DNA Marker

Seminar topic about DNA Markers

1. DNA Marker Presented by Satyaveer (Department of Fisheries Resource Management) College of Fisheries Mangalore

2. Marker Biochemical Molecular Morphological Based on Hybridization Based on PCR Protein banding pattern Isozyme

3. These are related to shape, size , colour and surface of various plants parts . Such characters used for the varietal identification. Advantages Readily available Usually require only simple equipment From the most direct measure of phenotype Disadvantage Require expertise on crop or species Subject to environmental influences Limited in number 1- Morphological markers

4. Such markers are related to the variation in protein and amino acid banding pattern. Gel Electrophoretic studies used for identification of biochemical markers. E.g.- Peroxidase , Acid Phosphatic , Esterase etc. Advantages : Require simple equipment A vigorous complement to the morphological assessment of variation. Disadvantages: Subjected to environment influences Limited in number 2. Protein (biochemical) Markers

5. DNA Sequence used to mark a particular location on a particular chromosomes. Molecular marker are polymorphic DNA or protein sequences that can be used to identify a chromosomal region. Two type of maker based on their origin 1- soluble protein (the gene products Isozymes / Allozymes ). 2- DNA Marker used for genetic stock identification and for resolving taxonomic ambiguity in fisheries. 3. Molecular Marker

6. Identity Correct label of animals. Similarity Degree of relatedness among animals. Structure Is possible to identify groups of related animals. Detection Possess some animal of the collection of particular allele of gene. Marker are useful in 4 types of measurement

7. Molecular markers allow working with genotype information directly. Analyze the effect of the genotype on the phenotype. Provide the breeder a tool to look into the ‘black box’ of the genotype. How can molecular markers help

8. The first priority for such research is the identification of genetic marker. Expertise has been developed for various classes of molecular markers, namely protein ( allozymes )and DNA Marker. In ichthyotaxonomy, DNA based molecular marker( Genetic Marker) plays an important role to identify the phylogenic trends of evolution. It can be described as a variation( which may arise due to mutation or alteration in the genomic loci) that can be observed. A genetic makers may be a short DNA sequence, such as a sequence surrounding a single base – pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites . Genetic Markers

9. “The green section indicates the presence of a desirable gene in an organism’ genetic code that associated with two genetic markers (red flags). Conti……..

10. DNA Marker The DNA marker s are based on polymorphism, detected at DNA level. Hence these are called as nuclear DNA markers or polymorphic DNA markers. Polymorphic DNA markers which can identification and analysis of new loci or gene in the genome (Chromosome).

11. DNA Markers = Direct reflection of genotype Two fish can display similar phenotypes, but be very different from a genetic point of view. e.g. Given fish genotypes with similar yield. In each genotype different genomic regions can be responsible for the high yield potential.

12. There are 2 main categories of Nuclear DNA Marker: Type I and type II Marker NBFGR ( Lucknow ) CMFRI (Kochi) CIFA ( Bhubaneshwar ) NIO (Goa) are the leading institution in India carrying out research in this field.

13. Minisatellites Microsatellites Random amplified polymorphic DNA(RAPD) Amplified fragment length polymorphism (AFLP) Single nucleotide polymorphism(SNP) Internal transcribed spacers(ITS) Mitochondria DNA (which in maternally inherited, Circular with genes in the 16-18 kilo base pair). Type II Markers are:-

14. Mutation : exp. The mutation is responsible for the change in the color of the fish. Basic type of DNA markers

15. RFLP Restriction fragment length polymorphism SSLP Simple sequence length polymorphism AFLP Amplified fragment length polymorphism RAPD Random amplification of polymorphic DNA VNTR Variable number tandem rep eat SNP Single nucleotide polymorphism STR Short tandem repeat SFP Single feature polymorphism DArT Diversity Arrays Technology RAD marker Restriction site associated DNA marker Now a days it is being replaced by various other method of DNA- marker like

16. Dominant markers allow for analyzing many loci at one time, e.g. RAPD Co- dominant markers analyze one locus at a time CO-dominant marker (RFLPs, Microsatellites,etc) They can be further categorized as dominant or co- dominant

17. Highly polymorphic – able to detect many different alleles. Highly informative – if one individual carries two different alleles we can visualize both. Easy, fast & inexpensive to screen. Easy availability. High reproducibility. Easy exchange of data between laboratories. Frequent occurrence in genome. Properties of marker

18. Genetic markers can be used to study the relationship between an inherited disease and its genetic cause. Genetic Markers have also been used to measure the genomic response to selection in livestock. Identify the phylogenetic relationship between the different species of fishes. Monitoring of inbreeding or other changes in the genetic composition of the stocks. Comparisons between hatchery and wild stocks. Basic function of all marker

19. Polymorphism information content (PIC) is the most important characteristics of a marker. From the allelic frequencies, the variability in the population can be assessed. A PIC value greater than 0.5 is considered highly informative, o.25-0.5 is reasonably informative and <0.25 is slightly informative other method such as Restriction endonuclease (RE) banding and fluorescent in situ hybridization (FISH) techniques are used for identification of fish population stock, species and sex chromosome in fish. Characteristics of Marker

20. To identify the stock accuracy To study genetic variation To study the phylogenetic relationship Conclusion

21. Ibrahim Okumus and Y. Çiftci / Turk. Turkish Journal of Fisheries and Aquatic Sciences 3: 51-79 (2003) ARIAGNA LARA,* JOSE LUIS PONCE DE, Molecular Ecology Resources (2010) 10, 421–430 Handbook of fisheries and Aquaculture, 2006 www.google.co.in/dnamarker/wikipedia/in MOLECULAR MARKERS IN ANIMAL GENOME ANALYSIS, Biotechnology in Animal Husbandry 25 (5-6), p 1267-1284, 2009 URL: http://www.jove.com/index/Details.stp?ID=1871 http:// www.ars.usda.gov/research/docs.htm?docid=7203&pf=1&cg_id=0 References