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Resource: Exploration of fine-scale recombination rate variation in the domestic horse
- Samantha K. Beeson,
- James R. Mickelson,
- and Molly E. McCue
Genome Res. October 2019 29: 1744-1752; Published in Advance August 21, 2019, doi:10.1101/gr.243311.118
...domestication has resulted in numerous breeds specialized for the purpose of performing work or participating in athletic competition, and genomic resources have been under development to enable investigation of the genetic bases for such traits. Low-resolution linkage maps for the domestic horse were first...
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Resource: A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate
- Martien A.M. Groenen,
- Per Wahlberg,
- Mario Foglio,
- Hans H. Cheng,
- Hendrik-Jan Megens,
- Richard P.M.A. Crooijmans,
- Francois Besnier,
- Mark Lathrop,
- William M. Muir,
- Gane Ka-Shu Wong,
- Ivo Gut,
- and Leif Andersson
Genome Res. March 2009 19: 510-519; Published in Advance December 16, 2008, doi:10.1101/gr.086538.108
...this table: In this window In a new window Table 1. Genetic and physical size of the chicken chromosomes Genome assembly and missing chromosomes Our new map consists of 34 linkage groups and covers at least 29 of the 38 autosomes. If the four new linkage groups (LG2–LG5) each represent an individual...
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RESOURCE: The First-Generation Whole-Genome Radiation Hybrid Map in the Horse Identifies Conserved Segments in Human and Mouse Genomes
- Bhanu P. Chowdhary,
- Terje Raudsepp,
- Srinivas R. Kata,
- Glenda Goh,
- Lee V. Millon,
- Veronica Allan,
- François Piumi,
- Gérard Guérin,
- June Swinburne,
- Matthew Binns,
- Teri L. Lear,
- Jim Mickelson,
- James Murray,
- Douglas F. Antczak,
- James E. Womack,
- and Loren C. Skow
Genome Res. April 1, 2003 13: 742-751; doi:10.1101/gr.917503
...to horse, human, and mouse. Discovery of these conserved linkages provides a quick comparative overview of smaller genomic blocks shared among the three species and signifies an important advance in accurate alignment of the three s. Overview The RH and comparative map presented here is the most elaborate...
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LETTER: A Comparative Gene Map of the Horse (Equus caballus)
- Alexandre R. Caetano,
- Yow-Ling Shiue,
- Leslie A. Lyons,
- Steven J. O'Brien,
- Thomas F. Laughlin,
- Ann T. Bowling,
- and James D. Murray
Genome Res. December 1, 1999 9: 1239-1249; doi:10.1101/gr.9.12.1239
...chromosome 3 by in situ hybridization. Cytogenet. &amp; Cell Genet. 82 : 112 – 113 . ↵ Lindgren G. , Sandberg K. , Persson H. , Marklund S. , Breen M. , Sandgren B. , Carlstén J. , Ellegren H. ( 1998 ) A primary male autosomal linkage map of the horse . Genome Res. 8 : 951 – 966 . ↵ Lyons L.A. , Laughlin T...
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Research: Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia
- Xiao Gou,
- Zhen Wang,
- Ning Li,
- Feng Qiu,
- Ze Xu,
- Dawei Yan,
- Shuli Yang,
- Jia Jia,
- Xiaoyan Kong,
- Zehui Wei,
- Shaoxiong Lu,
- Linsheng Lian,
- Changxin Wu,
- Xueyan Wang,
- Guozhi Li,
- Teng Ma,
- Qiang Jiang,
- Xue Zhao,
- Jiaqiang Yang,
- Baohong Liu,
- Dongkai Wei,
- Hong Li,
- Jianfa Yang,
- Yulin Yan,
- Guiying Zhao,
- Xinxing Dong,
- Mingli Li,
- Weidong Deng,
- Jing Leng,
- Chaochun Wei,
- Chuan Wang,
- Huaming Mao,
- Hao Zhang,
- Guohui Ding,
- and Yixue Li
Genome Res. August 2014 24: 1308-1315; Published in Advance April 10, 2014, doi:10.1101/gr.171876.113
...Gettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948. Gou et al. 1314 Genome Research www..org Li H. 2011. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical...
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RESOURCE: A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates
- Annelie Everts-van der Wind,
- Srinivas R. Kata,
- Mark R. Band,
- Mark Rebeiz,
- Denis M. Larkin,
- Robin E. Everts,
- Cheryl A. Green,
- Lei Liu,
- Shreedhar Natarajan,
- Tom Goldammer,
- Jun Heon Lee,
- Stephanie McKay,
- James E. Womack,
- and Harris A. Lewin
Genome Res. July 2004 14: 1424-1437; doi:10.1101/gr.2554404
...orientation of the linkage groups (Supplemental Table 1). The map contains 86 linkage groups assigned to all 29 autosomes and the X chromosome ( Table 1 ); 667 are framework markers ( Fig. 1 ). Relatively few markers are unlinked (n = 58), or linked with ambiguous placement (n = 63). Failure of these markers...
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LETTER: An Ordered Comparative Map of the Cattle and Human Genomes
- Mark R. Band,
- Joshua H. Larson,
- Mark Rebeiz,
- Cheryl A. Green,
- D. Wayne Heyen,
- Jena Donovan,
- Ryan Windish,
- Chad Steining,
- Prapti Mahyuddin,
- James E. Womack,
- and Harris A. Lewin
Genome Res. September 1, 2000 10: 1359-1368; doi:10.1101/gr.145900
...genes in public domain databases to create a whole- RH map. A COMPASS software tool facilitated the map-building process. The whole- cattle RH map was anchored with microsatellite markers from the existing cattle linkage maps. Construction of RH maps for all bovine autosomes and the X chromosome allowed...
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RESOURCE: High-Density Rat Radiation Hybrid Maps Containing Over 24,000 SSLPs, Genes, and ESTs Provide a Direct Link to the Rat Genome Sequence
- Anne E. Kwitek,
- Jo Gullings-Handley,
- Jiaming Yu,
- Danilo C. Carlos,
- Kimberly Orlebeke,
- Jeff Nie,
- Jeffrey Eckert,
- Angela Lemke,
- Jaime Wendt Andrae,
- Susan Bromberg,
- Dean Pasko,
- Dan Chen,
- Todd E. Scheetz,
- Thomas L. Casavant,
- M. Bento Soares,
- Val C. Sheffield,
- Peter J. Tonellato,
- and Howard J. Jacob
Genome Res. April 2004 14: 750-757; doi:10.1101/gr.1968704
.... ↵ Bihoreau, M., Sebag-Montefiore, L., Godfrey, R., Wallis, R., Brown, J., Danoy, P., Collins, S., Rouhard, M., Kaisaki, P., Lathrop, M., et al. 2001 . A high-resolution consensus linkage map of the rat, integrating radiation hybrid and genetic maps. Genomics 75 : 57 -69. ↵ Chowdhary, B., Raudsepp, T., Kata...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...phenotypic differences between breeds. Collectively, our work provides a road map for performing constraint-based analysis of genetic variation in other domesticated species with similar genomic resources, such as cattle, swine, and horses.ResultsA framework for evaluating gene sequence constraint metricsGenomic...
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REVIEW: Emerging Patterns of Comparative Genome Organization in Some Mammalian Species as Revealed by Zoo-FISH
- Bhanu P. Chowdhary,
- Terje Raudsepp,
- Lutz Frönicke,
- and Harry Scherthan
Genome Res. June 1, 1998 8: 577-589; doi:10.1101/gr.8.6.577
...–19 fission and 2–5 fusion events) leading to the pig, cattle, Indian muntjac, and horse karyotypes can be observed. Overall Conservation of Karyotypic Organization The accumulating gene mapping data across evolutionarily diverged species has progressively indicated that large genomic segments are conserved...

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