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6- GENE LINKAGE AND GENETIC MAPPING. Compiled by Siti Sarah Jumali Level 3 Room 14 Ext 2123. Linkage and crossing over. LINKAGE. Chromosome is a linkage group Linkage refers to: 1) 2 or more genes may be related on the same chromosome
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6- GENE LINKAGE AND GENETIC MAPPING Compiled by Siti Sarah Jumali Level 3 Room 14 Ext 2123
LINKAGE • Chromosome is a linkage group • Linkage refers to: • 1) 2 or more genes may be related on the same chromosome • Physically linked because eukaryotic chromosome contains a single, continuous linear molecule of DNA • 2) Genes that are close on the same chromosome tend to be transmitted as a unit • Indicate the linkage has an influence on the pattern
Bateson and Punnet discovered 2 traits that did not assort independently • They suggested that the transmission of these 2 traits from the parental generation to the F2 generation was somehow coupled and not easily assorted independently • This is due to linkage
LINKAGE CONT’D • Traits may not assort independently such as in Mendel’s law, where the traits did not segregate showing linkage • Therefore it produces bizarre phenotypic ratio than 9:3:3:1 to something like 15:1:1:4 • Chi-square (χ2) can be used to distinguish between linkage and independent assortment
Trihybrid cross- Lets consider this • Gray body, red eyes 1159 Yellow body, white eyes 1017 Gray body, white eyes 17 Yellow body, red eyes 12 Total 2205 • Red eyes, long wings 770 White eyes, miniature wings 716 Red eyes, miniature 401 White eyes, long wings 318 Total 2205 Nonparental offspring Nonparental offspring NonparentalOffsprings are called recombinant
Question ? • Why is the recombinant number so low?
Crossing over • May produce recombinant phenotypes or known as recombinant or nonparent • Because the genetic information recombine during Meiosis 1
Chi-square (χ2) • Is used to test goodness of fit between a genetic hypothesis and observed experimental data • Must 1st propose a hypothesis; • 2 genes are unlinked, therefore follow Mendel’s law • Null hypothesis is said to be null because it is assumed that there will be no difference between experimental data and observed data • If χ2 is low, accept hypothesis, genes assort independently • If χ2 is high, reject hypothesis, genes are linked
Chi-square (χ2) can be used to distinguish between linkage and independent assortment • χ2=Σ (o-e)2/ e; • Where o = observed value, e = expected outcome (theory) If the data do not fit, we will reject the idea that the genes assort independently and conclude that the genes are linked
Chi-square (χ2) analysis • The larger the chi-square, the smaller the p value • P value more than 5% will ensure acception of null hypothesis • 5% and below will cause rejection of null hypothesis
Experiment: Do the genes for flower color and pollen shape assort independently?
Mendel’s law overruled • Soon after Mendel's rules were rediscovered, it was found that some loci did not assort independently. • The simplest explanation is that the loci lie close to each other on the same chromosome. They are linked on the same chromosome.
Thomas Morgan • He did experiment on genetic mapping on X chromosome • He concluded that genes are located on the same X chromosome, so they are likely to be inherited together • Due to crossing over, X chromosome can exchange pieces of chromosomes and create new parental combination of alleles • The likelihood of crossing over depends on the distance between 2 genes. I f 2 genes are far apart from each other, crossing over is more likely to occur
CROSSOVER VALUE AND GENE MAPPING • Determining Map DistanceThe percent recombination is calculated as before. (# of recombinants ÷ # of offspring) x 100 = % of recombinants 1% recombination = 1 map unit, or 1 centimorgan, in honor of T.H. Morgan, one of the first persons to propose this linkage, and first to win a Nobel prize in genetics. • Two phenotypes are in very high frequency have the same phenotypes as the original parents (P1). These are called non-recombinants or parentals. • Two phenotypes are in low frequency and combine the phenotypes of the two original parents (P1). These are called recombinants or non-parentals.
Three-point cross • Determining gene order • The pair of phenotypes with the highest frequency is always the non-recombinant group. • The pair of phenotypes with the lowest frequency is always the double cross-over group. The probability of a double cross-over is approximately the product of the probability of the single cross-over. • compare the wild type class b+pr+c+ to the purple double cross-over class b+prc+ and we can see that the purple locus does not match indicating that the purple locus is in the middle. • Also note that as the parental phenotypes are composed of a gamete from the female that is either b pr c or b+ pr+ c+,
Determining Map Distance The next step is to set-up a table that is titled " number of recombinants between". The percent recombination is calculated as before. # of recombinants 100 x ----------------- = % of recombinants # of offspring thus for the distance from b to pr 887 100 x ----------------- = 5.9% or 5.9 m.u. 15,000 The distance from b to c, the two outside loci, (25.4 m.u.) is the sum of the distance from b to pr (5.9 m.u.) and the distance from pr to c (19.5 m.u.).