dna marker:

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DNA marker

Prepared byJitendra Kumar

MFK-1109Department of Fisheries Resource Management)

College of Fisheries, Mangalore

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What is molecular marker ?

DNA sequence used to mark a particular location on a particular chromosomes

genetic marker

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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

Genotype A Genotype B

Same Phenotypejitenderanduat@gmail.com

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How can molecular markers help?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

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Types of Marker by their origin

Soluble Proteins- the gene products (Isozymes / Allozymes)

DNA Marker (nDNA and mt DNA )

Mito-chondrial

DNANuclear DNA

0%50%

100%1%

99%DNA

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There are 2 main categories of DNA marker:

Type I and Type II Markers

Type I •Type I marker are the coding gene loci conserved across the species•Slightly polymorphic

Type II •Type II marker are derived mostly from non- coding sequences and are highly polymorphic•exp. Micro & Minisatellites

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Two basic types of DNA-markers

Mutations: Exp. the mutation is responsible for the change in the color of the Fish

-The most useful

- Difficult to find

Mutation = Marker

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Markers are useful in four types of measurements needed in this field:

• Identity: correct label of Animal?

• Similarity: degree of relatedness among Animal?

• Structure: is possible to identify groups of related Animal?

• Detection: posses some Animal of the collection a particular allele of a gene?

Understanding Germplasm Relationships

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Genetic 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 marker 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.

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Now a days it is being replaced by various other methods of DNA-marker like

• 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 repeat

• SNP Single nucleotide polymorphism

• STR   Short tandem repeat

• SFP   Single feature polymorphism

• DArT Diversity Arrays Technology

• RAD markers  Restriction site associated DNA markers

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They can be further categorized as dominant or co-dominant.

Dominant markers allow for analyzing many loci at

one time, e.g. RAPD.

Co-dominant markers analyze one locus at a

time.

Co-dominant markers (RFLPs, microsatellites,

etc)

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Markers: desired properties

• Highly polymorphic: able to detect many different alleles

• Highly informative; if one individual carries two different alleles we can visualize both (co-dominant)

• Easy, fast and inexpensive to screen

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Basic functions of all markers

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

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Conclusion

• To identify the stock accuracy

• To study genetic variation

• To study the phylogenetic relationship

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References

• 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

• http://www.google.co.in/imgres?q=gene+marker&hl=en&safe=active&gbv=2&biw=1280&bih=699&tbm=isch&tbnid=3O8vlSiXUk-IoM:&imgrefurl=http://medicineworld.org/news/news-archives/research-news/Oct-29-2007.html&docid=HOgYHw05OJswVM&imgurl=http://medicineworld.org/images/blogs/9-2007/gene-technology-7830.jpg&w=300&h=249&ei=KukmT9OhK4quiAe4qtjnBA&zoom=1

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