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BASSMAP
Tools for the genetic improvement of sea bass: Construction and preliminary application of a medium-density linkage and synteny map

Sea bass is one of the most economically important, captured and cultured marine species in Europe. Sea bass aquaculture maintains its position as one of the fastest-growing production activities in the world. From 1990 to 2001, sea bass production in the Mediterranean region grew 12.9 times and yielded 51 380 tons in 2001. However, 20 years of enlarged production of sea bass has not yet generated a single domesticated stock. A lack of genetic information strongly hampers the breeding and farming of this species towards the selective development of economically important features. There are several ways to improve the knowledge of the genetic base of this species for aquaculture. Constructing a first generation linkage and synteny map of the sea bass genome is one of them, supporting the fastest way to map and characterise genes that are responsible for commercially significant traits.


Sea bass (Dicentrarchus labrax) (Moronidae; Teleostei) is one of the most economically important, captured and cultured marine species in Europe. Sea bass aquaculture maintains its position as one of the fastest-growing production activities in the world. From 1990 to 2001 sea bass production in the Mediterranean region grew 12.9 times and yielded 51 380 tons in 2001. However, 20 years of enlarged production of sea bass has not yet generated a single domesticated stock. A lack of genetic information strongly hampers the breeding and farming of this species towards the selective development of economically important features. There are several ways to improve the knowledge of the genetic base of this species for aquaculture. Constructing a first generation linkage and synteny map of the sea bass genome is one of them, supporting the fastest way to map and characterise genes that are responsible for commercially significant traits.

Objectives
The objectives are:
1) to breed F1, meiotic gynogenetic, single and double haploid (mitotic) crosses of sea bass reference families in preparation for the mapping of type 1 and type 2 markers in order to generate a low density genetic linkage and synteny map
2) to provide DNA from the reference sea bass families, normal diploid, haploids, meiotic and mitotic gynogenetics to other mapping projects in an attempt to reduce duplication and speed up the acquisition of additional markers and genes on the map
3) to develop a partially characterised Bacterial Artificial Chromosome (BAC) library (1 000 Expressed Sequence Tags [EST] and 300+ markers identified to clones) for the long-term support of mapping and comparative genomic in this species
4) to develop and anchor a genetic linkage map using a mixed strategy including information on at least 200 dominant (Amplified Fragment Length Polymorphisms [AFLP]) markers and 200 co-dominant Short Tandem Repeat (STR), or DNA microsatellite markers
5) to develop a synteny map on the basis of ESTs for comparative mapping purposes
6) a pilot study based on the new medium-density genetic linkage map in the field of Quantitative Trait Loci (QTL): it includes the mapping of QTLs that control commercially significant traits such as sex, body length, body weight, body depth and some others.

Progress to Date
In April 2003, the following progress had been achieved.
Sixteen cross experiments were performed by employing 14 female and 10 male sea bass, and 35 different families were produced. From these, the outcrossed family F that consists of both parents and 50 F1 progeny was chosen as the reference panel to provide further mapping experiments. The samples taken serve as an RNA source for further construction of the complementary DNA (cDNA) library and isolating ESTs and as a DNA source for subsequent genotyping with polymorphic markers.
The sea bass BAC library was successfully constructed using DNA from the sperm of one of these males. The BAC clones have been reorganised as pools and superpools to provide for fast screening for suitable DNA markers by PCR.
The development of new microsatellite markers was successfully started using different enrichment and selective hybridisation protocols. Genotypes of the reference family F are being sent to the Roslin Institute for genetic linkage analysis.
Four types of cDNA libraries were generated based on total RNA preparations from the tissue of various sea bass developmental stages (embryo, larvae, juvenile and adult).
An official website of the project has been developed and activated at http://www.bassmap.org.
On a commercial farm, 58 female and 45 male sea bass were crossed to obtain reasonably large family sizes for subsequent QTL analysis.

Results
Intermediate results include the following:
1) The breeding of various types of F1 progeny was completed.
2) A BAC library consisting of 96 100 BAC clones, with a mean size of genomic DNA insertions of 150 kilobases, that corresponds to at least ten equivalents of the sea bass genome, has been constructed.
3) The development of new microsatellite markers is in progress.
4) Four types of cDNA libraries relating to different developmental stages of sea bass (embryo, larvae, juvenile and adult) were constructed.
5) An official website of the project (http://www.bassmap.org) was created. The prototype database (http://www.resspecies.org) for depositing data on pedigrees, markers and phenotypes has been developed.
6) All computing tools and software for genetic linkage analysis to generate the linkage map are accessible. The development of software for QTL analysis is almost finished.
7) A representative family sample of approximately 12 000 F1 progeny has been selected and is growing in commercial cages to provide a suitable DNA source for further QTL mapping.

Classified in FISHERIES AND AQUACULTURE

Scientist responsible for the project

Dr FILIP VOLCKAERT
Ch. de Bériotstraat 32
3000 Leuven
Belgium - BE

Phone: +32 16 323366
Fax: +32 16 324575
E-mail: filip.volckaert@bio.kuleuven.ac.be

References

Project ID QLRT-2000-01701
Organisation KATHOLIEKE UNIVERSITEIT LEUVEN
Area 5.1.2
Start date 01 November 2001
Duration (months) 48
Total cost 2 091 750 €
Total EC contribution   1 395 850 €
Status Ongoing
Web address of the project   http://www.bassmap.org

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