1 / 32

Bioinformatics

Lecture 7 Genome Mapping. Bioinformatics. Dr. Aladdin Hamwieh Khalid Al- shamaa Abdulqader Jighly. Aleppo University Faculty of technical engineering Department of Biotechnology. 2010-2011. independent assortment and punnett square. A dihybrid cross produces

chloe
Download Presentation

Bioinformatics

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Lecture 7 • Genome Mapping Bioinformatics Dr. Aladdin Hamwieh Khalid Al-shamaa Abdulqader Jighly Aleppo University Faculty of technical engineering Department of Biotechnology 2010-2011

  2. independent assortment and punnett square A dihybrid cross produces F2 progeny in the ratio 9:3:3:1.

  3. Crossover Independent assortment produces a recombinant frequency of 50 percent.

  4. Linkage • Loci that are close enough together on the same chromosome to deviate from independent assortment are said to display genetic linkage BUT • The linked loci that are far from each others are in danger of CROSSINGOVER

  5. Deviations from independent assortment In the early 1900s, William Bateson and R. C. Punnett were studying inheritance of two genes in the sweet pea. In a standard self of a dihybrid F1, the F2 did not show the 9:3:3:1 ratio predicted by the principle of independent assortment. In fact Bateson and Punnett noted that certain combinations of alleles showed up more often than expected, almost as though they were physically attached in some way. They had no explanation for this discovery.

  6. Deviations from independent assortment Thomas Hunt Morgan found a similar deviation from Mendel’s second law while studying two autosomal genes in Drosophila. Morgan proposed a hypothesis to explain the phenomenon of apparent allele association. One of the genes affected eye color (pr, purple, and pr, red), and the other wing length (vg, vestigial, and vg, normal). The wild-type alleles of both genes are dominant.

  7. When two genes are close together on the same chromosome pair (i.e., linked), they do not assort independently.

  8. Chiasmata (the visible manifestations of crossing-over): a cross-shaped structure forming the points of contact between non-sister chromatides of homologous chromosomes.

  9. Frequencies of recombinants arising from crossing-over. The frequencies of such recombinants are less than 50 percent.

  10. Linkage maps (distance between the genes.) • Recombinant frequencies are significantly lower than 50 percent and the recombinant frequency was 12.97 percent. (146+157) * 100 / 2335 = 12.97 • Morgan studied • linked genes, • proportion of recombinant progeny • varied considerably, • Morgan concluded actual distances separating genes on the chromosomes. • Alfred Sturtevant suggested that we can use this percentage of recombinants as a quantitative index of the linear distance between two genes on a genetic map, or linkage map.

  11. Linkage maps (distance between the genes.) • Sturtevant postulated the greater the distance between the linked genes, the greater the chance of crossovers in the region between the genes. • Sturtevant defined one genetic map unit (m.u.) as that distance between genes for which one product of meiosis in 100 is recombinant. Put another way, a recombinant frequency (RF) of 0.01 (1 percent) is defined as 1 m.u. A map unit is sometimes referred to as a centimorgan (cM) in honor of Thomas Hunt Morgan.

  12. A chromosome region containing three linked genes. Calculation of AB and AC distances leaves us with the two possibilities shown for the BC distance. Recombination between linked genes can be used to map their distance apart on the chromosome. The unit of mapping (1 m.u.) is defined as a recombinant frequency of 1 percent.

  13. example For the v and ctloci 89+94+3+5 =191 For the ctand cv, loci 45+40+3+5 = 93 For the v and cv, loci 45+40+89+94 = 268

  14. Mapping the12 chromosomes of tomatoes.

  15. Morphological Markers • Small Number • Limited genomic coverage • Could be influence by environment • Most of them exhibit dominance nature

  16. Linkage Mapping • Genes are points on the genome and there are a flanking regions around them link to these genes. • The central idea of the linkage mapping is to put a lot of points on the genome in order to get points that linked to another interesting points (genes). • These points that we add are called as: “MARKERS”

  17. Molecular Markers • Dominant or Co-dominant nature in different types: • Protein-based • Isozyme • Allozyme • Hybridization-based • RFLP • DArT • PCR-based • RAPD, AP-PCR • AFLP • STS (SSR, ISSR, SCAR, CAPS) • RGA • Single Nucleotide Polymorphism (SNP)

  18. Introduction • Molecular markers: • RFLP • AFLP • RAPD • SSR • SNP • STS • ISSR Genetic map of lentil RAPD AFLP SSR Hamwieh et al. 2005

  19. How to genotype? P2 P1 b a b b a a b bb a aaa b bba b bH

  20. P1 P2 P1 P2 Co-dominant Marker 1 2 3 4 5 6 7 8 9 10 11 12 13 14 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Dominant Marker

  21. P1 P2 P1 P2 Unaccepted Markers (RIL pop.) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Could be determined by Chi-square test Segregation distortion : Asegregationdistortion marker/gene produces a distortion in normal expected segregation

  22. Chi-Square • Obs.A=45 Exp.A=50 • Obs.B=55 Exp.B=50

  23. Chi-Square Table

  24. P1 P2 Recombinant Fraction 1 2 3 4 5 6 7 8 9 10 11 12 13 14 M1 M2

  25. LOD Score •A statistical estimate of whether two loci are likely to lie near each other on a chromosome and are therefore likely to be inherited together.

  26. Zmax A LOD score of three or more is generally taken to indicate that the two loci are close. M:Recombinant N: Total Number M-N: Non Recombinant • N=35 • M=7

  27. Mapping Function rAC = rAB + rBC - 2rABrBC Haldane's map function assumes that the probability of a crossover in one region is independent of the probability of a crossover in the second region. • Haldane • Kosambi rAC = rAB + rBC - 2CrABrBC C =coefficient of coincidence Kosambi's mapping function is based on empirical data regarding the proportion of double crossovers as the physical distance varies. Kosambi's function adjusts the map distance based on interference which changes the proportion of double crossovers.

  28. Thank you

More Related