotypic variation § Epigenetics different (diff methylation patterns) § Beckwith-Wiedemann syndrome – in one twin, not other 23.6 Quantitative trait loci are useful in studying multifactorial phenotypes • QTL –chromosome region has 1+ genes contributing to quantitative trait • Over time, diverge significantly and get 2 extremes. Then they are bred together for an F1 the nF2 shows different fractions of parental genomes =QTL mapping population • Find genomic differences and meas ure phenotypic expression through RFLPs, Microsatellites, and SNPs • IF linked to a QTL, diff genotypes at locus will differ in phenotypic expression o Called cosegregate o Linked • In AG (cattle, tomatoes, corn, rice) • Tomatoes -28+ QTLs à gene ORFX accounts for 30% variation in weight o Insert small QTL gene and decrease in size o Negative control • More compartments = larger Expression QTLs (eQTLs) and genetic disorders • Amount of RNA transcript made by gene • Identify genes responsible for common diseases o Asthma BIOS 206 –General Genetics Dr. Alan Christensen Chapter 25 Notes “Population and Evolutionary Genetics” • Evolution is a consequence of changes in genetic material through mutation and change in allele frequency in populations over time • Speciation –formation of new species (reproductively isolated) • Microevolution –within a species • Macro evolutionary –evolutionary events leading to new species 23.7 Genetic variation is present in most populations and species • Population –group of individuals belonging to same species • Gene pool –genetic information in population Detecting genetic variation by artificial selection • If no variation, selection wont have an effect • If variation, phenotype will change over generations Variations in nucleotide sequence • Compare nucleotide sequences (Adh in Drosophila) o Many mutations but only 2 alleles • Cystic fibrosis trans membrane conductance regulator (CFTR) o Loss of function, recessive o Secretes in glands and lungs o 1 mutation (3bp delete) accounts for 67% mutant alleles o Many silent mutations Explaining the high level of genetic variation in populations • Assumed selection would favor wild allele • Neutral theory –substitution mutations usually detrimental, few favorable • Some neutral so don’t get changed cuz no effect so stay there and mi ght fixate or be lost o Depends on population size, not natural selection o Some are kept through adaptation to environmental conditions • Some variation expected due to mutation and drift 23.8 Hardy-Weinberg law describes allele frequencies and genotype frequencies in populations • Assumptions o Frequencies of alleles in gene pool don’t change over time o If 2 alleles at locus, after 1 gen of mating, frequencies calculated with p +2pq+q =1 .49+.42+.09=1 Sperm fr(A)=.7 fr(a)=.3 Eggs fr(A)=.7 fr(AA)=.7x.7=.49 fr(Aa)=.3x.7=.21 fr(a)=.3 fr(Aa)=.3x.7=.21 fr(aa)=.3x.3=.09 F2 A .49+(.5x.42)=.7 .7+.3=1 a (.5x.42)+.09=.3 1. No selection 2. No new alleles or mutations 3. No migration 4. Large population 5. Random mating These can be used to see where evolution is occurring IMPORTANT CONSEQUENCES 1. Dominant traits don’t increase from gen to gen 2. Genetic variability maintained 3. Knowing frequency of one allele, can calculate other genotypes 23.9 Hardy-Weinberg law can be applied to human populations • HIV-1 homozygous people with CCR5 ( Δ32) gene that encodes a protein • This is a receptor for HIV -1 so it can enter cells • 32bp deletion in normal CCR51 gene (1) • Δ32/ Δ32 are resistant to mutation, 1/ Δ32 susceptible but progress slowly, 1/1 susceptible to STD HIV o Survey showed 89% population has 1 allele and 11% with Δ32 • Allele frequencies may change from one gen to next Testing for HWE in population • See if in equilibrium o Determine genotype frequencies (from phenotype or analyze protein/DNA sequence) o Calc allele frequencies o Use allele frequenc ies in parental to predict offspring 2 2 • Should fit p +2pq+q =1 • If not, evolving 283 individuals 233 1/1 57 1/Δ32 3 Δ32/Δ32 233 57 3 =.788 =.201 =.011 283 283 283 1freq =.89 = p Δ32freq =.11= q 2 2 1/1= p =(.89) =.792 1/Δ32=2pq=2(.89)(.11)=.196 2 2 Δ32/Δ32=q =(.11) =.012 • No evolution, not changing, in equilibrium Calculating frequencies for multiple alleles in population • ABO blood groups • 4 phenotypic combinations • p+q+r=1 Calculating allele frequencies for x -linked traits • Freq of x linked alleles in gene pool and freq of males expressing is same • Prob of male inheriting characteristic is equal to proportion of it in population 2 • Prob of female having allele is q • Color-blindness 8% males affected fr =.08 p =(.92) =. q =(.08) =.0064 2pq =.147=14.7%carriers Calculating heterozygote frequency • Cystic fibrosis • 1/2500=.0004 = q =√(.0004)=.02 • p=1-q=.98 • 2pq is heteros soooooo (2x.98x.02)=4% • Just an estimate! 23.10 Natural selection is a major force driving allele frequency change 1. Wallace-Darwin concept of natural selection 2. Variation in phenotypes 3. Many of variations are heritable 4. Reproduce in an exponential fashion. Competition among members to avoid predators and find mate 5. Some phenotypes are more successful than others • Populations and species change • Selection continues à new species Detecting natural selection in populations • Allele frequencies may change from one generation to next • Natural selection is the shift in allele frequencies Fitness and selection • Fitness (w) –organisms genetic contribution to future generations q0 • qg= 1+gq 0 • Conclusions from the sample o Weak selection can cause substantial change in allele frequencies o Selection is powerful force o Differences in fitness among genotypes must be large There are several types of selection • Directional selection –finches, shift to one end • Stabilizing selection –birth weight, both extremes selected against, increase at mean • Disruptive selection –drosophila, opposite of stabilizing selection, increase at extremes 23.11 Mutation creates new alleles in gene pool • Mutational event occur randomly • To figure out if mutation is significant in changing allele frequencies, measure rate they are produced • Dominant mutations, direct method 1. Distinctive phenotype 2. Fully expressed 3. Never produced by drugs or chemicals • Mutation rates can be stated as number of new mutant alleles per given number of gametes • Achondroplasia –dominant form of dwarfism o Estimate extent mutation can cause allele frequencies to change • In small populations, mutation can alter frequencies sufficiently 23.12 Migration and gene flow can alter allele frequencies • Migration –individual move between populations • Frequency of A on mainland is pm ' • pi= (1−m)p imp m • m is migrants from mainland to island • Change in allele frequency attributed to migration is proportional to differences in allele frequency between donor and recipient populations and to rate of migration 23.13 Genetic drift causes random changes in allele frequency in small populations • Genetic drift –random fluctuations in allele frequencies due to chance • Founder effect –when population originates from small numbers • Genetic bottleneck –when large population undergoes drastic, temporary reduction in numbers Founder effects in human populations • 4 forms of OCA (albinism) o Examine genetic basis for albinism o Could identify homozygous individuals and hetero carriers with PCR • Mutant allele specific to Navajo and arisen from 1 person in small population 23.14 Nonrandom mating changes genotype frequency but not allele frequency • Each genotype has same possibility of mating with any other genotype • Nonrandom mating doesn’t itself directly change allele frequency • Positive assertive mating –similar genotypes more likely to mate than dissimilar ones o Humans • Negative assertive mating –dissimilar genotypes more likely to mate o Plants Inbreeding • When mating individuals closely related than random people chosen • Mating among relatives • Increase homozygotes in population • Coefficient of inbreeding (F) –probability that 2 alleles are identical because from same copy of allele in ancestor o F = 1 àall homo and all same copy o F=0 à no person has 2 copies from same ancestor • Chance of having certain allele (50% for each parent back to original carrier) o Multiply .5 by how many generations • LOOK AT BOOK EXAMPLE 23.15 Reduced gene flow, selection, and genetic drift can lead to speciation • Species –interbreeding organisms reproductively isolated from other groups • No gene flow à population might diverge to where cant breed with other group • Macroevolution • Reproductive isolating mechanisms –barriers to prevent/reduce interbreeding between populations (ecological, behavioral, seasonal, mechanical, physiological) • Prezygotic isolating mechanisms –cant mate in first place • Postzygotic isolating mechanisms –barrier even when present and willing to mate o Viability and fertility of hybrids reduced o May be sterile hybrids o Hybrids viable and reproduce but offspring not good o Waste gametes and reduce fitness à will try to fix to make prezygotic barriers Changes leading to speciation • Atlantic and Pacific breeds • Were closet relatives genetically • 3 transocean pairs refused to mate • 4 other transocean had 33,45,67,86% likely to mate than same -ocean pairs • 1% viable offspring • Almost new species Rate of macroevolution and speciation • Millions of years? 100,000-10,000,000 yrs • Some faster (marine salmon, palm trees, brown algae) • 23,000 yrs new fish species in lake Apoyo • How find where came from? Phylogenetic, morphological and ecological analyses o PCR o Molecular clock –within the last 10,000 yrs 23.16 Phylogeny can be used to analyze evolutionary history Constructing phylogenetic trees from amino acid sequences • Cytochrome c –eukaryotic mitochondrial protein o Amino acid sequence changed slowly over time o Diverged from monkeys 20 mya • Genetic equidistance –diff in amino acid sequence between species proportional to evolutionary distance • Minimal mutational distance –nucleotide changes for all amino acid difference observed in protein • TREE Molecular clocks measure rate of evolutionary change • Molecular clocks –measure rate of change in sequences to infer evolutionary relationships and estimate time of divergence • Use fossil record Genomics and molecular evolution • Study origin, evolution, and function of gene duplications, evolution of human genome, and role of n atural selection in human adaptations • Compare to relatives and ancestors Complex origins of genome • Non-African populations had origins 50,000 ya • Paleogenomics –origin and dispersal of humans and history of genome • Neanderthals in Europe and western Asia 300 ,000 ya • Coexisted with humans • Sequenced a fossil of a Neanderthal skeleton o And living humans o Has same size as our genome o 99.7% identical o 98.8% same as chimpanzee • Might still carry Neanderthal genes (20% in population?) • Same ancestor 706,000 ya 1. No direct ancestors to humans 2. Interbreeding between humans and Neanderthals 3. Contributed to our genome 4. Share most genes and other sequences with them Our genome is a mosaic • Might be related to other species too • Another fossil showed close relation to Neanderthals and is currently in human DNA • Mosaics that have DNA from 1 or 2 other sources • Neanderthal and Denisovan genomes 40,000 -80,000 yrs old Special Topics 3 –DNA Forensics DNA profiles from very small evidence can be obtained Applications • Paternity and family relationship testing • Identification of plant materials • Verification of military casualties • Evolutionary studies 3.1 DNA profiling methods VNTR-Based DNA fingerprinting Variable number tandem repeats or microsatellites • Non-coding regions • 15-100bp long and 1-20 kb • Many different allele possibilities VNTR profile (DNA fingerprint) • Extract DNA and digest with restriction enzyme on either side of repeat • Separated by gel electrophoresis • Southern blot Limitation –requires lots of sample DNA • Used in paternity testing Autosomal STR DNA Profiling Short Tandem Repeats or microsatellites • 2-9 bp and repeated 7-40 times • Use 13 STR loci as a core set Forensic DNA analysis of STR loci • Primers tagged with 4 colored dyes • Size depends on number of repeats. Many loci one color and separated by length • Length measured by capillary electrophoresis (tubes filled with gel, put in DNA, electric current passes through) • Negative DNA moves to positive electrode • Make graph with peaks Y-Chromosome STR Profiling Primers only amplify on the Y chrom Limitation –can’t differentiate between dad, son, siblings cuz same Y chrom Can help with genetic genealogy studies Mitochondrial DNA Profiling Undergoes little recombination and is inherited mostly from mother. Hyper variable segment I and II • Compare DNA sequences Good cuz lots of them so can take small samples Limitation –cannot differentiate mothers and daughters/siblings Good for evolution, population, and genealogy Can help solve animal trafficking problems Single-Nucleotide Polymorphism Profiling SNP –bp change, insertions or deletions Random on mtDNA Every 500-1000 nucleotides Only 2 alleles Advantage –only need 2 primers plus one nucleotide (for PCR) • Sample can be degraded 3.2 Interpreting DNA profiles If profiles don’t match, then they are probably not the suspect If match, must examine the profile probability (random chance probability) –chance that random person would have same profile as evidence • Gene has 2 alleles, thus probability of hetero = 2pq 2 • 2 of same alleles = p • Method to multiply all frequencies of genotypes at each locus = product rule o Accepted in US courts Uniqueness of DNA profiles USA uses 13 loci to make DNA profiles Siblings have a 50% chance of inheriting 1 allele same, and 25% change of inheriting both alleles at a locus Parents can share with children, but less likely If siblings are considered, tables might not apply or might need adjusting The prosecutor’s Fallacy Have to have other evidence for the person to be guilty Could have human error, contamination, or deliberate tampering If doesn’t match, doesn’t mean innocent DNA profiles interpreted using context of all evidence in case DNA Profiles Databases CODIS –DNA profiles in USA with the FBI (11 million DNA profiles) Convicted offender database Forensic database –from crime scenes May be a question of privacy and rights Technical and Ethical issues surrounding DNA profiling Limitation –Most criminal cases have no DNA evidence • Cant be processes or backlogged Human error • Samples switched and innocent people convicted • Other DNA present at crime scene Degraded DNA and hard to interpret Deliberate tampering • Just a few cells or synthetic DNA • In future, might have to detect synthetic/cloned DNA (real DNA has methylation) Can you collect DNA without consent? Partial matches? • Use familial DNA testing • Ethical? DNA phenotyping –predict hair and eye color SPECIAL TOPIC 5 –Genetically Modified Foods GMO’s provide • Increased productivity • Reduced pesticide use • Enhanced flavor and nutrition Golden rice –has Vitamin A to help deficiencies Concerns • Safety and environmental WHAT ARE GM FOODS? • Organisms whose genome has been altered in a way that does not occur naturally • Transgenic –genes transferred between unrelated species • Cisgenic –transfer of genes within a species • This is a form of biotechnology • Most GMOs grown in 5 countries o USA has half and mostly soybeans and corn o Herbicide and insect resistance Herbicide-Resistance GM crops • 70% GM crops • Tolerance bacterial gene for Gylphosate –in Roundup • Problem: weeds become resistant to this also Insect-Resistant GM crops • Bt crops • CRY –a crystal protein that if ingested, will break down gut wall • Many different forms so select for one needed • Controversial cuz might hurt butterflies, and have bad things for humans GM crops for Direct Consumption • Few used for direct consumption (rice, squash, and papaya) • Golden rice o Serious need for people to get Vitamin A o Found in orange foods and leafy green vegi’s o Use different methods to get highest content METHODS USED TO CREATE GM PLANTS • Biolistic method o In vitro o Physically introduce DNA into cell o Gene gun o DNA coated particles • Agrobacterium tumefaciens-mediated transformation o Rhizobium radiobacter o Soil microbe to infect plant cells and cause tumors o Ti plasmid –puts part of t-DNA into plant o Ti plasmid is a transformation vector to insert cloned DNA into genes Selectable markers • Negative selection o Marker gene (resistance gene) o Incubated into medium with hygromycin (antibiotic that inhibits growth of euk cells) o Only resistance ones will survive • Positive selection o Phosphomannose isomerase (PMI) o In animals, not plants o Converts mannose and fructose interconnectedly o Survive on only mannose medium o Used for Golden Rice 2 Roundup-Ready Soybeans •
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