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Abstract
I abandoned my original career choice of high school teaching to pursue dentistry and soon abandoned that path for genetics. The latter decision was due to a challenge by a professor that led to me reading Nobel speeches by pioneer geneticists before I had formal exposure to the subject. Even then, I was 15 years into my career before my interest in rodent genomes gave way to mapping cattle genes. Events behind these twists and turns in my career path comprise the first part of this review. The remainder is a review of the development of the field of bovine genomics from my personal perspective. I have had the pleasure of working with outstanding graduate students, postdocs, and colleagues to contribute my small part to a discipline that has evolved from a few individuals mapping an orphan genome to a discipline underlying a revolution in animal breeding.
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Affiliation(s)
- James E. (Jim) Womack
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843–4467, USA
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Perelman PL, Pichler R, Gaggl A, Larkin DM, Raudsepp T, Alshanbari F, Holl HM, Brooks SA, Burger PA, Periasamy K. Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000 RAD and 15000 RAD. Sci Rep 2018; 8:1982. [PMID: 29386528 PMCID: PMC5792482 DOI: 10.1038/s41598-018-20223-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/11/2018] [Indexed: 01/08/2023] Open
Abstract
The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RAD and 15000RAD) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000RAD panel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000RAD panel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000RAD panel is an important high-resolution complement to the main 5000RAD panel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools.
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Affiliation(s)
- Polina L Perelman
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria
- Institute of Molecular and Cellular Biology and Novosibirsk State University, Novosibirsk, Russia
| | - Rudolf Pichler
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria
| | - Anna Gaggl
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
| | | | | | | | | | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni, Vienna, Austria
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria.
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Casas E, Kehrli ME. A Review of Selected Genes with Known Effects on Performance and Health of Cattle. Front Vet Sci 2016; 3:113. [PMID: 28018909 PMCID: PMC5156656 DOI: 10.3389/fvets.2016.00113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/28/2016] [Indexed: 11/21/2022] Open
Abstract
There are genetic conditions that influence production in dairy and beef cattle. The objective of this review was to describe relevant genetic conditions that have been associated with productivity and health in cattle. Genes or genomic regions that have been identified as a candidate for the condition will be included, and the genetic basis of the condition will be defined. Genes and genetic conditions included in this review are bovine leukocyte adhesion deficiency, deficiency of the uridine monophosphate synthase, bovine chronic interstitial nephritis, horn development, myostatin, complex vertebral malformation, leptin, osteopetrosis, apoptosis peptide activating factor 1, chondrodysplastic dwarfism, caseins, calpastatin, umbilical hernia, lactoglobulin, citrullinemia, cholesterol deficiency, prions, thyroglobulin, diacylglycerol acyltransferase, syndactyly, maple syrup urine disease, slick hair, Factor XI deficiency, and μ-Calpain. This review is not meant to be comprehensive, and relevant information is provided to ascertain genetic markers associated with the conditions.
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Affiliation(s)
- Eduardo Casas
- National Animal Disease Center, USDA, ARS, Ames, IA, USA
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Drögemüller C, Wöhlke A, Leeb T, Distl O. A 4 Mb high resolution BAC contig on bovine chromosome 1q12 and comparative analysis with human chromosome 21q22. Comp Funct Genomics 2010; 6:194-203. [PMID: 18629192 PMCID: PMC2447486 DOI: 10.1002/cfg.476] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2004] [Revised: 02/03/2005] [Accepted: 03/17/2005] [Indexed: 11/28/2022] Open
Abstract
The bovine RPCI-42 BAC library was screened to construct a sequence-ready ~4 Mb
single contig of 92 BAC clones on BTA 1q12. The contig covers the region between
the genes KRTAP8P1 and CLIC6. This genomic segment in cattle is of special interest
as it contains the dominant gene responsible for the hornless or polled phenotype in
cattle. The construction of the BAC contig was initiated by screening the bovine BAC
library with heterologous cDNA probes derived from 12 human genes of the syntenic
region on HSA 21q22. Contig building was facilitated by BAC end sequencing and
chromosome walking. During the construction of the contig, 165 BAC end sequences
and 109 single-copy STS markers were generated. For comparative mapping of 25
HSA 21q22 genes, genomic PCR primers were designed from bovine EST sequences
and the gene-associated STSs mapped on the contig. Furthermore, bovine BAC
end sequence comparisons against the human genome sequence revealed significant
matches to HSA 21q22 and allowed the in silico mapping of two new genes in cattle.
In total, 31 orthologues of human genes located on HSA 21q22 were directly mapped
within the bovine BAC contig, of which 16 genes have been cloned and mapped for the
first time in cattle. In contrast to the existing comparative bovine–human RH maps of
this region, these results provide a better alignment and reveal a completely conserved
gene order in this 4 Mb segment between cattle, human and mouse. The mapping of
known polled linked BTA 1q12 microsatellite markers allowed the integration of the
physical contig map with existing linkage maps of this region and also determined
the exact order of these markers for the first time. Our physical map and transcript
map may be useful for positional cloning of the putative polled gene in cattle. The
nucleotide sequence data reported in this paper have been submitted to EMBL and
have been assigned Accession Numbers AJ698510–AJ698674.
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Affiliation(s)
- Cord Drögemüller
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine, Hannover 30559, Germany.
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Brinkmeyer-Langford CL, Childers CP, Fritz KL, Gustafson-Seabury AL, Cothran M, Raudsepp T, Womack JE, Skow LC. A high resolution RH map of the bovine major histocompatibility complex. BMC Genomics 2009; 10:182. [PMID: 19393056 PMCID: PMC2682492 DOI: 10.1186/1471-2164-10-182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 04/24/2009] [Indexed: 11/10/2022] Open
Abstract
Background The cattle MHC is termed the bovine leukocyte antigen (BoLA) and, along with the MHCs of other ruminants, is unique in its genomic organization. Consequently, correct and reliable gene maps and sequence information are critical to the study of the BoLA region. The bovine genome sequencing project has produced two assemblies (Btau_3.1 and 4.0) that differ substantially from each other and from conventional gene maps in the BoLA region. To independently compare the accuracies of the different sequence assemblies, we have generated a high resolution map of BoLA using a 12,000rad radiation hybrid panel. Seventy-seven unique sequence tagged site (STS) markers chosen at approximately 50 kb intervals from the Btau 2.0 assembly and spanning the IIa-III-I and IIb regions of the bovine MHC were mapped on a 12,000rad bovine radiation hybrid (RH) panel to evaluate the different assemblies of the bovine genome sequence. Results Analysis of the data generated a high resolution RH map of BoLA that was significantly different from the Btau_3.1 assembly of the bovine genome but in good agreement with the Btau_4.0 assembly. Of the few discordancies between the RH map and Btau_4.0, most could be attributed to closely spaced markers that could not be precisely ordered in the RH panel. One probable incorrectly-assembled sequence and three missing sequences were noted in the Btau_4.0 assembly. The RH map of BoLA is also highly concordant with the sequence-based map of HLA (NCBI build 36) when reordered to account for the ancestral inversion in the ruminant MHC. Conclusion These results strongly suggest that studies using Btau_3.1 for analyses of the BoLA region should be reevaluated in light of the Btau_4.0 assembly and indicate that additional research is needed to produce a complete assembly of the BoLA genomic sequences.
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Affiliation(s)
- Candice L Brinkmeyer-Langford
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843-4458, USA.
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Kochan KJ, Amaral MEJ, Agarwala R, Schäffer AA, Riggs PK. Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis) chromosome 20. BMC Genomics 2008; 9:544. [PMID: 19014630 PMCID: PMC2621213 DOI: 10.1186/1471-2164-9-544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Accepted: 11/17/2008] [Indexed: 11/30/2022] Open
Abstract
Background Fluorescence of dyes bound to double-stranded PCR products has been utilized extensively in various real-time quantitative PCR applications, including post-amplification dissociation curve analysis, or differentiation of amplicon length or sequence composition. Despite the current era of whole-genome sequencing, mapping tools such as radiation hybrid DNA panels remain useful aids for sequence assembly, focused resequencing efforts, and for building physical maps of species that have not yet been sequenced. For placement of specific, individual genes or markers on a map, low-throughput methods remain commonplace. Typically, PCR amplification of DNA from each panel cell line is followed by gel electrophoresis and scoring of each clone for the presence or absence of PCR product. To improve sensitivity and efficiency of radiation hybrid panel analysis in comparison to gel-based methods, we adapted fluorescence-based real-time PCR and dissociation curve analysis for use as a novel scoring method. Results As proof of principle for this dissociation curve method, we generated new maps of river buffalo (Bubalus bubalis) chromosome 20 by both dissociation curve analysis and conventional marker scoring. We also obtained sequence data to augment dissociation curve results. Few genes have been previously mapped to buffalo chromosome 20, and sequence detail is limited, so 65 markers were screened from the orthologous chromosome of domestic cattle. Thirty bovine markers (46%) were suitable as cross-species markers for dissociation curve analysis in the buffalo radiation hybrid panel under a standard protocol, compared to 25 markers suitable for conventional typing. Computational analysis placed 27 markers on a chromosome map generated by the new method, while the gel-based approach produced only 20 mapped markers. Among 19 markers common to both maps, the marker order on the map was maintained perfectly. Conclusion Dissociation curve analysis is reliable and efficient for radiation hybrid panel scoring, and is more sensitive and robust than conventional gel-based typing methods. Several markers could be scored only by the new method, and ambiguous scores were reduced. PCR-based dissociation curve analysis decreases both time and resources needed for construction of radiation hybrid panel marker maps and represents a significant improvement over gel-based methods in any species.
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Affiliation(s)
- Kelli J Kochan
- Department of Animal Science, Texas A&M University, College Station, Texas, USA.
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Wunderlich KR, Abbey CA, Clayton DR, Song Y, Schein JE, Georges M, Coppieters W, Adelson DL, Taylor JF, Davis SL, Gill CA. A 2.5-Mb contig constructed from Angus, Longhorn and horned Hereford DNA spanning the polled interval on bovine chromosome 1. Anim Genet 2007; 37:592-4. [PMID: 17121607 DOI: 10.1111/j.1365-2052.2006.01538.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The polled locus has been mapped by genetic linkage analysis to the proximal region of bovine chromosome 1. As an intermediate step in our efforts to identify the polled locus and the underlying causative mutation for the polled phenotype, we have constructed a BAC-based physical map of the interval containing the polled locus. Clones containing genes and markers in the critical interval were isolated from the TAMBT (constructed from Angus and Longhorn genomic DNA) and CHORI-240 (constructed from horned Hereford genomic DNA) BAC libraries and ordered based on fingerprinting and the presence or absence of 80 STS markers. A single contig spanning 2.5 Mb was assembled. Comparison of the physical order of STSs to the corresponding region of human chromosome 21 revealed the same order of genes within the polled critical interval. This contig of overlapping BAC clones from horned and polled breeds is a useful resource for SNP discovery and characterization of positional candidate genes.
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Affiliation(s)
- K R Wunderlich
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA
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Jann OC, Aerts J, Jones M, Hastings N, Law A, McKay S, Marques E, Prasad A, Yu J, Moore SS, Floriot S, Mahé MF, Eggen A, Silveri L, Negrini R, Milanesi E, Ajmone-Marsan P, Valentini A, Marchitelli C, Savarese MC, Janitz M, Herwig R, Hennig S, Gorni C, Connor EE, Sonstegard TS, Smith T, Drögemüller C, Williams JL. A second generation radiation hybrid map to aid the assembly of the bovine genome sequence. BMC Genomics 2006; 7:283. [PMID: 17087818 PMCID: PMC1636650 DOI: 10.1186/1471-2164-7-283] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Accepted: 11/06/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several approaches can be used to determine the order of loci on chromosomes and hence develop maps of the genome. However, all mapping approaches are prone to errors either arising from technical deficiencies or lack of statistical support to distinguish between alternative orders of loci. The accuracy of the genome maps could be improved, in principle, if information from different sources was combined to produce integrated maps. The publicly available bovine genomic sequence assembly with 6x coverage (Btau_2.0) is based on whole genome shotgun sequence data and limited mapping data however, it is recognised that this assembly is a draft that contains errors. Correcting the sequence assembly requires extensive additional mapping information to improve the reliability of the ordering of sequence scaffolds on chromosomes. The radiation hybrid (RH) map described here has been contributed to the international sequencing project to aid this process. RESULTS An RH map for the 30 bovine chromosomes is presented. The map was built using the Roslin 3000-rad RH panel (BovGen RH map) and contains 3966 markers including 2473 new loci in addition to 262 amplified fragment-length polymorphisms (AFLP) and 1231 markers previously published with the first generation RH map. Sequences of the mapped loci were aligned with published bovine genome maps to identify inconsistencies. In addition to differences in the order of loci, several cases were observed where the chromosomal assignment of loci differed between maps. All the chromosome maps were aligned with the current 6x bovine assembly (Btau_2.0) and 2898 loci were unambiguously located in the bovine sequence. The order of loci on the RH map for BTA 5, 7, 16, 22, 25 and 29 differed substantially from the assembled bovine sequence. From the 2898 loci unambiguously identified in the bovine sequence assembly, 131 mapped to different chromosomes in the BovGen RH map. CONCLUSION Alignment of the BovGen RH map with other published RH and genetic maps showed higher consistency in marker order and chromosome assignment than with the current 6x sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.
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Affiliation(s)
- Oliver C Jann
- Division of Genetics & Genomics, Roslin Institute, Roslin, Midlothian, Edinburgh, EH25 9PS, UK
| | - Jan Aerts
- Division of Genetics & Genomics, Roslin Institute, Roslin, Midlothian, Edinburgh, EH25 9PS, UK
| | - Michelle Jones
- Division of Genetics & Genomics, Roslin Institute, Roslin, Midlothian, Edinburgh, EH25 9PS, UK
| | - Nicola Hastings
- Division of Genetics & Genomics, Roslin Institute, Roslin, Midlothian, Edinburgh, EH25 9PS, UK
| | - Andy Law
- Division of Genetics & Genomics, Roslin Institute, Roslin, Midlothian, Edinburgh, EH25 9PS, UK
| | | | - Elisa Marques
- University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Aparna Prasad
- University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Jody Yu
- University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | | | - Sandrine Floriot
- Laboratoire de Génétique Biochimique et Cytogénétique, INRA-CRJ, 78350 Jouy-en-Josas, France
| | - Marie-Françoise Mahé
- Laboratoire de Génétique Biochimique et Cytogénétique, INRA-CRJ, 78350 Jouy-en-Josas, France
| | - André Eggen
- Laboratoire de Génétique Biochimique et Cytogénétique, INRA-CRJ, 78350 Jouy-en-Josas, France
| | - Licia Silveri
- Laboratoire de Génétique Biochimique et Cytogénétique, INRA-CRJ, 78350 Jouy-en-Josas, France
- Istituto di Zootecnica, Università Cattolica del S. Cuore via E. Parmense 84, 29100 Piacenza, Italy
| | - Riccardo Negrini
- Istituto di Zootecnica, Università Cattolica del S. Cuore via E. Parmense 84, 29100 Piacenza, Italy
| | - Elisabetta Milanesi
- Istituto di Zootecnica, Università Cattolica del S. Cuore via E. Parmense 84, 29100 Piacenza, Italy
| | - Paolo Ajmone-Marsan
- Istituto di Zootecnica, Università Cattolica del S. Cuore via E. Parmense 84, 29100 Piacenza, Italy
| | - Alessio Valentini
- Department of Animal Productions, University of Tuscia, Viterbo, Italy
| | | | - Maria C Savarese
- Department of Animal Productions, University of Tuscia, Viterbo, Italy
| | - Michal Janitz
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ralf Herwig
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Steffen Hennig
- RZPD German Resource Center for Genome Research, 14059 Berlin, Germany
| | - Chiara Gorni
- Istituto di Zootecnica, Università Cattolica del S. Cuore via E. Parmense 84, 29100 Piacenza, Italy
- Parco Tecnologico Padano, via Einstein, Polo Universitario, Lodi 26900, Italy
| | - Erin E Connor
- USDA-ARS, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Tad S Sonstegard
- USDA-ARS, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Timothy Smith
- USDA-ARS U.S. Meat Animal Research Center P.O. Box 166 Clay Center, NE 68933-0166, USA
| | - Cord Drögemüller
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany
| | - John L Williams
- Division of Genetics & Genomics, Roslin Institute, Roslin, Midlothian, Edinburgh, EH25 9PS, UK
- Parco Tecnologico Padano, via Einstein, Polo Universitario, Lodi 26900, Italy
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Thomsen B, Horn P, Panitz F, Bendixen E, Petersen AH, Holm LE, Nielsen VH, Agerholm JS, Arnbjerg J, Bendixen C. A missense mutation in the bovine SLC35A3 gene, encoding a UDP-N-acetylglucosamine transporter, causes complex vertebral malformation. Genome Res 2005; 16:97-105. [PMID: 16344554 PMCID: PMC1356133 DOI: 10.1101/gr.3690506] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The extensive use of a limited number of elite bulls in cattle breeding can lead to rapid spread of recessively inherited disorders. A recent example is the globally distributed syndrome Complex Vertebral Malformation (CVM), which is characterized by misshapen and fused vertebrae around the cervico-thoracic junction. Here, we show that CVM is caused by a mutation in the Golgi-resident nucleotide-sugar transporter encoded by SLC35A3. Thus, the disease showed complete cosegregation with the mutation in a homozygous state, and proteome patterns indicated abnormal protein glycosylation in tissues of affected animals. In addition, a yeast mutant that is deficient in the transport of UDP-N-acetylglucosamine into its Golgi lumen can be rescued by the wild-type SLC35A3 gene, but not by the mutated gene. These results provide the first demonstration of a genetic disorder associated with a defective SLC35A3 gene, and reveal a new mechanism for malformation of the vertebral column caused by abnormal nucleotide-sugar transport into the Golgi apparatus.
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Affiliation(s)
- Bo Thomsen
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, DK-8830 Tjele, Denmark
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Snelling WM, Gautier M, Keele JW, Smith TPL, Stone RT, Harhay GP, Bennett GL, Ihara N, Takasuga A, Takeda H, Sugimoto Y, Eggen A. Integrating linkage and radiation hybrid mapping data for bovine chromosome 15. BMC Genomics 2004; 5:77. [PMID: 15473903 PMCID: PMC526187 DOI: 10.1186/1471-2164-5-77] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2004] [Accepted: 10/08/2004] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Bovine chromosome (BTA) 15 contains a quantitative trait loci (QTL) for meat tenderness, as well as several breaks in synteny with human chromosome (HSA) 11. Both linkage and radiation hybrid (RH) maps of BTA 15 are available, but the linkage map lacks gene-specific markers needed to identify genes underlying the QTL, and the gene-rich RH map lacks associations with marker genotypes needed to define the QTL. Integrating the maps will provide information to further explore the QTL as well as refine the comparative map between BTA 15 and HSA 11. A recently developed approach to integrating linkage and RH maps uses both linkage and RH data to resolve a consensus marker order, rather than aligning independently constructed maps. Automated map construction procedures employing this maximum-likelihood approach were developed to integrate BTA RH and linkage data, and establish comparative positions of BTA 15 markers with HSA 11 homologs. RESULTS The integrated BTA 15 map represents 145 markers; 42 shared by both data sets, 36 unique to the linkage data and 67 unique to RH data. Sequence alignment yielded comparative positions for 77 bovine markers with homologs on HSA 11. The map covers approximately 32% of HSA 11 sequence in five segments of conserved synteny, another 15% of HSA 11 is shared with BTA 29. Bovine and human order are consistent in portions of the syntenic segments, but some rearrangement is apparent. Comparative positions of gene markers near the meat tenderness QTL indicate the region includes separate segments of HSA 11. The two microsatellite markers flanking the QTL peak are between defined syntenic segments. CONCLUSIONS Combining data to construct an integrated map not only consolidates information from different sources onto a single map, but information contributed from each data set increases the accuracy of the map. Comparison of bovine maps with well annotated human sequence can provide useful information about genes near mapped bovine markers, but bovine gene order may be different than human. Procedures to connect genetic and physical mapping data, build integrated maps for livestock species, and connect those maps to more fully annotated sequence can be automated, facilitating the maintenance of up-to-date maps, and providing a valuable tool to further explore genetic variation in livestock.
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Affiliation(s)
- Warren M Snelling
- USDA, ARS, U.S. Meat Animal Research Center, Spur 18D, Clay Center, Nebraska 68933-0166, USA
| | - Mathieu Gautier
- Biochemical Genetics and Cytogenetics Unit, Department of Animal Genetics, Laboratory of Genetics and Biochemistry, INRA-CRJ 78350 Jouy-en-Josas, France
| | - John W Keele
- USDA, ARS, U.S. Meat Animal Research Center, Spur 18D, Clay Center, Nebraska 68933-0166, USA
| | - Timothy PL Smith
- USDA, ARS, U.S. Meat Animal Research Center, Spur 18D, Clay Center, Nebraska 68933-0166, USA
| | - Roger T Stone
- USDA, ARS, U.S. Meat Animal Research Center, Spur 18D, Clay Center, Nebraska 68933-0166, USA
| | - Gregory P Harhay
- USDA, ARS, U.S. Meat Animal Research Center, Spur 18D, Clay Center, Nebraska 68933-0166, USA
| | - Gary L Bennett
- USDA, ARS, U.S. Meat Animal Research Center, Spur 18D, Clay Center, Nebraska 68933-0166, USA
| | - Naoya Ihara
- Shirakawa Institute of Animal Genetics, Livestock Technology Association of Japan, Fukushima, Japan
| | - Akiko Takasuga
- Shirakawa Institute of Animal Genetics, Livestock Technology Association of Japan, Fukushima, Japan
| | - Haruko Takeda
- Shirakawa Institute of Animal Genetics, Livestock Technology Association of Japan, Fukushima, Japan
| | - Yoshikazu Sugimoto
- Shirakawa Institute of Animal Genetics, Livestock Technology Association of Japan, Fukushima, Japan
| | - André Eggen
- Biochemical Genetics and Cytogenetics Unit, Department of Animal Genetics, Laboratory of Genetics and Biochemistry, INRA-CRJ 78350 Jouy-en-Josas, France
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11
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De Donato M, Brenneman R, Stelly D, Womack J, Taylor J. A methodological approach for the construction of a radiation hybrid map of bovine chromosome 5. Genet Mol Biol 2004. [DOI: 10.1590/s1415-47572004000100005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- M. De Donato
- Texas A&M University, USA; Universidad de Oriente, Venezuela
| | - R.A. Brenneman
- Texas A&M University, USA; Omaha's Henry Doorly Zoo, USA
| | | | | | - J.F. Taylor
- Texas A&M University, USA; University of Missouri, USA
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12
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Drögemüller C, Bader A, Wöhlke A, Kuiper H, Leeb T, Distl O. A high-resolution comparative RH map of the proximal part of bovine chromosome 1. Anim Genet 2002; 33:271-9. [PMID: 12139506 DOI: 10.1046/j.1365-2052.2002.00866.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Current comparative maps between human chromosome 21 and the proximal part of cattle chromosome 1 are insufficient to define chromosomal rearrangements because of the low density of mapped genes in the bovine genome. The recently completed sequence of human chromosome 21 facilitates the detailed comparative analysis of corresponding segments on BTA1. In this study eight bovine bacterial artificial chromosome (BAC) clones containing bovine orthologues of human chromosome 21 genes, i.e. GRIK1, CLDN8, TIAM1, HUNK, SYNJ1, OLIG2, IL10RB, and KCNE2 were physically assigned by fluorescence in situ hybridization (FISH) to BTA1q12.1-q12.2. Sequence tagged site (STS) markers derived from these clones were mapped on the 3000 rad Roslin/Cambridge bovine radiation hybrid (RH) panel. In addition to these eight novel markers, 17 known markers from previously published BTA1 linkage or RH maps were also mapped on the Roslin/Cambridge bovine RH panel resulting in an integrated map with 25 markers of 355.4 cR(3000) length. The human-cattle genome comparison revealed the existence of three chromosomal breakpoints and two probable inversions in this region.
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Affiliation(s)
- C Drögemüller
- Institute of Animal Breeding and Genetics, School of Veterinary Medicine Hannover, Germany.
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Goldammer T, Kata SR, Brunner RM, Dorroch U, Sanftleben H, Schwerin M, Womack JE. A comparative radiation hybrid map of bovine chromosome 18 and homologous chromosomes in human and mice. Proc Natl Acad Sci U S A 2002; 99:2106-11. [PMID: 11854506 PMCID: PMC122326 DOI: 10.1073/pnas.042688699] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A comprehensive radiation hybrid (RH) map and a high resolution comparative map of Bos taurus (BTA) chromosome 18 were constructed, composed of 103 markers and 76 markers, respectively, by using a cattle-hamster somatic hybrid cell panel and a 5,000 rad whole-genome radiation hybrid (WGRH) panel. These maps include 65 new assignments (56 genes, 3 expressed-sequence tags, 6 microsatellites) and integrate 38 markers from the first generation WGRH(5,000) map of BTA18. Fifty-nine assignments of coding sequences were supported by somatic hybrid cell mapping to markers on BTA18. The total length of the comprehensive map was 1666 cR(5,000). Break-point positions within the chromosome were refined and a new telomeric RH linkage group was established. Conserved synteny between cattle, human, and mouse was found for 76 genes of BTA18 and human chromosomes (HSA) 16 and 19 and for 34 cattle genes and mouse chromosomes (MMU) 7 and 8. The new RH map is potentially useful for the identification of candidate genes for economically important traits, contributes to the expansion of the existing BTA18 gene map, and provides new information about the chromosome evolution in cattle, humans, and mice.
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Affiliation(s)
- Tom Goldammer
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA
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Affiliation(s)
- Melissa S Ashwell
- USDA, ARS, Beltsville Agricultural Research Center, Beltsville, MD, USA.
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Band MR, Larson JH, Rebeiz M, Green CA, Heyen DW, Donovan J, Windish R, Steining C, Mahyuddin P, Womack JE, Lewin HA. An ordered comparative map of the cattle and human genomes. Genome Res 2000; 10:1359-68. [PMID: 10984454 PMCID: PMC310912 DOI: 10.1101/gr.145900] [Citation(s) in RCA: 191] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A cattle-human whole-genome comparative map was constructed using parallel radiation hybrid (RH) mapping in conjunction with EST sequencing, database mining for unmapped cattle genes, and a predictive bioinformatics approach (COMPASS) for targeting specific homologous regions. A total of 768 genes were placed on the RH map in addition to 319 microsatellites used as anchor markers. Of these, 638 had human orthologs with mapping data, thus permitting construction of an ordered comparative map. The large number of ordered loci revealed > or =105 conserved segments between the two genomes. The comparative map suggests that 41 translocation events, a minimum of 54 internal rearrangements, and repositioning of all but one centromere can account for the observed organizations of the cattle and human genomes. In addition, the COMPASS in silico mapping tool was shown to be 95% accurate in its ability to predict cattle chromosome location from random sequence data, demonstrating this tool to be valuable for efficient targeting of specific regions for detailed mapping. The comparative map generated will be a cornerstone for elucidating mammalian chromosome phylogeny and the identification of genes of agricultural importance."Ought we, for instance, to begin by discussing each separate species-in virtue of some common element of their nature, and proceed from this as a basis for the consideration of them separately?" from Aristotle, On the Parts of Animals, 350 B.C.E.
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Affiliation(s)
- M R Band
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Rexroad CE, Owens EK, Johnson JS, Womack JE. A 12,000 rad whole genome radiation hybrid panel for high resolution mapping in cattle: characterization of the centromeric end of chromosome 1. Anim Genet 2000; 31:262-5. [PMID: 11086535 DOI: 10.1046/j.1365-2052.2000.00641.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have constructed a 12,000 rad bovine whole-genome radiation hybrid panel (BovR12) to complement the 5000 rad panel (BovR5) currently available to the bovine genomics research community. Initial characterization with markers from chromosome 1 reveals a higher frequency of breakage between adjacent markers and subsequently a larger number of 'linkage' groups on this chromosome. For this set of markers, the retention frequency is also higher than in BovR5.
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Affiliation(s)
- C E Rexroad
- USDA-ARS, US Meat Animal Research Center, Clay Center, NE 68933-0166, USA
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