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Generation of highly informative DNA markers and genetic marker maps of Salmonid fishes - SALMAP


Production and characterisation of highly informative DNA markers with particular stress on micro-satellites in Atlantic salmon (Salmo salar), rainbow trout (Oncorhyncits mykiss) and brown trout (Salmo trlitta). Run characterised markers through reference families, some of which also are typed for alloenzymes, to provide recombination data for linkage analysis. Typing of traditional, diploid pedigrees will allow for sex linkage analysis. Carry out genetic linkage analysis and construct species-specific low-resolution genetic maps, embracing mostly anonymous markers but also enzyme loci (rainbow trout). Depending on the success rate of cross-reacting markers and the degree of inter-specific conservation of marker linkage groups: identify anchor loci in a comparative Salmonid map.
State of progress

At the end of the first reporting period of the project the state of progress is as follows:

Atlantic salmon: 278 (256 from Atlantic salmon + 22 from rainbow trout) micro-satellite loci have been identified and partially characterised and so far 55 (38 from Atlantic salmon + 17 from rainbow trout) have been fully characterised. No markers have been genotyped in the reference families since these will be slaughtered in month 14 and DNA made available in month 15 or 16.

Rainbow trout: 172 (155 from rainbow trout + 17 from Atlantic salmon) micro-satellite loci have been identified and 124 (116 from rainbow trout + 8 from Atlantic salmon) have been fully characterised. 108 micro-satellite loci and 6 RAPDs have been genotyped in reference families resulting in the identification of 20 linkage groups by the Canadian group and 2 linkage groups were identified by the French group.

Brown trout: 89 micro-satellite loci from rainbow trout (50) and Atlantic salmon (39) have been identified and 63 micro-satellite loci have been fully characterised (41 from rainbow trout + 22 from Atlantic salmon). 15 have been genotyped in reference families resulting in the identification of 3 linkage groups.


Within the first 12 months of this project, 430 micro-satellite PCR assays have been described for salmonids - this represents one of the largest such data base generated to date. In isolating these micro-satellites, several experimental approaches have been tested. Screening of a range of fragment lengths has identified an optimal insert length of 300-500 bp for PCR amenable micro-satellite typing. Micro-satellite library enrichment protocols have been successfully employed for several of the libraries developed. Finally, the first micro-satellite-based linkage groups have been described for rainbow and brown trout.

Future actions

Research will continue towards the genetic mapping of the three salmonid species as outlined in the work program. Work will concentrate on describing the first micro-satellite based linkage groups in Atlantic salmon, exploiting markers generated within the project as well as those published elsewhere. In a similar manner the existing linkage groups for brown and rainbow trout will be further developed. Successful completion of this work will result in low-resolution genome maps suitable for future QTL exploitation and bloodstock management.
Description of work

The SALMAP consortium will isolate and characterise highly informative DNA markers using standard molecular genetics methods (e.g. Screening genomic libraries for micro-satellite positive clones, DNA sequencing, PCR analysis) from three species of salmonid fish: Atlantic salmon, Rainbow trout and Brown trout. Major efforts will be placed on the isolation, sequencing and characterisation of micro-satellite markers, predominantly of the dinucleotide repeat type. Tri- and tetranucleotide repeat micro-satellites will also to some extent be isolated. Segregation studies, using PCR and electrophoretic techniques, of these markers in appropriate reference families will be carried out. Subsequent linkage analysis of the segregation data, using contemporary and consensus computer programs, will enable the construction of species specific linkage maps and possible salmonid comparative maps.


Ullevaalsveien 72
0033 Oslo

Participants (5)

Danish Institute of Animal Science
Blichers Alle
8830 Tjele
Institut National de Recherche Agronomique
Domaine De Vilvert
78352 Jouy-en-josas
University Road
90 Galway
University of Guelph
Department Of Zoology
N1G 2W1 Guelph, Ontario
University of Stirling
United Kingdom

FK9 4LA Stirling