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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
...of variation, have propelled the domestic dog to new levels as a system for understanding fundamental principles in mammalian biology. Central to this advance are more than 350 recognized breeds, each a closed population that has undergone selection for unique features. Genetic variation in the domestic dog...
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Research: Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation
- Xin Li,
- San-Gang He,
- Wen-Rong Li,
- Ling-Yun Luo,
- Ze Yan,
- Dong-Xin Mo,
- Xing Wan,
- Feng-Hua Lv,
- Ji Yang,
- Ya-Xi Xu,
- Juan Deng,
- Qiang-Hui Zhu,
- Xing-Long Xie,
- Song-Song Xu,
- Chen-Xi Liu,
- Xin-Rong Peng,
- Bin Han,
- Zhong-Hui Li,
- Lei Chen,
- Jian-Lin Han,
- Xue-Zhi Ding,
- Renqing Dingkao,
- Yue-Feng Chu,
- Jin-Yan Wu,
- Li-Min Wang,
- Ping Zhou,
- Ming-Jun Liu,
- and Meng-Hua Li
Genome Res. September 2022 32: 1669-1684; Published in Advance August 10, 2022, doi:10.1101/gr.276769.122
..., China ↵13 These authors contributed equally to this work. Corresponding authors: menghua.li@cau.edu.cn, liumingjun@xjaas.netAbstractUnderstanding the genetic mechanisms of phenotypic variation in hybrids between domestic animals and their wild relatives may aid germplasm innovation. Here, we report...
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Research: A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids
- Bridgett M. vonHoldt,
- John P. Pollinger,
- Dent A. Earl,
- James C. Knowles,
- Adam R. Boyko,
- Heidi Parker,
- Eli Geffen,
- Malgorzata Pilot,
- Wlodzimierz Jedrzejewski,
- Bogumila Jedrzejewska,
- Vadim Sidorovich,
- Claudia Greco,
- Ettore Randi,
- Marco Musiani,
- Roland Kays,
- Carlos D. Bustamante,
- Elaine A. Ostrander,
- John Novembre,
- and Robert K. Wayne
Genome Res. August 2011 21: 1294-1305; Published in Advance May 12, 2011, doi:10.1101/gr.116301.110
...increase the resolution of demographic history and ancestry in wild relatives. We use a SNP genotyping microarray developed for the domestic dog to assay variation in over 48K loci in wolf-like species worldwide. Despite the high mobility of these large carnivores, we find distinct hierarchical population...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...graph pans can reveal trait-associated complex SVs.Natural selection, domestication, and selective breeding have shaped the genetic and phenotypic variation of modern cattle (Bos taurus). Hundreds of cattle breeds are recognized worldwide belonging to the indicine (Bos taurus indicus) or taurine (Bos...
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Research: Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity
- Conor J. Kelly,
- Carol G. Chitko-McKown,
- and Edward B. Chuong
Genome Res. August 2022 32: 1474-1486; Published in Advance August 10, 2022, doi:10.1101/gr.276241.121
...networks.Modern cattle were domesticated 10,000 years ago and are an important livestock species (Troy et al. 2001; Orozco-terWengel et al. 2015). Cattle exhibit extensive phenotypic diversity, with over 1000 recognized breeds and closely related subspecies. Understanding the evolution and genetic basis...
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Research: Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor
- Brennan Decker,
- Brian W. Davis,
- Maud Rimbault,
- Adrienne H. Long,
- Eric Karlins,
- Vidhya Jagannathan,
- Rebecca Reiman,
- Heidi G. Parker,
- Cord Drögemüller,
- Jason J. Corneveaux,
- Erica S. Chapman,
- Jeffery M. Trent,
- Tosso Leeb,
- Matthew J. Huentelman,
- Robert K. Wayne,
- Danielle M. Karyadi,
- and Elaine A. Ostrander
Genome Res. November 2015 25: 1646-1655; Published in Advance July 31, 2015, doi:10.1101/gr.190314.115
...16 genes with strong Figure 1. Founder-inherited versus somatic variation in CTVT. (A) Fraction of SNVs from 186 sequenced canids found in canine dbSNP (mean 32.65%). Sequenced canids included the two host dogs, 64 dogs representing 40 modern breeds, 27 dogs representing 12 ancient breeds, 86 outbred...
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PERSPECTIVE: The canine genome
- Elaine A. Ostrander and
- Robert K. Wayne
Genome Res. December 2005 15: 1706-1716; doi:10.1101/gr.3736605
...a primer to use the dog genome by first focusing on its evolutionary history. We overview the relationship of dogs to wild canids and discuss their origin and domestication. Dogs clearly originated from a substantial number of gray wolves and dog breeds define distinct genetic units that can be divided...
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Dog Special/Letters: Short interspersed elements (SINEs) are a major source of canine genomic diversity
- Wei Wang and
- Ewen F. Kirkness
Genome Res. December 2005 15: 1798-1808; doi:10.1101/gr.3765505
...of identity-by-descent, and easy typing methodologies, that make these abundant variations a valuable additional resource for identifying the ancestral relationships between different dog breeds, and between domesticated dogs and wild canids. It is also relevant to note that recent observations of extensive...
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Research: The recombination landscape of the zebra finch Taeniopygia guttata genome
- Niclas Backström,
- Wolfgang Forstmeier,
- Holger Schielzeth,
- Harriet Mellenius,
- Kiwoong Nam,
- Elisabeth Bolund,
- Matthew T. Webster,
- Torbjörn Öst,
- Melanie Schneider,
- Bart Kempenaers,
- and Hans Ellegren
Genome Res. April 2010 20: 485-495; Published in Advance March 31, 2010, doi:10.1101/gr.101410.109
...structured dog breeds (Sutter et al. 2004), a useful approach for trait mapping will be to use within-population LD to map candidate regions and then combine information from several populations for fine-tuned mapping of causative variants. The significant heterogeneity in recombination rate observed...
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COMMENTARY: Canid genomics: Mapping genes for behavior in the silver fox
- Tyrone C. Spady and
- Elaine A. Ostrander
Genome Res. March 2007 17: 259-263; Published in Advance February 6, 2007, doi:10.1101/gr.6055807
..., and studies of canid phylogenetic relationships show that gray wolves are the sole progenitor to the domestic dog ( Clutton-Brock 1995 ; Vila et al. 1997 , 1999b ; Wayne et al. 1997 ) ( Fig. 1B ). The study of genetic diversity across canids indicates that dogs first originated in East Asia and subsequently...

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