Chromosome or gene mapping &Linkage analysis

Describes chromosome mapping and linkage analysis.

1. Chromosome or Gene Mapping & Linkage Analysis Mrs.R.Gloria Jemmi Christobel Assistant Professor Department of Biochemistry V.V.Vanniaperumal College for Women Virudhunagar, Tamil Nadu, India.

2. Chromosome OR Gene Mapping Gene mapping describes the methods used to identify the locus of a gene and the distances between genes. The essence of all genome mapping is to place a collection of molecular markers onto their respective positions on the genome. Molecular markers come in all forms. Genes can be viewed as one special type of genetic markers in the construction of genome maps, and mapped the same way as any other markers. In 1911, by Thomas Hunt Morgan, gene for eyecolor was located on the X chromosome of fruit fly. E.B. Wilson attributed the sex-linked genes responsible for color-blindness and hemophilia in human beings to be located on the Xchromosome,similar to the many X-linked factors being described by the Morgan group in flies.

3. Picture showing loci in chromosome 3 3p21, 3p22.1 are the locus of various genes or sequences

4. What are molecular markers? It is a DNA sequence readily detected and their inheritance is easily monitored. It is polymorphic(more than one allele occupy the locus in a population) Includes; Biochemical & genetic markers Genetic markers- RFLP, RAPD, SSR,SNP, VNTR etc…. Biochemical markers-genes that code for proteins

5. There are two distinctive types of "Maps" used in the field of genome mapping: genetic maps and physical maps. Genetic maps' distances are based on the genetic linkage information Physical maps use actual physical distances usually measured in number of base pairs. While the physical map could be a more "accurate" representation of the genome, genetic maps often offer insights into the nature of different regions of the chromosome, e.g. the genetic distance to physical distance ratio varies greatly at different genomic regions which reflects different recombination rates, and such rate is often indicative of euchromatic (usually gene-rich) vs heterochromatic (usually gene poor) regions of the genome.

6. Genetic mapping Usually done by collecting samples (saliva, blood or tissue) from members with prominent trait or tissue & from members who doesn’t have the same. DNA isolated from the samples Examined for the difference in the DNA pattern in person with disease and person who don’t have the disease. Unique DNA pattern is termed as polymorphism or marker The important step in building a genetic map is the development of genetic marker -any sequence feature that can be faithfully distinguished from the two parents can be used as a genetic marker Closer two markers pass on together to the next generation. “Co-segregation " patterns of all markers can be used to reconstruct their order

7. The genotypes of each genetic marker are recorded for both parents and each individual in the following generations . The quality of genetic map depends on : number of genetic markers on the map and the size of the mapping population . Linkage for the newly viewed marker with the other genetic markers are calculated and the actual gene loci are then bracketed in a region between the two nearest neighboring markers . Process repeated to look for more markers till the causative locus identified. The great advantage of genetic mapping is that it can identify the relative position of genes based solely on their phenotypic effect

8. Genetic mapping is a way to identify exactly which chromosome has which gene and exactly pinpointing where that gene lies on that particular chromosome. Mapping also acts as a method in determining which gene is most likely recombine based on the distance between two genes. The distance between two genes is measured in units known as centimorgan . A centimorgan is a distance between genes for which one product of meiosis in one hundred is recombinant . DNA sequence features that satisfy this requirement are – Restriction Fragment Length Polymorphism (RFLP) – Simple Sequence Length Polymorphism (SSLP) – Single Nucleotide Polymorphism (SNP)

9. Physical mapping – Uses molecular biology techniques to examine DNA molecules directly. – Based on these techniques map construction is done. – These maps show the positions of sequence features , including genes . The most important techniques used in physical mapping are as follows: – Restriction Mapping – Fluorescent in situ Hybridization (FISH) – Sequence Tagged Site (STS) Mapping

10. There are two methods for scoring an RFLP – Southern hybridization – PCR Two types of SSLPs are- – Minisatellites (VNTRs) – Microsatellites (STRs ) Mapping of SSLPs are done by PCR There are some positions in the genome where some individuals have one nucleotide while others have another known as SNP SNPs enable very detailed genome maps to be constructed .

11. Mapping SNPS: These are mainly based on oliginucleotide hybridization analysis which includes - – DNA Chip Technology – Solution Hybridization – Oligonucleotide Ligation Assay – Amplification Refractory Mutation Assay (ARMS Test)

12. Example for mapping the difference in traits of dominant and recessive in RFLP sequence:

13. Linkage • Genetic linkage describes the way in which two genes that are located close to each other on a chromosome are often inherited together Genes on the same chromosome are said to be exhibit linkage and are called linked genes Linkage is based on crossing over frequency

14. Chromosomes are inherited as intact units, so it was reasoned that the alleles of some pairs of genes will be inherited together because they are on the same chromosome . This is the principle of genetic linkage, Pairs of genes were either inherited independently, as expected for genes in different chromosomes, or, if they showed linkage, then it was only partial linkage : sometimes they were inherited together and sometimes they were not The frequency with which the genes are unlinked by crossovers will be directly proportional to how far apart they are on their chromosome. The recombination frequencyis therefore a measure of the distance between two genes If you work out the recombination frequencies for different pairs of genes, you can construct a map of their relative positions on the chromosome

15. Two types of Linkage: Complete and incomplete linkage

16. What is linkage anlaysis ? Genetic Linkage Analysis is a power tool to detect the chromosomal locations of diseases genes Statistical method for mapping heritable trait genes to their chromosome locations Techniques of Linkage Analysis Recombination Fraction LOD score Haldane mapping function

17. Recombination Fraction Recombination fraction is a measure of the distance between two loci. Two loci that show 1% recombination are defined as being 1 centimorgan ( cM ) apart on a genetic map. 1 map unit = 1 cM ( centimorgan ) Two genes that undergo independent assortment have recombination frequency of 50 percent and are located on nonhomologous chromosomes or far apart on the same chromosome = unlinked Genes with recombination frequencies less than 50 are on the same chromosome = linked Probability of a marker and a susceptibility locus segregating independently(may be represented as θ) Ratio of the number of recombined gametes to the total number of gametes produced If θ = 0.5 No linkage If θ < 0.5 Linkage

18. LOD scores Statistical measure of the likelihood of genetic linkage between two loci Test to compare the likelihood that two loci are linked, vs. the likelihood that the two loci are unlinked LOD – logarithm of the odd LOD calculations: LOD(Z) = log10 ( probability of birth sequences with a given linkage/probability of birth sequences with no linkage) A LOD score, higher than 3.0 is generally accepted as evidence for linkage A LOD score lower than -2.0 is accepted as evidence against linkage

19. Haldane’s Mapping functions Mapping functions are used to translate recombination fractions into genetic distances A genetic map function M gives a relations i.e. r = M(d), connecting recombination fraction rand genetic map According to Haldane’s dM = -1/2ln(1-2r) where dM is the distance between marker loci , r is the recombination frequency, dM is expressed in Morgan, so r = ½(1-exp (-2dM))

20. Some of the tools for Linkage Analysis JoinMap Vitesse MAPMAKER HOMOG LOT LInkageMapView

21. THANK YOU