Skip to main content
NCBI home page
BMC Genomics logoLink to BMC Genomics
. 2005 Apr 18;6:54. doi: 10.1186/1471-2164-6-54

Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss)

Caird E Rexroad III 1,✉, Maria F Rodriguez 1, Issa Coulibaly 1, Karim Gharbi 2, Roy G Danzmann 2, Jenefer DeKoning 3, Ruth Phillips 3, Yniv Palti 1
PMCID: PMC1090573  PMID: 15836796

Abstract

Background

Comparative genomics, through the integration of genetic maps from species of interest with whole genome sequences of other species, will facilitate the identification of genes affecting phenotypes of interest. The development of microsatellite markers from expressed sequence tags will serve to increase marker densities on current salmonid genetic maps and initiate in silico comparative maps with species whose genomes have been fully sequenced.

Results

Eighty-nine polymorphic microsatellite markers were generated for rainbow trout of which at least 74 amplify in other salmonids. Fifty-five have been associated with functional annotation and 30 were mapped on existing genetic maps. Homologous sequences were identified for 20 of the EST containing microsatellites to identify comparative assignments within the tetraodon, mouse, and/or human genomes.

Conclusion

The addition of microsatellite markers constructed from expressed sequence tag data will facilitate the development of high-density genetic maps for rainbow trout and comparative maps with other salmonids and better studied species.

Background

Genome research in agriculturally important species is facilitated by the availability of species-specific molecular genetic tools and resources such as chromosome maps and large volumes of sequence data. Recently such resources have been developed for important aquaculture species including rainbow trout, which are also widely used as a model system for carcinogenesis, toxicological, and comparative immunological research [1].

Several genetic maps [2-4] consisting primarily of type II markers [5] (amplified fragment length polymorphism simple sequence repeats) have been utilized in the identification of qualitative and quantitative trait loci (QTL) [6] associated with rainbow trout production traits. This includes QTL for natural killer cell-like activity, temperature tolerance, spawning date, body weight, resistance to infectious pancreatic necrosis virus (IPNV), resistance to infectious hematopoietic necrosis virus (IHNV), embryonic development rate, and albinism [7-19]. Although the genetic improvement of these traits through selective breeding would benefit the aquaculture industry, these QTL span large chromosomal intervals and will not be practical for marker assisted selection [20] without additional mapping. The current rainbow trout genetic maps lack marker densities and comparative information necessary to conduct fine mapping aimed at reducing QTL interval sizes, developing practical marker assisted selection schemes, and selection of comparative positional candidates [21] to specifically identify the gene(s) affecting traits of interest.

The recent evolutionary divergence of the salmonids [22] and the importance of many of these species to aquaculture will allow for comparative QTL mapping. For example, the development of genetic linkage maps for Atlantic salmon and Arctic char [23-25] has enabled the identification of QTLs for growth characteristics, disease resistance, and temperature tolerance in those species [18,26,27]. The development of microsatellites markers from EST sequences will facilitate the use of genome information in salmonids species by 1) increasing Type II [5] marker densities on genetic maps; 2) integrating physical and genetic maps; 3) developing comparative genetic maps among salmonids; and 4) developing comparative maps with aquatic model organisms such as zebrafish, fugu, and tetraodon and with better studied avian and mammalian species. This comparative information will aid in the identification of positional candidate genes [28] for production traits in salmonid aquaculture and for basic research which utilizes rainbow trout as model organism.

An expressed sequence tag (EST) [29] project was initiated for rainbow trout with the following aims: 1) identify as many unique transcribed sequences as possible; 2) annotate sequence data with information from other species; 3) develop functional genome tools for rainbow trout; and 4) identify microsatellite and single nucleotide polymorphism (SNP) genetic markers for the construction of high-density chromosome maps [30]. Sequences from a normalized cDNA library (NCCCWA 1RT) constructed from brain, gill, liver, muscle, kidney, and spleen tissue resulted in the creation of the Rainbow Trout Gene Index (RTGI) [31]. Microsatellite marker development was conducted simultaneously with the sequencing phase of the project through hybridization of (GT)11 and (GA)11 probes to high-density filters representing 27,648 clones from the library. Positive clones were selected for further analyses resulting in 89 polymorphic microsatellite markers derived from ESTs, 30 which were informative in mapping reference families, 55 were associated with functional annotation, and 20 for which comparative mapping assignments were determined.

Results

Marker development

Hybridization of high-density filters representing 27,648 cDNA clones from a normalized cDNA library with (GA)11 and (GT)11 oligonucleotide probes identified 415 clones potentially containing microsatellite repeats. Forward and reverse sequencing for 384 of these clones resulted in 755 sequences of good quality (PHRED score > 20 over 100 bp [32]). Dinucleotide microsatellite repeat were identified from 181 clone sequences. Analysis of redundancy identified 161 unique sequences. PCR primer design was possible for 128 of the 161 sequences which were assigned locus names using OMM5000 nomenclature (in-house terminology for microsatellite markers derived from ESTs). PCR optimization was successful for 93 of the 128 primer pairs. Testing for polymorphism in three reference parents and five doubled haploids resulted in the development of 89 polymorphic microsatellites markers with an average of 4.52 alleles (range 2–7), 40% of which were duplicated as determined by the observance of multiple alleles in clonal lines (see Additional File 1). Cross-amplification in other salmonid species using PCR conditions that were optimized for rainbow trout was determined (Table 1) to be similar to markers from previous publications [33].

Table 1.

Cross-species amplification. Cross-species amplification allele size range information (bp) for microsatellite markers generated from rainbow trout ESTs

Locus Artic Char Brook Trout Atlantic Salmon Brown Trout Chinook Salmon Coho Salmon Sockeye Salmon Cutthroat Trout
OMM5000 253–255 260–294 256 239–254 250–260 256 251–263 240–252
OMM5001 87 89 87 85 97 89 97–109 123–151
OMM5002 142–155 - 165–265 336–346 274–282 139–151 139–151 277
OMM5003 177 176–179 173 179–183 179 168–184 173–186 176–181
OMM5004 187 189 185–187 187 187 150–164 193 189–193
OMM5005 201–203 195–202 219 196–207 186–187 189 191 200–204
OMM5006 - 225–231 - 205–245 203 207–209 201 211–236
OMM5007 162–167 182–187 181–192 166 170–176 180–199 156–170 147–163
OMM5008 259 247 223–255 253–261 246–95 227–252 232 236–254
OMM5009 247 335–363 - 266 279–283 410 - 303–331
OMM5010 288–334 - 346–370 350–358 305–332 341–346 294–297 362
OMM5011 214–248 217–248 213–248 214–233 224–244 227–247 228–249 224–246
OMM5012 170–188 202–208 186 199–201 174–184 175–190 196–223 169–187
OMM5013 - 107 98 98–111 111–135 96–220 126 102–187
OMM5014 - - - 201–208 185–202 181–198 - 230–262
OMM5015 228 228 228 228 228 228 228 228
OMM5016 239 - 239 239 198 249–311 189 231–236
OMM5017 203–234 195–200 188–200 208–256 217–237 190–201 193 184–209
OMM5018 192 215–231 182–199 198 184–192 - - 186–215
OMM5019 298 256–268 269–335 298–321 269–279 272–275 - 272–282
OMM5020 262 262 262–275 262 256–259 255–258 256–261 261–263
OMM5023 131 131 122 122 130–136 122 122 126–142
OMM5024 198 202 170 194–195 209–230 - - 212–214
OMM5025 154 152 160 160 186–188 158 164 160
OMM5029 210–214 209–227 192–211 193–215 208 207–213 210 203–228
OMM5030 135–187 135–137 140–187 137–139 129–141 150–164 129–141 141–155
OMM5031 145 143 102–144 129–144 142–155 136 142–144 140
OMM5032 198 - 178 216–218 191–201 159 175–179 179–187
OMM5033 284 - 274–280 225 - 243 254–279 260–295
OMM5034 239–287 264 238–240 238–263 239–275 236–269 236–267 246–269
OMM5037 - 266 262–268 260–293 251 254–281 264–272 260–285
OMM5039 284 280 274–280 268 248–286 243–308 282–286 260
OMM5041 168 185–187 172 170 170–173 183–187 132 132–189
OMM5042 133 140 - 127–137 122 - - -
OMM5043 122 122 126 114–128 – 112–114 112–122 112–131
OMM5044 206 199 - 230 242 - - 199–217
OMM5047 - - 317–328 245–251 257–258 261 190 257–263
OMM5050 242 247–249 251 240 243 245–247 246–248 251–261
OMM5051 174–192 190 179 201–218 212–214 190–191 - 195–206
OMM5053 134–198 - - - 122 248 202 228–237
OMM5054 172–240 171–265 161–240 172–241 171–240 171–265 172–241 162–278
OMM5055 217–219 190–220 190–212 190–212 221 225–243 221 219
OMM5056 254–280 268–299 - 196 186 282–319 - 218–253
OMM5058 - - 216–219 239–244 198–204 192 231–235 194–209
OMM5059 151 - 157 145–172 134 124–135 121–127 126–136
OMM5060 105–164 165 - 160 164 164 164 105–164
OMM5061 400 354–358 291–293 274–282 275 274 262 274–278
OMM5062 229 225 200 192–212 223–233 212–231 221–241 222–240
OMM5063 - 148–195 207–243 203–237 150–154 237–282 154–182 178–220
OMM5064 272–274 92–110 276–283 274 290–319 283–285 279 95–286
OMM5067 153–186 153–164 185–187 171–185 153–186 153–164 171–192 153–187
OMM5072 160–164 161–167 171 170–187 146–158 158–164 158–167 164–170
OMM5074 306–344 247–260 242 238–244 245–253 232 228–233 241–244
OMM5075 214 206–208 - 189–191 186 192–198 194 208–229
OMM5077 368 372 377 383 373 377–380 365 334–354
OMM5088 174 168 - 153 159–161 153 168 159–174
OMM5089 - - 134–167 - 154–161 132–140 134–146 -
OMM5090 153 152–255 153 249–255 153–269 249–255 153–255 239–248
OMM5091 276 201–210 178 201–205 221–262 368 223–244 265–283
OMM5092 161 161 186 186 202–208 192–217 - -
OMM5093 285 285 285 285 285 285 285 285
OMM5099 244 243 228 219–234 278–296 260–268 214–254 213–260
OMM5100 137–185 - 182 138–143 173 - 160–173 167–201
OMM5106 358–388 328–353 260–271 261 306–322 361–395 257–274 273–318
OMM5107 258–264 255 250–254 264 - 254 255 -
OMM5108 265 251 265–271 256 263–292 260–262 251–271 256–267
OMM5109 256 254–256 256–271 260–263 256 254–256 260–262 262–271
OMM5112 194 198 194–218 196 193–202 189–196 189 193–206
OMM5113 - 320–368 - 274–320 - 286–304 - 243–288
OMM5117 135–142 138 142 125–140 138 125–140 138 137–154
OMM5121 230 228–230 156–173 166–176 166–267 178–230 173–175 197–222
OMM5124 271–281 271–277 - 272–273 258 266 269 280
OMM5125 256 262–264 254 250–252 256–277 250–260 256–260 256–260
OMM5126 295–299 286 295–299 286–290 286 286–291 286 286–307
% Amp. 87 83 83 97 94 93 85 94
Open in a new tab

Functional annotation

Functional annotations were associated with ESTs by BLAST analyses of the RTGI which previously included EST sequence data for the clones described in this manuscript. The highest scoring matches all had E-values ranging from 0 to 10-40 and percent identities ranging from 91–100 % (see Additional File 2). TIGR gene index annotation for tentative consensus sequences (TCs) includes three levels of significance based on percent identity: matches in the range of 90 to 100% are categorized as "homologues," matches in the range of 70–90% are categorized as "similar," and matches less than 70% are categorized as "weakly similar." Annotation of ESTs in this manuscript resulted in 10 highly significant matches to genome sequences, 8 categorized as homologues, 28 as similar, 9 as weakly similar, and 41 for which no associations were determined Locus or gene symbols from Locus Link [34] or UniProt [35] were added to 8 loci designated as homologues.

Genetic and comparative mapping

Linkage analyses of 33 informative markers resulted in the assignment of 30 markers to linkage groups (see Additional File 3). Twenty-three markers were informative in the reference families of Sakamoto et al. [3] and 7 markers were placed on the map of Nichols et al. [2] in addition to 3 which were not included into previous linkage groups (Table 2). Comparisons to zebrafish and fugu databases identified homologous assignments for 16 ESTs each (see Additional File 4 and Additional File 5), however, the chromosomal assignments in these 2 species are not yet available.

Table 2.

Identification of homologous segments between rainbow trout, human, mouse and tetraodaon chromosomes. Rainbow trout linkage group nomenclature is from Nichols et al. (2003a)

Locus Rainbow Trout Linkage Group Tetraodon (TNI) Human (HSA) Mouse (MMU)
OMM5000 27 8 19 7
OMM5002 21 6 10
OMM5003 23
OMM5005 11 2 13 14
OMM5012 23
OMM5017 20 3
OMM5019 9 17 11
OMM5023 22
OMM5025 8
OMM5026 29
OMM5029 12
OMM5033 16
OMM5034 19 8
OMM5041 12 10 3 3
OMM5045 19 12 12 16
OMM5051 ? 2
OMM5056 ? 10 14
OMM5057 9
OMM5059 13 5
OMM5062 27
OMM5065 25
OMM5077 25 X
OMM5088 19
OMM5090 21
OMM5093 ? 4 5
OMM5099 7 6 8 15
OMM5100 15 19
OMM5106 14
OMM5107 22 9
OMM5108 20
OMM5109 31
OMM5112 23
OMM5113 6 10
OMM5117 10 14
OMM5121 31 6
OMM5126 21
OMM5127 9 16 7
Open in a new tab

Discussion

Microsatellite marker development

Marker development strategies for the construction of high-density genetic maps typically utilize random or targeted approaches. Random approaches are commonly employed in the early phases of the map construction and are characterized by the use of sequence data not associated with mapping or functional annotation for marker development. In targeted approaches, commonly employed to increase marker density in a specific chromosome region or to map genes of interest, only sequence data meeting specified parameters with respect to mapping or function are utilized for marker development. Our approach for increasing the marker densities of rainbow trout genetic maps was a hybrid of random and targeted approaches. Although clones for marker development were not chosen based on functional annotation, the sequence data utilized were known to be transcribed. The benefit of this approach is that these microsatellites are Type I and II markers [5], serving to increase marker densities on both genetic and comparative maps. Similar strategies have been employed in the development of microsatellite markers for other agriculturally important animals including sheep, turkey, cattle, catfish, and pig [36-40].

Cross amplification within the salmonidae

Salmonids are believed to have diverged from a common tetraploid ancestor some 25 million years ago [22]. As a result of this evolutionarily recent divergence, microsatellite markers can be used in the development of comparative genetic maps among the salmonidae. Cross-species amplification was obtained for 74 markers and ranged between 83% and 97% per species, with observed polymorphism that ranged between 36% and 82% per marker. Sampling additional individuals from multiple populations is likely to increase observations of polymorphism. This high level of cross-amplification and polymorphism should facilitate the development of comparative and genetic maps for the salmonids.

Functional annotation

The RTGI was used to associate ESTs with functional annotation as their sequence data was previously included in RTGI Version 4.0. Unfortunately, 42% of the markers were not associated with any annotation, demonstrating an overall lack of functional annotation of the rainbow trout transcriptome.

Genetic and comparative mapping

The goal of the activities outlined in this manuscript was to identify homologous regions of chromosomes between rainbow trout and species for which there is an abundance of genome information including whole genome sequence. Eight regions of homology were identified between trout and tetraodon, seven with human, and 10 with mouse (Table 2). Although mapping single loci does not identify segments of conserved synteny, the homologies reported in this paper are supported by the examination of direct comparative information between tetraodon and human and mouse. For instance, OMM5000 was observed to be homologous with TNI 8, HSA19, and MMU7. The NCBI human/mouse comparative map [41] reveals a homologous region between HSA 19 and MMU 7, and the tetraodon comparative map [42,43] reveals regions of homology between TNI8 and both HSA19 and MMU7. Similar analyses of comparative assignments in two or more species supported our findings for every marker reported.

Conclusion

This project was initiated at a time where very little sequence data was publicly available for salmonid species. Now the RTGI contains over 150,000 ESTs which represent ~ 50,000 unique sequences. Current methods to develop new microsatellite markers from EST sequences would most likely replace hybridization with an in silico strategy on the RTGI data set. Therefore, the continuation of microsatellite marker development from expressed sequence tag data is feasible and will be useful for developing comparative maps with other salmonids and with better studied species.

Methods

Identification of cDNA clones with microsatellites

A rainbow trout normalized cDNA library was constructed using mRNA from brain, gill, liver, spleen, kidney, and muscle tissues. The library was plated, picked, and arrayed into 384-well plates. Sets of 72 plates were gridded onto single 20 cm2 positively charged nylon membranes for hybridization experiments. One high-density membrane (representing 27,648 clones) was hybridized overnight at 65°C with radioactively (32P) labeled (GA)11 and (GT)11 oligonucleotide probes using standard protocols [44]. Membranes were removed from hybridization solution, washed, and exposed to storage phosphor screens for 1 hour. The phosphor screens were scanned on a Storm (Amersham Biosciences Corp, Piscataway, NJ) and positive clones identified.

Sequencing and primer design

Positive clones were re-arrayed into 96-well plates and grown overnight. DNA was isolated for each clone using manufacturer's standard miniprep protocols for the BioRobot 8000 (QIAGEN, Valencia, CA, USA). Sequencing reactions were carried out using ABI Dye Terminator Chemistry (Applied Biosystems, Foster City, CA, USA) using SP6 and T7 primers. Sequencing reactions were purified and electrophoresed on an ABI3700. Sequences were trimmed for quality and vector using PHRED and Cross_match [32]. Consensus sequences were constructed for clones having multiple sequence data files. Those containing microsatellites were analyzed for redundancy within the dataset and previously discovered salmonid microsatellites using Vector NTI Suite 6.0 (InforMax, Bethesda, MD). PCR primer pairs were designed to amplify unique microsatellite sequences using Oligo 6.0 [45].

PCR and genotyping

PCR primer pairs were obtained from commercial sources with the forward primers labeled with FAM, HEX, or NED. Primer pairs were optimized by varying annealing temperatures and MgCl2 concentrations to amplify in rainbow trout (Kamloop strain), the clone of origin, and a negative control with no DNA. Reactions (11 μl total volume) included 25 ng DNA, 1.5–2.5 mM MgCl2, 2.0 μM of each primer, 200 μM dNTPs, 1 × manufacturer's reaction buffer, and 0.5 unit AmpliTaq Gold Polymerase (ABI, Foster City, CA). Amplifications were conducted in an MJ Research PTC 200 DNA Engine thermal cycler (MJ Research, Waltham, MA) as follows: an initial denaturation at 94°C for 10 min, 36 cycles consisting of 94°C for 30 s, annealing temperature for 30 s, 72°C extension for 30 s; followed by a final extension of 72°C for 10 min. Successfully optimized primer pairs were used to amplify DNA from the three reference family parents [3] and five doubled haploid clonal lines (OSU, Arlee, Swanson, Hot Creek, and Clearwater [46]). Cross-species amplifications were attempted in two samples representing various other salmonids including cutthroat, Sockeye, Kokanee, Chinook, Atlantic salmon, brown trout, brook trout, and Artic char. PCR products were electrophoresed and verified by visualization in 3% agarose gels. PCR reactions were then combined according to label and size. Typical combinations of markers for capillary electrophoresis were made by combining PCR reactions for markers having alleles of at least 100 bp (based on agarose results) difference in size and different fluorescent labels. One microliter of each PCR product was added to 20 microliters of water, of which one microliter was added to 12 microliters of HiDi formamide and 0.5 microliters of ROX standard for genotyping for electrophoresis on an ABI PRISM3700 DNA Analyzer or an ABI PRISM 3100 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). Genescan output files were analyzed using Genotyper 3.5 software (Applied Biosystems, Foster City, CA, USA). Markers for which the parents of the reference families were informative were genotyped on the offspring. Markers not informative on the Sakamoto et al. [3] map having been associated with mapping annotation were genotyped on the reference families of Nichols et al. [2].

Annotation

A FASTA file was generated containing clone sequence data for use in standalone BLAST with the goal of obtaining functional and mapping annotation. Functional annotation was associated by comparison to the RTGI Version 4.0 (Appendix 2) [31]. Mapping annotation was obtained by comparisons to sequence data from the Tetraodon Genome Browser [47] and zebrafish, fugu, human and mouse genome sequences from NCBI (Appendices 4 and 5) [48].

Authors' contributions

CER conceived the study and participated in its design and coordination and drafted the manuscript. MFR, IC and YP assisted in genotyping analyses, RGD and KG conducted linkage analysis on the Sakamoto et al. [3] reference families and JD and RP conducted mapping in the doubled haploid crosses [2]. All authors read and approved the final manuscript.

Supplementary Material

Additional File 1

Appendix 1. Microsatellite marker information including GenBank accessions, duplication status, allele size ranges, repeat motif, primer sequences, and optimized PCR conditions.

Click here for file (206KB, doc)
Additional File 2

Appendix 2. Functional Annotation. Tentative annotation assigned to marker ESTs acquired via BLAST of the rainbow trout gene index version 4.0. Markers identified as homologues are annotated with gene or locus name symbols from UniProt [35] or NCBI.

Click here for file (151.5KB, doc)
Additional File 3

Appendix 3. Mapping information for rainbow trout microsatellites. Each marker which was informative for mapping is included with cross, closest marker locus name, linkage group, and map position.

Click here for file (84KB, doc)
Additional File 4

Appendix 4. In silico derived comparative mapping information I. BLAST was used to identify similar sequences between mouse, human, zebrafish, and pufferfish.

Click here for file (437KB, doc)
Additional File 5

Appendix 5. In silico derived comparative mapping information II. BLAST was used to identify similar sequences with tetraodon.

Click here for file (98KB, doc)

Acknowledgments

Acknowledgements

The authors thank Roseanna Athey, Renee Fincham, Ashley Gustafson, and Connie Briggs for their technical contributions to this manuscript and Krista Nichols and Robert Drew for their assistance in linkage analyses with doubled haploid crosses. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S Department of Agriculture.

Contributor Information

Caird E Rexroad, III, Email: crexroad@ncccwa.ars.usda.gov.

Maria F Rodriguez, Email: frodriguez@ncccwa.ars.usda.gov.

Issa Coulibaly, Email: icoulibaly@ncccwa.ars.usda.gov.

Karim Gharbi, Email: kgharbi@uoguelph.ca.

Roy G Danzmann, Email: rdanzman@uoguelph.ca.

Jenefer DeKoning, Email: dekoning@vancouver.wsu.edu.

Ruth Phillips, Email: phllipsr@vancouver.wsu.edu.

Yniv Palti, Email: ypalti@ncccwa.ars.usda.gov.

References

  1. Thorgaard GH, Bailey GS, Williams D, Buhler DR, Kaattari SL, Ristow SS, Hansen JD, Winton JR, Bartholomew JL, Nagler JJ, Walsh PJ, Vijayan MM, Devlin RH, Hardy RW, Overturf KE, Young WP, Robison BD, Rexroad C, Palti Y. Status and opportunities for genomics research with rainbow trout. Comp Biochem Physiol B Biochem Mol Biol. 2002;133:609–646. doi: 10.1016/S1096-4959(02)00167-7. [DOI] [PubMed] [Google Scholar]
  2. Nichols KM, Young WP, Danzmann RG, Robison BD, Rexroad C, Noakes M, Phillips RB, Bentzen P, Spies I, Knudsen K, Allendorf FW, Cunningham BM, Brunelli J, Zhang H, Ristow S, Drew R, Brown KH, Wheeler PA, Thorgaard GH. A consolidated linkage map for rainbow trout (Oncorhynchus mykiss) Anim Genet. 2003;34:102–115. doi: 10.1046/j.1365-2052.2003.00957.x. [DOI] [PubMed] [Google Scholar]
  3. Sakamoto T, Danzmann RG, Gharbi K, Howard P, Ozaki A, Khoo SK, Woram RA, Okamoto N, Ferguson MM, Holm LE, Guyomard R, Hoyheim B. A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates. Genetics. 2000;155:1331–1345. doi: 10.1093/genetics/155.3.1331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Young WP, Wheeler PA, Coryell VH, Keim P, Thorgaard GH. A detailed linkage map of rainbow trout produced using doubled haploids. Genetics. 1998;148:839–850. doi: 10.1093/genetics/148.2.839. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. O'Brien SJ, Womack JE, Lyons LA, Moore KJ, Jenkins NA, Copeland NG. Anchored reference loci for comparative genome mapping in mammals. Nat Genet. 1993;3:103–112. doi: 10.1038/ng0293-103. [DOI] [PubMed] [Google Scholar]
  6. Lander ES, Botstein D. Mapping complex genetic traits in humans: new methods using a complete RFLP linkage map. Cold Spring Harb Symp Quant Biol. 1986;51 Pt 1:49–62. doi: 10.1101/sqb.1986.051.01.007. [DOI] [PubMed] [Google Scholar]
  7. Danzmann RG, Jackson TR, Ferguson MM. Epistasis in allelic expression at upper temperature tolerance QTL in rainbow trout. Aquaculture. 1999;173:45–58. doi: 10.1016/S0044-8486(98)00465-7. [DOI] [Google Scholar]
  8. Jackson TR, Ferguson MM, Danzmann RG, Fishback AG, Ihssen PE, O'Connel M, Crease TJ. Identification of two QTL influencing upper temperature tolerance in three rainbow trout (Oncorhychus mykiss) half-sib families. Heredity. 1998;80:143–151. doi: 10.1038/sj.hdy.6882890. [DOI] [Google Scholar]
  9. Nakamura K, Ozaki A, Akutsu T, Iwai K, Sakamoto T, Yoshizaki G, Okamoto N. Genetic mapping of the dominant albino locus in rainbow trout (Oncorhynchus mykiss) Mol Genet Genomics. 2001;265:687–693. doi: 10.1007/s004380100464. [DOI] [PubMed] [Google Scholar]
  10. Nichols KM, Bartholomew J, Thorgaard GH. Mapping multiple genetic loci associated with Ceratomyxa shasta resistance in Oncorhynchus mykiss. Dis Aquat Organ. 2003;56:145–154. doi: 10.3354/dao056145. [DOI] [PubMed] [Google Scholar]
  11. Nichols KM, Wheeler PA, Thorgaard GH. Quantitative Trait Loci Analyses for Meristic Traits in Oncorhynchus mykiss. Environmental Biology of Fishes. 2004;69:317–331. doi: 10.1023/B:EBFI.0000022905.72702.0e. [DOI] [Google Scholar]
  12. O'Malley KG, Sakamoto T, Danzmann RG, Ferguson MM. Quantitative trait Loci for spawning date and body weight in rainbow trout: testing for conserved effects across ancestrally duplicated chromosomes. J Hered. 2003;94:273–284. doi: 10.1093/jhered/esg067. [DOI] [PubMed] [Google Scholar]
  13. Ozaki A, Sakamoto T, Khoo S, Nakamura K, Coimbra MR, Akutsu T, Okamoto N. Quantitative trait loci (QTLs) associated with resistance/susceptibility to infectious pancreatic necrosis virus (IPNV) in rainbow trout (Oncorhynchus mykiss) Mol Genet Genomics. 2001;265:23–31. doi: 10.1007/s004380000392. [DOI] [PubMed] [Google Scholar]
  14. Perry GM, Danzmann RG, Ferguson MM, Gibson JP. Quantitative trait loci for upper thermal tolerance in outbred strains of rainbow trout (Oncorhynchus mykiss) Heredity. 2001;86:333–341. doi: 10.1046/j.1365-2540.2001.00838.x. [DOI] [PubMed] [Google Scholar]
  15. Robison BD, Wheeler PA, Sundin K, Sikka P, Thorgaard GH. Composite interval mapping reveals a major locus influencing embryonic development rate in rainbow trout (Oncorhynchus mykiss) J Hered. 2001;92:16–22. doi: 10.1093/jhered/92.1.16. [DOI] [PubMed] [Google Scholar]
  16. Rodriguez MF, LaPatra S, Williams S, Famula T, May B. Genetic markers associated with resistance to infectious hematopoietic necrosis in rainbow and steelhead trout (Oncorhynchus mykiss) backcrosses. Aquaculture. 2004;241:93–115. doi: 10.1016/j.aquaculture.2004.08.003. [DOI] [Google Scholar]
  17. Sakamoto T, Danzmann RG, Okamoto N, Ferguson MM, Ihssen PE. Linkage analysis of quantitative trait loci associated with spawning time in rainbow trout (Oncorhynchus mykiss) Aquaculture. 1999;173:33–43. doi: 10.1016/S0044-8486(98)00463-3. [DOI] [Google Scholar]
  18. Somorjai IM, Danzmann RG, Ferguson MM. Distribution of temperature tolerance quantitative trait loci in Arctic charr (Salvelinus alpinus) and inferred homologies in rainbow trout (Oncorhynchus mykiss) Genetics. 2003;165:1443–1456. doi: 10.1093/genetics/165.3.1443. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Zimmerman AM, Evenhuis JP, Thorgaard GH, Ristow SS. A single major chromosomal region controls natural killer cell-like activity in rainbow trout. Immunogenetics. 2004;55:825–835. doi: 10.1007/s00251-004-0645-6. [DOI] [PubMed] [Google Scholar]
  20. Soller M. Genetic Mapping of the Bovine Genome Using Deoxyribonucleic Acid-Level Markers to Identify Loci Affecting Quantitative Traits of Economic Importance. J Dairy Sci. 1990;73:2628–2646. [Google Scholar]
  21. Womack JE, Kata SR. Bovine genome mapping: evolutionary inference and the power of comparative genomics. Curr Opin Genet Dev. 1995;5:725–733. doi: 10.1016/0959-437X(95)80004-O. [DOI] [PubMed] [Google Scholar]
  22. Allendorf FW, Thorgaard GH. Tetraploidy and the evolution of salmonid fishes. In: Turner BJ, editor. Evolutionary Genetics of Fishes. New York, Plenum Press; 1984. pp. 1–46. [Google Scholar]
  23. Gilbey J, Verspoor E, McLay A, Houlihan D. A microsatellite linkage map for Atlantic salmon (Salmo salar) Anim Genet. 2004;35:98–105. doi: 10.1111/j.1365-2052.2004.01091.x. [DOI] [PubMed] [Google Scholar]
  24. Moen T, Hoyheim B, Munck H, Gomez-Raya L. A linkage map of Atlantic salmon (Salmo salar) reveals an uncommonly large difference in recombination rate between the sexes. Anim Genet. 2004;35:81–92. doi: 10.1111/j.1365-2052.2004.01097.x. [DOI] [PubMed] [Google Scholar]
  25. Woram RA, McGowan C, Stout JA, Gharbi K, Ferguson MM, Hoyheim B, Davidson EA, Davidson WS, Rexroad C, Danzmann RG. A genetic linkage map for Arctic char (Salvelinus alpinus): evidence for higher recombination rates and segregation distortion in hybrid versus pure strain mapping parents. Genome. 2004;47:304–315. doi: 10.1139/g03-127. [DOI] [PubMed] [Google Scholar]
  26. Moen T, Fjalestad KT, Munck H, Gomez-Raya L. A multistage testing strategy for detection of quantitative trait Loci affecting disease resistance in Atlantic salmon. Genetics. 2004;167:851–858. doi: 10.1534/genetics.103.013227. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Reid DP, Szanto A, Glebe B, Danzmann RG, Ferguson MM. QTL for body weight and condition factor in Atlantic salmon (Salmo salar): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus) Heredity. 2004. [DOI] [PubMed]
  28. Collins FS. Positional cloning moves from perditional to traditional. Nat Genet. 1995;9:347–350. doi: 10.1038/ng0495-347. [DOI] [PubMed] [Google Scholar]
  29. Adams MD, Soares MB, Kerlavage AR, Fields C, Venter JC. Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library. Nat Genet. 1993;4:373–380. doi: 10.1038/ng0893-373. [DOI] [PubMed] [Google Scholar]
  30. Rexroad CE, Lee Y, Keele JW, Karamycheva S, Brown G, Koop B, Gahr SA, Palti Y, Quackenbush J. Sequence analysis of a rainbow trout cDNA library and creation of a gene index. Cytogenet Genome Res. 2003;102:347–354. doi: 10.1159/000075773. [DOI] [PubMed] [Google Scholar]
  31. RTGI The TIGR Rainbow Trout Gene Index http://www.tigr.org/tigr-scripts/tgi/T_index.cgi?species=r_trout
  32. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998;8:175–185. doi: 10.1101/gr.8.3.175. [DOI] [PubMed] [Google Scholar]
  33. Rexroad CE, Palti Y. Development of Ninety-Seven Polymorphic Microsatellite Markers for rainbow trout (Oncorhynchus mykiss) Transactions of the American Fisheries Society. 2003;132:1214–1221. doi: 10.1577/T02-086. [DOI] [Google Scholar]
  34. LocusLink Locus Link http://www.ncbi.nlm.nih.gov/LocusLink/
  35. UniProt UniProt http://www.pir.uniprot.org/cgi-bin/upEntry?id=Q8AWF1
  36. DeSilva U, Franklin IR, Maddox JF, van Hest B, Adelson DL. Systematic screening of sheep skin cDNA libraries for microsatellite sequences. Cytogenet Genome Res. 2003;102:79–84. doi: 10.1159/000075729. [DOI] [PubMed] [Google Scholar]
  37. Dranchak PK, Chaves LD, Rowe JA, Reed KM. Turkey microsatellite loci from an embryonic cDNA library. Poult Sci. 2003;82:526–531. doi: 10.1093/ps/82.4.526. [DOI] [PubMed] [Google Scholar]
  38. Karsi A, Cao D, Li P, Patterson A, Kocabas A, Feng J, Ju Z, Mickett KD, Liu Z. Transcriptome analysis of channel catfish (Ictalurus punctatus): initial analysis of gene expression and microsatellite-containing cDNAs in the skin. Gene. 2002;285:157–168. doi: 10.1016/S0378-1119(02)00414-6. [DOI] [PubMed] [Google Scholar]
  39. Grosse WM, Kappes SM, McGraw RA. Linkage mapping and comparative analysis of bovine expressed sequence tags (ESTs) Anim Genet. 2000;31:171–177. doi: 10.1046/j.1365-2052.2000.00625.x. [DOI] [PubMed] [Google Scholar]
  40. Rohrer GA, Fahrenkrug SC, Nonneman D, Tao N, Warren WC. Mapping microsatellite markers identified in porcine EST sequences. Anim Genet. 2002;33:372–376. doi: 10.1046/j.1365-2052.2002.00880.x. [DOI] [PubMed] [Google Scholar]
  41. NCBIComparativeMap NCBI Comparative Map
  42. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biemont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 2004;431:946–957. doi: 10.1038/nature03025. [DOI] [PubMed] [Google Scholar]
  43. The Tetraodon Genome Browser http://www.genoscope.cns.fr/externe/tetranew/
  44. Sambrook J, Russell D. Molecular cloning : a laboratory manual. 3rd ed. Cold Spring Harbor, N.Y., Cold Spring Harbor Laboratory Press; 2001. [Google Scholar]
  45. Rychlik W, Rhoads RE. A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res. 1989;17:8543–8551. doi: 10.1093/nar/17.21.8543. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Young WP, Wheeler PA, Fields RD, Thorgaard GH. DNA fingerprinting confirms isogenicity of androgenetically derived rainbow trout lines. J Hered. 1996;87:77–80. doi: 10.1093/oxfordjournals.jhered.a022960. [DOI] [PubMed] [Google Scholar]
  47. The Tetraodon Genome Browser http://www.genoscope.cns.fr/externe/tetranew/
  48. NCBI National Center for Biotechnology Information

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Additional File 1

Appendix 1. Microsatellite marker information including GenBank accessions, duplication status, allele size ranges, repeat motif, primer sequences, and optimized PCR conditions.

Click here for file (206KB, doc)
Additional File 2

Appendix 2. Functional Annotation. Tentative annotation assigned to marker ESTs acquired via BLAST of the rainbow trout gene index version 4.0. Markers identified as homologues are annotated with gene or locus name symbols from UniProt [35] or NCBI.

Click here for file (151.5KB, doc)
Additional File 3

Appendix 3. Mapping information for rainbow trout microsatellites. Each marker which was informative for mapping is included with cross, closest marker locus name, linkage group, and map position.

Click here for file (84KB, doc)
Additional File 4

Appendix 4. In silico derived comparative mapping information I. BLAST was used to identify similar sequences between mouse, human, zebrafish, and pufferfish.

Click here for file (437KB, doc)
Additional File 5

Appendix 5. In silico derived comparative mapping information II. BLAST was used to identify similar sequences with tetraodon.

Click here for file (98KB, doc)

Articles from BMC Genomics are provided here courtesy of BMC

RESOURCES