dna marker:
DESCRIPTION
What is molecular marker ? DNA sequence used to mark a particular location on a particular chromosomesTRANSCRIPT
DNA marker
Prepared byJitendra Kumar
MFK-1109Department of Fisheries Resource Management)
College of Fisheries, Mangalore
What is molecular marker ?
DNA sequence used to mark a particular location on a particular chromosomes
genetic marker
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 [email protected]
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
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
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
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
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
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.
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
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)
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
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
Conclusion
• To identify the stock accuracy
• To study genetic variation
• To study the phylogenetic relationship
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
