Searching journal content for articles similar to Ideraabdullah et al. 14 (10a): 1880.

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Resource: GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis
- Robyn L. Ball,
- Molly A. Bogue,
- Hongping Liang,
- Anuj Srivastava,
- David G. Ashbrook,
- Anna Lamoureux,
- Matthew W. Gerring,
- Alexander S. Hatoum,
- Matthew J. Kim,
- Hao He,
- Jake Emerson,
- Alexander K. Berger,
- David O. Walton,
- Keith Sheppard,
- Baha El Kassaby,
- Francisco Castellanos,
- Govindarajan Kunde-Ramamoorthy,
- Lu Lu,
- John Bluis,
- Sejal Desai,
- Beth A. Sundberg,
- Gary Peltz,
- Zhuoqing Fang,
- Gary A. Churchill,
- Robert W. Williams,
- Arpana Agrawal,
- Carol J. Bult,
- Vivek M. Philip,
- and Elissa J. Chesler
Genome Res. January 2024 34: 145-159; Published in Advance January 30, 2024, doi:10.1101/gr.278157.123
...-relevant traits have been characterized in mice and made publicly available. New strains and populations including consomics, the collaborative cross, expanded BXD, and inbred wild-derived strains add to existing complex disease mouse models, mapping populations, and sensitized backgrounds for engineered...
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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
...activity (Tanaka et al. 1991). Yang et al. (2011) reported that the origins and compositions of the s of classical inbred strains depend on the use of wild-derived inbred strains as reference s to infer subspecific origin. This is because some wild-derived inbred strains suffered intersubspecific...
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Research: Inference of selective forces on house mouse genomes during secondary contact in East Asia
- Kazumichi Fujiwara,
- Shunpei Kubo,
- Toshinori Endo,
- Toyoyuki Takada,
- Toshihiko Shiroishi,
- Hitoshi Suzuki,
- and Naoki Osada
Genome Res. March 2024 34: 366-375; Published in Advance March 20, 2024, doi:10.1101/gr.278828.123
...this (Scavetta and Tautz 2010; Cocquet et al. 2012). Morgan and Pardo-Manuel (2017) showed that the subspecies musculus tended to have higher Sly/Slx copy numbers than other subspecies, but their analyzed samples were biased toward wild-derived inbred lines (Morgan and Pardo-Manuel de Villena 2017). Therefore...
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LETTER: Significant gene content variation characterizes the genomes of inbred mouse strains
- Gene Cutler,
- Lisa A. Marshall,
- Ni Chin,
- Helene Baribault,
- and Paul D. Kassner
Genome Res. December 2007 17: 1743-1754; Published in Advance November 7, 2007, doi:10.1101/gr.6754607
...in independent C57BL/6J mouse samples (data not shown). The strains with the largest numbers of CNVs (SPRET/EiJ, CZECHII/EiJ, PWK/PhJ, MOLF/EiJ, JF1/Ms, CAST/EiJ), being wild-derived, are the most genetically distant from the reference C57BL/6J strain as one would expect. Likewise, the strains with the fewest...
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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
...: Their APOA2 sequence had an Ala 61 -to-Val 61 substitution, and none of them were wild-derived strains (all were inbred laboratory mice). The other APOA2 types each had at least one wild-derived strain: “a” type contains M. m. castaneus, M. m. musculus , and M. m. molossinus (a mixture of the previous two...
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LETTER: Segmental Phylogenetic Relationships of Inbred Mouse Strains Revealed by Fine-Scale Analysis of Sequence Variation Across 4.6 Mb of Mouse Genome
- Kelly A. Frazer,
- Claire M. Wade,
- David A. Hinds,
- Nila Patil,
- David R. Cox,
- and Mark J. Daly
Genome Res. August 2004 14: 1493-1500; doi:10.1101/gr.2627804
...mouse strains is needed. Here, we use high-density oligonucleotide arrays to discover an extremely dense set of SNPs in 13 classical and two wild-derived inbred strains in five genomic intervals totaling 4.6 Mb of DNA sequence, and then analyze the segmental haplotype structure defined by these high...
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LETTER: A high-resolution multistrain haplotype analysis of laboratory mouse genome reveals three distinctive genetic variation patterns
- Jinghui Zhang,
- Kent W. Hunter,
- Michael Gandolph,
- William L. Rowe,
- Richard P. Finney,
- Jenny M. Kelley,
- Michael Edmonson,
- and Kenneth H. Buetow
Genome Res. February 2005 15: 241-249; doi:10.1101/gr.2901705
..., a third haplotype was found in the wild-derived strains PERA/Pk, PERC/Ei, and ZALENDE/Ei but not in the laboratory inbred strains. Haplotypes of the last two SNPs polymorphic in domesticus strains (marked by red asterisks in Fig. 7A ) in segment 1 are biallelic (among the wild-derived domesticus strains...
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Review: Contrasting genetic architectures in different mouse reference populations used for studying complex traits
- David A. Buchner and
- Joseph H. Nadeau
Genome Res. June 2015 25: 775-791; Published in Advance May 7, 2015, doi:10.1101/gr.187450.114
...corresponding investigations in humans (Schughart et al. 2013). Insights from mouse models Initially, investigators relied on existing genetic and phenotypic diversity among the many inbred strains of mice. Thousands and perhaps millions of DNA sequence variants that differ among these strains contribute...
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Research: Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection
- Caroline Durrant,
- Hanna Tayem,
- Binnaz Yalcin,
- James Cleak,
- Leo Goodstadt,
- Fernando Pardo-Manuel de Villena,
- Richard Mott,
- and Fuad A. Iraqi
Genome Res. August 2011 21: 1239-1248; Published in Advance April 14, 2011, doi:10.1101/gr.118786.110
...involved contrasts between wild-derived founder strains and therefore would not segregate between classical inbred strains. Use of variation data from the genomes of the CC founder strains refined these QTLs further and suggested several candidate genes. These results support the use of the CC...
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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
...strains, including five classical inbred strains (A/J, C57BL/6J, 129S1/SvImJ, NOD/LtJ, and NZO/H1LtJ) and three wild-derived strains representing the three Mus musculus subspecies (CAST/EiJ, PWK/PhJ, and WSB/EiJ). The eight founder strains capture a level of genetic diversity unsurpassed by any existing...

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