Genetic mapping in Atlantic salmon (Salmo salar) and brown trout (Salmo trutta)

McGowan, Colin (1996) Genetic mapping in Atlantic salmon (Salmo salar) and brown trout (Salmo trutta). Doctoral (PhD) thesis, Memorial University of Newfoundland.

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Abstract

Segregation analysis of polymorphic genetic markers was performed using the hybrid progeny of a brown trout (Salmo trutta) x Atlantic salmon (Salmo salar) cross. Three types of genetic markers, 1) RAPDs (randomly amplified polymorphic DNA), 2) microsatellites and 3) ESTs (expressed sequence tags) were examined. -- 1) Of the 271 random primers tested, 151 (56%) generated distinct, reproducible band patterns. A total 893 loci were scored, of which 126 could be attributed to the Atlantic salmon component of the genome and 173 to that of the brown trout. The majority (594) of loci were held in common by both parents. Three and 13 heterozygous loci were identified in the Atlantic salmon and brown trout parents, respectively. All of the markers segregated in a normal (1:1) manner. No linkage was observed in Atlantic salmon. Thirteen significant (P<0.05) pair-wise associations were identified in brown trout, five of which were highly significant (P<0.001). -- The RAPD procedure was also used for bulked segregant analysis of Atlantic salmon male and female DNA, to search for a sex-specific marker. A total of 1152 loci were screened using 200 different primers; however none were tightly linked to a male sex determining factor. -- 2) Two hybrid families were screened for polymorphisms at 14 microsatellite loci which have been described in previous studies. Seven and eight heterozygous markers were identified in the Atlantic salmon and brown trout parents, respectively. Segregation ratios of variant alleles in the hybrid offspring, were normal (1:1) in all but one case. In brown trout, seven significant (P<0.05) linkages were detected among microsatellite and RAPD loci, three of which were highly significant (P<0.001). In Atlantic salmon, five significant (P<0.05) linkages were identified, three of which were highly significant (P<0.001). Of three tightly linked microsatellite pairs identified in Atlantic salmon, only two are conserved in brown trout. -- 3) The partial sequences of 41 ESTs, isolated from two cDNA libraries, were submitted, by e-mail, for comparison with entries in the EMBL and GenBank data bases. Twenty of the sequences were similar to genes of known protein function, 12 of which were used as probes to search for RFLPs in the genomic DNA of Atlantic salmon and brown trout parents. Five different probes detected RFLPs, but multiple banding patterns were difficult to interpret. Variant alleles at a locus detected with the fibrinogen EST segregated normally (1:1) in hybrid offspring. Linkage was not observed between the fibrinogen marker and any of the microsatellite or RAPD loci. -- Three and six, highly significant (P<0.001), new linkage groups are reported for Atlantic salmon and brown trout, respectively. Linkage analysis using the hybrid offspring of these two species has been a success, however, faster gains may result from more extensive outbreeding prior to hybridization.

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