Influence of immune-relevant genotype on the reproductive success of a salmonid alternative mating strategy.

Major histocompatibility complex (MHC) and immune-relevant gene markers were used to evaluate differences in reproductive success (RS) among naturally spawning coho salmon Oncorhynchus kisutch mate pairs involving an alternative male reproductive phenotype, known as jacks. These mate pairs included both hatchery-reared and wild origin fish such that three classes were evaluated in two consecutive years (2005 and 2006) using a previously constructed multigenerational genetic pedigree: wild × wild (W × W), hatchery × hatchery (H × H) and wild × hatchery (W × H). Oncorhynchus kisutch jack mate pairs mated randomly based on immune-relevant genotype in both years; a result consistent with the opportunistic mating strategy of jacks. An association between greater number of alleles shared at three immune-relevant gene markers and increased RS was found for: W × H mate pairs in 2005 (BHMS429), W × H pairs in 2006 (SsalR016TKU) and W × W pairs in 2006 (OMM3085). No correlation between immune gene diversity and RS was found for H × H pairs in either year. The results suggest that the influence of immune-relevant genotype on mating success may be different for jacks when compared with previous studies of large adult male O. kisutch.

Duplicated Clock genes with unique polyglutamine domains provide evidence for nonhomologous recombination in Chinook salmon (Oncorhynchus tshawytscha).

Circadian rhythms underlie diverse life functions ranging from cellular activities to behavior. Multiple clock genes play a central role in the generation of these rhythms. We partially characterized two copies of the Clock gene from Chinook salmon (Oncorhynchus tshawytscha), OtsClock1a and OtsClock1b. The 6,460 bp OtsClock1a sequence contains 16 exons, 15 introns and encompasses three highly conserved domains indicating it is a novel member of the bHLH-PAS superfamily of transcription factors. The second copy, OtsClock1b, consists of five exons and five introns spanning 1,945 bp. A polyglutamine repeat motif (PolyQ), characteristic of a majority of CLOCK proteins, is present in both OTSCLOCK1a and OTSCLOCK1b. However, the Chinook PolyQ domains are uniquely positioned inside the gene. Interestingly, a 1,200 bp non-coding segment located downstream of the OtsClock1a PolyQ domain is absent from OtsClock1b. This insertion/deletion is 91% similar to the Salmo salar Transferrin gene. A phylogenetic analysis of 11 CLOCK proteins shows that OtsClock1a and OtsClock1b are paralogs which likely arose subsequent to the salmonid genome-wide duplication event. Ultimately, the Chinook salmon Clock genes are key components to our understanding the genetic mechanisms underlying temporally regulated life history traits in Pacific salmonids.

Quantitative trait loci for spawning date and body weight in rainbow trout: testing for conserved effects across ancestrally duplicated chromosomes.

We incorporated 69 microsatellite loci into an existing data set of 132 markers to test for quantitative trait loci (QTLs) affecting spawning date and body weight in a backcross between two outbred strains of rainbow trout (Oncorhynchus mykiss). Twenty-six linkage groups were identified and synteny of duplicated microsatellite markers was used to confirm 13 homeologous chromosome pairs. Gene-centromere data were used to localize the centromeres for 13 linkage groups whose orientations were previously unknown. We applied a combination of interval mapping and single marker analysis to the segregating maternal and paternal alleles at 201 microsatellite loci. Four spawning date QTLs with suggestive evidence for an additional two QTLs were detected in female trout spawning at 3 and 4 years of age. Similarly we detected three QTLs for body weight in females at 2 years of age plus four suggestive QTLs for this trait. We found marginal evidence that three pairs of ancestral homeologues contained detectable QTLs for the same trait. In one of the three pairs of homeologues, the duplicated QTL regions mapped to the same relative chromosomal location, while the exact localization of the QTL position in one of the other pairs was difficult to infer since it was based on data from a male-derived map. The existing data were unable to refute a hypothesis that duplicated functional genes will be maintained within the telomeric regions of salmonids due to preferential male-mediated crossing over in this region. Two of the four spawning date QTLs were detected on linkage groups with unknown homeologous relationships. QTLs with possible pleiotropic effects on both spawning date and body size were localized to two linkage groups.