A COMPARATIVE ANALYSIS OF THE RAINBOW TROUT GENOME WITH TWO OTHER SPECIES OF FISH (ARCTIC CHARR AND ATLANTIC SALMON) WITHIN THE TETRAPLOID DERIVATIVE SALOMIDAE FAMILY (SUBFAMILY: SALMONINAE)

Authors: DANZMANN, RG - UNIVERSITY OF GUELPH; CAIRNEY, M - UNIVERSITY OF STIRLING; FERGUSON, MM - UNIVERSITY OF GUELPH; GHARBI, K - UNIVERSITY OF GUELPH; GUYOMARD, R - INRA; HOLM, L - DANISH INST OF AGRICULTUR; HOYHEIM, B - NORWEGIAN SCHOOL OF VET; Leder, Erica; OKAMOTO, N - INSTITUTE FOR RES AND INN; OZAKI, A - INST FOR RES AND INNOVA; Rexroad, Caird; SAKOMOTO, T - INST FOR RESEARCH ANDINNO; TAGGART, JB - UNIVERSITY OF STIRLING; WORAM, RA - UNIVERSITY OF GUELPH

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/20/2005
Publication Date: 12/1/2005
Citation: Danzmann, R., Cairney, M., Ferguson, M., Gharbi, K., Guyomard, R., Holm, L., Hoyheim, B., Leder, E.H., Okamoto, N., Ozaki, A., Rexroad III, C.E., Sakomoto, T., Taggart, J., Woram, R. 2005. A comparative analysis of the rainbow trout genome with two other species of fish (arctic charr and atlantic salmon) within the tetraploid derivative salomidae family (subfamily: salmoninae). Genome 2005 Dec;48(6):1037-51.

Interpretive Summary: Genetic improvement strategies aimed at increasing production efficiencies for agriculturally important species are enhanced by the use of molecular genetic technologies. DNA markers are being used to identify genes affecting production traits through genetic mapping and to characterize the genetic makeup of broodstock populations. The evolutionarily recent divergence of the salmonids presents the opportunity to use molecular technologies developed for one of these species in the others. We report the use of microsatellite markers to integrate the genetic maps of three salmonids important to aquaculture: rainbow trout, Atlantic salmon, and Artic char. This information will aid breeders in the use of DNA marker information between species and support selective breeding schemes for aquaculture production.

Technical Abstract: We updated the genetic map of rainbow trout (Oncorhynchus mykiss) for two outcrossed mapping panels, and used this map to assess the putative chromosome structure, and recombination rate differences among linkage groups. We then used the rainbow trout sex specific maps to make comparisons with two other ancestrally polyploid species of salmonid fishes, Arctic charr (Salvelinus alpinus), and Atlantic salmon (Salmo salar), to: identify homeologous chromosome affinities within each species and ascertain homologous chromosome relationships among the species. Salmonid fishes exhibit a wide range of sex-specific differences in recombination rate with some species having the largest differences for any vertebrate species studied to date. Our current estimate of female : male recombination rates in rainbow trout is 4.31 : 1. Chromosome structure and/or size is associated with recombination rate differences between the sexes in rainbow trout. Linkage groups derived from presumptive acrocentric type chromosomes were observed to have much lower sex-specific differences in recombination rate than metacentric type linkage groups. Arctic charr is karyotypically the least derived species (i.e. possessing a high number of acrocentric chromosomes) and Atlantic salmon is the most derived (i.e. possessing a number of whole-arm fusions). Atlantic salmon have the largest female : male recombination ratio difference (i.e. 16.81 : 1) in comparison to rainbow trout, and Arctic charr (1.69 : 1). Comparisons of recombination rates between homologous segments of linkage groups among species indicated that when significant experiment-wise differences were detected (7 / 24 tests), recombination rates were generally higher in the species with a less derived chromosome structure (6 / 7 significant comparisons). Greater similarity in linkage group syntenies were observed between Atlantic salmon and rainbow trout suggesting their closer phylogenetic affinities, and most interspecific linkage group comparisons support a model that suggests whole chromosome arm translocations have occurred in the evolution of this group. However, some possible exceptions were detected and these findings are discussed in relation to their influence on segregation distortion patterns. We also report unusual meiotic segregation patterns in a female parent involving the duplicated (homeologous) linkage group pair 12/16 and discuss several models that may account for these patterns.