Genetic maps characterizing the inheritance patterns of traits and markers have been developed and utilized for a wide range of species and applications associated with studies addressing biomedical, agricultural, ecological and evolutionary questions. These applications often target the discovery of allelic variation affecting traits and have the eventual goal of identifying the exact DNA sequences underlying phenotypes [1
]. Other studies highlight differences in recombination rates between the sexes as observed in the earliest linkage maps [2
], or suggest mechanisms of chromosomal evolution through the identification of regions of conserved synteny across species. For instance, comparisons of conserved synteny and conserved gene orders have been conducted extensively within the vertebrates [5
]. Whole genome sequences have enabled comparative genomic studies which employ computational approaches [9
], including the identification of functional elements [10
]. As a result, one additional goal for mapping in species not having access to a whole genome reference sequence is to develop high-density comparative maps with whole genome sequences of related species. This may be accomplished through genetic, cytogenetic, radiation hybrid, bacterial artificial chromosome (BAC), and integrated mapping approaches [12
]. These maps not only enable the use of information across species, but may be used within a species to aid whole genome sequence assembly [17
The construction of genetic maps for many species begins by genotyping reference families with markers such as microsatellites [18
] which were initially developed for population genetic analyses. Microsatellites are often the marker of choice as they exhibit co-dominant inheritance, have high degrees of heterozygosity, are widely distributed throughout the genome, and may provide comparative information between closely related species[19
]. When associated with a gene, these markers can provide comparative information across a great diversity of taxa. The limiting factors of microsatellites for map construction are the time and resources required for marker development and genotyping. Alternatively, amplified fragment length polymorphisms (AFLPs) [20
] and random amplified polymorphic DNAs (RAPDs) [21
] markers are inexpensive to develop and are conducive to high throughput genotyping protocols. Although large numbers of loci can be mapped rather inexpensively in a short amount of time, these markers are not associated with unique sequences and are specific to each mapping population. These efforts result in first generation linkage maps containing hundreds of markers which represent much of the genome with a low resolution of microsatellites [22
]. As additional markers become available, including those associated with candidate genes, second generation maps containing several hundred to over one thousand markers spanning the entire genome at higher resolutions are constructed [29
]. The ultimate genetic maps have sub-centiMorgan (cM) resolution and include anywhere from thousands to millions of markers [39
]. Currently, high-density mapping efforts for human, model organism, and agriculturally important species with whole genome sequences are using single nucleotide polymorphism (SNP) [42
] markers. Similar to microsatellites, SNPs are abundant, widely distributed throughout the genome, and are associated with a unique sequence. Although SNPs are amenable to genotyping with high-throughput protocols, they are less polymorphic and will require large numbers of crosses for mapping.
The status of rainbow trout genetic maps has progressed significantly over the last decade due to interest in their economic impacts as an aquaculture species and on sport fisheries, and as a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition [43
]. Rainbow trout have a genome size estimated to be 2.4 × 109
]. While the karyotype of this species varies from 2 N = 58–64, the number of chromosome arms is conserved at 104. An evolutionarily recent whole genome duplication event is estimated to have occurred 25–100 mya [45
], and the genome is estimated to be 1/3 of the way along the process of re-diploidization, [46
]. Several laboratories have constructed genetic maps including AFLPs, microsatellites, and SNPs to identify quantitative trait loci (QTL) affecting time to hatch, development rate, growth, thermal tolerance, natural killer cell-like activity, albinism and disease resistance [47
]. The first genetic map based on molecular markers was constructed by Young et al
] who observed the inheritance of 476 loci (332 AFLPs) on 76 doubled haploid fish. The resulting map contained 31 large linkage groups and spanned a total of 2627.5 cM. In 2000, Sakamoto et al
] mapped 208 loci (191 microsatellites) to 29 linkage groups by genotyping 186 fish from 3 backcross families. This effort revealed large recombination rate differences between the sexes (3.25:1 female to male) and a female map length over 1000 cM Morgans which is an underestimation as acknowledged by the authors. In 2003, Nichols et al
] added to the map of Young et al
], ordering 1359 loci consisting primarily of 973 AFLPs and 226 microsatellites, and forming 30 large linkage groups with a map length of 4590 cM. Most recently, Guyomard et al.
] used 120 offspring from two doubled haploid mitogynogenetic families to map 903 microsatellite loci with a map length of 2750 cM. Concurrently, Phillips et al
] integrated the cytogenetic and genetic maps by assigning linkage groups from Nichols et al
] to specific chromosomes of the OSU doubled haploid line. Using microsatellites as comparative loci between salmonids, Danzmann et al.
] added genetic markers to the map of Sakamoto et al
], reporting homeologous chromosome arm assignments within species resulting from the genome duplication event and pairwise homologous assignments between rainbow trout, artic char and Atlantic salmon.
In an effort to support the selective breeding of rainbow trout for aquaculture production efficiency, we constructed a genetic map to identify QTL affecting important traits and facilitate positional candidate cloning [63
]. Most of the markers mapped were anonymous microsatellites from random enriched libraries, but our focus was to add markers with comparative information between the trout genome and other salmonids, and with the genome sequences of model fish species. By genotyping 30 offspring from each of 5 outbred families related to our broodstock germplasm, 1124 loci were ordered into 29 linkage groups representing each chromosome. This allowed for the observation of differences in recombination rate between the sexes and the creation of comparative maps. Anchoring of EST sequence on the genome sequences of other fishes has enabled the construction of comparative maps to facilitate genome research in regions of interest. The development and mapping of a large number of microsatellite loci will facilitate genome mapping efforts in rainbow trout and other salmonids.