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Resource: Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle
- Alexander S. Leonard,
- Xena M. Mapel,
- and Hubert Pausch
Genome Res. February 2024 34: 300-309; Published in Advance February 14, 2024, doi:10.1101/gr.278267.123
...-eQTL for STN1 and MYH7 and SV-sQTL for CEP89 and ASAH2. Extensive linkage disequilibrium between small and structural variation results in only 28 additional eQTL and 17 sQTL discovered when including SVs, although many top associated SVs are compelling candidates.Assigning functional information to genetic...
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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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Research: Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome
- Jessica Stapley,
- Tim R. Birkhead,
- Terry Burke,
- and Jon Slate
Genome Res. April 2010 20: 496-502; Published in Advance March 31, 2010, doi:10.1101/gr.102095.109
...on finescale patterns of linkage disequilibrium. Hum Mol Genet 13: 577–588. KhatkarM, Nicholas F, Collins A, Zenger K, Cavanagh J, BarrisW, Schnabel R, Taylor J, RaadsmaH. 2008. Extent of -wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics 9: 187...
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Research: After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection
- Amine Namouchi,
- Xavier Didelot,
- Ulrike Schöck,
- Brigitte Gicquel,
- and Eduardo P.C. Rocha
Genome Res. April 2012 22: 721-734; Published in Advance February 29, 2012, doi:10.1101/gr.129544.111
...linkage disequilibrium (y-axis) and genomic distance between pairs of SNPs (x-axis). (Blue line) LD computed using all SNPs; (red line) LD after excluding SNPs identified in recombination tracts. Namouchi et al. 726 Genome Research www..org This is also well below the extant G+C composition...
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Resource: Analysis of copy number variations among diverse cattle breeds
- George E. Liu,
- Yali Hou,
- Bin Zhu,
- Maria Francesca Cardone,
- Lu Jiang,
- Angelo Cellamare,
- Apratim Mitra,
- Leeson J. Alexander,
- Luiz L. Coutinho,
- Maria Elena Dell'Aquila,
- Lou C. Gasbarre,
- Gianni Lacalandra,
- Robert W. Li,
- Lakshmi K. Matukumalli,
- Dan Nonneman,
- Luciana C. de A. Regitano,
- Tim P.L. Smith,
- Jiuzhou Song,
- Tad S. Sonstegard,
- Curt P. Van Tassell,
- Mario Ventura,
- Evan E. Eichler,
- Tara G. McDaneld,
- and John W. Keele
Genome Res. May 2010 20: 693-703; Published in Advance March 8, 2010, doi:10.1101/gr.105403.110
...Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here, we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR...
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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
...provided evidence of linkage disequilibrium with flanking SNPs (McCarroll et al. 2008), a significant portion of CNVs fell in genomic regions not well-covered by SNP arrays, such as SDs, and thus were not genotyped (Locke et al. 2006; Estivill and Armengol 2007; Campbell et al. 2011). Combining CNV and SNP...
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Method: ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage
- Xiran Liu,
- Lorin Crawford,
- and Sohini Ramachandran
Genome Res. December 2025 35: 2691-2700; Published in Advance November 19, 2025, doi:10.1101/gr.280440.125
...selection using summary data from -wide association studies. Bioinformatics 32: 1493–1501. doi:10.1093/bioinformatics/btw018 ↵Berisa T, Pickrell JK. 2015. Approximately independent linkage disequilibrium blocks in human populations. Bioinformatics 32: 283–285. doi:10.1093/bioinformatics/btv546 ↵Blei DM...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
.... https://zenodo.org/records/6617246 ↵Li N, Stephens M. 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165: 2213–2233. doi:10.1093/genetics/165.4.2213 ↵Li JH, Mazur CA, Berisa T, Pickrell JK. 2021. Low-pass sequencing...
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Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
...et al. 2023). However, the majority of these variants are of small effects, are in linkage disequilibrium (LD) with nearby variants, and are located in noncoding regions of the , potentially influencing complex phenotypes via regulating intermediate molecular phenotypes, such as gene expression...
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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
...height than c.3768_3769insA and was also associated with breed standard weight (Supplemental Fig. S10; Zhou and Stephens 2012). All three variants were in close proximity but were not in linkage disequilibrium (LD) (Fig. 3C; Supplemental Fig. S11). Conversely, since c.1978_1981delACAG has a similar...
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