A First Generation BAC-based Physical Map of the Rainbow Trout Genome

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2009 Oct 10

PMID 19814815

Citations 27

Authors

Yniv Palti

Ming-Cheng Luo

Yuqin Hu

Carine Genet

Frank M You

Roger L Vallejo

Gary H Thorgaard

Paul A Wheeler

Caird E Rexroad 3rd

Affiliations

Soon will be listed here.

Abstract

Background: Rainbow trout (Oncorhynchus mykiss) 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 (QTL) have been identified for production and life-history traits in rainbow trout. A bacterial artificial chromosome (BAC) physical map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS) for improving rainbow trout aquaculture production. This resource will also facilitate efforts to obtain and assemble a whole-genome reference sequence for this species.

Results: The physical map was constructed from DNA fingerprinting of 192,096 BAC clones using the 4-color high-information content fingerprinting (HICF) method. The clones were assembled into physical map contigs using the finger-printing contig (FPC) program. The map is composed of 4,173 contigs and 9,379 singletons. The total number of unique fingerprinting fragments (consensus bands) in contigs is 1,185,157, which corresponds to an estimated physical length of 2.0 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.

Conclusion: 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 200 microsatellites isolated from BAC end sequences and by identifying BACs that harbor more than 300 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.

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References

Gahr S, Palti Y, Rexroad 3rd C . Genomic characterization of a novel pair of ID genes in the rainbow trout (Oncorhynchus mykiss). Anim Genet. 2004; 35(4):317-20. DOI: 10.1111/j.1365-2052.2004.01142.x. View

OMalley K, Sakamoto T, Danzmann R, Ferguson M . Quantitative trait loci for spawning date and body weight in rainbow trout: testing for conserved effects across ancestrally duplicated chromosomes. J Hered. 2003; 94(4):273-84. DOI: 10.1093/jhered/esg067. View

Young W, Wheeler P, Fields R, Thorgaard G . DNA fingerprinting confirms isogenicity of androgenetically derived rainbow trout lines. J Hered. 1996; 87(1):77-80. DOI: 10.1093/oxfordjournals.jhered.a022960. View

Guyomard R, Mauger S, Tabet-Canale K, Martineau S, Genet C, Krieg F . A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms. BMC Genomics. 2006; 7:302. PMC: 1698487. DOI: 10.1186/1471-2164-7-302. View

Danzmann R, Davidson E, Ferguson M, Gharbi K, Koop B, Hoyheim B . Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon). BMC Genomics. 2008; 9:557. PMC: 2632648. DOI: 10.1186/1471-2164-9-557. View

Nichols K, Young W, Danzmann R, Robison B, Rexroad C, Noakes M . A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Anim Genet. 2003; 34(2):102-15. DOI: 10.1046/j.1365-2052.2003.00957.x. View

Xu P, Wang S, Liu L, Thorsen J, Kucuktas H, Liu Z . A BAC-based physical map of the channel catfish genome. Genomics. 2007; 90(3):380-8. DOI: 10.1016/j.ygeno.2007.05.008. View

Nichols K, Broman K, Sundin K, Young J, Wheeler P, Thorgaard G . Quantitative trait loci x maternal cytoplasmic environment interaction for development rate in Oncorhynchus mykiss. Genetics. 2006; 175(1):335-47. PMC: 1774986. DOI: 10.1534/genetics.106.064311. View

Rexroad 3rd C, Palti Y, Gahr S, Vallejo R . A second generation genetic map for rainbow trout (Oncorhynchus mykiss). BMC Genet. 2008; 9:74. PMC: 2605456. DOI: 10.1186/1471-2156-9-74. View

10.

Johnson N, Vallejo R, Silverstein J, Welch T, Wiens G, Hallerman E . Suggestive association of major histocompatibility IB genetic markers with resistance to bacterial cold water disease in rainbow trout (Oncorhynchus mykiss). Mar Biotechnol (NY). 2008; 10(4):429-37. DOI: 10.1007/s10126-007-9080-7. View

11.

Rise M, von Schalburg K, Brown G, Mawer M, Devlin R, Kuipers N . Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res. 2004; 14(3):478-90. PMC: 353236. DOI: 10.1101/gr.1687304. View

12.

Palti Y, Gahr S, Hansen J, Rexroad 3rd C . Characterization of a new BAC library for rainbow trout: evidence for multi-locus duplication. Anim Genet. 2004; 35(2):130-3. DOI: 10.1111/j.1365-2052.2004.01112.x. View

13.

Phillips R, Nichols K, Dekoning J, Morasch M, Keatley K, Rexroad 3rd C . Assignment of rainbow trout linkage groups to specific chromosomes. Genetics. 2006; 174(3):1661-70. PMC: 1667062. DOI: 10.1534/genetics.105.055269. View

14.

Lathrop G, Lalouel J, Julier C, Ott J . Strategies for multilocus linkage analysis in humans. Proc Natl Acad Sci U S A. 1984; 81(11):3443-6. PMC: 345524. DOI: 10.1073/pnas.81.11.3443. View

15.

Raposo M, Raymond M, Deschepper C . M13-tailed primers improve the readability and usability of microsatellite analyses performed with two different allele-sizing methods. Biotechniques. 2001; 31(1):24-6, 28. View

16.

Nichols K, Bartholomew J, Thorgaard G . Mapping multiple genetic loci associated with Ceratomyxa shasta resistance in Oncorhynchus mykiss. Dis Aquat Organ. 2003; 56(2):145-54. DOI: 10.3354/dao056145. View

17.

OConnell J, Weeks D . The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance. Nat Genet. 1995; 11(4):402-8. DOI: 10.1038/ng1295-402. View

18.

Nichols K, Edo A, Wheeler P, Thorgaard G . The genetic basis of smoltification-related traits in Oncorhynchus mykiss. Genetics. 2008; 179(3):1559-75. PMC: 2475755. DOI: 10.1534/genetics.107.084251. View

19.

Haidle L, Janssen J, Gharbi K, Moghadam H, Ferguson M, Danzmann R . Determination of quantitative trait loci (QTL) for early maturation in rainbow trout (Oncorhynchus mykiss). Mar Biotechnol (NY). 2008; 10(5):579-92. PMC: 2516301. DOI: 10.1007/s10126-008-9098-5. View

20.

Rozen S, Skaletsky H . Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 1999; 132:365-86. DOI: 10.1385/1-59259-192-2:365. View