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Chen Y, Zhang T, Xian M, Zhang R, Yang W, Su B, Yang G, Sun L, Xu W, Xu S, Gao H, Xu L, Gao X, Li J. A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation. Commun Biol 2022; 5:353. [PMID: 35418663 PMCID: PMC9008013 DOI: 10.1038/s42003-022-03298-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/21/2022] [Indexed: 12/02/2022] Open
Abstract
Drung cattle (Bos frontalis) have 58 chromosomes, differing from the Bos taurus 2n = 60 karyotype. To date, its origin and evolution history have not been proven conclusively, and the mechanisms of chromosome fusion and environmental adaptation have not been clearly elucidated. Here, we assembled a high integrity and good contiguity genome of Drung cattle with 13.7-fold contig N50 and 4.1-fold scaffold N50 improvements over the recently published Indian mithun assembly, respectively. Speciation time estimation and phylogenetic analysis showed that Drung cattle diverged from Bos taurus into an independent evolutionary clade. Sequence evidence of centromere regions provides clues to the breakpoints in BTA2 and BTA28 centromere satellites. We furthermore integrated a circulation and contraction-related biological process involving 43 evolutionary genes that participated in pathways associated with the evolution of the cardiovascular system. These findings may have important implications for understanding the molecular mechanisms of chromosome fusion, alpine valleys adaptability and cardiovascular function.
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Affiliation(s)
- Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Tianliu Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Ming Xian
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Rui Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Weifei Yang
- 1 Gene Co., Ltd, 310051, Hangzhou, P.R. China
- Annoroad Gene Technology (Beijing) Co., Ltd, 100176, Beijing, P.R. China
| | - Baqi Su
- Drung Cattle Conservation Farm in Jiudang Wood, Drung and Nu Minority Autonomous County, Gongshan, 673500, Kunming, Yunnan, P.R. China
| | - Guoqiang Yang
- Livestock and Poultry Breed Improvement Center, Nujiang Lisu Minority Autonomous Prefecture, 673199, Kunming, Yunnan, P.R. China
| | - Limin Sun
- Yunnan Animal Husbandry Service, 650224, Kunming, Yunnan, P.R. China
| | - Wenkun Xu
- Yunnan Animal Husbandry Service, 650224, Kunming, Yunnan, P.R. China
| | - Shangzhong Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China.
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China.
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Holečková B, Schwarzbacherová V, Galdíková M, Koleničová S, Halušková J, Staničová J, Verebová V, Jutková A. Chromosomal Aberrations in Cattle. Genes (Basel) 2021; 12:1330. [PMID: 34573313 PMCID: PMC8468509 DOI: 10.3390/genes12091330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 02/04/2023] Open
Abstract
Chromosomal aberrations and their mechanisms have been studied for many years in livestock. In cattle, chromosomal abnormalities are often associated with serious reproduction-related problems, such as infertility of carriers and early mortality of embryos. In the present work, we review the mechanisms and consequences of the most important bovine chromosomal aberrations: Robertsonian translocations and reciprocal translocations. We also discuss the application of bovine cell cultures in genotoxicity studies.
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Affiliation(s)
- Beáta Holečková
- Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (V.S.); (M.G.); (S.K.); (J.H.); (A.J.)
| | - Viera Schwarzbacherová
- Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (V.S.); (M.G.); (S.K.); (J.H.); (A.J.)
| | - Martina Galdíková
- Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (V.S.); (M.G.); (S.K.); (J.H.); (A.J.)
| | - Simona Koleničová
- Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (V.S.); (M.G.); (S.K.); (J.H.); (A.J.)
| | - Jana Halušková
- Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (V.S.); (M.G.); (S.K.); (J.H.); (A.J.)
| | - Jana Staničová
- First Faculty of Medicine, Charles University in Prague, Salmovská 1, 121 08 Prague, Czech Republic;
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia;
| | - Valéria Verebová
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia;
| | - Annamária Jutková
- Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (V.S.); (M.G.); (S.K.); (J.H.); (A.J.)
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3
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Udroiu I, Sgura A. Cytogenetic tests for animal production: state of the art and perspectives. Anim Genet 2017; 48:505-515. [DOI: 10.1111/age.12581] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2017] [Indexed: 01/07/2023]
Affiliation(s)
- I. Udroiu
- Dipartimento di Scienze; Università Roma Tre; Viale G. Marconi 446 00146 Rome Italy
| | - A. Sgura
- Dipartimento di Scienze; Università Roma Tre; Viale G. Marconi 446 00146 Rome Italy
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Vozdova M, Sebestova H, Kubickova S, Cernohorska H, Awadova T, Vahala J, Rubes J. Impact of Robertsonian translocation on meiosis and reproduction: an impala (Aepyceros melampus) model. J Appl Genet 2014; 55:249-58. [DOI: 10.1007/s13353-014-0193-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 01/03/2014] [Accepted: 01/08/2014] [Indexed: 11/27/2022]
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5
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Ducos A, Revay T, Kovacs A, Hidas A, Pinton A, Bonnet-Garnier A, Molteni L, Slota E, Switonski M, Arruga MV, van Haeringen WA, Nicolae I, Chaves R, Guedes-Pinto H, Andersson M, Iannuzzi L. Cytogenetic screening of livestock populations in Europe: an overview. Cytogenet Genome Res 2008; 120:26-41. [PMID: 18467823 DOI: 10.1159/000118738] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2007] [Indexed: 11/19/2022] Open
Abstract
Clinical animal cytogenetics development began in the 1960's, almost at the same time as human cytogenetics. However, the development of the two disciplines has been very different during the last four decades. Clinical animal cytogenetics reached its 'Golden Age' at the end of the 1980's. The majority of the laboratories, as well as the main screening programs in farm animal species, presented in this review, were implemented during that period, under the guidance of some historical leaders, the first of whom was Ingemar Gustavsson. Over the past 40 years, hundreds of scientific publications reporting original chromosomal abnormalities generally associated with clinical disorders (mainly fertility impairment) have been published. Since the 1980's, the number of scientists involved in clinical animal cytogenetics has drastically decreased for different reasons and the activities in that field are now concentrated in only a few laboratories (10 to 15, mainly in Europe), some of which have become highly specialized. Currently between 8,000 and 10,000 chromosomal analyses are carried out each year worldwide, mainly in cattle, pigs, and horses. About half of these analyses are performed in one French laboratory. Accurate estimates of the prevalence of chromosomal abnormalities in some populations are now available. For instance, one phenotypically normal pig in 200 controlled in France carries a structural chromosomal rearrangement. The frequency of the widespread 1;29 Robertsonian translocation in cattle has greatly decreased in most countries, but remains rather high in certain breeds (up to 20-25% in large beef cattle populations, even higher in some local breeds). The continuation, and in some instances the development of the chromosomal screening programs in farm animal populations allowed the implementation of new and original scientific projects, aimed at exploring some basic questions in the fields of chromosome and/or cell biology, thanks to easier access to interesting biological materials (germ cells, gametes, embryos ...).
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Affiliation(s)
- A Ducos
- INRA-ENVT, UMR 444 Génétique Cellulaire, Toulouse, France.
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6
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Basrur PK, Stranzinger G. Veterinary cytogenetics: past and perspective. Cytogenet Genome Res 2008; 120:11-25. [PMID: 18467822 DOI: 10.1159/000118737] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2008] [Indexed: 11/19/2022] Open
Abstract
Cytogenetics was conceived in the late 1800s and nurtured through the early 1900s by discoveries pointing to the chromosomal basis of inheritance. The relevance of chromosomes to human health and disease was realized more than half a century later when improvements in techniques facilitated unequivocal chromosome delineation. Veterinary cytogenetics has benefited from the information generated in human cytogenetics which, in turn, owes its theoretical and technical advancement to data gathered from plants, insects and laboratory mammals. The scope of this science has moved from the structure and number of chromosomes to molecular cytogenetics for use in research or for diagnostic and prognostic purposes including comparative genomic hybridization arrays, single nucleotide polymorphism array-based karyotyping and automated systems for counting the results of standard FISH preparations. Even though the counterparts to a variety of human diseases and disorders are seen in domestic animals, clinical applications of veterinary cytogenetics will be less well exploited mainly because of the cost-driven nature of demand on diagnosis and treatment which often out-weigh emotional and sentimental attachments. An area where the potential of veterinary cytogenetics will be fully exploited is reproduction since an inherited aberration that impacts on reproductive efficiency can compromise the success achieved over the years in animal breeding. It is gratifying to note that such aberrations can now be tracked and tackled using sophisticated cytogenetic tools already commercially available for RNA expression analysis, chromatin immunoprecipitation, or comparative genomic hybridization using custom-made microarray platforms that allow the construction of microarrays that match veterinary cytogenetic needs, be it for research or for clinical applications. Judging from the technical refinements already accomplished in veterinary cytogenetics since the 1960s, it is clear that the importance of the achievements to date are bound to be matched or out-weighed by what awaits to be accomplished in the not-too-far future.
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Affiliation(s)
- P K Basrur
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada.
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Stranzinger GF, Steiger D, Kneubuhler J, Hagger C. Y chromosome polymorphism in various breeds of cattle (Bos taurus) in Switzerland. J Appl Genet 2007; 48:241-5. [PMID: 17666776 DOI: 10.1007/bf03195218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The evolutionary development of mammals involves mutations and fixations of chromosomal types. The Y chromosome polymorphism in cattle is important for the breeding strategy, since chromosomal incompatibilities in crossings result in fertility problems. In bulls of various breeds in Switzerland, data on chromosome status have been collected for over 20 years. Data from 7 years were analysed in this study through chromosome measurements and their normalization. Some highly significant differences were found between the 7 groups of breeds, especially between Holsteins and the original Swiss breeds Braunvieh and Simmental. Fleckvieh (purebred or crossbred) did not differ significantly from Black or Red Holsteins. The results were discussed with respect to fertility problems. The observed Y chromosome polymorphism should be taken into account in breeding, and research in this field should be continued.
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Affiliation(s)
- Gerald F Stranzinger
- Breeding Biology Group, Swiss Federal Institute of Technology (ETHZ), Zürich, Switzerland
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McRae AF, Beraldi D. Examination of a region showing linkage map discrepancies across sheep breeds. Mamm Genome 2006; 17:346-53. [PMID: 16596456 DOI: 10.1007/s00335-005-0087-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Accepted: 01/11/2006] [Indexed: 12/23/2022]
Abstract
The availability of accurate linkage maps is an important step for the localization of genetic variants of interest. However, most studies in livestock assume the published map is applicable in their population despite the large differences between the breeds of a species. A region of sheep Chromosome 1 was previously identified as providing evidence for a marker order inconsistent with the published linkage map. In this study the identified region was investigated in more detail. Four microsatellite markers covering the central 5 cM of the inconsistent region and two flanking markers were genotyped in three sheep breeds, a commercial population (Charollais), an experimental population (Scottish Blackface), and a feral population (Soay). With the inclusion of the published linkage map, this provided evidence for three different marker orders across four sheep populations. Evidence for selection in this region was investigated using both a single-point allelic competition model and a multipoint allele-sharing statistic. Only the Charollais population provided evidence for selection, with significant transmission bias observed at marker BM7145. The implications of variation in linkage maps on the design and analysis of fine-mapping studies are discussed.
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Affiliation(s)
- Allan F McRae
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom.
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Ahrens E, Stranzinger G. Comparative chromosomal studies of E. caballus (ECA) and E. przewalskii (EPR) in a female F1 hybrid. J Anim Breed Genet 2005; 122 Suppl 1:97-102. [PMID: 16130463 DOI: 10.1111/j.1439-0388.2005.00494.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previous research revealed that the karyotypes of Equus przewalskii (2n = 66) and Equus caballus (2n = 64) differ by one pair of metacentric chromosomes, present in ECA but not in EPR, and two pairs of acrocentric chromosomes found only in the EPR karyotype. The formation of a trivalent during meiosis in a male F1 hybrid and the homologies in G-banding patterns suggest that ECA 5 corresponds to two acrocentric EPR chromosomes resulting from a Robertsonian fusion or fission event. Chromosomal investigations of a female interspecies F1 hybrid including banded karyograms and fluorescence in situ hybridization (FISH) studies focusing on the p and q arm of ECA 5 were conducted. Q- and G-banding patterns of E. caballus, E. przewalskii and the hybrid revealed interspecies homology between all chromosome pairs except for ECA 5, EPR 23 and EPR 24, which were unique for that particular species. Furthermore, they indicated homology between ECA 5p and EPR 23 as well as between ECA 5q and EPR 24. FISH revealed hybridization of the BACs laminin beta 3 (LAM B3) and laminin gamma 2 (LAM C2) to ECA 5p and EPR 23. However, nuclear factor I (NFIA) and immunoglobulin lambda (IGL@), primarily assigned to ECA 5q, mapped to ECA 7 and EPR 6 respectively. Thus the karyotypes of E. caballus and E. przewalskii differ solely by one Robertsonian translocation (ECA 5 =EPR 23 + EPR 24).
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Affiliation(s)
- E Ahrens
- Department of Animal Sciences, Swiss Federal Institute of Technology, Zurich, Switzerland
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10
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Kaupe B, Kollers S, Fries R, Erhardt G. Mapping of CYP11B and a putative CYHR1 paralogous gene to bovine chromosome 14 by FISH. Anim Genet 2005; 35:478-9. [PMID: 15566480 DOI: 10.1111/j.1365-2052.2004.01200.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- B Kaupe
- Institut für Tierzucht und Haustiergenetik, Justus-Liebig-Universität, Ludwigstrasse 21b, Giessen, Germany
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