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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...was associated with behavioral trait data collected from 46,000 dogs. Further, lineage-specific variation was associated with genes in neurodevelopmental coexpression networks, suggesting that the accumulation of many small effect variants drove behavioral diversification between breeds (Dutrow et al. 2022...
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Research: Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
- Aitor Serres-Armero,
- Brian W. Davis,
- Inna S. Povolotskaya,
- Carlos Morcillo-Suarez,
- Jocelyn Plassais,
- David Juan,
- Elaine A. Ostrander,
- and Tomas Marques-Bonet
Genome Res. May 2021 31: 762-774; Published in Advance April 16, 2021, doi:10.1101/gr.266049.120
...study of structural variation as it relates to breed-specific phenotypes is lacking. We have generated whole CNV maps for more than 300 canids. Our data set extends the canine structural variation landscape to more than 100 dog breeds, including novel variants that cannot be assessed using microarray...
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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
...body size in dogs.An additional variant revealed by this study that may correspond to a breed trait is the stop-gained at position p.Glu391* in CSF1 in Chows. The variant was homozygous in all six unrelated Chows, heterozygous in one of five Elos, and absent from two Eurasiers, the latter two breeds...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...except for the three taurine breeds) were separated. The Hereford breed for the ARS-UCD1.2 assembly was also separated. This offered an excellent chance to explain the three-cross breeding breed Beefmaster, which carries about one-half Brahman ancestry (India indicine) and one-fourth each of Hereford...
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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...using Picard MarkDuplicates tool v.3.1.0 (http://broadinstitute.github.io/picard), and called variants using DeepVariant v1.5.0 (Poplin et al. 2018). We then filtered for sites with genotype 1/1 and a “PASS” filter value, meaning that all or nearly all reads support an alternative sequence...
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Research: Worldwide patterns of genomic variation and admixture in gray wolves
- Zhenxin Fan,
- Pedro Silva,
- Ilan Gronau,
- Shuoguo Wang,
- Aitor Serres Armero,
- Rena M. Schweizer,
- Oscar Ramirez,
- John Pollinger,
- Marco Galaverni,
- Diego Ortega Del-Vecchyo,
- Lianming Du,
- Wenping Zhang,
- Zhihe Zhang,
- Jinchuan Xing,
- Carles Vilà,
- Tomas Marques-Bonet,
- Raquel Godinho,
- Bisong Yue,
- and Robert K. Wayne
Genome Res. February 2016 26: 163-173; Published in Advance December 17, 2015, doi:10.1101/gr.197517.115
...of breed and village dogs, which concluded that dogs originated inCentral Asia (Shannon et al. 2015). Consequently, we test for alternative regions of origin with a geographically broad sample of gray wolves. The release of the boxer in 2005 (Lindblad-Toh et al. 2005) provided a high-quality dog reference...
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Resource: Mapping DNA structural variation in dogs
- Wei-Kang Chen,
- Joshua D. Swartz,
- Laura J. Rush,
- and Carlos E. Alvarez
Genome Res. March 2009 19: 500-509; Published in Advance November 17, 2008, doi:10.1101/gr.083741.108
...be common within breed classes ( Figs. 2 , 3 ). Some other CNVs could have preceded the divergence of dog breed classes and others may have occurred independently in different breeds. View larger version: In this window In a new window Figure 2. Copy number variants (CNVs) in the four main classes of dog...
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ARTICLE: Extensive and breed-specific linkage disequilibrium in Canis familiaris
- Nathan B. Sutter,
- Michael A. Eberle,
- Heidi G. Parker,
- Barbara J. Pullar,
- Ewen F. Kirkness,
- Leonid Kruglyak,
- and Elaine A. Ostrander
Genome Res. December 2004 14: 2388-2396; Published in Advance November 15, 2004, doi:10.1101/gr.3147604
...intervals, each 5 Mb in length and composed of five clusters of sequence variants spaced 800 kb-1.6 Mb apart. These intervals are located on canine chromosomes 1, 2, 3, 34, and 37, and none is under obvious selective pressure. Approximately 20 unrelated dogs were assayed from each of five breeds: Akita...
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Research: Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations
- Mirte Bosse,
- Hendrik-Jan Megens,
- Ole Madsen,
- Richard P.M.A. Crooijmans,
- Oliver A. Ryder,
- Frédéric Austerlitz,
- Martien A.M. Groenen,
- and M. Angeles R. de Cara
Genome Res. July 2015 25: 970-981; Published in Advance June 10, 2015, doi:10.1101/gr.187039.114
...of the population, aswell as to potentially select variants that have fitness consequences (Frankham et al. 2002). Conservation programs usually use small numbers of breeding individuals, and thus, genetic variation can decrease rapidly. In commercial breeding programs, artificial selection can lead to a reduction...

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