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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
.... maculatus Jp163B, and X. couchianus), laboratory fish that were maintained by inter-strain cross (X. hellerii), and a wild population (i.e., wild caught X. maculatus), four fish per cohort were resequenced. Short sequencing reads were mapped to corresponding assemblies using Bowtie 2 (Langmead and Salzberg...
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Resource: Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource
- Elizabeth G. King,
- Chris M. Merkes,
- Casey L. McNeil,
- Steven R. Hoofer,
- Saunak Sen,
- Karl W. Broman,
- Anthony D. Long,
- and Stuart J. Macdonald
Genome Res. August 2012 22: 1558-1566; Published in Advance April 10, 2012, doi:10.1101/gr.134031.111
..., with on average 12 of the 15 founders present. A feature of the DSPR, in common with the Collaborative Cross (Churchill et al. 2004) and the Arabidopsis MAGIC lines (Kover et al. 2009), is that phenotyping a single panel of strains allows one to simultaneously interrogate a large amount of genetic and functional...
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Method: Joint genotyping on the fly: Identifying variation among a sequenced panel of inbred lines
- Eric A. Stone
Genome Res. May 2012 22: 966-974; Published in Advance February 23, 2012, doi:10.1101/gr.129122.111
..., Frieman MB Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M, Frieman MB, et al. 2011. Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res 21: 1213–1222. ↵ Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, Fitz J...
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LETTER: Genetic and Haplotype Diversity Among Wild-Derived Mouse Inbred Strains
- Folami Y. Ideraabdullah,
- Elena de la Casa-Esperón,
- Timothy A. Bell,
- David A. Detwiler,
- Terry Magnuson,
- Carmen Sapienza,
- and Fernando Pardo-Manuel de Villena
Genome Res. October 2004 14: 1880-1887; doi:10.1101/gr.2519704
.... We estimate that 50% of the total variation identified in M. musculus may be recovered in intrasubspecific crosses. Alleles at variants positions can be classified into 164 strain distribution patterns, a number exceeding those reported and predicted in panels of classical inbred strains. The number...
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Resource: The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains
- Toyoyuki Takada,
- Toshinobu Ebata,
- Hideki Noguchi,
- Thomas M. Keane,
- David J. Adams,
- Takanori Narita,
- Tadasu Shin-I,
- Hironori Fujisawa,
- Atsushi Toyoda,
- Kuniya Abe,
- Yuichi Obata,
- Yoshiyuki Sakaki,
- Kazuo Moriwaki,
- Asao Fujiyama,
- Yuji Kohara,
- and Toshihiko Shiroishi
Genome Res. August 2013 23: 1329-1338; Published in Advance April 19, 2013, doi:10.1101/gr.156497.113
...analyses of a wide-range of complex traits, which would otherwise require many different crosses between classical inbred strains. Methods All Supplemental Material (Supplemental Data 1–3; Supplemental Tables S7–S12) is available on the FTP site of the NIG Mouse Genome Database (ftp...
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ARTICLE: Combining Mouse Congenic Strains and Microarray Gene Expression Analyses to Study a Complex Trait: The NOD Model of Type 1 Diabetes
- Iain A. Eaves,
- Linda S. Wicker,
- Ghassan Ghandour,
- Paul A. Lyons,
- Laurence B. Peterson,
- John A. Todd,
- and Richard J. Glynne
Genome Res. February 1, 2002 12: 232-243; Published in Advance January 13, 2003, doi:10.1101/gr.214102
...Combining Mouse Congenic Strains and Microarray Gene Expression Analyses to Study a Complex Trait: The NOD Model of Type 1 Diabetes Iain A. Eaves 1 , Linda S. Wicker 2 , 5 , Ghassan Ghandour 3 , Paul A. Lyons 1 , Laurence B. Peterson 4...
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Methods: Haplotype Analysis in Multiple Crosses to Identify a QTL Gene
- Xiaosong Wang,
- Ron Korstanje,
- David Higgins,
- and Beverly Paigen
Genome Res. September 2004 14: 1767-1772; Published in Advance August 12, 2004, doi:10.1101/gr.2668204
...?”: Deciding when one has demonstrated specific genetic causation in complex diseases and quantitative traits. Am. J. Hum. Genet. 73 : 711 -719. ↵ Park, Y.G., Clifford, R., Buetow, K.H., and Hunter, K.W. 2003 . Multiple cross and inbred strain haplotype mapping of complex-trait candidate genes. Genome Res. 13...
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Research: Identifying multiple causative genes at a single GWAS locus
- Michael J. Flister,
- Shirng-Wern Tsaih,
- Caitlin C. O'Meara,
- Bradley Endres,
- Matthew J. Hoffman,
- Aron M. Geurts,
- Melinda R. Dwinell,
- Jozef Lazar,
- Howard J. Jacob,
- and Carol Moreno
Genome Res. December 2013 23: 1996-2002; Published in Advance September 4, 2013, doi:10.1101/gr.160283.113
...for ZFN-induced mutations by PCR amplification with the vendor-supplied primers (Supplemental Table 2) and assayed with the SURVEYOR Mutation Detection kit (Transgenomic, Inc.). Mutant alleles were then confirmed by Sanger sequencing. F0 animals were back-crossed to the parental strain, and multiple pairs...
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Research: Genetic analysis of complex traits in the emerging Collaborative Cross
- David L. Aylor,
- William Valdar,
- Wendy Foulds-Mathes,
- Ryan J. Buus,
- Ricardo A. Verdugo,
- Ralph S. Baric,
- Martin T. Ferris,
- Jeff A. Frelinger,
- Mark Heise,
- Matt B. Frieman,
- Lisa E. Gralinski,
- Timothy A. Bell,
- John D. Didion,
- Kunjie Hua,
- Derrick L. Nehrenberg,
- Christine L. Powell,
- Jill Steigerwalt,
- Yuying Xie,
- Samir N.P. Kelada,
- Francis S. Collins,
- Ivana V. Yang,
- David A. Schwartz,
- Lisa A. Branstetter,
- Elissa J. Chesler,
- Darla R. Miller,
- Jason Spence,
- Eric Yi Liu,
- Leonard McMillan,
- Abhishek Sarkar,
- Jeremy Wang,
- Wei Wang,
- Qi Zhang,
- Karl W. Broman,
- Ron Korstanje,
- Caroline Durrant,
- Richard Mott,
- Fuad A. Iraqi,
- Daniel Pomp,
- David Threadgill,
- Fernando Pardo-Manuel de Villena,
- and Gary A. Churchill
Genome Res. August 2011 21: 1213-1222; Published in Advance March 15, 2011, doi:10.1101/gr.111310.110
.... Abstract The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome...
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Research: Genetic analysis in the Collaborative Cross breeding population
- Vivek M. Philip,
- Greta Sokoloff,
- Cheryl L. Ackert-Bicknell,
- Martin Striz,
- Lisa Branstetter,
- Melissa A. Beckmann,
- Jason S. Spence,
- Barbara L. Jackson,
- Leslie D. Galloway,
- Paul Barker,
- Ann M. Wymore,
- Patricia R. Hunsicker,
- David C. Durtschi,
- Ginger S. Shaw,
- Sarah Shinpock,
- Kenneth F. Manly,
- Darla R. Miller,
- Kevin D. Donohue,
- Cymbeline T. Culiat,
- Gary A. Churchill,
- William R. Lariviere,
- Abraham A. Palmer,
- Bruce F. O'Hara,
- Brynn H. Voy,
- and Elissa J. Chesler
Genome Res. August 2011 21: 1223-1238; Published in Advance July 6, 2011, doi:10.1101/gr.113886.110
...diversity. The existing panel of common inbred strains reflects historical selection biases, and existing recombinant inbred panels have low allelic diversity. All such populations may be subject to consequences of inbreeding depression. The Collaborative Cross (CC) is a mouse reference population with high...
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