BACKGROUND
rainbow trout  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  <cit> .
coupling great interest in this species as a research model with the need for genetic improvement for aquaculture justifies the continued development of genome resources facilitating selective breeding.
genome size estimates derived from molecular weight of dna per cell for rainbow trout and other salmonids vary from  <dig>  to  <dig>  ×  <dig> bp  <cit> .
as with most salmonids, rainbow trout experienced a recent genome duplication event resulting in a semi-tetraploid state  <cit> .
our physical mapping experience with bacs from the swanson library has demonstrated that duplicated loci can be detected by dna fingerprinting  <cit> .
additionally, bacs that represent one of two duplicated loci were shown by fluorescent in-situ hybridization  to distinctly hybridize to a specific chromosome pair  <cit> .
therefore, it is likely that the vast majority of the duplicated loci contain enough sequence variation to allow correct assembly of a physical map using bac dna fingerprinting.
current genomic resources available for rainbow trout research include multiple bacterial artificial chromosome  libraries  <cit> ; doubled haploid  clonal lines  <cit> ; genetic maps  <cit> ; a large est database  <cit> ; and dna microarrays  <cit> .
seven rainbow trout bac libraries were constructed to date.
two libraries constructed in japan  <cit>  contain average insert sizes of  <dig> kb and  <dig> kb, and provide haploid genome coverages of  <dig>  fold and  <dig>  fold, respectively.
however, they have not been arrayed in plates and library screening tools are not available.
one bac library from the swanson male homozygous line and one from the osu female homozygous line were commercially constructed by amplicon express inc. in  <dig>  both libraries were prepared from partial digestions with hindiii.
the osu bac library has  <dig>  clones with an average insert size of  <dig> kb .
the swanson bac library has  <dig>  clones with an average insert size of  <dig> kb .
hindiii bac dna fingerprinting for local physical mapping of  <dig> type-i markers in the swanson library demonstrated the library's utility for identifying duplicated loci and confirmed its 10× coverage  <cit> .
both libraries have been used for genomic sequencing and genetic mapping of loci of interest  <cit> .
an additional 5× genome coverage swanson dh yy male library  was constructed at the children's hospital oakland research institute  in  <dig> using ecori partial digestion of genomic dna with an estimated average insert size of  <dig> kb.
an additional two new libraries were prepared by amplicon express in  <dig>  the two new 5× genome coverage swanson dh yy male libraries  were prepared using bamhi and ecori partial genomic digestion to complement the 10x hindiii swanson library and have estimated insert sizes of  <dig> kb.
the four swanson dh yy male libraries described above were prepared using genomic dna from the same swanson doubled-haploid clonal line that is propagated and maintained at the lab of gary thorgaard in washington state university.
two genetic maps with improved marker densities were recently developed for rainbow trout by inra  <cit>  and the ncccwa  <cit> .
the inra map is based on a panel of two dh gynogenetic lines.
it has more than  <dig> microsatellites over  <dig> linkage groups and a total length of  <dig>  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  <dig>  microsatellite loci over  <dig> linkage groups and a total length of  <dig>  cm .
the rainbow trout haploid karyotype is composed of  <dig> chromosome arms, but chromosome numbers can vary among rainbow trout populations in concordance with their native geographic distribution  <cit> .
therefore, anchoring the genetic linkage groups to the physical chromosome arms was a crucial task accomplished by phillips et al.
<cit>  using bacs as fish probes.
the range of the haploid chromosome number  is between  <dig> and  <dig>  <cit> .
the karyotype of the swanson dh line is composed of 2n =  <dig>  <cit> .
the offspring of "hybrids" between strains with different chromosome number are viable and they can be used for genetic mapping as two uni-armed  chromosomes from the parent with 2n =  <dig> will align with a di-armed  chromosome from the parent with 2n =  <dig>  a comparative cytogenetic map of the rainbow trout and atlantic salmon using fish with bacs that harbor type-i markers and microsatellites is being developed in a coordinated effort  <cit> .
this cytogenetic map and the comparative genetic map of danzmann et al.
<cit>  provide a frame-work for future high resolution trout-salmon comparative genome maps.
qualitative/quantitative trait loci  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  <cit> , resistance to ihnv  <cit>  and to ipnv  <cit> , killer cell-like activity  <cit> , upper thermal tolerance  <cit> , embryonic developmental rate  <cit> , spawning time  <cit> , confinement stress response  <cit>  and smoltification  <cit> .
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  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 effect.
this can be overcome by whole genome association studies and other approaches that capture effects of most qtl that contribute to the population-wide variation in a trait such as genomic selection.
recently we demonstrated the feasibility of low resolution ld association studies in rainbow trout  <cit> .
in the absence of whole genome sequence assembly, the robust integrated physical and genetic map that we aim to construct will provide better resolution than the current genetic maps for ordering of genetic markers and estimating physical distances between markers, thus facilitating whole genome association studies rainbow trout.
several bac-based physical maps were constructed in recent years for economically important aquaculture species including tilapia  <cit> , atlantic salmon  <cit>  and catfish  <cit> .
here we report the construction of the first physical map of the rainbow trout genome using a 10× genome coverage bac library derived from the swanson dh clonal line.
RESULTS
bac fingerprinting and contigs assembly
we used the 4-color high-information-content fingerprinting  snapshot method of luo et al.
<cit>  to fingerprint all the clones from the 10x hindiii bac library  and  <dig>  clones from the chori- <dig> 5x ecori library.
after editing with fpminer software  82% bac fingerprints from the 10x library and 50% from the chori- <dig> library were assembled into physical contigs using fpc software  with a tolerance of  <dig>  bp and an initial cutoff of  <dig> e- <dig> , followed by dqer and several rounds of end-to-end merging and single-to-end merging at progressively lower cutoff stringencies.
the current version of the map is composed of  <dig>  clones of which  <dig>  are assembled into  <dig>  contigs and  <dig>  remained singletons .
the average number of bacs per contig is  <dig> , and the distribution of the number of bacs per contig is shown in figure  <dig>  the average number of fingerprinting fragments per bac is  <dig> , and the average insert size for this library is  <dig> kb  <cit> .
therefore, each fragment is estimated on average to represent  <dig>  kb of genome dna.
the total number of unique fingerprinting fragments  in contigs is  <dig> , <dig>  which corresponds to an estimated physical length of  <dig>  gb .
the average number of consensus bands  per contig is  <dig>  and the estimated contig size is  <dig> kb.
the number of contigs in this assembly is similar to the first generation atlantic salmon physical map, which resulted in  <dig>  contigs and  <dig>  singletons with an average contig length of  <dig> kb from fingerprinting of a  <dig> x library  <cit> .
the rainbow trout physical map can be searched and viewed online via webfpc:
validation of contigs
the physical map assembly was validated by: 1) comparing contigs assembly to the probe hybridization results and agarose gel fingerprinting contigs of palti et al.
<cit> ; and 2) anchoring large contigs to the microsatellite-based genetic linkage map of rexroad et al.
<cit> .
in the first approach we evaluated the contig assignments of  <dig> clones that were positive by probe hybridization to  <dig> type i markers .
most of the clones  that were positive for a single probe and were also assembled into a single contig by palti et al.
<cit>  also clustered inside a single contig in this physical map, confirming the reliability of this assembly.
only one marker  was truly split into two contigs in the physical map where five clones clustered in contig  <dig> and four clustered in contig  <dig>  the other  <dig> clones that did not cluster in the major contig of clones positive to each marker did not cluster with other positive clones either, likely representing the fraction of mis-assembled clones.
an additional  <dig> clones  that were positive to the markers of palti et al.
failed our fingerprinting editing criteria and were excluded from the current fpc assembly.
overall, the current assembly of 93% of the clones was in agreement with our previous work and only  <dig> clones  were likely mis-assembled.
a the contig numbers are in parenthesis.
b clones that were not fingerprinted successfully and did not pass the editing step of the analysis.
c gtpbp-gi- <dig> and gtpbp-gi- <dig> appear tightly linked on contig  <dig>  but the respective positive bacs do not overlap.
this may be caused by local tandem duplication of this locus.
in the second validation approach,  <dig> of the largest contigs were anchored to the genetic linkage map using  <dig> microsatellite markers isolated from bac end sequences  and reported here for the first time, and three microsatellites that were previously isolated from other clones in the contigs .
two to four markers were developed per contig from clones that were distal to each other on the contig as illustrated in figure  <dig>  all of the  <dig> markers were placed on the rainbow trout genetic map by two-point linkage analysis.
markers from  <dig> of the  <dig> contigs displayed close genetic linkage of  <dig> cm -  <dig> cm.
the other two contigs  were likely mis-joined as for each contig two of the three markers were closely linked and the third marker was mapped to another linkage group .
those two were also the largest contigs with  <dig> and  <dig> clones and estimated length of  <dig>  mb and  <dig>  mb, respectively.
the ratio of physical to genetic linkage distances varied among the contigs we sampled, which is similar to other vertebrate genomes  <cit> .
we will be able to better investigate this relationship in the rainbow trout genome when we will have a comprehensive and robust integration between the physical and genetic maps.
in terms of number of contigs,  <dig> of  <dig>  are in agreement with the genetic map.
in terms of genome coverage in number of markers,  <dig> of  <dig>  are in agreement between the physical and genetic maps.
this 8%-18% error rate is higher then the 5% estimated for the catfish physical map of quiniou et al.
<cit>  or the 4% rate detected in the 3-color hicf physical map of the maize genome  <cit> .
however, the whole assembly error rate for this trout physical map is likely lower than the estimate of 18% or even 8% as this validation was heavily skewed toward the largest contigs, and indeed the two mis-joined contigs were also the largest contigs.
all clones were from the 10x hindiii yy male swanson doubled haploid bac library .
a number of q-clones in parenthesis.
clones that were assigned to a contig but may be false positives  are marked by fpc as q-clones.
b two point linkage recombination between markers from the two most distant clones in the contig.
c additional markers that were previously isolated from other bacs in the contigs were linked to the new bac end sequence microsatellites by two point linkage analysis and included in this table.
contig 84: omm3090/mhci-a  <cit> ; contig260: omm3079/tap <dig>  <cit> ; contig 791: omm3183/tlr8a .
fpc identified  <dig>  questionable  clones in  <dig> contigs in this physical map .
q-clones are the result of false overlaps between dna fingerprinting patterns, which can be caused by the presence of chimerical clones in the bac library, cross-contamination between neighboring wells, large repetitive regions of the genome or duplicated regions that are frequent in the trout genome.
the occurrence of q-clones in this assembly  is lower than the 4%-11% reported for other hicf projects  <cit> .
however, the fraction of contigs with q-clones in this assembly  is similar to the catfish physical map assembly of xu et al.
<cit> .
the initial high cutoff stringency and relatively deep genome coverage that we used likely contributed to the lower fraction of q-clones in this assembly.
the quality of this physical map was validated, but it could still benefit from better computational tools for identifying q-clones.
clearly, the assembly of physical maps can be significantly improved by identifying the specific q-clones in each contig, which in turn will enable evaluation of their location within the contig and relationship to the neighboring clones.
as a proof of concept, the computational approach for improving physical maps assembly that is currently being developed by frenkel et al.
<cit>  was tested on the two large mis-joined contigs that we identified in this assembly and correctly identified the specific q-clones causing the mis-joining of the contigs and how they should be split into smaller contigs that would also be in good agreement with the genetic map .
contig  <dig> that was also analyzed by this approach was found to be an intact contig, which is also in agreement with our results .
taken together the results of this analysis illustrate that better handling of q-clones by the assembly software can dramatically improve physical maps.
CONCLUSIONS
the production and validation of the first physical map of the rainbow trout genome is described in this paper.
we are currently integrating this map with the genetic map using more than  <dig> microsatellites isolated from bac end sequences and by identifying bacs that harbor more than  <dig> previously mapped markers.
the availability of an integrated physical and genetic map will enable detailed comparative genome analyses, fine mapping of qtl, positional cloning, selection of positional candidate genes for economically important traits and the incorporation of mas into rainbow trout breeding programs.
a comprehensive integrated map can also provide a minimal tiling path for genome sequencing and a framework for whole genome sequence assembly.

 rainbow trout 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. coupling great interest in this species as a research model with the need for genetic improvement for aquaculture justifies the continued development of genome resources facilitating selective breeding. genome size estimates derived from molecular weight of dna per cell for rainbow trout and other salmonids vary from to × bp. as with most salmonids, rainbow trout experienced a recent genome duplication event resulting in a semi-tetraploid state. our physical mapping experience with bacs from the swanson library has demonstrated that duplicated loci can be detected by dna fingerprinting. additionally, bacs that represent one of two duplicated loci were shown by fluorescent in-situ hybridization to distinctly hybridize to a specific chromosome pair. therefore, it is likely that the vast majority of the duplicated loci contain enough sequence variation to allow correct assembly of a physical map using bac dna fingerprinting. current genomic resources available for rainbow trout research include multiple bacterial artificial chromosome libraries; doubled haploid clonal lines; genetic maps; a large est database; and dna microarrays. seven rainbow trout bac libraries were constructed to date. two libraries constructed in japan contain average insert sizes of kb and kb, and provide haploid genome coverages of fold and fold, respectively. however, they have not been arrayed in plates and library screening tools are not available. one bac library from the swanson male homozygous line and one from the osu female homozygous line were commercially constructed by amplicon express inc. in both libraries were prepared from partial digestions with hindiii. the osu bac library has clones with an average insert size of kb. the swanson bac library has clones with an average insert size of kb. hindiii bac dna fingerprinting for local physical mapping of type-i markers in the swanson library demonstrated the library's utility for identifying duplicated loci and confirmed its 10× coverage. both libraries have been used for genomic sequencing and genetic mapping of loci of interest. an additional 5× genome coverage swanson dh yy male library was constructed at the children's hospital oakland research institute in using ecori partial digestion of genomic dna with an estimated average insert size of kb. an additional two new libraries were prepared by amplicon express in the two new 5× genome coverage swanson dh yy male libraries were prepared using bamhi and ecori partial genomic digestion to complement the 10x hindiii swanson library and have estimated insert sizes of kb. the four swanson dh yy male libraries described above were prepared using genomic dna from the same swanson doubled-haploid clonal line that is propagated and maintained at the lab of gary thorgaard in washington state university. two genetic maps with improved 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 microsatellites over linkage groups and a total length of 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 microsatellite loci over linkage groups and a total length of cm. the rainbow trout haploid karyotype is composed of chromosome arms, but chromosome numbers can vary among rainbow trout populations in concordance with their native geographic distribution. therefore, anchoring the genetic linkage groups to the physical chromosome arms was a crucial task accomplished by phillips et al. using bacs as fish probes. the range of the haploid chromosome number is between and. the karyotype of the swanson dh line is composed of 2n =. the offspring of "hybrids" between strains with different chromosome number are viable and they can be used for genetic mapping as two uni-armed chromosomes from the parent with 2n = will align with a di-armed chromosome from the parent with 2n = a comparative cytogenetic map of the rainbow trout and atlantic salmon using fish with bacs that harbor type-i markers and microsatellites is being developed in a coordinated effort. this cytogenetic map and the comparative genetic map of danzmann et al. provide a frame-work for future high resolution trout-salmon comparative genome maps. qualitative/quantitative trait loci 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 and to ipnv, killer cell-like activity, upper thermal tolerance, embryonic developmental rate, spawning time, confinement stress response 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 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 effect. this can be overcome by whole genome association studies and other approaches that capture effects of most qtl that contribute to the population-wide variation in a trait such as genomic selection. recently we demonstrated the feasibility of low resolution ld association studies in rainbow trout. in the absence of whole genome sequence assembly, the robust integrated physical and genetic map that we aim to construct will provide better resolution than the current genetic maps for ordering of genetic markers and estimating physical distances between markers, thus facilitating whole genome association studies rainbow trout. several bac-based physical maps were constructed in recent years for economically important aquaculture species including tilapia, atlantic salmon and catfish. here we report the construction of the first physical map of the rainbow trout genome using a 10× genome coverage bac library derived from the swanson dh clonal line.  bac fingerprinting and contigs assembly we used the 4-color high-information-content fingerprinting snapshot method of luo et al. to fingerprint all the clones from the 10x hindiii bac library and clones from the chori- 5x ecori library. after editing with fpminer software 82% bac fingerprints from the 10x library and 50% from the chori- library were assembled into physical contigs using fpc software with a tolerance of bp and an initial cutoff of e-, followed by dqer and several rounds of end-to-end merging and single-to-end merging at progressively lower cutoff stringencies. the current version of the map is composed of clones of which are assembled into contigs and remained singletons. the average number of bacs per contig is, and the distribution of the number of bacs per contig is shown in figure the average number of fingerprinting fragments per bac is, and the average insert size for this library is kb. therefore, each fragment is estimated on average to represent kb of genome dna. the total number of unique fingerprinting fragments in contigs is, which corresponds to an estimated physical length of gb. the average number of consensus bands per contig is and the estimated contig size is kb. the number of contigs in this assembly is similar to the first generation atlantic salmon physical map, which resulted in contigs and singletons with an average contig length of kb from fingerprinting of a x library. the rainbow trout physical map can be searched and viewed online via webfpc: validation of contigs the physical map assembly was validated by: 1) comparing contigs assembly to the probe hybridization results and agarose gel fingerprinting contigs of palti et al.; and 2) anchoring large contigs to the microsatellite-based genetic linkage map of rexroad et al.. in the first approach we evaluated the contig assignments of clones that were positive by probe hybridization to type i markers. most of the clones that were positive for a single probe and were also assembled into a single contig by palti et al. also clustered inside a single contig in this physical map, confirming the reliability of this assembly. only one marker was truly split into two contigs in the physical map where five clones clustered in contig and four clustered in contig the other clones that did not cluster in the major contig of clones positive to each marker did not cluster with other positive clones either, likely representing the fraction of mis-assembled clones. an additional clones that were positive to the markers of palti et al. failed our fingerprinting editing criteria and were excluded from the current fpc assembly. overall, the current assembly of 93% of the clones was in agreement with our previous work and only clones were likely mis-assembled. a the contig numbers are in parenthesis. b clones that were not fingerprinted successfully and did not pass the editing step of the analysis. c gtpbp-gi- and gtpbp-gi- appear tightly linked on contig but the respective positive bacs do not overlap. this may be caused by local tandem duplication of this locus. in the second validation approach, of the largest contigs were anchored to the genetic linkage map using microsatellite markers isolated from bac end sequences and reported here for the first time, and three microsatellites that were previously isolated from other clones in the contigs. two to four markers were developed per contig from clones that were distal to each other on the contig as illustrated in figure all of the markers were placed on the rainbow trout genetic map by two-point linkage analysis. markers from of the contigs displayed close genetic linkage of cm - cm. the other two contigs were likely mis-joined as for each contig two of the three markers were closely linked and the third marker was mapped to another linkage group. those two were also the largest contigs with and clones and estimated length of mb and mb, respectively. the ratio of physical to genetic linkage distances varied among the contigs we sampled, which is similar to other vertebrate genomes. we will be able to better investigate this relationship in the rainbow trout genome when we will have a comprehensive and robust integration between the physical and genetic maps. in terms of number of contigs, of are in agreement with the genetic map. in terms of genome coverage in number of markers, of are in agreement between the physical and genetic maps. this 8%-18% error rate is higher then the 5% estimated for the catfish physical map of quiniou et al. or the 4% rate detected in the 3-color hicf physical map of the maize genome. however, the whole assembly error rate for this trout physical map is likely lower than the estimate of 18% or even 8% as this validation was heavily skewed toward the largest contigs, and indeed the two mis-joined contigs were also the largest contigs. all clones were from the 10x hindiii yy male swanson doubled haploid bac library. a number of q-clones in parenthesis. clones that were assigned to a contig but may be false positives are marked by fpc as q-clones. b two point linkage recombination between markers from the two most distant clones in the contig. c additional markers that were previously isolated from other bacs in the contigs were linked to the new bac end sequence microsatellites by two point linkage analysis and included in this table. contig 84: omm3090/mhci-a; contig260: omm3079/tap; contig 791: omm3183/tlr8a. fpc identified questionable clones in contigs in this physical map. q-clones are the result of false overlaps between dna fingerprinting patterns, which can be caused by the presence of chimerical clones in the bac library, cross-contamination between neighboring wells, large repetitive regions of the genome or duplicated regions that are frequent in the trout genome. the occurrence of q-clones in this assembly is lower than the 4%-11% reported for other hicf projects. however, the fraction of contigs with q-clones in this assembly is similar to the catfish physical map assembly of xu et al.. the initial high cutoff stringency and relatively deep genome coverage that we used likely contributed to the lower fraction of q-clones in this assembly. the quality of this physical map was validated, but it could still benefit from better computational tools for identifying q-clones. clearly, the assembly of physical maps can be significantly improved by identifying the specific q-clones in each contig, which in turn will enable evaluation of their location within the contig and relationship to the neighboring clones. as a proof of concept, the computational approach for improving physical maps assembly that is currently being developed by frenkel et al. was tested on the two large mis-joined contigs that we identified in this assembly and correctly identified the specific q-clones causing the mis-joining of the contigs and how they should be split into smaller contigs that would also be in good agreement with the genetic map. contig that was also analyzed by this approach was found to be an intact contig, which is also in agreement with our results. taken together the results of this analysis illustrate that better handling of q-clones by the assembly software can dramatically improve physical maps.  the production and validation of the first physical map of the rainbow trout genome is described in this paper. we are currently integrating this map with the genetic map using more than microsatellites isolated from bac end sequences and by identifying bacs that harbor more than previously mapped markers. the availability of an integrated physical and genetic map will enable detailed comparative genome analyses, fine mapping of qtl, positional cloning, selection of positional candidate genes for economically important traits and the incorporation of mas into rainbow trout breeding programs. a comprehensive integrated map can also provide a minimal tiling path for genome sequencing and a framework for whole genome sequence assembly. 
the map assembly was validated by 1) comparison with probe hybridization results and agarose gel fingerprinting contigs; and 2) anchoring large contigs to the microsatellite-based genetic linkage map. we are currently integrating this map with the ncccwa genetic map using more than microsatellites isolated from bac end sequences and by identifying bacs that harbor more than previously mapped markers. the availability of an integrated physical and genetic map will enable detailed comparative genome analyses, fine mapping of qtl, positional cloning, selection of positional candidate genes for economically important traits and the incorporation of mas into rainbow trout breeding programs. coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. many quantitative trait loci have been identified for production and life-history traits in rainbow trout. a bacterial artificial chromosome physical map is needed to facilitate fine mapping of qtl and the selection of positional candidate genes for incorporation in marker-assisted selection for improving rainbow trout aquaculture production. rainbow trout are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. the production and validation of the first bac physical map of the rainbow trout genome is described in this paper. the physical map was constructed from dna fingerprinting of bac clones using the 4-color high-information content fingerprinting method. the clones were assembled into physical map contigs using the finger-printing contig program. the total number of unique fingerprinting fragments in contigs is, which corresponds to an estimated physical length of gb.
 rainbow trout are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. many quantitative trait loci have been identified for production and life-history traits in rainbow trout. a bacterial artificial chromosome physical map is needed to facilitate fine mapping of qtl and the selection of positional candidate genes for incorporation in marker-assisted selection for improving rainbow trout aquaculture production. this resource will also facilitate efforts to obtain and assemble a whole-genome reference sequence for this species.  the physical map was constructed from dna fingerprinting of bac clones using the 4-color high-information content fingerprinting method. the clones were assembled into physical map contigs using the finger-printing contig program. the map is composed of contigs and singletons. the total number of unique fingerprinting fragments in contigs is, which corresponds to an estimated physical length of gb. the map assembly was validated by 1) comparison with probe hybridization results and agarose gel fingerprinting contigs; and 2) anchoring large contigs to the microsatellite-based genetic linkage map.  the production and validation of the first bac physical map of the rainbow trout genome is described in this paper. we are currently integrating this map with the ncccwa genetic map using more than microsatellites isolated from bac end sequences and by identifying bacs that harbor more than previously mapped markers. the availability of an integrated physical and genetic map will enable detailed comparative genome analyses, fine mapping of qtl, positional cloning, selection of positional candidate genes for economically important traits and the incorporation of mas into rainbow trout breeding programs. 