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Resource: An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Can Yuan,
- Lijing Tang,
- Thomas Lopdell,
- Vyacheslav A. Petrov,
- Claire Oget-Ebrad,
- Gabriel Costa Monteiro Moreira,
- José Luis Gualdrón Duarte,
- Arnaud Sartelet,
- Zhangrui Cheng,
- Mazdak Salavati,
- D. Claire Wathes,
- Mark A. Crowe,
- GplusE Consortium,
- Wouter Coppieters,
- Mathew Littlejohn,
- Carole Charlier,
- Tom Druet,
- Michel Georges,
- and Haruko Takeda
Genome Res. October 2023 33: 1848-1864; Published in Advance September 26, 2023, doi:10.1101/gr.277947.123
...expressed genes, 14,289 genes were retained for eQTL analyses in blood and 15,458 in liver. All samples were genotyped with a high-density SNV array interrogating 777,962 variants and imputed to whole using Minimac4 (Das et al. 2016) and the 264 sequenced Holstein animals as reference. This yielded usable...
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LETTER: Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle
- Miri Cohen-Zinder,
- Eyal Seroussi,
- Denis M. Larkin,
- Juan J. Loor,
- Annelie Everts-van der Wind,
- Jun-Heon Lee,
- James K. Drackley,
- Mark R. Band,
- A.G. Hernandez,
- Moshe Shani,
- Harris A. Lewin,
- Joel I. Weller,
- and Micha Ron
Genome Res. July 2005 15: 936-944; doi:10.1101/gr.3806705
.... Cancer 2 : 48 -58. ↵ Grisart, B., Coppieters, W., Farnir, F., Karim, L., Ford, C., Berzi, P., Cambisano, N., Mni, M., Reid, S., Simon, P., et al. 2002 . Positional candidate cloning of a QTL in dairy cattle: Identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield...
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Resource: Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle
- Lingzhao Fang,
- Wentao Cai,
- Shuli Liu,
- Oriol Canela-Xandri,
- Yahui Gao,
- Jicai Jiang,
- Konrad Rawlik,
- Bingjie Li,
- Steven G. Schroeder,
- Benjamin D. Rosen,
- Cong-jun Li,
- Tad S. Sonstegard,
- Leeson J. Alexander,
- Curtis P. Van Tassell,
- Paul M. VanRaden,
- John B. Cole,
- Ying Yu,
- Shengli Zhang,
- Albert Tenesa,
- Li Ma,
- and George E. Liu
Genome Res. May 2020 30: 790-801; Published in Advance May 18, 2020, doi:10.1101/gr.250704.119
...in brain regions (Fig. 5B). By examining quantitative trait loci (QTL) of 19 milk-relevant traits in cattle QTLdb, we confirmed that brain-specific genes were significantly enriched for genes (i.e., closest genes to the lead SNPs) associated with milk production traits (e.g., milk yield and fat...
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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
...al. 2002 . Positional candidate cloning of a QTL in dairy cattle: Identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Res. 12 : 222 –231. ↵ Grobet, L., Martin, L.J., Poncelet, D., Pirottin, D., Brouwers, B., Riquet, J., Schoeberlein...
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PERSPECTIVE: Advances in livestock genomics: Opening the barn door
- James E. Womack
Genome Res. December 2005 15: 1699-1705; doi:10.1101/gr.3809105
...ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle. Genome Res. 15 : 936 -944. ↵ Collins, F.S., Green, E.D., Guttmacher, A.E., and Guyer, M.S. 2003 . US National Human Genome Research Institute, a vision for the future of genomics research...

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