Rainbow trout (Oncorhynchus mykiss) are the most-widely cultivated cold freshwater fish in the world and are considered by many to be the "aquatic lab-rat". Interests in the utilization of rainbow trout as a model species for genome-related research activities focusing on carcinogenesis, toxicology, comparative immunology, disease ecology, physiology, transgenics, evolutionary genetics, and nutrition have been well documented . Rainbow trout are cultured on every continent except Antarctica, with 2008 global production estimated at 576,289 metric tons and valued at $2.39 billion . Coupling great interest in this species as a research model with the need for genetic improvement for aquaculture production efficiency and product quality justifies the continued development of genome resources facilitating selective breeding.
The rainbow trout genome is large and complex. Genome size estimates derived from determining the molecular weight of DNA per cell for rainbow trout and other salmonids vary from 2.4 to 3.0 × 109 bp [3, 4]. As with most salmonids, rainbow trout experienced a recent genome duplication event resulting in a semi-tetraploid state (i.e. after an autotetraploid event in the salmonids, their genome is undergoing reversion to a diploid state) . All ray-finned fishes share an additional (3R) round of ancestral genome duplication in their evolutionary history compared to mammals and birds, but the salmonids' common ancestor underwent an additional recent (4R) whole genome duplication event and more than half of the loci are still duplicated . In addition, it is estimated that 50% to 60% of the rainbow trout genome contains interspersed repeat sequences (Genet et al.: Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes, submitted).
Current genomic resources available for rainbow trout research include multiple bacterial artificial chromosome (BAC) libraries and a BAC fingerprinting physical map [6–8]; a database of ~200,000 BAC end sequences (BES) (Genet et al.: Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes, submitted); doubled haploid (DH) clonal lines [9–12]; multiple genetic maps based on clonal lines and outbred populations [4, 13–16]; large expressed sequence tag (EST) databases and a reference transcriptome [17–19]; a microRNAs database  and high density DNA microarrays [21, 22].
Two microsatellite-based genetic maps with medium to high marker densities were recently developed for rainbow trout by INRA  and the NCCCWA . The INRA map is based on a panel of two DH gynogenetic lines. It has more than 900 microsatellites over 31 linkage groups and a total length of 2,750 cM (average resolution of 3 cM). The NCCCWA map is based on a panel of five families that represent the starting genetic material of the NCCCWA selective breeding program. It has 1,124 microsatellite loci over 29 linkage groups and a total length of 2,927 cM (average resolution of 2.6 cM). The linkage groups from the two microsatellite genetic maps were anchored to the physical chromosomes using fluorescent in-situ hybridization and were found to represent 52 chromosome arms [23, 24].
Qualitative/quantitative trait loci (QTL) mapping experiments in rainbow trout have been very successful because of their high fecundity, external fertilization, and ease of gamete handling and manipulation. Many QTL have been identified for production and life-history traits including resistance to the parasite C. shasta , resistance to IHNV [26, 27] and to IPNV , whirling disease resistance , Killer cell-like activity , upper thermal tolerance [31, 32], embryonic development rate [9, 33, 34], spawning time [35, 36], confinement stress response , early maturation  and smoltification . The availability of a BAC physical map integrated with the genetic map will facilitate fine mapping of QTL, the selection of positional candidate genes and the incorporation of marker-assisted selection (MAS) into rainbow trout breeding programs. A major shortcoming of QTL studies is that they are limited to the variation present in a limited number of families and typically do not detect loci with small effects. This can be overcome by whole genome association studies and other approaches, such as genomic selection, that capture the effects of most QTL that contribute to the population-wide variation in a trait. Recently we demonstrated the feasibility of low resolution LD association studies in rainbow trout [40, 41]. In the absence of a reference genome sequence assembly, a robust integrated physical and genetic map will provide better resolution than the current genetic maps for ordering of genetic markers and estimating physical distances between markers, thus facilitating future whole genome association studies in rainbow trout.
The first BAC-based physical map of the rainbow trout genome was recently assembled using DNA fingerprints of 154,439 clones from the 10X HindIII Swanson library . The map contains 4,173 contigs and 9,379 singletons. The physical length of the map contigs was estimated to be approximately 2.0 Gb, which represents approximately 80% of rainbow trout genome. Here we report the construction of the first integrated physical and genetic map of the rainbow trout genome using microsatellites isolated from BAC end sequences and PCR superpools for library screening and identification of BACs that harbor previously mapped markers. This integrated map provides a frame work for a robust composite genome map and future reference genome sequence assemblies.