1
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Faster deterministic algorithm for Co-Path Set. INFORM PROCESS LETT 2023. [DOI: 10.1016/j.ipl.2022.106335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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2
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Hughes JF, Skaletsky H, Pyntikova T, Koutseva N, Raudsepp T, Brown LG, Bellott DW, Cho TJ, Dugan-Rocha S, Khan Z, Kremitzki C, Fronick C, Graves-Lindsay TA, Fulton L, Warren WC, Wilson RK, Owens E, Womack JE, Murphy WJ, Muzny DM, Worley KC, Chowdhary BP, Gibbs RA, Page DC. Sequence analysis in Bos taurus reveals pervasiveness of X-Y arms races in mammalian lineages. Genome Res 2020; 30:1716-1726. [PMID: 33208454 PMCID: PMC7706723 DOI: 10.1101/gr.269902.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/28/2020] [Indexed: 12/28/2022]
Abstract
Studies of Y Chromosome evolution have focused primarily on gene decay, a consequence of suppression of crossing-over with the X Chromosome. Here, we provide evidence that suppression of X-Y crossing-over unleashed a second dynamic: selfish X-Y arms races that reshaped the sex chromosomes in mammals as different as cattle, mice, and men. Using super-resolution sequencing, we explore the Y Chromosome of Bos taurus (bull) and find it to be dominated by massive, lineage-specific amplification of testis-expressed gene families, making it the most gene-dense Y Chromosome sequenced to date. As in mice, an X-linked homolog of a bull Y-amplified gene has become testis-specific and amplified. This evolutionary convergence implies that lineage-specific X-Y coevolution through gene amplification, and the selfish forces underlying this phenomenon, were dominatingly powerful among diverse mammalian lineages. Together with Y gene decay, X-Y arms races molded mammalian sex chromosomes and influenced the course of mammalian evolution.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | | | | | - Terje Raudsepp
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Laura G Brown
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | | | - Ting-Jan Cho
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - Shannon Dugan-Rocha
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ziad Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Colin Kremitzki
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Catrina Fronick
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Tina A Graves-Lindsay
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Lucinda Fulton
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Wesley C Warren
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Richard K Wilson
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Elaine Owens
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - James E Womack
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - William J Murphy
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bhanu P Chowdhary
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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3
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Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators. Nat Genet 2017; 49:387-394. [PMID: 28135246 PMCID: PMC5359078 DOI: 10.1038/ng.3778] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/29/2016] [Indexed: 12/14/2022]
Abstract
After birds diverged from mammals, different ancestral autosomes evolved into sex chromosomes in each lineage. In birds, females are ZW and males ZZ, but in mammals females are XX and males XY. We sequenced the chicken W chromosome, compared its gene content with our reconstruction of the ancestral autosomes, and followed the evolutionary trajectory of ancestral W-linked genes across birds. Avian W chromosomes evolved in parallel with mammalian Y chromosomes, preserving ancestral genes through selection to maintain the dosage of broadly-expressed regulators of key cellular processes. We propose that, like the human Y chromosome, the chicken W chromosome is essential for embryonic viability of the heterogametic sex. Unlike other sequenced sex chromosomes, the chicken W did not acquire and amplify genes specifically expressed in reproductive tissues. We speculate that the pressures that drive the acquisition of reproduction related genes on sex chromosomes may be specific to the male germ line.
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4
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Soh YQS, Alföldi J, Pyntikova T, Brown LG, Graves T, Minx PJ, Fulton RS, Kremitzki C, Koutseva N, Mueller JL, Rozen S, Hughes JF, Owens E, Womack JE, Murphy WJ, Cao Q, de Jong P, Warren WC, Wilson RK, Skaletsky H, Page DC. Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes. Cell 2014; 159:800-13. [PMID: 25417157 DOI: 10.1016/j.cell.2014.09.052] [Citation(s) in RCA: 213] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 09/04/2014] [Accepted: 09/22/2014] [Indexed: 01/27/2023]
Abstract
We sequenced the MSY (male-specific region of the Y chromosome) of the C57BL/6J strain of the laboratory mouse Mus musculus. In contrast to theories that Y chromosomes are heterochromatic and gene poor, the mouse MSY is 99.9% euchromatic and contains about 700 protein-coding genes. Only 2% of the MSY derives from the ancestral autosomes that gave rise to the mammalian sex chromosomes. Instead, all but 45 of the MSY's genes belong to three acquired, massively amplified gene families that have no homologs on primate MSYs but do have acquired, amplified homologs on the mouse X chromosome. The complete mouse MSY sequence brings to light dramatic forces in sex chromosome evolution: lineage-specific convergent acquisition and amplification of X-Y gene families, possibly fueled by antagonism between acquired X-Y homologs. The mouse MSY sequence presents opportunities for experimental studies of a sex-specific chromosome in its entirety, in a genetically tractable model organism.
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Affiliation(s)
- Y Q Shirleen Soh
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jessica Alföldi
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | | | - Laura G Brown
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Tina Graves
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA
| | - Patrick J Minx
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA
| | - Robert S Fulton
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA
| | - Colin Kremitzki
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA
| | - Natalia Koutseva
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Jacob L Mueller
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Steve Rozen
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
| | | | - Elaine Owens
- College of Veterinary Medicine and Biomedical Sciences, 4458 Texas A&M University, College Station, TX 77843, USA
| | - James E Womack
- College of Veterinary Medicine and Biomedical Sciences, 4458 Texas A&M University, College Station, TX 77843, USA
| | - William J Murphy
- College of Veterinary Medicine and Biomedical Sciences, 4458 Texas A&M University, College Station, TX 77843, USA
| | - Qing Cao
- BACPAC Resources, Children's Hospital Oakland, 747 52nd Street, Oakland, CA 94609, USA
| | - Pieter de Jong
- BACPAC Resources, Children's Hospital Oakland, 747 52nd Street, Oakland, CA 94609, USA
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA
| | - Helen Skaletsky
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - David C Page
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA.
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5
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Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho TJ, Koutseva N, Zaghlul S, Graves T, Rock S, Kremitzki C, Fulton RS, Dugan S, Ding Y, Morton D, Khan Z, Lewis L, Buhay C, Wang Q, Watt J, Holder M, Lee S, Nazareth L, Alföldi J, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature 2014; 508:494-9. [PMID: 24759411 PMCID: PMC4139287 DOI: 10.1038/nature13206] [Citation(s) in RCA: 432] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/06/2014] [Indexed: 12/31/2022]
Abstract
The human X and Y chromosomes evolved from an ordinary pair of autosomes, but
millions of years ago genetic decay ravaged the Y chromosome, and only three percent of
its ancestral genes survived. We reconstructed the evolution of the Y chromosome across
eight mammals to identify biases in gene content and the selective pressures that
preserved the surviving ancestral genes. Our findings indicate that survival was
non-random, and in two cases, convergent across placental and marsupial mammals. We
conclude that the Y chromosome's gene content became specialized through selection
to maintain the ancestral dosage of homologous X-Y gene pairs that function as broadly
expressed regulators of transcription, translation and protein stability. We propose that
beyond its roles in testis determination and spermatogenesis, the Y chromosome is
essential for male viability, and plays unappreciated roles in Turner syndrome and in
phenotypic differences between the sexes in health and disease.
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Affiliation(s)
- Daniel W Bellott
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Jennifer F Hughes
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Helen Skaletsky
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Laura G Brown
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Tatyana Pyntikova
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Ting-Jan Cho
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Natalia Koutseva
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Sara Zaghlul
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Tina Graves
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Susie Rock
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Colin Kremitzki
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Robert S Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yan Ding
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Donna Morton
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ziad Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lora Lewis
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Christian Buhay
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Qiaoyan Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jennifer Watt
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michael Holder
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sandy Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lynne Nazareth
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jessica Alföldi
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Steve Rozen
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - David C Page
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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6
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Filipović V, Kartelj A, Matić D. An electromagnetism metaheuristic for solving the Maximum Betweenness Problem. Appl Soft Comput 2013. [DOI: 10.1016/j.asoc.2012.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. Nature 2012; 483:82-6. [PMID: 22367542 PMCID: PMC3292678 DOI: 10.1038/nature10843] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 01/10/2012] [Indexed: 11/16/2022]
Abstract
The human X and Y chromosomes evolved from an ordinary pair of autosomes during the past 200–300 million years1–3. Due to genetic decay, the human MSY (male-specific region of Y chromosome) retains only three percent of the ancestral autosomes’ genes4,5. This evolutionary decay was driven by a series of five “stratification” events. Each event suppressed X-Y crossing over within a chromosome segment or “stratum”, incorporated that segment into the MSY, and subjected its genes to the erosive forces that attend the absence of crossing over2,6. The last of these events occurred 30 million years ago (mya), or 5 million years before the human and Old World monkey (OWM) lineages diverged. Although speculation abounds regarding ongoing decay and looming extinction of the human Y chromosome7–10, remarkably little is known about how many MSY genes were lost in the human lineage in the 25 million years that have followed its separation from the OWM lineage. To explore this question, we sequenced the MSY of the rhesus macaque, an OWM, and compared it to the human MSY. We discovered that, during the last 25 million years, MSY gene loss in the human lineage was limited to the youngest stratum (stratum 5), which comprises three percent of the human MSY. Within the older strata, which collectively comprise the bulk of the human MSY, gene loss evidently ceased more than 25 mya. Likewise, the rhesus MSY has not lost any older genes (from strata 1–4) during the past 25 million years, despite major structural differences from the human MSY. The rhesus MSY is simpler, with few amplified gene families or palindromes that might enable intrachromosomal recombination and repair. We present an empirical reconstruction of human MSY evolution in which each stratum transitioned from rapid, exponential loss of ancestral genes to strict conservation through purifying selection.
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8
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KOMATSU M, FUJIMORI Y, SATO Y, OKAMURA H, SASAKI S, ITOH T, MORITA M, NAKAMURA R, OE T, FURUTA M, YASUDA J, KOJIMA T, WATANABE T, HAYASHI T, MALAU-ADULI AE, TAKAHASHI H. Nucleotide polymorphisms and the 5′-UTR transcriptional analysis of the bovine growth hormone secretagogue receptor 1a (GHSR1a) gene. Anim Sci J 2010; 81:530-50. [DOI: 10.1111/j.1740-0929.2010.00797.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Karere GM, Lyons LA, Froenicke L. Enhancing radiation hybrid mapping through whole genome amplification. Hereditas 2010; 147:103-12. [PMID: 20536549 DOI: 10.1111/j.1601-5223.2010.02166.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Radiation hybrid (RH) mapping is limited by the inherent genomic instability of RH clones entailing both, limited DNA sample amounts and genomic heterogeneity of the clones. Here the instability of RH clones is quantified and the suitability of the multiple strand displacement whole genome amplification method (WGA) for radiation hybrid mapping is assessed. To quantify the instability of RH clones, eleven clones of a 10,000(Rad) rhesus macaque radiation hybrid panel were passaged ten times and analyzed by interspersed repeat sequence specific quantitative PCR and by genotyping of 46 macaque chromosome 5 STS markers. The quantitative PCR data indicate an average loss of 55% of the donor DNA over 10 passages. Over the same period, a dropout of 46.2% of the STS markers was observed. These data indicate a genome wide half-life of the donor DNA of 8.7 passages and of 10.6 passages for the chromosome 5 markers. The genotyping data of the genomic RH DNA were compared to three sets of WGA experiments: 1) single wgaDNA amplifications, 2) six WGA replicates, and 3) re-amplification of wga DNA. The assays demonstrated concordance rates of 97.6%, 98% and 99.3%, respectively, and indicated the marker specificity of some repeated WGA dropouts. The study confirms that WGA is suitable for RH mapping studies should enable the accurate analysis of almost an infinite numbers of markers. WGA will allow the analysis of earliest RH clone passages, thus limiting their heterogeneity and RH mapping artifacts.
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Affiliation(s)
- Genesio M Karere
- Department of Population Health and Reproduction, School of Veterinary Medicine, California National Primate Research Center, University of California - Davis, Davis, California, USA
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10
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Localization of 31 porcine transcripts to the pig genome by SSRH radiation hybrid mapping. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0024-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Verma S, Goldammer T, Aitken R. Cloning and expression of activation induced cytidine deaminase from Bos taurus. Vet Immunol Immunopathol 2009; 134:151-9. [PMID: 19766322 DOI: 10.1016/j.vetimm.2009.08.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Revised: 07/21/2009] [Accepted: 08/24/2009] [Indexed: 12/13/2022]
Abstract
Activation induced cytidine deaminase is an enzyme crucial to somatic hypermutation and gene conversion, processes that are essential for the diversification of Ig V genes. The bovine Ig repertoire appears to be diversified by mechanisms that are significantly different to those that operate in humans and mice. This study set out to test the hypothesis that differences in the organization, coding sequence, expression or genomic location of the bovine AICDA gene enables the encoded enzyme to catalyse the unusual Ig diversification mechanism seen in cattle as well as conventional antigen-driven mutation. Characterization of bovine AICDA excluded the first two possibilities. AICDA expression was detected in lymphoid tissues from neonatal and older cattle, but AICDA cDNA could not be detected in muscle tissue. The pattern of gene expression did not therefore differ from that in other vertebrates. The AICDA cDNA was cloned and expressed successfully in Escherichia coli generating a phenotype consistent with the mutating action of this deaminase. Using a whole genome radiation hybrid panel, bovine AICDA was mapped to a region of bovine chromosome 5 syntenic with the location of human AICDA on chromosome 12. We conclude that the unusual nature of Ig diversification in cattle is unlikely to be attributable to the structure, sequence, activity or genomic location of bovine AICDA.
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Affiliation(s)
- Subhash Verma
- Division of Infection and Immunity, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, UK
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12
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Williams JL, Dunner S, Valentini A, Mazza R, Amarger V, Checa ML, Crisà A, Razzaq N, Delourme D, Grandjean F, Marchitelli C, García D, Pérez Gomez R, Negrini R, Ajmone Marsan P, Levéziel H. Discovery, characterization and validation of single nucleotide polymorphisms within 206 bovine genes that may be considered as candidate genes for beef production and quality. Anim Genet 2009; 40:486-91. [DOI: 10.1111/j.1365-2052.2009.01874.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Polymorphism identification, RH mapping and association of placental lactogen gene with milk production traits of dairy cows. Animal 2009; 3:1-5. [DOI: 10.1017/s1751731108003054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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14
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Ajmone Marsan P, Gorni C, Milanesi E, Mazza R, van Eijk MJT, Peleman JD, Williams JL. Assessment of AFLP marker behaviour in enriching STS radiation hybrid maps. Anim Genet 2008; 39:383-94. [PMID: 18573125 DOI: 10.1111/j.1365-2052.2008.01747.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Radiation hybrid (RH) mapping provides a powerful tool to build high-resolution maps of genomes. Here, we demonstrate the use of the AFLP technique for high-throughput typing of RH cell lines. Cattle were used as the model species because an RH panel was available to investigate the behaviour of AFLP markers within the microsatellite- and STS-based maps of this species. A total of 747 AFLP markers were typed on the TM112 RH radiation panel and 651 of these were assigned by two-point analysis to the 29 bovine autosomes and sex chromosomes. AFLP markers were added to the 1222 microsatellite and STS markers that were included in earlier RH maps. Multipoint maps were constructed for seven example chromosomes, which retained 248 microsatellite and STS markers, and added 123 AFLP markers at LOD 4. The addition of the AFLP markers increased the number of markers by 42.1% and the map length by 10.4%. The AFLP markers showed lower retention frequency (RF) values than the STS markers. The comparison of RF values in AFLP markers and their corresponding AFLP-derived STSs demonstrated that the lower RF values were due to the lower detection sensitivity of the AFLP technique. Despite these differences, AFLP and AFLP-derived STS markers mapped to identical or similar positions. These results demonstrate that it is possible to merge AFLP and microsatellite markers in the same map. The application of AFLP technology could permit the rapid construction of RH maps in species for which extensive genome information and large numbers of SNP and microsatellite markers are not available.
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Affiliation(s)
- P Ajmone Marsan
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, 29100 Piacenza, Italy.
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15
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Pelissier P, Delourme D, Germot A, Blanchet X, Becila S, Maftah A, Leveziel H, Ouali A, Bremaud L. An original SERPINA3 gene cluster: elucidation of genomic organization and gene expression in the Bos taurus 21q24 region. BMC Genomics 2008; 9:151. [PMID: 18384666 PMCID: PMC2373789 DOI: 10.1186/1471-2164-9-151] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Accepted: 04/02/2008] [Indexed: 12/18/2022] Open
Abstract
Background The superfamily of serine proteinase inhibitors (serpins) is involved in numerous fundamental biological processes as inflammation, blood coagulation and apoptosis. Our interest is focused on the SERPINA3 sub-family. The major human plasma protease inhibitor, α1-antichymotrypsin, encoded by the SERPINA3 gene, is homologous to genes organized in clusters in several mammalian species. However, although there is a similar genic organization with a high degree of sequence conservation, the reactive-centre-loop domains, which are responsible for the protease specificity, show significant divergences. Results We provide additional information by analyzing the situation of SERPINA3 in the bovine genome. A cluster of eight genes and one pseudogene sharing a high degree of identity and the same structural organization was characterized. Bovine SERPINA3 genes were localized by radiation hybrid mapping on 21q24 and only spanned over 235 Kilobases. For all these genes, we propose a new nomenclature from SERPINA3-1 to SERPINA3-8. They share approximately 70% of identity with the human SERPINA3 homologue. In the cluster, we described an original sub-group of six members with an unexpected high degree of conservation for the reactive-centre-loop domain, suggesting a similar peptidase inhibitory pattern. Preliminary expression analyses of these bovSERPINA3s showed different tissue-specific patterns and diverse states of glycosylation and phosphorylation. Finally, in the context of phylogenetic analyses, we improved our knowledge on mammalian SERPINAs evolution. Conclusion Our experimental results update data of the bovine genome sequencing, substantially increase the bovSERPINA3 sub-family and enrich the phylogenetic tree of serpins. We provide new opportunities for future investigations to approach the biological functions of this unusual subset of serine proteinase inhibitors.
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Affiliation(s)
- Patrick Pelissier
- INRA, UMR 1061 Unité de Génétique Moléculaire Animale, Université de Limoges, IFR 145, Faculté des Sciences et Techniques, 87060 Limoges, France.
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16
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Guo H, Liu WS, Takasuga A, Eyer K, Landrito E, Xu SZ, Gao X, Ren HY. Mapping, expression, and association study of the bovine PSMC1 gene. Biochem Genet 2008; 46:347-55. [PMID: 18247114 DOI: 10.1007/s10528-008-9151-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 11/16/2007] [Indexed: 11/27/2022]
Abstract
The 26S ATP-dependent protease is composed of a 20S catalytic proteasome and two PA700 regulatory modules; it plays a central role in many regulatory pathways, such as cell cycle regulation, differentiation, and apoptosis. The PA700 complex is composed of multiple subunits, including at least six related ATPases and approximately 15 non-ATPase polypeptides. PSMC1 (proteasome 26S subunit, ATPase, 1) is one of these ATPases. In this study, we amplified a fragment of 507 bp from intron 9 of the bovine PSMC1 gene and found a SNP (G/A) at position 216 in the PCR fragment. Genotyping of 138 animals from four beef breeds revealed that the average frequency for allele A (G-base) was 0.4271 (0.3269-0.5517); for allele B (A-base) it was 0.5729 (0.4483-0.6731). This SNP is significantly associated with average daily feed intake (P < 0.01), average daily gain, finishing average daily gain, body length, ratio of feed to meat, backfat thickness, and loin-muscle area (P < 0.05). Our experimental data showed that animals with an AA genotype have a significantly lower food intake, grow faster, are longer in the body, and have less backfat and bigger loin muscle; hence, their ratio of feed to meat is significantly lower. We believe that the PSMC1 SNP is a potential candidate marker for marker-assisted selection in these traits. We also found that the bovine PSMC1 gene was expressed mainly in lung, testis, and spleen. In addition, we mapped the bovine PSMC1 gene on BTA10 by an RH mapping method.
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Affiliation(s)
- H Guo
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100094, P.R. China
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17
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Coleman SJ, Gong G, Gaile DP, Chowdhary BP, Bailey E, Liu L, MacLeod JN. Evaluation of Compass as a comparative mapping tool for ESTs using horse radiation hybrid maps. Anim Genet 2008; 38:294-302. [PMID: 17539974 DOI: 10.1111/j.1365-2052.2007.01603.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Loci for 9322 equine expressed sequence tags (ESTs) were predicted using the Comparative Mapping by Annotation and Sequence Similarity (Compass) strategy in order to evaluate the programme's ability to make accurate locus predictions in species with comparative gene maps. Using human genome sequence information from Build 35 (May 2004) and published marker information from the radiation hybrid (RH) maps for equine chromosomes (ECA) 17 and X, 162 ESTs were predicted to locations on ECA17 and 328 ESTs to locations on ECAX by selection of the 'top blast hit'. The locations of 30 ESTs were assessed experimentally by RH mapping analysis to evaluate the accuracy of the Compass predictions. The data revealed that 53% (16 of 30) of the ESTs predicted on ECA17 and ECAX mapped to those chromosomes. Analysis of the results suggested the need to identify expressed orthologous sequences in order to generate more accurate predictions for ESTs. Locus predictions were reassessed with three modifications to the Compass strategy's orthologue selection parameters. Selection of the 'top gene hit' improved accuracy to 72% (21 of 29), while selection of the 'top expressed gene hit' improved accuracy to 86% (24 of 28). Using the default Compass parameters with the UniGene database improved prediction accuracy to 96% (22 of 23); however, this level of accuracy came with a substantial decrease in the total number of predictions. When used with optimized prediction parameters, the Compass strategy can be a practical in silico map location prediction tool for large EST sample sets from unsequenced animal genomes.
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Affiliation(s)
- S J Coleman
- Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA.
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18
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A new 4016-marker radiation hybrid map for porcine-human genome analysis. Mamm Genome 2008; 19:51-60. [PMID: 18188646 DOI: 10.1007/s00335-007-9081-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Accepted: 11/02/2007] [Indexed: 10/22/2022]
Abstract
We constructed a 5000-rad comprehensive radiation hybrid (RH) map of the porcine (Sus scrofa) genome and compared the results with the human genome. Of 4475 typed markers, 4016 (89.7%) had LOD >5 compared with the markers used in our previous RH map by means of two-point analysis and were grouped onto the 19 porcine chromosomes (SSCs). All mapped markers had LOD >3 as determined by RHMAPPER analysis. The current map comprised 430 microsatellite (MS) framework markers, 914 other MS markers, and 2672 expressed sequence tags (ESTs). The whole-genome map was 8822.1 cR in length, giving an average marker density of 0.342 Mb/cR. The average retention frequency was 35.8%. Using BLAST searches of porcine ESTs against the RefSeq human nucleotide and amino acid sequences (release 22), we constructed high-resolution comparative maps of each SSC and each human chromosome (HSA). The average distance between ESTs in the human genome was 1.38 Mb. SSC contained 50 human chromosomal syntenic groups, and SSC11, SSC12, and SSC16 were only derived from the HSA13q, HSA17, and HSA5 regions, respectively. Among 38 porcine terminal regions, we found that at least 20 regions have been conserved between the porcine and human genomes; we also found four paralogous regions for the major histocompatibility complex (MHC) on SSC7, SSC2, SSC4, and SSC1.
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19
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Yu SL, Chung HJ, Sang BC, Park CS, Lee JH, Yoon DH, Lee SH, Choi KD. Identification of differentially expressed genes in distinct skeletal muscles in cattle using cDNA microarray. Anim Biotechnol 2008; 18:275-85. [PMID: 17934901 DOI: 10.1080/10495390701413391] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The 788-gene microarray was manufactured using selected elements from three different cDNA libraries in order to identify molecular processes that determine phenotypic characteristics between loin (M. longissimus thoracis) and round (M. semimembranosus) muscles. Microarray analyses identified 24 differentially expressed genes between the two muscles investigated. Five of the genes were verified by quantitative RT-PCR and three of them were mapped on bovine chromosomes using 5,000 rad bovine radiation hybrid (RH) panel. The map locations indicated that they were mapped in the same chromosomal regions where IMF and growth QTLs were located, suggesting that they are most possible positional candidate genes for the traits.
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Affiliation(s)
- S L Yu
- Division of Animal Science and Resources, Chungnam National University, Daejeon, Korea
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20
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Cargill EJ, Paetzold L, Womack JE. Radiation hybrid mapping and comparative sequence analysis of bovine RIG-I and MAVS genes. ACTA ACUST UNITED AC 2007; 17:314-8. [PMID: 17312953 DOI: 10.1080/10425170600857582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Retinoic acid inducible gene I (RIG-I) and mitochondrial antiviral signaling (MAVS) proteins have recently been found to operate in a pathway for the detection and subsequent elimination of replicating viral genomes. Because of this innate immunity role, RIG-I and MAVS are candidates for studies of disease resistance. The objectives of this work were to (1) radiation hybrid (RH) map bovine RIG-I and MAVS and (2) perform comparative sequence analysis of partial genomic sequence from each gene. Using a bovine 5000(rad) RH panel, RIG-I was localized to BTA08 (LOD > 12) and MAVS was localized to BTA13 (LOD > 12). RIG-I exon 14 and partial MAVS exon five were sequenced in nine breeds and compared with available sequence from the Bovine Genome Project. RIG-I exon 14 and partial MAYS exon five were conserved in all samples examined. One T-A transversion SNP was found in intronic sequence downstream of RIG-I exon 14.
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Affiliation(s)
- Edward J Cargill
- Department of Pathobiology, College of Veterinary Medicine, Texas A & M University, College Station, TX 77843-4467, USA
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21
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Schäffer AA, Rice ES, Cook W, Agarwala R. rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control. Bioinformatics 2007; 23:1156-8. [PMID: 17332018 PMCID: PMC2266093 DOI: 10.1093/bioinformatics/btm077] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
UNLABELLED rh_tsp_map is a software package for computing radiation hybrid (RH) maps and for integrating physical and genetic maps. It solves the central mapping instances by reducing them to the traveling salesman problem (TSP) and using a modification of the CONCORDE package to solve the TSP instances. We present some of the features added between the initial rh_tsp_map version 1.0 and the current version 3.0, emphasizing the automation of many steps and addition of various checks designed to find problems with the input data. Iterations of improved input data followed by fast re-computation of the maps improves the quality of the final maps. AVAILABILITY rh_tsp_map source code and documentation including a tutorial is available at ftp://ftp.ncbi.nih.gov/pub/agarwala/rhmapping/rh_tsp_map.tar.gz. CONCORDE modified for RH mapping is available in the directory http://www.isye.gatech.edu/~wcook/rh/. The QSopt library needed for CONCORDE is available at http://www2.isye.gatech.edu/~wcook/qsopt/downloads/downloads.htm
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Affiliation(s)
- Alejandro A Schäffer
- National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
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22
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Dierks C, Mömke S, Drögemüller C, Leeb T, Chowdhary BP, Distl O. A high-resolution comparative radiation hybrid map of equine chromosome 4q12-q22. Anim Genet 2006; 37:513-7. [PMID: 16978184 DOI: 10.1111/j.1365-2052.2006.01510.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
In this study, we present a comprehensive 5000-rad radiation hybrid map of a 40-cM region on equine chromosome 4 (ECA4) that contains quantitative trait loci for equine osteochondrosis. We mapped 29 gene-associated sequence tagged site markers using primers designed from equine expressed sequence tags or BAC clones in the ECA4q12-q22 region. Three blocks of conserved synteny, showing two chromosomal breakpoints, were identified in the segment of ECA4q12-q22. Markers from other segments of HSA7q mapped to ECA13p and ECA4p, and a region of HSA7p was homologous to ECA13p. Therefore, we have improved the resolution of the human-equine comparative map, which allows the identification of candidate genes underlying traits of interest.
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Affiliation(s)
- C Dierks
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17p, 30559 Hannover, Germany
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23
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Boneker C, Kuiper H, Drögemüller C, Chowdhary BP, Distl O. Molecular characterization of the equine collagen, type IX, alpha 2 (COL9A2) gene on horse chromosome 2p16-->p15. Cytogenet Genome Res 2006; 115:107-14. [PMID: 17065790 DOI: 10.1159/000095229] [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] [Received: 01/30/2006] [Accepted: 03/24/2006] [Indexed: 11/19/2022] Open
Abstract
The mammalian collagen, type IX, alpha 2 gene (COL9A2) encodes the alpha-2 chain of type IX collagen and is located on horse chromosome 2p16-->p14 harbouring a quantitative trait locus for osteochondrosis. We isolated a bacterial artificial chromosome (BAC) clone containing the equine COL9A2 gene and determined the complete genomic sequence of this gene. Cloning and characterization of equine COL9A2 revealed that the equine gene consists of 32 exons spanning approximately 15 kb. The COL9A2 transcript encodes a single protein of 688 amino acids. Thirty two single nucleotide polymorphisms (SNPs) equally distributed in the gene were detected in a mutation scan of eight unrelated Hanoverian warmblood stallions, including one SNP that affects the amino acid sequence of COL9A2. Comparative analyses between horse, human, mouse and rat indicate that the chromosomal location of equine COL9A2 is in agreement with known chromosomal synteny relationships. The comparison of the gene structure and transcript revealed a high degree of conservation towards the other mammalian COL9A2 genes. We chose three informative SNPs for association and linkage disequilibrium tests in three to five paternal half-sib families of Hanoverian warmblood horses consisting of 44 to 75 genotyped animals. The test statistics did not reach the significance threshold of 5% and so we could not show an association of COL9A2 with equine osteochondrosis.
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Affiliation(s)
- C Boneker
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
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24
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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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25
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Abbasi AR, Ihara N, Khalaj M, Sugimoto Y, Kunieda T. An integrated radiation hybrid map of bovine chromosome 18 that refines a critical region associated with multiple ocular defects in cattle. Anim Genet 2006; 37:58-61. [PMID: 16441298 DOI: 10.1111/j.1365-2052.2005.01372.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Congenital multiple ocular defects (MOD) of Japanese black cattle is a hereditary ocular disorder with an autosomal recessive mode of inheritance showing developmental defects of the lens, retina and iris, persistent embryonic eye vascularization and microphthalmia. The MOD locus has been mapped by linkage analysis to a 6.6-cM interval on the proximal end of bovine chromosome 18, which corresponds to human chromosome 16q and mouse chromosome 8. To refine the MOD region in cattle, we constructed an integrated radiation hybrid (RH) map of the proximal region of bovine chromosome 18, which consisted of 17 genes and 10 microsatellite markers, using the SUNbRH7000 panel. Strong conservation of gene order was found among the corresponding chromosomal regions in cattle, human and mouse. The MOD-critical region was fine mapped to a 59.5-cR region that corresponds to a 6.3-Mb segment of human chromosome 16 and a 4.8-Mb segment of mouse chromosome 8. Several positional candidate genes, including FOXC2 and USP10, were identified in this region.
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Affiliation(s)
- A R Abbasi
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
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26
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Guo H, Liu WS, Takasuga A, Eyer K, Landrito E, Xu SZ, Gao X, Ren HY. Mapping of the CCK, PSMC2, PSMC4, PSMD1, CPB1 and PSPH genes in cattle. Anim Genet 2006; 37:73-5. [PMID: 16441302 DOI: 10.1111/j.1365-2052.2005.01403.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- H Guo
- Laboratory of Molecular Biology and Animal Breeding, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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27
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Itoh T, Watanabe T, Sugimoto Y, Takasuga A. Radiation hybrid mapping of seven bovine genes encoding transcription factors involved in adipogenesis. Anim Genet 2006; 37:78-9. [PMID: 16441304 DOI: 10.1111/j.1365-2052.2005.01402.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- T Itoh
- Livestock Improvement Association of Japan, Inc., Maebashi, Gunma 351-0211, Japan
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28
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Taylor KH, Taylor JF, White SN, Womack JE. Identification of genetic variation and putative regulatory regions in bovine CARD15. Mamm Genome 2006; 17:892-901. [PMID: 16897345 DOI: 10.1007/s00335-005-0148-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Accepted: 04/05/2006] [Indexed: 11/30/2022]
Abstract
Mutations in caspase recruitment domain 15 (CARD15) are associated with susceptibility to Crohn's disease and Blau Syndrome. We performed comparative analyses of the bovine, murine, and human CARD15 transcripts to elucidate functionality of bovine CARD15 and examine its potential role in bovine disease resistance. Comparative analyses of intronic sequence across seven divergent species were performed to identify putative regulatory element binding motifs. High levels of interspecies conservation in sequence, genomic structure, and protein domains were detected indicating common functionality for CARD15 in cattle, human, and mouse. We identified species-specific regulatory elements in the 5' and 3' untranslated regions, suggesting that modes of regulation may have diverged across species. Thirty-one conserved putative regulatory element binding motifs were identified in the CARD15 intronic sequence of seven species. To assess the extent of genetic diversity within bovine CARD15, 41 individuals from two subspecies were sequenced and screened for polymorphisms. Thirty-six single nucleotide polymorphisms (SNPs) were identified. Finally, 20 subspecies-specific haplotypes were predicted with 7 and 13 unique haplotypes explaining the diversity within B. taurus taurus and B. taurus indicus animals, respectively. Strong evidence for a simple causal relationship between these SNP loci and their haplotypes with Johne's disease was not detected.
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Affiliation(s)
- Kristen H Taylor
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas 77843-4467, USA
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29
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Dranchak PK, Ekenstedt KJ, Valberg SJ, Chowdhary BP, Raudsepp T, Mickelson JR. Chromosomal assignments for the equine AMPK family genes. Anim Genet 2006; 37:293-4. [PMID: 16734697 DOI: 10.1111/j.1365-2052.2006.01431.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: 11/30/2022]
Affiliation(s)
- P K Dranchak
- Department of Veterinary Biomedical Sciences, University of Minnesota, 1988 Fitch Ave, St Paul, 55108, USA
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30
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Willcocks S, Yamakawa Y, Stalker A, Coffey TJ, Goldammer T, Werling D. Identification and gene expression of the bovine C-type lectin Dectin-1. Vet Immunol Immunopathol 2006; 113:234-42. [PMID: 16797084 DOI: 10.1016/j.vetimm.2006.04.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Revised: 04/10/2006] [Accepted: 04/19/2006] [Indexed: 11/22/2022]
Abstract
C-type lectin receptors (CTLR) are cell-surface signalling molecules that recognize a range of highly conserved pathogen molecules and instigate the appropriate immune response. Here, we report the cloning, sequencing, mapping and expression pattern of the bovine C-type lectin domain family 7, member A (CLEC7A; synonyms CLCSF12, Dectin-1). We identified two isoforms, similar to the human system, with a long and short neck. Overall, the organization of the two bovine CLEC7A genes is similar to that of humans and mice. The CLEC7A gene maps on Bos taurus chromosome 5 (BTA5). mRNA transcripts for CLEC7A were detected in bone-marrow cells, monocytes, macrophages and dendritic cells and NK cells, but not in CD4(+) T-cells or CD21(+) B-cells. The increased knowledge of the genomic organization of the bovine CTLR genes may promote our understanding of their evolution and help in the identification of bovine genes underlying disease-resistance traits.
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Affiliation(s)
- S Willcocks
- Royal Veterinary College, Department of Pathology and Infectious Diseases, Hawkshead Lane, Hatfield, AL9 7TA, UK
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31
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Wittwer C, Chowdhary BP, Distl O. Radiation hybrid mapping of equine CDK2, DGKA, DNAJC14, MMP19, CTSL and GAS1. Anim Genet 2006; 36:536-7. [PMID: 16293143 DOI: 10.1111/j.1365-2052.2005.01381.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C Wittwer
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Germany
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Leeb T, Vogl C, Zhu B, de Jong PJ, Binns MM, Chowdhary BP, Scharfe M, Jarek M, Nordsiek G, Schrader F, Blöcker H. A human-horse comparative map based on equine BAC end sequences. Genomics 2006; 87:772-6. [PMID: 16603334 DOI: 10.1016/j.ygeno.2006.03.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Revised: 12/15/2005] [Accepted: 03/04/2006] [Indexed: 11/18/2022]
Abstract
In an effort to increase the density of sequence-based markers for the horse genome we generated 9473 BAC end sequences (BESs) from the CHORI-241 BAC library with an average read length of 677 bp. BLASTN searches with the BESs revealed 4036 meaningful hits (E <or= 10(-5)) in the human genome that provide useful markers for the human-horse comparative map. The 4036 BLASTN hits allowed the anchoring of 3079 BAC clones to the human genome, on average one corresponding equine BAC clone per megabase of human DNA. We used the BLASTN anchored BESs for an in silico prediction of the gene content and chromosome assignment of comparatively mapped equine BAC clones. As a first verification of our in silico mapping strategy we placed 19 equine BESs with matches to HSA6 onto the RH map. All markers were assigned to the predicted localizations on ECA10, ECA20, and ECA31, respectively.
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Affiliation(s)
- Tosso Leeb
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany.
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Looft C, Paul S, Philipp U, Regenhard P, Kuiper H, Distl O, Chowdhary BP, Leeb T. Sequence analysis of a 212 kb defensin gene cluster on ECA 27q17. Gene 2006; 376:192-8. [PMID: 16723195 DOI: 10.1016/j.gene.2006.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Accepted: 03/10/2006] [Indexed: 11/22/2022]
Abstract
Defensins are a family of evolutionary ancient antimicrobial peptides consisting of three sub-families: alpha-, beta- and theta-defensins. This investigation was focused on the genomic characterization of equine beta-defensins and the investigation of the potential clustering of beta-defensin genes in the equine genome. Six genomic BAC clones were isolated from the CHORI-241 library and one of these was mapped by FISH to ECA 27q17. This location was confirmed by RH-mapping. The contiguous 212 kb sequence of this clone was determined. Sequence analysis revealed the identification of ten pseudogenes and nine genes, six of which were highly homologous to human beta-defensin DEFB4. Clustering of the beta-defensin genes was confirmed and the order of the genes on the analyzed BAC was related to the corresponding defensin cluster on HSA 8. The knowledge about the sequence and the genomic structure of the equine beta-defensin genes will improve the classification of different paralogous defensin genes and is a prerequisite for subsequent functional studies. Additionally, the first alpha-defensin-like sequence outside the groups of primates, lagomorphs and rodents (glires) was identified.
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Affiliation(s)
- Christian Looft
- Institute of Animal Breeding and Husbandry, Christian Albrecht University of Kiel, D-24098 Kiel, Germany
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34
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Weikard R, Goldammer T, Laurent P, Womack JE, Kuehn C. A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits. BMC Genomics 2006; 7:53. [PMID: 16542434 PMCID: PMC1475854 DOI: 10.1186/1471-2164-7-53] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Accepted: 03/16/2006] [Indexed: 11/25/2022] Open
Abstract
Background A number of different quantitative trait loci (QTL) for various phenotypic traits, including milk production, functional, and conformation traits in dairy cattle as well as growth and body composition traits in meat cattle, have been mapped consistently in the middle region of bovine chromosome 6 (BTA6). Dense genetic and physical maps and, ultimately, a fully annotated genome sequence as well as their mutual connections are required to efficiently identify genes and gene variants responsible for genetic variation of phenotypic traits. A comprehensive high-resolution gene-rich map linking densely spaced bovine markers and genes to the annotated human genome sequence is required as a framework to facilitate this approach for the region on BTA6 carrying the QTL. Results Therefore, we constructed a high-resolution radiation hybrid (RH) map for the QTL containing chromosomal region of BTA6. This new RH map with a total of 234 loci including 115 genes and ESTs displays a substantial increase in loci density compared to existing physical BTA6 maps. Screening the available bovine genome sequence resources, a total of 73 loci could be assigned to sequence contigs, which were already identified as specific for BTA6. For 43 loci, corresponding sequence contigs, which were not yet placed on the bovine genome assembly, were identified. In addition, the improved potential of this high-resolution RH map for BTA6 with respect to comparative mapping was demonstrated. Mapping a large number of genes on BTA6 and cross-referencing them with map locations in corresponding syntenic multi-species chromosome segments (human, mouse, rat, dog, chicken) achieved a refined accurate alignment of conserved segments and evolutionary breakpoints across the species included. Conclusion The gene-anchored high-resolution RH map (1 locus/300 kb) for the targeted region of BTA6 presented here will provide a valuable platform to guide high-quality assembling and annotation of the currently existing bovine genome sequence draft to establish the final architecture of BTA6. Hence, a sequence-based map will provide a key resource to facilitate prospective continued efforts for the selection and validation of relevant positional and functional candidates underlying QTL for milk production and growth-related traits mapped on BTA6 and on similar chromosomal regions from evolutionary closely related species like sheep and goat. Furthermore, the high-resolution sequence-referenced BTA6 map will enable precise identification of multi-species conserved chromosome segments and evolutionary breakpoints in mammalian phylogenetic studies.
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Affiliation(s)
- Rosemarie Weikard
- Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere (FBN), 19196 Dummerstorf; Germany
| | - Tom Goldammer
- Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere (FBN), 19196 Dummerstorf; Germany
| | - Pascal Laurent
- Laboratoire de Génétique et de Cytogénétique, INRA, Jouy-en-Josas, 78350, France
| | | | - Christa Kuehn
- Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere (FBN), 19196 Dummerstorf; Germany
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35
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Ponsuksili S, Brunner RM, Goldammer T, Kühn C, Walz C, Chomdej S, Tesfaye D, Schellander K, Wimmers K, Schwerin M. Bovine NALP5, NALP8, and NALP9 Genes: Assignment to a QTL Region and the Expression in Adult Tissues, Oocytes, and Preimplantation Embryos. Biol Reprod 2006; 74:577-84. [PMID: 16339045 DOI: 10.1095/biolreprod.105.045096] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A 3204-bp full-length cDNA of bovine NALP9 was cloned and its genomic organization was analyzed. The 2988-bp open reading frame covers 9 exons and encodes a deduced protein of 996 amino acids containing Pyrin, Nacht and leucine-rich repeat domains like the human NALP gene family members. Mapping with the WGRH5000 panel and fluorescence in situ hybridization assigned NALP9 in close vicinity to BM2078 (LOD score 25.71; distance 0.0 cR5000) on bovine chromosome 18, BTA18q25-q26, within a previously identified QTL region for reproductive traits flanked by the bovine marker BM2078 and TGLA227. BAC contig analysis revealed that NALP9, NALP8, and NALP5 map in this QTL region. Temporospatial expression of these members of the NALP gene family was monitored. Among the adult tissues examined, transcripts of NALP8 and NALP9 were detected exclusively in testis and ovary, whereas transcripts of the NALP5 gene are limited to the ovary. The transcripts of NALP9, NALP8, and NALP5 were detected in oocytes before and after in vitro maturation and with a gradual decline from 2-cell to 8-cell stage, suggesting no reactivation at the time of bovine maternal to embryonic transition. Assignment to a QTL region for reproductive traits and preferential expression of NALP9, NALP8, and NALP5 in oocyte, germinal lineage, and gonad cells may suggest their functional relevance to reproduction and possible contribution to phenotypic variation.
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Affiliation(s)
- Siriluck Ponsuksili
- Research Group Functional Genomics, Research Institute for the Biology of Farm Animals (FBN), 18196 Dummerstorf, Germany
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36
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Böneker C, Müller D, Kuiper H, Drögemüller C, Chowdhary BP, Distl O. Assignment of the COL8A2 gene to equine chromosome 2p15-p16 by FISH and confirmation by RH mapping. Anim Genet 2006; 36:444-5. [PMID: 16167992 DOI: 10.1111/j.1365-2052.2005.01330.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- C Böneker
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
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37
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Müller D, Kuiper H, Böneker C, Mömke S, Drögemüller C, Chowdhary BP, Distl O. Assignment of BGLAP, BMP2, CHST4, SLC1A3, SLC4A1, SLC9A5 and SLC20A1 to equine chromosomes by FISH and confirmation by RH mapping. Anim Genet 2006; 36:457-61. [PMID: 16167999 DOI: 10.1111/j.1365-2052.2005.01347.x] [Citation(s) in RCA: 3] [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)
- D Müller
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
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38
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Brunner RM, Kata SR, Womack JE, Goldammer T. Assignment of the bovine tumor protein D52 gene (TPD52) to the distal half of BTA14 with somatic and radiation cell hybrid panel mapping. Cytogenet Genome Res 2005; 111:96. [PMID: 16097081 DOI: 10.1159/000085676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- R M Brunner
- Research Institute for the Biology of Farm Animals Dummerstorf, Dummerstorf, Germany
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39
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Gasbarra D, Sillanpää MJ. Constructing the parental linkage phase and the genetic map over distances <1 cM using pooled haploid DNA. Genetics 2005; 172:1325-35. [PMID: 16301209 PMCID: PMC1456229 DOI: 10.1534/genetics.105.044271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A new statistical approach for construction of the genetic linkage map and estimation of the parental linkage phase based on allele frequency data from pooled gametic (sperm or egg) samples is introduced. This method can be applied for estimation of recombination fractions (over distances <1 cM) and ordering of large numbers (even hundreds) of closely linked markers. This method should be extremely useful in species with a long generation interval and a large genome size such as in dairy cattle or in forest trees; the conifer species have haploid tissues available in megagametophytes. According to Mendelian expectation, two parental alleles should occur in gametes in 1:1 proportions, if segregation distortion does not occur. However, due to mere sampling variation, the observed proportions may deviate from their expected value in practice. These deviations and their dependence along the chromosome can provide information on the parental linkage phase and on the genetic linkage map. Usefulness of the method is illustrated with simulations. The role of segregation distortion as a source of these deviations is also discussed. The software implementing this method is freely available for research purposes from the authors.
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40
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Itoh T, Watanabe T, Ihara N, Mariani P, Beattie CW, Sugimoto Y, Takasuga A. A comprehensive radiation hybrid map of the bovine genome comprising 5593 loci. Genomics 2005; 85:413-24. [PMID: 15780744 DOI: 10.1016/j.ygeno.2004.12.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Accepted: 12/29/2004] [Indexed: 11/17/2022]
Abstract
A bovine whole genome 7000-rad radiation hybrid (RH) panel, SUNbRH(7000-rad), was constructed to build a high-resolution RH map. The Shirakawa-USDA linkage map served as a scaffold to construct a framework map of 3216 microsatellites on which 2377 ESTs were ordered. The resulting RH map provided essentially complete coverage across the genome, with 1 cR7000 corresponding to 114 kb, and a cattle-human comparative map of 1716 bovine genes and sequences annotated in the human genome, which covered 79 and 72% of the bovine and human genomes, respectively. We then integrated the bovine RH and comparative maps with BAC fingerprint information in to construct a detailed, BAC-based physical map covering a reported 40-cM quantitative trait locus region for intramuscular fat or "marbling" on BTA 4. In summary, the new, high-resolution SUNbRH7000-rad, comparative, Shirakawa-USDA linkage, and BAC fingerprint maps provide a set of genomic tools for fine mapping regions of interest in cattle.
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Affiliation(s)
- Tomohito Itoh
- Shirakawa Institute of Animal Genetics, Odakura, Nishigo, Nishi-shirakawa, Fukushima 961-8061, Japan
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41
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Müller D, Kuiper H, Böneker C, Mömke S, Drögemüller C, Chowdhary BP, Distl O. Physical mapping of the PTHR1 gene to equine chromosome 16q21.2. Anim Genet 2005; 36:282-4. [PMID: 15932428 DOI: 10.1111/j.1365-2052.2005.01298.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D Müller
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine, Hannover, Germany
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42
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Müller D, Kuiper H, Mömke S, Böneker C, Drögemüller C, Chowdhary BP, Distl O. Assignment of the COMP gene to equine chromosome 21q12-q14 by FISH and confirmation by RH mapping. Anim Genet 2005; 36:277-9. [PMID: 15932424 DOI: 10.1111/j.1365-2052.2005.01294.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- D Müller
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
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43
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Böneker C, Kuiper H, Wöhlke A, Drögemüller C, Chowdhary BP, Distl O. Assignment of the COL16A1 gene to equine chromosome 2p15.1-p15.3 by FISH and confirmation by RH mapping. Anim Genet 2005; 36:262-3. [PMID: 15932413 DOI: 10.1111/j.1365-2052.2005.01273.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C Böneker
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
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44
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Li GH, Liu WS, Takasuga A, Watanabe T, Carpio CM, Rink A, Sugimoto Y, Ponce de León FA, Beattie CW. Characterization and RH mapping of bovine microsatellites generated from a microdissected BTA20-specific DNA library. Anim Genet 2005; 36:146-51. [PMID: 15771726 DOI: 10.1111/j.1365-2052.2005.01258.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bovine chromosome 20 (BTA20) is associated with several quantitative trait loci (QTL) for meat tenderness, birth weight, milk yield and composition. Fine mapping of these QTL requires the development of additional informative markers to increase the resolution of the BTA20 genetic and physical maps. A BTA20-specific library was constructed by means of microdissection and microcloning, and screened for dinucleotide repeats with (CA)16 and (GT)16 oligos. A total of 60 new microsatellites (MS) were developed and characterized for polymorphism using the U.S. Department of Agriculture (USDA)/Meat Animal Research Center (MARC) bovine reference family, of which 53 markers were informative in this family. The number of alleles for these loci varied from 1 to 14, with an average of 6.5. Thirty-three of these MSs, together with 105 markers previously mapped to BTA20, were scored on a 7000-rad cattle-hamster whole-genome radiation hybrid panel (SUNbRH), resulting in a high-resolution RH7000 rad map for BTA20.
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Affiliation(s)
- G-H Li
- Department of Animal Biotechnology, University of Nevada, Reno, NV 89557, USA
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45
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Leeb T, Bruhn O, Philipp U, Kuiper H, Regenhard P, Paul S, Distl O, Chowdhary BP, Kalm E, Looft C. Assignment of the equine S100A7 gene (psoriasin 1) to chromosome 5p12→p13 by fluorescence in situ hybridization and radiation hybrid mapping. Cytogenet Genome Res 2005; 109:533. [PMID: 15906470 DOI: 10.1159/000084216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- T Leeb
- Institute of Animal Breeding and Genetics, School of Veterinary Medicine Hannover, Hannover; Germany
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46
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Goldammer T, Kata SR, Brunner RM, Kühn C, Weikard R, Womack JE, Schwerin M. High-resolution comparative mapping between human chromosomes 4 and 8 and bovine chromosome 27 provides genes and segments serving as positional candidates for udder health in cattle. Genomics 2004; 84:696-706. [PMID: 15475247 DOI: 10.1016/j.ygeno.2003.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2003] [Accepted: 12/10/2003] [Indexed: 11/30/2022]
Abstract
To get more information about the order of genes located in Bos taurus (BTA) chromosome 27 segments, supposed to harbor loci influencing clinical mastitis and somatic cell count, and to identify genes that serve as positional candidates for the mentioned traits, we constructed a high-resolution, comparative, and comprehensive gene map for BTA27. The map includes 57 loci in a 5000-rad cattle-hamster whole genome radiation hybrid panel supported by 50 syntenic assignments in a cattle-murine somatic hybrid cell panel. Thirty-eight new loci (36 genes, 2 microsatellites) together with repeated mappings of 5 genes and 7 microsatellites and integration of existing data from 7 microsatellites were used to generate a comprehensive RH5000 map. The RH map, constructed at lod score criterion 8 using the software RHMAP v.3.0, consisted of three linkage groups 23, 22, and 590 cR5000 in length. Gene assignments on BTA27 and the localization of 8 more genes on BTA8 and BTA14 previously predicted on BTA8/BTA27 and BTA14/BTA27 narrowed down significantly the chromosome break points between the three cattle chromosomes and segments on Homo sapiens chromosomes HSA4 and HSA8. Defined evolutionary break points increase the accuracy of comparative in silico mapping of further human genes in conserved chromosome segments of BTA27.
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Affiliation(s)
- Tom Goldammer
- Research Unit Molecular Biology, Research Institute for the Biology of Farm Animals (FBN), D-18196 Dummerstorf, Germany.
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47
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Everts-van der Wind A, Kata SR, Band MR, Rebeiz M, Larkin DM, Everts RE, Green CA, Liu L, Natarajan S, Goldammer T, Lee JH, McKay S, Womack JE, Lewin HA. A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates. Genome Res 2004; 14:1424-37. [PMID: 15231756 PMCID: PMC442159 DOI: 10.1101/gr.2554404] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using cattle ESTs that were targeted to gaps in the existing cattle-human comparative map, as well as to sparsely populated map intervals. A total of 870 targeted markers were added, bringing the number of markers mapped on the RH(5000) panel to 1913. Of these, 1463 have significant BLASTN hits (E < e(-5)) against the human genome sequence. A cattle-human comparative map was created using human genome sequence coordinates of the paired orthologs. One-hundred and ninety-five conserved segments (defined by two or more genes) were identified between the cattle and human genomes, of which 31 are newly discovered and 34 were extended singletons on the first-generation map. The new map represents an improvement of 20% genome-wide comparative coverage compared with the first-generation map. Analysis of gene content within human genome regions where there are gaps in the comparative map revealed gaps with both significantly greater and significantly lower gene content. The new, more detailed cattle-human comparative map provides an improved resource for the analysis of mammalian chromosome evolution, the identification of candidate genes for economically important traits, and for proper alignment of sequence contigs on cattle chromosomes.
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48
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Yap IV, Schneider D, Kleinberg J, Matthews D, Cartinhour S, McCouch SR. A graph-theoretic approach to comparing and integrating genetic, physical and sequence-based maps. Genetics 2004; 165:2235-47. [PMID: 14704199 PMCID: PMC1462874 DOI: 10.1093/genetics/165.4.2235] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
For many species, multiple maps are available, often constructed independently by different research groups using different sets of markers and different source material. Integration of these maps provides a higher density of markers and greater genome coverage than is possible using a single study. In this article, we describe a novel approach to comparing and integrating maps by using abstract graphs. A map is modeled as a directed graph in which nodes represent mapped markers and edges define the order of adjacent markers. Independently constructed graphs representing corresponding maps from different studies are merged on the basis of their common loci. Absence of a path between two nodes indicates that their order is undetermined. A cycle indicates inconsistency among the mapping studies with regard to the order of the loci involved. The integrated graph thus produced represents a complete picture of all of the mapping studies that comprise it, including all of the ambiguities and inconsistencies among them. The objective of this representation is to guide additional research aimed at interpreting these ambiguities and inconsistencies in locus order rather than presenting a "consensus order" that ignores these problems.
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Affiliation(s)
- Immanuel V Yap
- Department of Plant Breeding, Cornell University, Ithaca, New York 14853, USA
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49
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McKay SD, White SN, Kata SR, Loan R, Womack JE. The bovine 5' AMPK gene family: mapping and single nucleotide polymorphism detection. Mamm Genome 2004; 14:853-8. [PMID: 14724738 DOI: 10.1007/s00335-003-2276-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2003] [Accepted: 07/18/2003] [Indexed: 10/26/2022]
Abstract
The 5'-AMP-activated protein kinase (AMPK) family is an ancient stress response system whose primary function is regulation of cellular ATP. Activation of AMPK, which is instigated by environmental and nutritional stresses, initiates energy-conserving measures that protect the cell by inhibition and phosphorylation of key enzymes in energy-consuming biochemical pathways. The seven genes that comprise the bovine AMPK family were mapped in cattle by using a radiation hybrid panel. The seven genes mapped to six different cattle chromosomes, each with a LOD score greater than 10.0. PRKAA1 mapped to BTA 20, PRKAA2 and PRKAB2 to BTA 3, PRKAB1 to BTA 17, PRKAG1 to BTA 5, PRKAG2 to BTA 4, and PRKAG3 to BTA 2. Five of the seven genes mapped to regions expected from human/cattle comparative maps. PRKAB2 and PRKAG3, however, have not been mapped in humans. We predict these genes to be located on HSA 1 and 2, respectively. Additionally, one synonymous and one non-synonymous single nucleotide polymorphism (SNP) were detected in PRKAG3 in Bos taurus cattle. In an effort to determine ancestral origins, various herds of mixed breed cattle as well as other ruminant species were characterized for sequence variation in this region of PRKAG3. Owing to the physiological importance of this gene family, we believe that its individual genes are candidate genes for conferring resistance to diseases in cattle.
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Affiliation(s)
- Stephanie D McKay
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843-4467, USA
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50
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Goldammer T, Zerbe H, Molenaar A, Schuberth HJ, Brunner RM, Kata SR, Seyfert HM. Mastitis increases mammary mRNA abundance of beta-defensin 5, toll-like-receptor 2 (TLR2), and TLR4 but not TLR9 in cattle. CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY 2004; 11:174-85. [PMID: 14715566 PMCID: PMC321333 DOI: 10.1128/cdli.11.1.174-185.2004] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Coordination of the primary defense mechanisms against pathogens relies on the appropriate expression of pathogen recognition receptors (PRRs) triggering the early release of effector molecules of the innate immune system. To analyze the impact of this system on the counteraction of infections of the mammary gland (mastitis), we characterized the bovine gene encoding the key PRR Toll-like receptor 9 (TLR9) and mapped its precise position on chromosome BTA22. The sequence information was used to establish real-time PCR quantification assays to measure the mRNA abundances of TLR9, TLR2, and TLR4 together with those of beta-defensin 5 (BNBD5), an early bactericidal effector molecule of the innate system, in healthy and infected mammary glands. Mastitis strongly increased (4- to 13-fold) the mRNA abundances of all of these genes except TLR9. Slight subclinical infections already caused a substantial increase in the copy numbers, though they did so the least for TLR9. Induction was not systemic, since mRNA abundance was low in uninfected control quarters of the udder but high in the severely infected quarters of the same animal. The number of TLR2 copies correlated well with those of TLR4, indicating coordinated regulation of these two PRRs during infection of the udder. Their coordinated regulation explains our unexpected observation that pure Staphylococcus aureus infections caused a strong increase also in TLR4 mRNA abundance. In situ hybridizations revealed that BNBD5 is expressed predominantly in the mammary epithelial cells (MEC) of the infected gland. Our data therefore suggest a significant contribution of the innate immune system to counteract mastitis and attribute a prominent effector function to the MEC.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Cattle
- Chromosome Mapping
- DNA, Complementary/genetics
- DNA-Binding Proteins/genetics
- Female
- Gene Expression
- Immunity, Innate
- Mammary Glands, Animal/immunology
- Mammary Glands, Animal/pathology
- Mastitis, Bovine/genetics
- Mastitis, Bovine/immunology
- Mastitis, Bovine/pathology
- Membrane Glycoproteins/genetics
- Molecular Sequence Data
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Cell Surface/genetics
- Sequence Homology, Amino Acid
- Staphylococcus aureus/pathogenicity
- Toll-Like Receptor 2
- Toll-Like Receptor 4
- Toll-Like Receptor 9
- Toll-Like Receptors
- beta-Defensins/genetics
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Affiliation(s)
- T Goldammer
- Molecular Biology Research Division, Research Institute for the Biology of Farm Animals, 18196 Dummerstorf, Germany
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