title: A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae).
abstract: We updated the genetic map of rainbow trout (Oncorhynchus mykiss) for 2 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 2 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) compared with 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.
authors.affiliation: Department of Integrative Biology, University of Guelph, ON, Canada. rdanzman@uoguelph.ca
authors.forename: Roy G
authors.initials: RG
authors.lastname: Danzmann
authors.forename: Margaret
authors.initials: M
authors.lastname: Cairney
authors.forename: William S
authors.initials: WS
authors.lastname: Davidson
authors.forename: Moira M
authors.initials: MM
authors.lastname: Ferguson
authors.forename: Karim
authors.initials: K
authors.lastname: Gharbi
authors.forename: Rene
authors.initials: R
authors.lastname: Guyomard
authors.forename: Lars-Erik
authors.initials: LE
authors.lastname: Holm
authors.forename: Erica
authors.initials: E
authors.lastname: Leder
authors.forename: Nobuaki
authors.initials: N
authors.lastname: Okamoto
authors.forename: Akiyuki
authors.initials: A
authors.lastname: Ozaki
authors.forename: Caird E
authors.initials: CE
authors.lastname: Rexroad
authors.forename: Takashi
authors.initials: T
authors.lastname: Sakamoto
authors.forename: John B
authors.initials: JB
authors.lastname: Taggart
authors.forename: Rachael A
authors.initials: RA
authors.lastname: Woram
mesh_terms: D000818:Animals; D020090:Chromosome Segregation; D005260:Female; D016678:Genome; D008297:Male; D017686:Oncorhynchus mykiss / Q000235:genetics*; D011123:Polyploidy; D011995:Recombination, Genetic; D020317:Salmo salar / Q000235:genetics*; D017422:Sequence Analysis, DNA