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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
...an increased count of repeats in Hereford relative to Simmental and other white-headed cattle breeds from the graph alignment coverage, suggesting a large under-assembly in the current Hereford-based cattle reference , which had fewer copies. Our work shows that exploiting assembly path similarities within...
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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
....marques@upf.eduAbstractExtreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive -wide...
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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
...in tropical and subtropical climates. The observation of breed-specific sequence in each breed and the level of diversity among global cattle adapted and selected in specific environments indicate the need to include a broader sampling of existing breeds to improve the pan representation. A pan incorporating...
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Resource: The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
- Zhengcao Li,
- Xiaohong Liu,
- Chen Wang,
- Zhenyang Li,
- Bo Jiang,
- Ruifeng Zhang,
- Lu Tong,
- Youping Qu,
- Sheng He,
- Haifan Chen,
- Yafei Mao,
- Qingnan Li,
- Torsten Pook,
- Yu Wu,
- Yanjun Zan,
- Hui Zhang,
- Lu Li,
- Keying Wen,
- and Yaosheng Chen
Genome Res. October 2023 33: 1833-1847; Published in Advance November 1, 2023, doi:10.1101/gr.277638.122
...emerged as an important driving force for evolution and phenotypic variation in various organisms, yet their contributions to genetic diversity and adaptation in domesticated animals remain largely unknown. Here we constructed a pan based on 250 sequenced individuals from 32 pig breeds in Eurasia...
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Method: Variations in antibody repertoires correlate with vaccine responses
- Yana Safonova,
- Sung Bong Shin,
- Luke Kramer,
- James Reecy,
- Corey T. Watson,
- Timothy P.L. Smith,
- and Pavel A. Pevzner
Genome Res. April 2022 32: 791-804; Published in Advance March 31, 2022, doi:10.1101/gr.276027.121
...cattle for ongoing breeding programs.IntroductionThe challenge of identifying variations in immunoglobulin genes that affect vaccine responseAlthough vaccination is a primary tool to control the spread of viral and bacterial diseases, the success of vaccines at the population level does not always...
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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
..., which are only biological important for the given traits in certain physiological stages or environmental conditions.Due to the large amount of linkage disequilibrium (LD) among genomic markers within a single cattle breed (e.g., Holstein), traditional single-component prediction models (e.g., GBLUP...
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Resource: Copy number variation of individual cattle genomes using next-generation sequencing
- Derek M. Bickhart,
- Yali Hou,
- Steven G. Schroeder,
- Can Alkan,
- Maria Francesca Cardone,
- Lakshmi K. Matukumalli,
- Jiuzhou Song,
- Robert D. Schnabel,
- Mario Ventura,
- Jeremy F. Taylor,
- Jose Fernando Garcia,
- Curtis P. Van Tassell,
- Tad S. Sonstegard,
- Evan E. Eichler,
- and George E. Liu
Genome Res. April 2012 22: 778-790; Published in Advance February 2, 2012, doi:10.1101/gr.133967.111
...content of unique CNVs among the Angus individuals. A total of 23.4Mbp of large SDs is shared among the four cattle breeds (36% of the intervals and 43% by base pair) (Supplemental Fig. S1). We found the greatest CNV diversity for the indicine Nelore individual, BINE, with a total of 245 CNVs...
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Research: Identification of copy number variants in horses
- Ryan Doan,
- Noah Cohen,
- Jessica Harrington,
- Kylee Veazy,
- Rytis Juras,
- Gus Cothran,
- Molly E. McCue,
- Loren Skow,
- and Scott V. Dindot
Genome Res. May 2012 22: 899-907; Published in Advance March 1, 2012, doi:10.1101/gr.128991.111
...variations among diverse cattle breeds. Genome Res 20: 693–703. ↵ Livak KJ, Schmittgen TD Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-ΔΔ C(T)) method. Methods 25: 402–408. ↵ McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM...
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Research: Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle
- Naveen Kumar Kadri,
- Chad Harland,
- Pierre Faux,
- Nadine Cambisano,
- Latifa Karim,
- Wouter Coppieters,
- Sébastien Fritz,
- Erik Mullaart,
- Denis Baurain,
- Didier Boichard,
- Richard Spelman,
- Carole Charlier,
- Michel Georges,
- and Tom Druet
Genome Res. October 2016 26: 1323-1332; Published in Advance August 11, 2016, doi:10.1101/gr.204214.116
.... These can be used to map quantitative trait loci (QTL) affecting individual variation in -wide or global recombination rate (GRR). Such GWAS have been conducted in humans (Kong et al. 2008, 2014; Chowdhury et al. 2009; Fledel-Alon et al. 2011), cattle (Sandor et al. 2012; Ma et al. 2015), and sheep...
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Resource: Haplotype-resolved 3D chromatin architecture of the hybrid pig
- Yu Lin,
- Jing Li,
- Yiren Gu,
- Long Jin,
- Jingyi Bai,
- Jiaman Zhang,
- Yujie Wang,
- Pengliang Liu,
- Keren Long,
- Mengnan He,
- Diyan Li,
- Can Liu,
- Ziyin Han,
- Yu Zhang,
- Xiaokai Li,
- Bo Zeng,
- Lu Lu,
- Fanli Kong,
- Ying Sun,
- Yongliang Fan,
- Xun Wang,
- Tao Wang,
- An'an Jiang,
- Jideng Ma,
- Linyuan Shen,
- Li Zhu,
- Yanzhi Jiang,
- Guoqing Tang,
- Xiaolan Fan,
- Qingyou Liu,
- Hua Li,
- Jinyong Wang,
- Li Chen,
- Liangpeng Ge,
- Xuewei Li,
- Qianzi Tang,
- and Mingzhou Li
Genome Res. February 2024 34: 310-325; Published in Advance March 13, 2024, doi:10.1101/gr.278101.123
...in the eighteenth century, and especially since the strong genetic selection of inbred commercial lines within the past 70 years (Groenen et al. 2012), many of these breeds show remarkable phenotypic diversity and genetic adaptations that provide a sufficient number of segregating sites to distinguish allele...
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