Molecular Tools for Aiding and Breeding of Aquaculture Species Masters in Aquaculture and Fisheries Genetic and Selection 2014 Tamara Moedas nº 47853;

Molecular Tools for Aiding and Breeding of Aquaculture Species

Masters in Aquaculture and Fisheries Genetic and Selection

2014Tamara Moedas nº 47853; Catarina Ferreira nº 35671

Molecular Tools

• Allozyme markers;

• Mitochondrial DNA markers (mtDNA);

• Restriction fragment length polymorphism (RFLP);

• Random amplified polymorphic DNA (RAPD);

• Amplified fragment length polymorphism (AFLP);

• Microsatellite markers;

• Single nucleotide polymorphism (SNP);

• Expressed sequence tags (ESTs).

Allozyme Markers

• Advantages:

o Low cost;o the rapid technique;o Ease to use;o Usually used in fishery

genetics.

• Disadvantages:

o Heterozygote deficiencies due to null alleles;

o Limited number of available allozyme loci precludes their use in large-scale genome mapping;

o Changes in DNA sequence reduce the level of detectable variation

o Are not selectively neutral.

Mitochondrial DNA Markers

• Advantages:

o High levels of polymorphism;

o It evolves much faster than coding regions of DNA;

o Multiple copies in each cell.

• Disadvantages:

o Back mutation;o Parallel substitution;o Rate heterogeneity or

mutational hot spots.

Restriction fragment length polymorphism (RFLP)

• Advantage:

o Codominant markers.

• Disadvantages:

o Low level of polymorphism;

o Low power in revealing genetic variation;

o Difficult and time-consuming to develop markers in species lacking molecular information.

Random Amplified Polymorphic DNA Markers (RAPD)

• Advantages:

o High levels of polymorphisms;

o Allows the simultaneous analysis of many loci;

o Markers are inherited in dominant fashion.

• Disadvantage:

o Special equipment.

Amplified Fragment Length Polymorphism (AFLP)

• Advantages:

o Analysis many loci simultaneously;

o Revealed polymorphisms;

o Inherited as dominant markers;

o High reproducibility.

• Disadvantage:

o Special equipment.

Microsatellite markers

• Advantages:

o Hight Abundant in all species;

o Distributed in the genome on all chromosomes;

o Loci are small;o Polymorphic;o Codominant markers.

• Disadvantage:

o Hight expensive.

Single Nucleotide Polymorphism (SNP)

• Advantages:

o Most abundant polymorphism in organism;

o Reveal hidden polymorphism;

o Co-dominant markers.

• Disadvantages:

o Requires specialized equipment;

o Large-scale analysis, depends on the availability of expensive, cutting-edge equipment.

Expressed sequence tags (ESTs)

• Advantages:

o Identify genes and analyze their expression by expression profiling;

o Rapid and at genes expressed in specific tissue types;

o Development of cDNA microarrays;

o Great value in genome mapping.

o Disadvantage:

o Identification of polymorphic ESTs is necessary for genome mapping.

Conclusions

Markers Linking Mapping

Population Studies

Maternal Linkage

Hybrid Identific

-ation

Physical Mapping

Comparati- ve

MappingPolymorph

-ism

AllozymeMarkers LOW

mtDNA

RFLP LOW

RAPD INTERMEDIATE

AFLP HIGH

Microsat-ellites

markersHIGH

SNP HIGH

EST’s LOW

Biblography• Liu, Z. J., Cordes, J. F., 2004. “DNA marker technologies and their

applications in aquaculture genetics”. Aquaculture 238, pp. 1-37;

• Magoulas, A.. “Application of molecular markers to aquaculture

and broodstock management with special emphasis on

microsatellite DNA”. CIHEM-Options Mediterraneennes, pp. 153-

168;• Chauhan,T., Rajiv, K.,2010. “Molecular markers and their

applications in fisheries and aquaculture”. University of Delhi, Delhi, India.