ch 7 linkage, recomb, eukaryotic gene mapping

mendels segregation and independent assortment

segregation: each diploig org has 2 alleles at locus separate in meiosis, one allele into each gamete
indepednent assortment: 2 alleles at locus separate independently of alleles at other loci

results in recombination- alleles in new combos

chromosome theory of inheritance

segregation: diploid org has 2 alleles for characteristic, each at same position/locus on ½ hom chrom. segregate in meiosis, each gamete 1 homolog

independent assortment: meiosis, each pair of hom chrom assort independent of other pairs

more genes than chromosome, gene must present on same and not asssort independent

genes close together are linked and in same linkage group

travel together in meiosis and arrive at same gamete not assort independent

linked genes and crossing over, what is it

genes occasionally switch from one hom chrom HC to other thru crossing over

results in recomb: break up association of genes close together on same chromosome

linking and crossing over is opposite

linking keeps genes together

crossing over mixes them up and makes new combos of genes

cross linkage notation

need to know genotypes and arrangement of genes on chromosome

for example homo dom at 2 link loci x homo rec is AA BB x aa bb and would be

A B a b
—— x ——
A B a b

horizontal line is HC

f1 progeny will be

A B
——
a b

complete linkage compared with independent assortment

located very close together on same chromosome, no cross over

new combos only if physical connection between allleles were broken

nonrecombinant gametes

gametes that contain only original combinations of alleles that were present in the parents, parental gamete

parental progeny

independent assortment outcomes in testcross

hetero parent would produce 4 types of gametes

2 nonrecomb with og combs of alleles and 2 new combos of alleles

1:1 equal proportion

4 gametes join with single from homo parent to produce 4 kinds progeny in equal proportion

recombinant gametes

gametes with new combos of alleles are recomb

cross over in linked genes

cross over in prophase 1 of meiosis, exchange genetic material between nonsister chromatids

single crossover: 2 chromatids that didnt are unchanged, gametes receiving are nonrecomb. other 2 which did cross over, new combos of alleles, gametes are recomb. so each meiosis has 2 nonrecomb and 2 recomb. so thats why impossible to determine whether genes on same chromosome w crossing over or different chromosome if cross over in every meiosis

for closely link genes: cross over not every meiosis. in meiosis without cross over only nonrecomb. in single crossover, half recomb and half nonrecomb. total percent of recomb always ½ percent of meiosis with cross over. only 50% result gametes are recomb. fequency of recomb alwasys ½ cross over and max proportion of recomb is 50%

result of testcross is mostly nonrecomb and few recomb

calculate recomb frequency

percent of recomb progeny in cross or rate or recomb

number of recomb progeny/total x 100

coupling and repulsion

wild type alleles found on one chromosome and mutant on another. coupling or cis configuration

each chromosome contains one wild type and one mutant allele. repulsion or trans configuration

test for independent assortment

genes linked if more nonrecomb than recomb

sometimes difference isnt as obvious

use chi square of independence

construct table of observed progeny like punnett square, genotypes from segregation of alleles at one locus on top and other on side, compute total for each row and column and grand total, use totals to compute expected values

compute expect numbers for each combo of genotype under assumption that segregation of alelles at 1 locus independent of other. if independent, expected number is row total x column total over grand total

calculate chi square value so same formula, add for 4 types of progeny.

degrees of freedom. number of rows minus 1 times columns minus 1. so dof is 1.

gene map with recomb frequency

two genes far apart more likely to crossover than close together

genetic recomb are genetic maps and physcial distance are physical maps

measure distance in map unit, 1% recomb rate is 1 mu centiMogans or cM. approx additive

but remember

1. cant distinguish between genes on diff chromosomes and far apart on same chromosome. if 50% recomb, they are in diff link groups so ither diff chromosome or far apart on same

2. testcross for 2 genes far apart on same chromosome tend to understestimate true physical distance. cross doest reveal double crossovers. double crossover is 2 separate crossover in 2 loci. single crossover produce combo of alleles not present on og, 2nd crossover between same 2 genes reverse effects to restore og parents. so cant distingish between 2 strand double crossover or when no cross over at all

genetic map with 2 point test cross

each testcross, one parent is hetero and recomb frequency calculated for each pair of genes. testcross btwn two genes is two pt testcross or 2pt cross. 50% recomb frquency is independent.

3pt testcross to map 3 linked genes

order of 3 genes can be establiushed in single set of progeny, some double crossover detected, provide more map distance

2 types of single crossovers and a double crossover, so 2 recombs and 2 nonrecomb

middle allele is diff so in fouble crossover, only middle allele should differ from alleles in nonrecomb progeny

genetic map

set up 3 pt testcross. hetero for all loci and homo rec. order abirtrarily assigned because we dont know middle and make hetero in coupling although can be repulsion

progeny hetero with domininat and progeny homo with rec. with 2 classes possible for each of 3, all 8 phenotypic classes present, in some 3 pt rosses, one or more phenotype may be missing if number of progeny limited. absense of a class can be least frequebt abd order

determine gene order

identify middle locus by examin diuble cross over progeny

which are nonrecomb, 2 most numerous class of progeny

next double crossover progeny which is 2 least number

which gene is middle? draw chromosome of hetero with all 3 possible gene order and see if double crossover produce combo of genes observe in double crossover progeny. so like which one is only one different from nonrecomb.

determine location: 4 remaining are single crossover. compare with nonrecomb. so if we had xyz, in that order, for x-y, find which one only change for yz and then y-z, find one change only z

calculate recomb frequency
1. add all recomb progeny divide by total times 100. include all single and double. so add the 2 singles that are differnet for “yz“ and double and same for other by “z“ and double. and thats the distance.

interference and coeff of coincidence

interference: degree to which one crossover interfere with additional crossover in same region

coeff of coincidence: ratio of observed double crossover to expected. observe/expected. for expected you mutliply the map distances as decimals by total.

interference is 1-coeff of coincidence. and its a percent. so wtv interferance is is that much of double crossover progeny expected not obserbed bc of interference.

wghen interference is complete and no double crossover progeny observe, coeff is 0 and interferance is 1

if crossover increases probabiltiy of another crossover nearby, we see more double crossover, then coeff is greater than 1 and interferance is negative

effect of multiple crossover

if we examine only alleles at loci on either side of both crossover events:

two strand double crossover result in no new combo of aleles and no recomb

three strand double crossover result in 2/4 gametes recomb

four strand double crossover result in all 4 gamete recomb

so 2 strand: 0% recomb
3 strand: 50% recomb
4: 100% recomb

all types of double crossover average of 50% recomb gametes

some multiple crossover go undetected, map distances based on recomb understimate true physical distances bc some multiple crossover not detected aomng progeny of cross. when genes together, multiply clrossover unlikely, genetic distances accurately correspond to phsical distance. but as distance increase, more multiply crossover, so we have map functions

map human genes

use pedigree data to analyze linkage, use several families and pedigrees.

map with molecular markers

genetic markers: variable genes with easily observable phenotypes whose inheritance an be studied.

cosegregation of two or more markers is stdied, map distances based on rates of recomb btwn markers