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KSU / BSCI / BSC 30156 / What is synteny in genetics?

What is synteny in genetics?

What is synteny in genetics?

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Elements of Genetics (Dr. Groff)  


What is synteny in genetics?



Exam 2 Study Guide (Scantron 3/12,  Written 3/14)  

Highlight: Key Term Highlight: Important Concept Highlight: Formula  

I highly recommend reading the powerpoint transcripts on Blackboard and doing  practice problems from the text-helpful when studying!

 

I tried to break down the study guide Dr. Groff provided as best I could-short and  sweet and to the point!  

Genetic Linkage and Mapping  

Mendelian Inheritance- alleles of different genes sort independently during meiosis  (NOT linked)  

In reality- many alleles are linked (especially if close together on a chromosome)  and travel together  

All genes on one chromosome- a linkage group  


How many phenotypes are possible?



Genetic map: used to diagram the order of genes along a chromosome  Linkage  Don't forget about the age old question of What is meant by direct material?

 -Chromosomes made up of way more than one gene  

 -Synteny groups: blocks of genes ordered the same way; conserved across  species due to shared ancestry  

 -Chromosomes called linkage groups  

 -Humans: 22 autosomal linkage groups, X and Y linkage groups (sex  chromosomes)  

 -Linkage: two genes on same chromosome

 -Genes close together usually transmitted from parent to offspring as a  group  

 -Far apart genes may assort independently due to crossing over  (consistent with Mendel)  

Bateson & Punnett-discovered 2 traits (didn’t assort independently)   -1905: first researchers to demonstrate not all traits assort independently  


What is a three factor cross?



Don't forget about the age old question of How do we reconstruct a crime scene?

 -Crosses involving flower color and pollen length of the sweet pea: offspring  didn’t display a 9:3:3:1 phenotypic ratio expected from  

 dihybrid crosses  

 -Suggested that traits were coupled to one another  We also discuss several other topics like Who founded the 1st lab dedicated to psychology & separated psychology from philosophy for the first time?
Don't forget about the age old question of Decriminalization refers to what?

Early studies leading to understanding of genetic linkage  

 -Drosophila geneticists observed outcomes of crosses where phenotypic  ratios didn’t fit expected ratio for Mendelian crosses  

 -More than expected numbers of parental & nonrecombinant progeny and  very few recombinant  

 -If genes are close together chances of crosscover is small: a large  number of nonrecombinant (resembling parentals) expected  If you want to learn more check out Criminology is the study of what?

 -MAX recombination frequency is 50%; genes close together have RF well  below 50%  

Crossing over may produce recombinant genotype  

 -Genetic recombination by crossing over can produce new combination of  alleles on chromosomes  

 -Cells containing new allelic combinations: nonparental or  recombinant cells  

 -Cells containing original allele combination: parental cells  

Morgan provided evidence for linkage of X-linked genes and proposed crossing  over between X chromosomes  We also discuss several other topics like Starch means what?

 -Studied X-linked inheritance patterns  

 -Three traits used: body color, eye color and wing shape

 -Eight phenotypic classes expected  

 -Parental combinations most prevalent in offspring; the three traits  were found on X chromosome and inherited together  

 -Offspring not containing parental combination: crossing over  between homologous X chromosomes  

 -3 hypotheses explaining results  

 -All three genes on same chromosome  

 -Crossing over produces new combination of alleles   -Likelihood of crossing over depends on distance between two genes  Likelihood of crossing over between two genes depends on distance between them   -Far apart genes more likely to cross over than close together  

Frequency of recombination (RF) between two genes used to calculate map  distance along a chromosome  

 -% recombinant offspring correlated to distance between genes  

 -Construction of a genetic linkage map involves a testcross (typically  involve individual heterozygous for traits being mapped, and an  

 individual homozygous recessive for traits being mapped)  

 -Testcrosses allow researcher to distinguish between recombinant and  nonrecombinant offspring  

 -Recombinant have different combinations of alleles than parental  strains  

 -Nonrecombinant have same combinations of alleles as one of  parental strains  

 -Crossing over during meiosis produces recombinant   -Recombinant fewer than nonrecombinant  

 -Map distance: (# recombinant offspring)/ (total # offspring) X 100   -Total includes recombinant & nonrecombinant  

 -Units: map units (mu) or centiMorgans (cm)

 -1 mu/cm: 1 % RF  

Three-gene crosses (trihybrid) can be used to determine order and distance  between linked genes  

 -Procedure (VERY important; 20% of exam 2 grade, included in written  portion; refer to example problem from class in Module 2  

 folder)  

 1. Order 8 allele combinations (2 highest parentals, 2 lowest double  crossovers, 4 intermediate single crossovers)  

 2. # progeny  

 3. What allele is in the middle (what has flipped?)   4. Calculate genetic distance, interference  

 -Double crossovers underestimate the distance between genes further apart  Interference can influence # double crossovers occurring in a short region  

 -Probability of a double crossover in a trihybrid cross EQUAL to product of  recombination frequency between genes  

 -This probability, when multiplied by total # offspring, should  EQUAL observed # double crossovers  

 -Rarely occurs due to positive interference  

 -When a crossover occurs in an area of a chromosome: usually  decreases probability a second crossover will occur  

 -To calculate interference: first calculate a coefficient of coincidence (C); C  is EQUAL to (observed double crossovers)/(expected  

 double crossovers)  

 -Interference (I)= 1-C  

Quantitative Traits and Heritability  

Quantitative traits  

 -Majority of phenotypic traits in plants & animals are quantitative (complex)   -Quantitative traits

 -Continuous distribution, not discrete classes  

 -Affected by many genes  

 -Affected by environmental factors  

 -Multifactorial diseases: polygenic human diseases influenced by  environment; examples are diabetes, heart diseases,  

 schizophrenia, autism  

 -Categorized as anatomical, physiological and behavioral (as well as human  diseases analogous to quantitative traits)  

Phenotype  

 -Inherited DNA sequence variation produces allelic variation that creates  variation in phenotypic traits  

 -When we refer to alleles and mutations creating allelic variation: referring  to very specific types of DNA sequences  

Phenotype represents an interplay of the underlying genetic architecture of an  organism AND the environment  

 -Temperature sensitive alleles in animals (example from lecture)  

 -Phenotypic plasticity: single genotype producing different phenotypes in  different environments  

 -Majority of phenotypic traits polygenic (influenced by more than one gene)   -Quantitative trait loci (QTL) mapping  

 -Variation in QTLs underlies phenotypic variation & evolution over a  long-time scale  

 -Some traits controlled by a few QTLs others by many  

 -Epistasis: interaction between two or more genes that influence the same  phenotypic trait; genes can work with or against each other  

 -Pleiotropy: one gene influences several phenotypic traits; master regulator  genes (developmental control) show pleiotropy  

Components of phenotypic variation

 -Variance  

 -Phenotypic variance (VP or VT): sum of variance due to differences  among genotypes (genetic variance, VG) & variance due to  

 direct effects of the environment (environmental variance, VE)   -VP=VG+VE

 -Two components of genetic variance: additive genetic variance (VA) &  dominant genetic variance (VD)  

 -VG=VA+VDof

 -Additive variance: variance in a trait due to the effects of each  individual allele being added together, without any interactions   with other alleles or genes  

 -Dominant variance: variance due to interactions between alleles:  synergy, effects due to two alleles interacting to make the trait  

 greater/lesser than the sum of the two alleles acting alone   -Dominance variance not directly inherited from parent to offspring  

 -Due to interaction of genes from both parents within the  individual; only one allele passed from each parent to offspring  

 -Phenotypic traits: contribution of heritable genetic factors (broad-sense  heritability) & measurement errors  

and environmental effects  

Heritability 

-How much of variation in a trait is due to variation in genetic factors (as opposed  to environmental)  

-Describes the proportion of genetic variance (VG) to total variance  -2 types  

 -Broad-sense heritability (H2): ratio of total genetic variance to total  phenotypic variance

 -Can be partitioned into contribution of additive genetic factors  (narrow-sense heritability), dominance effects, gene-gene interactions (epistasis) &  gene-environment interaction  

 -H2=VG/VP  

 -Narrow-sense heritability (h2): ratio of additive genetic variance to total  phenotypic variance  

 -h2=VA/VP  

 -Proportion of variability that can be passed from parent to offspring   -Only VA enables a response to selection  

 -WHEN h2=0, none of phenotypic variance among individuals is due  to additive genetic differences (VA=0) and offspring will not closely resemble their  parents for the trait of interest for genetic reasons  

 -WHEN h2=1, all variation among individuals due to heritable genetic  differences (VP=VA) and offspring will resemble their parents very closely  

Polygenic inheritance, additive genes & a continuum of phenotypes  

Nilsson-Eble studied how continuous variation is related to polygenic inheritance  of color in wheat  

 -Trait (color) determined by two genes (each having red and white alleles);  different allele combinations contribute to color in an additive manner (doses) &  display partial dominance (heterozygotes intermediate); three genes controlling  “redness” of wheat (RESULT)  

 -With two additive genes, have 5 phenotypic classes in F2 offspring of true breeding strains instead of 3 classes with one additive gene  

 -# phenotypic classes when there are n diallelic additive loci: (2n+1)   -With 3 diallelic loci, 7 phenotypic classes expected  

 -With 4 additive genes, 9 phenotypic classes expected  

Heritability values relevant only to particular groups raised in a particular  environment  

Heritability describes amount phenotypic variation due to genetic variation for a  particular population raised in a PARTICULAR ENVIRONMENT

Not able to determine relative contribution of genetics and environment in  producing a given trait  

Selective breeding: way of estimating heritability  

Response to selection in an artificial selection experiment: most common way to  estimate narrow-sense heritability  

 -Also known as realized heritability  

Narrow-sense heritability: proportion of variance in phenotype which can be used  to predict changes in population when selection is practiced  

 -Important: can aid in predicting outcome of selective breeding

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