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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 2023 33: 463-477; Published in Advance April 3, 2023, doi:10.1101/gr.277372.12
...to deletions (94,422 vs. 33,571), suggesting recent active LINE expansions in sheep. Nearly half of the SVs display low to moderate linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 27, 2023 ; Published in Advance March 27, 2023, doi:10.1101/gr.277372.122
...linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified 865 population-stratified SVs including 122 SVs possibly derived in the domestication process among 690 individuals from sheep...
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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
...the high-quality assemblies of a male Pamir argali (O. ammon polii, 2n = 56), a female Tibetan sheep (O. aries, 2n = 54), and a male hybrid of Pamir argali and domestic sheep, and the high-throughput sequencing of 425 ovine animals, including the hybrids of argali and domestic sheep. We detected genomic...
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RESOURCE: A Comprehensive Genetic Map of the Cattle Genome Based on 3802 Microsatellites
- Naoya Ihara,
- Akiko Takasuga,
- Kazunori Mizoshita,
- Haruko Takeda,
- Mayumi Sugimoto,
- Yasushi Mizoguchi,
- Takashi Hirano,
- Tomohito Itoh,
- Toshio Watanabe,
- Kent M. Reed,
- Warren M. Snelling,
- Steven M. Kappes,
- Craig W. Beattie,
- Gary L. Bennett,
- and Yoshikazu Sugimoto
Genome Res. October 2004 14: 1987-1998; doi:10.1101/gr.2741704
....P., Freking, B.A., Beh, K.J., Cockett, N.E., Kang, N., et al. 2001 . An enhanced linkage map of the sheep comprising more than 1000 loci. Genome Res. 11 : 1275 -1289. ↵ Mohrenweiser, H.W., Tsujimoto, S., Gordon, L., and Olsen, A.S. 1998 . Regions of sex-specific hypo- and hyper-recombination identified...
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LETTER: An Ordered Comparative Map of the Cattle and Human Genomes
- Mark R. Band,
- Joshua H. Larson,
- Mark Rebeiz,
- Cheryl A. Green,
- D. Wayne Heyen,
- Jena Donovan,
- Ryan Windish,
- Chad Steining,
- Prapti Mahyuddin,
- James E. Womack,
- and Harris A. Lewin
Genome Res. September 1, 2000 10: 1359-1368; doi:10.1101/gr.145900
...BM1348 and C4BPB , apparently because of the high frequency of breakage between these loci. BTA14 is another example where a paucity of known markers affects mapping efficiency. The RH map of BTA14 contains five linkage groups even though recombination data shows tight linkage between markers from...
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ARTICLE: An integrated map of human chromosome 6p23.
- M G Olavesen,
- A F Davies,
- S J Broxholme,
- J L Wixon,
- G Senger,
- D Nizetic,
- R D Campbell,
- and J Ragoussis
Genome Res. November 1995 5: 342-358; doi:10.1101/gr.5.4.342
.... Millasseau, P. Vaysseix, G. and Lathrop. M. 1992. A second-generation linkage map of the human . Nature 359: 794 – 801. Zehetner, G. , Lehrach. H. Zehetner, G. and Lehrach. H. 1994. The Reference Library System-Sharing biological material and experimental data. Nature 367: 489 – 491. Genome Res Genome...
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PERSPECTIVE: The opossum genome: Insights and opportunities from an alternative mammal
- Paul B. Samollow
Genome Res. August 2008 18: 1199-1215; doi:10.1101/gr.065326.107
...recombination rates among vertebrates. The published M. domestica linkage map, comprising 150 loci in eight autosomal linkage groups and spanning 86%–89% of the physical ( Samollow et al. 2007 ), yields a sex-averaged total map-length estimate of only 866 centiMorgans (cM), which is considerably shorter than...
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RESOURCE: Initial sequence and comparative analysis of the cat genome
- Joan U. Pontius,
- James C. Mullikin,
- Douglas R. Smith,
- Agencourt Sequencing Team,
- Kerstin Lindblad-Toh,
- Sante Gnerre,
- Michele Clamp,
- Jean Chang,
- Robert Stephens,
- Beena Neelam,
- Natalia Volfovsky,
- Alejandro A. Schäffer,
- Richa Agarwala,
- Kristina Narfström,
- William J. Murphy,
- Urs Giger,
- Alfred L. Roca,
- Agostinho Antunes,
- Marilyn Menotti-Raymond,
- Naoya Yuhki,
- Jill Pecon-Slattery,
- Warren E. Johnson,
- Guillaume Bourque,
- Glenn Tesler,
- NISC Comparative Sequencing Program,
- and Stephen J. O’Brien
Genome Res. November 2007 17: 1675-1689; doi:10.1101/gr.6380007
...in the cat than FeLV or RD114 sequences ( Fig. 4 ; Supplemental Fig. S3; Table 3 ). Identification of 327,000 new SNPs, 208,177 new STR loci, and a mosaic pattern of homozygosity useful for linkage disequilibrium mapping of complex traits in the cat ( Fig. 5 ). A dynamic online browser of Genome Annotation...
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Letter: A novel active endogenous retrovirus family contributes to genome variability in rat inbred strains
- Yongming Wang,
- František Liška,
- Claudia Gosele,
- Lucie Šedová,
- Vladimír Křen,
- Drahomíra Křenová,
- Zoltán Ivics,
- Norbert Hubner,
- and Zsuzsanna Izsvák
Genome Res. January 2010 20: 19-27; Published in Advance November 3, 2009, doi:10.1101/gr.100073.109
...status of RnERV-K8e in different inbred strains, genomic PCR was employed to screen eight genomic loci for the presence or absence of the identified full-length elements on a panel of 21 inbred strains. RnERV-K8e copies were detected at genomic loci of chr 1, chr 5, chr 6, chr 7, and chr 8 in all...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...number of unique loci, with the highest number observed in the Diannan small-ear pig and the lowest in the Jiaxing Black pig (Supplemental Fig. S4).To confirm that this data set is suitable for assessing the performance of HITSNP, we inferred the population structure of pigs by applying this data set...
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