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Lawson JM, Salem SE, Miller D, Kahler A, van den Boer WJ, Shilton CA, Sever T, Mouncey RR, Ward J, Hampshire DJ, Foote AK, Bryan JS, Juras R, Pynn OD, Davis BW, Bellone RR, Raudsepp T, de Mestre AM. Naturally occurring horse model of miscarriage reveals temporal relationship between chromosomal aberration type and point of lethality. Proc Natl Acad Sci U S A 2024; 121:e2405636121. [PMID: 39102548 PMCID: PMC11331123 DOI: 10.1073/pnas.2405636121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/04/2024] [Indexed: 08/07/2024] Open
Abstract
Chromosomal abnormalities are a common cause of human miscarriage but rarely reported in any other species. As a result, there are currently inadequate animal models available to study this condition. Horses present one potential model since mares receive intense gynecological care. This allowed us to investigate the prevalence of chromosomal copy number aberrations in 256 products of conception (POC) in a naturally occurring model of pregnancy loss (PL). Triploidy (three haploid sets of chromosomes) was the most common aberration, found in 42% of POCs following PL over the embryonic period. Over the same period, trisomies and monosomies were identified in 11.6% of POCs and subchromosomal aberrations in 4.2%. Whole and subchromosomal aberrations involved 17 autosomes, with chromosomes 3, 4, and 20 having the highest number of aberrations. Triploid fetuses had clear gross developmental anomalies of the brain. Collectively, data demonstrate that alterations in chromosome number contribute to PL similarly in women and mares, with triploidy the dominant ploidy type over the key period of organogenesis. These findings, along with highly conserved synteny between human and horse chromosomes, similar gestation lengths, and the shared single greatest risk for PL being advancing maternal age, provide strong evidence for the first animal model to truly recapitulate many key features of human miscarriage arising due to chromosomal aberrations, with shared benefits for humans and equids.
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Affiliation(s)
- Jessica M. Lawson
- Department of Pathobiology and Population Sciences, Royal Veterinary College, LondonAL9 7TA, UK
| | - Shebl E. Salem
- Department of Biomedical Sciences, Baker Institute for Animal Health, Cornell University, Ithaca, NY14853
| | - Donald Miller
- Department of Biomedical Sciences, Baker Institute for Animal Health, Cornell University, Ithaca, NY14853
| | - Anne Kahler
- Department of Pathobiology and Population Sciences, Royal Veterinary College, LondonAL9 7TA, UK
| | - Wilhelmina J. van den Boer
- Department of Biomedical Sciences, Baker Institute for Animal Health, Cornell University, Ithaca, NY14853
| | - Charlotte A. Shilton
- Department of Pathobiology and Population Sciences, Royal Veterinary College, LondonAL9 7TA, UK
| | - Tia Sever
- Department of Biomedical Sciences, Baker Institute for Animal Health, Cornell University, Ithaca, NY14853
| | - Rebecca R. Mouncey
- Department of Pathobiology and Population Sciences, Royal Veterinary College, LondonAL9 7TA, UK
| | - Jenna Ward
- Department of Biomedical Sciences, Baker Institute for Animal Health, Cornell University, Ithaca, NY14853
| | - Daniel J. Hampshire
- Department of Pathobiology and Population Sciences, Royal Veterinary College, LondonAL9 7TA, UK
| | - Alastair K. Foote
- Rossdales Laboratories, Rossdales Ltd, Beaufort Cottages Stables, NewmarketCB8 8JS, UK
| | - Jill S. Bryan
- Rossdales Laboratories, Rossdales Ltd, Beaufort Cottages Stables, NewmarketCB8 8JS, UK
| | - Rytis Juras
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX77843
| | - Oliver D. Pynn
- Rossdales Veterinary Surgeons, Rossdales Ltd, Beaufort Cottages Stables, NewmarketCB8 8JS, UK
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX77843
| | - Rebecca R. Bellone
- Department of Population Health and Reproduction, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA95617
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA95617
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX77843
| | - Amanda M. de Mestre
- Department of Biomedical Sciences, Baker Institute for Animal Health, Cornell University, Ithaca, NY14853
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2
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De Coster T, Zhao Y, Tšuiko O, Demyda-Peyrás S, Van Soom A, Vermeesch JR, Smits K. Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection. Sci Rep 2024; 14:2003. [PMID: 38263320 PMCID: PMC10805710 DOI: 10.1038/s41598-023-48103-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/22/2023] [Indexed: 01/25/2024] Open
Abstract
In different species, embryonic aneuploidies and genome-wide errors are a major cause of developmental failure. The increasing number of equine embryos being produced worldwide provides the opportunity to characterize and rank or select embryos based on their genetic profile prior to transfer. Here, we explored the possibility of generic, genome-wide preimplantation genetic testing concurrently for aneuploidies (PGT-A) and monogenic (PGT-M) traits and diseases in the horse, meanwhile assessing the incidence and spectrum of chromosomal and genome-wide errors in in vitro-produced equine embryos. To this end, over 70,000 single nucleotide polymorphism (SNP) positions were genotyped in 14 trophectoderm biopsies and corresponding biopsied blastocysts, and in 26 individual blastomeres from six arrested cleavage-stage embryos. Subsequently, concurrent genome-wide copy number detection and haplotyping by haplarithmisis was performed and the presence of aneuploidies and genome-wide errors and the inherited parental haplotypes for four common disease-associated genes with high carrier frequency in different horse breeds (GBE1, PLOD1, B3GALNT2, MUTYH), and for one color coat-associated gene (STX17) were compared in biopsy-blastocyst combinations. The euploid (n = 12) or fully aneuploid (n = 2) state and the inherited parental haplotypes for 42/45 loci of interest of the biopsied blastocysts were predicted by the biopsy samples in all successfully analyzed biopsy-blastocyst combinations (n = 9). Two biopsies showed a loss of maternal chromosome 28 and 31, respectively, which were confirmed in the corresponding blastocysts. In one of those biopsies, additional complex aneuploidies not present in the blastocyst were found. Five out of six arrested embryos contained chromosomal and/or genome-wide errors in most of their blastomeres, demonstrating their contribution to equine embryonic arrest in vitro. The application of the described PGT strategy would allow to select equine embryos devoid of genetic errors and pathogenetic variants, and with the variants of interest, which will improve foaling rate and horse quality. We believe this approach will be a gamechanger in horse breeding.
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Affiliation(s)
- T De Coster
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Y Zhao
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - O Tšuiko
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - S Demyda-Peyrás
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Department of Animal Production, Veterinary School, National University of La Plata, La Plata, Argentina
| | - A Van Soom
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium
| | - J R Vermeesch
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - K Smits
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium.
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3
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Shilton CA, Kahler A, Roach JM, Raudsepp T, de Mestre AM. Lethal variants of equine pregnancy: is it the placenta or foetus leading the conceptus in the wrong direction? Reprod Fertil Dev 2022; 35:51-69. [PMID: 36592981 DOI: 10.1071/rd22239] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Embryonic and foetal loss remain one of the greatest challenges in equine reproductive health with 5-10% of established day 15 pregnancies and a further 5-10% of day 70 pregnancies failing to produce a viable foal. The underlying reason for these losses is variable but ultimately most cases will be attributed to pathologies of the environment of the developing embryo and later foetus, or a defect intrinsic to the embryo itself that leads to lethality at any stage of gestation right up to birth. Historically, much research has focused on the maternal endometrium, endocrine and immune responses in pregnancy and pregnancy loss, as well as infectious agents such as pathogens, and until recently very little was known about the both small and large genetic variants associated with reduced foetal viability in the horse. In this review, we first introduce key aspects of equine placental and foetal development. We then discuss incidence, risk factors and causes of pregnancy loss, with the latter focusing on genetic variants described to date that can impact equine foetal viability.
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Affiliation(s)
- Charlotte A Shilton
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Herts, AL9 7TA, UK
| | - Anne Kahler
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Herts, AL9 7TA, UK
| | - Jessica M Roach
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Herts, AL9 7TA, UK
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA
| | - Amanda M de Mestre
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Herts, AL9 7TA, UK
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4
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Djangwani J, Abong' GO, Njue LG, Kaindi DWM. Sero-prevalence and risk factors of Brucella presence in farm bulk milk from open and zero grazing cattle production systems in Rwanda. Vet Med Sci 2021; 7:1656-1670. [PMID: 34237200 PMCID: PMC8464226 DOI: 10.1002/vms3.562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Animal and human brucelloses have been reported in Rwanda, human brucellosis being linked to drinking inadequately heat-treated milk. However, information on Brucella detection and prevalence in milk produced in Rwanda is limited. OBJECTIVES To determine the sero-prevalence and risk factors of Brucella in farm bulk milk from zero and open grazing cattle production systems in Rwanda. METHODS A total of 330 farm bulk milk samples were collected from 198 zero grazing farms and 132 open grazing farms in a cross-sectional study in Rwanda. Sero-prevalence of Brucella in milk was analysed using indirect enzyme-linked immunosorbent assay. A questionnaire was administered to farmers to determine the risk factors of milk contamination with Brucella. RESULTS Anti-Brucella antibodies were prevalent in 19.7% (95% confidence interval (CI), 15.5-24.4) of the 330 collected farm bulk milk. Sero-prevalence was significantly higher (p < 0.05) in open grazing farms (37.9% [50/132]) than in zero grazing farms (7.6% [15/198]). Practising open grazing system (odds ratio, OR = 69.5; 95% CI = 1.6-3033.6), history of abortion (OR = 19.5; 95% CI = 8.1-46.8) and placenta retention (OR = 4.2; 95% CI = 1.7-10.3) were the significant risk factors for the presence of anti-Brucella antibodies in milk. CONCLUSION Notably, more than a third of farm bulk milk from open grazing farms in Rwanda contains Brucella antibodies. Considering the zoonotic nature of Brucella, there is a need to reinforce brucellosis control programs in the country.
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Affiliation(s)
- Juvenal Djangwani
- College of Agriculture and Veterinary Sciences, Department Food Science, Nutrition and Technology, University of Nairobi, Kangemi, Nairobi, Kenya.,College of Agriculture, Animal Sciences and Veterinary Medicine, School of Agriculture and Food Sciences, University of Rwanda, Musanze, Rwanda
| | - George Ooko Abong'
- College of Agriculture and Veterinary Sciences, Department Food Science, Nutrition and Technology, University of Nairobi, Kangemi, Nairobi, Kenya
| | - Lucy Gicuku Njue
- College of Agriculture and Veterinary Sciences, Department Food Science, Nutrition and Technology, University of Nairobi, Kangemi, Nairobi, Kenya
| | - Dasel Wambua Mulwa Kaindi
- College of Agriculture and Veterinary Sciences, Department Food Science, Nutrition and Technology, University of Nairobi, Kangemi, Nairobi, Kenya
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Djangwani J, Ooko Abong’ G, Gicuku Njue L, Kaindi DWM. Brucellosis: Prevalence with reference to East African community countries - A rapid review. Vet Med Sci 2021; 7:851-867. [PMID: 33421354 PMCID: PMC8136958 DOI: 10.1002/vms3.425] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 11/22/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Brucellosis is a zoonotic disease which is endemic to certain regions of the world including Sub-Saharan Africa. The aim of this article is to provide a recent and rapid review on brucellosis prevalence in East African Community (EAC) countries. Literature was obtained using Google Scholar search engine and screened for relevancy and fulfilment of criteria to 1, 17, 4, 4, 30 and 29 articles retained for brucellosis prevalence in Burundi, Kenya, Rwanda, South Sudan, Tanzania and Uganda. Recent literature (published in the last decade 2010 to 2019) was considered for prevalence results in this review. In EAC, livestock had an animal-level prevalence of 0.2% to 43.8%, 0.0% to 20.0% and 0.0% to 13.8% for cattle, goats and sheep respectively. In humans, the prevalence varied mostly between 0.0% and 35.8%. In conclusion, brucellosis is quite prevalent in the region. The reported prevalence calls for plans or more efforts from individual member countries and from EAC, as a region, to control brucellosis.
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Affiliation(s)
- Juvenal Djangwani
- College of Agriculture and Veterinary SciencesDepartment of Food Science, Nutrition and TechnologyUniversity of NairobiKangemiKenya
- College of Agriculture, Animal Sciences and Veterinary MedicineSchool of Agriculture and Food SciencesUniversity of RwandaMusanzeRwanda
| | - George Ooko Abong’
- College of Agriculture and Veterinary SciencesDepartment of Food Science, Nutrition and TechnologyUniversity of NairobiKangemiKenya
| | - Lucy Gicuku Njue
- College of Agriculture and Veterinary SciencesDepartment of Food Science, Nutrition and TechnologyUniversity of NairobiKangemiKenya
| | - Dasel W. M. Kaindi
- College of Agriculture and Veterinary SciencesDepartment of Food Science, Nutrition and TechnologyUniversity of NairobiKangemiKenya
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6
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Chromosome Abnormalities and Fertility in Domestic Bovids: A Review. Animals (Basel) 2021; 11:ani11030802. [PMID: 33809390 PMCID: PMC8001068 DOI: 10.3390/ani11030802] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary In domestic bovids, numerical autosome abnormalities have been rarely reported, as they present abnormal animal phenotypes quickly eliminated by breeders. However, numerical abnormalities involving sex chromosomes and structural (balanced) chromosome anomalies have been more frequently detected because they are most often not phenotypically visible to breeders. For this reason, these chromosome abnormalities, without a cytogenetic control, escape animal selection, with subsequent deleterious effects on fertility, especially in female carriers. Abstract After discovering the Robertsonian translocation rob(1;29) in Swedish red cattle and demonstrating its harmful effect on fertility, the cytogenetics applied to domestic animals have been widely expanded in many laboratories in order to find relationships between chromosome abnormalities and their phenotypic effects on animal production. Numerical abnormalities involving autosomes have been rarely reported, as they present abnormal animal phenotypes quickly eliminated by breeders. In contrast, numerical sex chromosome abnormalities and structural chromosome anomalies have been more frequently detected in domestic bovids because they are often not phenotypically visible to breeders. For this reason, these chromosome abnormalities, without a cytogenetic control, escape selection, with subsequent harmful effects on fertility, especially in female carriers. Chromosome abnormalities can also be easily spread through the offspring, especially when using artificial insemination. The advent of chromosome banding and FISH-mapping techniques with specific molecular markers (or chromosome-painting probes) has led to the development of powerful tools for cytogeneticists in their daily work. With these tools, they can identify the chromosomes involved in abnormalities, even when the banding pattern resolution is low (as has been the case in many published papers, especially in the past). Indeed, clinical cytogenetics remains an essential step in the genetic improvement of livestock.
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Magata F, Urakawa M, Matsuda F, Oono Y. Developmental kinetics and viability of bovine embryos produced in vitro with sex-sorted semen. Theriogenology 2020; 161:243-251. [PMID: 33340757 DOI: 10.1016/j.theriogenology.2020.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/03/2020] [Accepted: 12/06/2020] [Indexed: 02/06/2023]
Abstract
The present study aimed to elucidate the developmental kinetics, growth potential, and viability of bovine embryos produced in vitro with sexed semen. Bovine oocytes were fertilized in vitro using unsorted and X-sorted semen from the same Holstein bulls, and the kinetics of in vitro development were continuously monitored for 10 d through time-lapse cinematography. The blastocyst formation rate was lower in the X-sorted group than in the unsorted group (P < 0.01), whereas the normal fertilization rate did not differ between groups. Morphokinetic evaluation revealed that the incidence of blastomere fusion during the first cleavage division, termed reverse cleavage, was higher in the X-sorted group (P < 0.01). Furthermore, embryos produced with X-sorted semen showed slower growth throughout the developmental period than embryos produced with unsorted semen (P < 0.01). The cell number of the trophectoderm and inner cell mass of blastocysts was reduced in the X-sorted group (P < 0.01). In embryos that developed to the blastocyst stage, the hatchability (P < 0.05), chromosomal normality (P < 0.01), and survivability after the conventional frozen-thawing process (P < 0.05) were reduced in the X-sorted group compared to that in the unsorted group, indicating a compromised viability of embryos derived from X-sorted semen. Taken together, the first cleavage dysmorphism, delayed embryo growth, and impaired viability of embryos developed to the blastocyst stage may explain the mechanism of reduced fertility in embryos derived from sexed semen. The kinetic evaluation of early embryo development and de-selection of embryos presenting the aberrant first cleavage would be valid for clinical application to produce sexed embryos with high implantation potential.
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Affiliation(s)
- F Magata
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro, Hokkaido, Japan; Department of Veterinary Medical Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - M Urakawa
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro, Hokkaido, Japan
| | - F Matsuda
- Department of Veterinary Medical Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Y Oono
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro, Hokkaido, Japan
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Häfliger IM, Agerholm JS, Drögemüller C. Constitutional trisomy 20 in an aborted Holstein fetus with pulmonary hypoplasia and anasarca syndrome. Anim Genet 2020; 51:988-989. [PMID: 33006153 DOI: 10.1111/age.13008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Irene Monika Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Jørgen Steen Agerholm
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, 1870, Denmark
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
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9
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Shilton CA, Kahler A, Davis BW, Crabtree JR, Crowhurst J, McGladdery AJ, Wathes DC, Raudsepp T, de Mestre AM. Whole genome analysis reveals aneuploidies in early pregnancy loss in the horse. Sci Rep 2020; 10:13314. [PMID: 32769994 PMCID: PMC7415156 DOI: 10.1038/s41598-020-69967-z] [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: 03/04/2020] [Accepted: 07/20/2020] [Indexed: 01/10/2023] Open
Abstract
The first 8 weeks of pregnancy is a critical time, with the majority of pregnancy losses occurring during this period. Abnormal chromosome number (aneuploidy) is a common finding in human miscarriage, yet is rarely reported in domestic animals. Equine early pregnancy loss (EPL) has no diagnosis in over 80% of cases. The aim of this study was to characterise aneuploidies associated with equine EPL. Genomic DNA from clinical cases of spontaneous miscarriage (EPLs; 14-65 days of gestation) and healthy control placentae (various gestational ages) were assessed using a high density genotyping array. Aneuploidy was detected in 12/55 EPLs (21.8%), and 0/15 healthy control placentae. Whole genome sequencing (30X) and digital droplet PCR (ddPCR) validated results. The majority of these aneuploidies have never been reported in live born equines, supporting their embryonic/fetal lethality. Aneuploidies were detected in both placental and fetal compartments. Rodents are currently used to study how maternal ageing impacts aneuploidy risk, however the differences in reproductive biology is a limitation of this model. We present the first evidence of aneuploidy in naturally occurring equine EPLs at a similar rate to human miscarriage. We therefore suggest the horse as an alternative to rodent models to study mechanisms resulting in aneuploid pregnancies.
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Affiliation(s)
- Charlotte A Shilton
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, University of London, London, UK
| | - Anne Kahler
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, University of London, London, UK
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | | | | | | | - D Claire Wathes
- Department of Production and Population Health, The Royal Veterinary College, University of London, Hatfield, UK
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Amanda M de Mestre
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, University of London, London, UK.
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10
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Bickhart DM, McClure JC, Schnabel RD, Rosen BD, Medrano JF, Smith TPL. Symposium review: Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection. J Dairy Sci 2020; 103:5278-5290. [PMID: 32331872 DOI: 10.3168/jds.2019-17693] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/03/2019] [Indexed: 11/19/2022]
Abstract
The cattle reference genome assembly has underpinned major innovations in beef and dairy genetics through genome-enabled selection, including removal of deleterious recessive variants and selection for favorable alleles affecting quantitative production traits. The initial reference assemblies, up to and including UMD3.1 and Btau4.1, were based on a combination of clone-by-clone sequencing of bacterial artificial chromosome clones generated from blood DNA of a Hereford bull and whole-genome shotgun sequencing of blood DNA from his inbred daughter/granddaughter named L1 Dominette 01449 (Dominette). The approach introduced assembly gaps, misassemblies, and errors, and it limited the ability to assemble regions that undergo rearrangement in blood cells, such as immune gene clusters. Nonetheless, the reference supported the creation of genotyping tools and provided a basis for many studies of gene expression. Recently, long-read sequencing technologies have emerged that facilitated a re-assembly of the reference genome, using lung tissue from Dominette to resolve many of the problems and providing a bridge to place historical studies in common context. The new reference, ARS-UCD1.2, successfully assembled germline immune gene clusters and improved overall continuity (i.e., reduction of gaps and inversions) by over 250-fold. This reference properly places nearly all of the legacy genetic markers used for over a decade in the industry. In this review, we discuss the improvements made to the cattle reference; remaining issues present in the assembly; tools developed to support genome-based studies in beef and dairy cattle; and the emergence of newer genome assembly methods that are producing even higher-quality assemblies for other breeds of cattle at a fraction of the cost. The new frontier for cattle genomics research will likely include a transition from the individual Hereford reference genome, to a "pan-genome" reference, representing all the DNA segments existing in commonly used cattle breeds, bringing the cattle reference into line with the current direction of human genome research.
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Affiliation(s)
- D M Bickhart
- US Dairy Forage Research Center, Agricultural Research Service, USDA, Madison, WI 53705.
| | - J C McClure
- US Dairy Forage Research Center, Agricultural Research Service, USDA, Madison, WI 53705
| | - R D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, 65211; MU Institute for Data Science and Informatics, University of Missouri, Columbia, 65211
| | - B D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - J F Medrano
- Department of Animal Science, University of California Davis, 95616
| | - T P L Smith
- Meat Animal Research Center, Agricultural Research Service, USDA, Clay Center, NE 68933
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11
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Häfliger IM, Seefried F, Drögemüller C. Trisomy 29 in a stillborn Swiss Original Braunvieh calf. Anim Genet 2020; 51:483-484. [PMID: 32196694 DOI: 10.1111/age.12929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2020] [Indexed: 01/28/2023]
Affiliation(s)
- Irene Monika Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
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12
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Häfliger IM, Wiedemar N, Švara T, Starič J, Cociancich V, Šest K, Gombač M, Paller T, Agerholm JS, Drögemüller C. Identification of small and large genomic candidate variants in bovine pulmonary hypoplasia and anasarca syndrome. Anim Genet 2020; 51:382-390. [PMID: 32069517 DOI: 10.1111/age.12923] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2020] [Indexed: 12/25/2022]
Abstract
The pulmonary hypoplasia and anasarca syndrome (PHA) is a congenital lethal disorder, which until now has been reported in cattle and sheep. PHA is characterized by extensive subcutaneous fetal edema combined with hypoplasia or aplasia of the lungs and dysplasia of the lymphatic system. PHA is assumed to be of genetic etiology. This study presents the occurrence of PHA in two different cattle breeds and their genetic causation. Two PHA cases from one sire were observed in Slovenian Cika cattle. Under the assumption of monogenic inheritance, genome-wide homozygosity mapping scaled down the critical regions to 3% of the bovine genome including a 43.6 Mb-sized segment on chromosome 6. Whole-genome sequencing of one case, variant filtering against controls and genotyping of a larger cohort of Cika cattle led to the detection of a likely pathogenic protein-changing variant perfectly associated with the disease: a missense variant on chromosome 6 in ADAMTS3 (NM_001192797.1: c.1222C>T), which affects an evolutionary conserved residue (NP_001179726.1: p.(His408Tyr)). A single PHA case was found in Danish Holstein cattle and was whole-genome sequenced along with its parents. However, as there was no plausible private protein-changing variant, mining for structural variation revealed a likely pathogenic trisomy of the entire chromosome 20. The identified ADAMTS3 associated missense variant and the trisomy 20 are two different genetic causes, which shows a compelling genetic heterogeneity for bovine PHA.
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Affiliation(s)
- I M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - N Wiedemar
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - T Švara
- Veterinary Faculty, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - J Starič
- Veterinary Faculty, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - V Cociancich
- Veterinary Faculty, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - K Šest
- Veterinary Faculty, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - M Gombač
- Veterinary Faculty, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - T Paller
- Veterinary Faculty, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - J S Agerholm
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, C 1870, Denmark
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
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13
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Magata F, Tsuchiya K, Okubo H, Ideta A. Application of intracytoplasmic sperm injection to the embryo production in aged cows. J Vet Med Sci 2018; 81:84-90. [PMID: 30473579 PMCID: PMC6361645 DOI: 10.1292/jvms.18-0284] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Reduction in oocyte quality is a major factor responsible for declining fertility associated with maternal aging in cows. The objective of the present study was to determine whether
intracytoplasmic sperm injection (ICSI) could increase the efficiency of embryo production in older cows. We used cows aged 30 to 50 months or >120 months, which were defined as young or
aged, respectively. The distribution of cortical granules in oocytes was affected by age as older cows had lower proportion of oocytes with mature cytoplasm containing evenly dispersed
cortical granules compared to young cows. Although fertilization rates did not differ significantly between the two groups after in vitro fertilization (IVF), the rate of
abnormal fertilization was higher, and the numbers of total and diploid blastocysts were lower for aged cows compared to young cows. However, in the embryos produced by ICSI, there was no
significant difference in these parameters between young and aged cows. Although ICSI did not improve the blastocyst development rate, ICSI increased the proportion of diploid blastocysts in
aged cows compared to IVF. In conclusion, maternal aging may negatively affect cytoplasmic maturation of bovine oocytes, which could be associated with abnormal fertilization or low
developmental competence of oocytes. Our data also suggests beneficial effects of ICSI on the production of chromosomally normal embryos in aged cows.
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Affiliation(s)
- Fumie Magata
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro, Hokkaido 080-1407, Japan.,Department of Veterinary Medical Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kanami Tsuchiya
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro, Hokkaido 080-1407, Japan
| | - Haruna Okubo
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro, Hokkaido 080-1407, Japan
| | - Atsushi Ideta
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro, Hokkaido 080-1407, Japan
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Abstract
Recognition and detailed description of malformations and aberrations in domestic animals may be very useful in cognition of the problem and in creating breeding programs. The aim of this study was to describe a rare case of sternal (pectoral) ectopia cordis in a calf. A female calf of the Limousin breed born in Poland in 2011 was subjected to euthanasia because the heart was situated outside the chest. The carcass of the calf was subjected to anatomical examination in which alterations in cardiovascular system and in the structure of the sternum were observed. Cytogenetic studies were performed to find out if the karyotype of the calf was normal. Elongation of the ascending aorta was observed and the pattern of aortic branching was aberrant similarly to that found in dogs, not cattle. The systemic circulation was found to be linked to pulmonary circulation due to persisting large calibre arterial duct. Each of the ventricles had its own cardiac apex and walls of the ventricles manifested a similar width. The atria were slightly altered. A single, short and dilated blood vessel (pulmonary vein) evacuated its content to the left atrium. Pericardium formed no pericardial sac. Radiogram of the sternum demonstrated a ring-resembling shape and 12 (6 pairs) cartilaginous bars of the sternum (sternebrae). A normal female karytotype (60, XX) indicated that this malformation was not caused by an abnormal number of chromosomes (aneuploidy).
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Citek J, Rubes J, Hajkova J. Short communication: Robertsonian translocations, chimerism, and aneuploidy in cattle. J Dairy Sci 2009; 92:3481-3. [PMID: 19528626 DOI: 10.3168/jds.2009-2099] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The aim of this study was to evaluate frequencies of Robertsonian translocations, aneuploidy, and chimerism in Holstein-Friesian, Czech Simmental, and different beef breeds in the Czech Republic from 1996 to 2007. A total of 2,425 animals were examined: 2,377 males, (991 Holstein-Friesians, 1,218 Czech Simmental sires, 168 sires of beef breeds) and 48 females. Translocation was found in 10 Czech Simmental sires, 2 Highland, 1 Charolais, and 3 Blonde d' Aquitaine sires, and in 13 females. Chimerism (XX/XY) was found in 9 Czech Simmental sires, and in 5 Holstein-Friesian sires; XXX trisomy was found in 2 heifers and XXY trisomy in 3 Charolais sires. We recommend that animals with such anomalies should be disqualified from siring stock bulls.
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Affiliation(s)
- J Citek
- Department of Genetics, South Bohemia University, Studentska 13, CZ 370 05 Ceske Budejovice, Czech Republic
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16
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Rybar R, Kopecka V, Prinosilova P, Kubickova S, Veznik Z, Rubes J. Fertile bull sperm aneuploidy and chromatin integrity in relationship to fertility. ACTA ACUST UNITED AC 2009; 33:613-22. [PMID: 19751362 DOI: 10.1111/j.1365-2605.2009.00989.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aneuploidy is associated with spontaneous abortions, perinatal mortality, mental retardation and with embryonic and foetal mortality. Most of these abnormalities originate as a result of meiosis errors during gametogenesis. The main purpose of the study was to analyse frequency of aneuploidies of sex chromosomes and chromosome 6 by three-colour fluorescence in situ hybridization (FISH) in 47 young bulls, candidates for artificial insemination programme with cryopreserved semen and to investigate the influence of aneuploidies and disturbed sperm chromatin integrity on non-return rates, the frequencies of abortions, perinatal mortality and stillbirths. The average frequencies of spermatozoa with disomy for chromosomes X, Y, XY and 6 were 0.032, 0.005, 0.003 and 0.039% respectively. The incidence of XX66, YY66 and XY66 diploidy was 0.017, 0.006 and 0.015% respectively. Frequencies of meiotic II errors were significantly higher than meiotic I errors (p < 0.01). More X bearing spermatozoa than Y bearing spermatozoa were detected (5151 vs. 5022; p < 0.01). Sperm chromatin damage expressed by DNA fragmentation index (DFI) was 5.3 +/- 3.7 and percentage of cells with defective chromatin condensation (HDS) was 1.4 +/- 0.8. No correlation was found between sperm aneuploidy and basic sperm analysis. The relationship was found between non-return rate and total aneuploidy (r = -0.310; p = 0.036). Significant correlation was found between sex disomy, total aneuploidy (disomy of chromosomes 6, X, Y and XY spermatozoa and diploidy) and stillbirths (r = 0.390; p = 0.013; and r = 0.331; p = 0.037). Chromosome 6 disomy correlated with perinatal mortality (r = 0.317; p = 0.047). HDS correlated significantly with total aneuploidy (r = 0.449; p = 0.002). Our study indicated that aneuploidy frequencies in young fertile bull spermatozoa are relatively low. Nevertheless, there exists a variability in aneuploidy frequencies amongst bulls, which appears to be able to have an influence on the fertility of these animals.
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Affiliation(s)
- R Rybar
- Department of Genetics and Reproduction, Veterinary Research Institute, 621 00 Brno, Czech Republic.
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18
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Rubes J, Kubickova S, Pagacova E, Cernohorska H, Di Berardino D, Antoninova M, Vahala J, Robinson TJ. Phylogenomic study of spiral-horned antelope by cross-species chromosome painting. Chromosome Res 2008; 16:935-47. [PMID: 18704723 DOI: 10.1007/s10577-008-1250-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 06/23/2008] [Accepted: 06/23/2008] [Indexed: 11/28/2022]
Abstract
Chromosomal homologies have been established between cattle (Bos taurus, 2n = 60) and eight species of spiral-horned antelope, Tribe Tragelaphini: Nyala (Tragelaphus angasii, 2n = 55male/56female), Lesser kudu (T. imberbis, 2n = 38male,female), Bongo (T. eurycerus, 2n = 33male/34female), Bushbuck (T. scriptus, 2n = 33male/34female), Greater kudu (T. strepsiceros, 2n = 31male/32female), Sitatunga (T. spekei, 2n = 30male,female) Derby eland (Taurotragus derbianus 2n = 31male/32female) and Common eland (T. oryx 2n = 31male/32female). Chromosomes involved in centric fusions in these species were identified using a complete set of cattle painting probes generated by laser microdissection. Our data support the monophyly of Tragelaphini and a clade comprising T. scriptus, T. spekei, T. euryceros and the eland species T. oryx and T. derbianus, findings that are largely in agreement with sequence-based molecular phylogenies. In contrast, our study suggests that the arid adaptiveness of T. oryx and T. derbianus is recent. Finally, we have identified the presence of the rob(1;29) fusion as an evolutionary marker in most of the tragelaphid species investigated. This rearrangement is associated with reproductive impairment in cattle and raises questions whether subtle distinctions in breakpoint location or differential rescue during meiosis underpin the different outcomes detected among these lineages.
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Affiliation(s)
- Jiri Rubes
- Department of Genetics and Reproduction, Veterinary Research Institute, Brno, Czech Republic.
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Gómez MC, Pope CE, López M, Dumas C, Giraldo A, Dresser BL. Chromosomal Aneuploidy in African Wildcat Somatic Cells and Cloned Embryos. CLONING AND STEM CELLS 2006; 8:69-78. [PMID: 16776599 DOI: 10.1089/clo.2006.8.69] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In the present study, we compared the incidence of aneuploidy in in vitro fertilized domestic cat embryos (DSH-IVF) with that of African Wildcat (AWC) cloned embryos reconstructed with AWC fibroblast donor cells from different passages (AWC-NT). Fibroblast cells were cultured to passages 1 (P1), 3 (P3), 4 (P4), and 9 (P9), after which cells at each passage were karyotyped and serum-starved before being frozen for nuclear transfer. AWC-NT embryos were produced by fusion of a single AWC somatic cell at P1, P3, P4, or P9 to enucleated domestic cat cytoplast derived from in vitro matured (IVU) oocytes. DSH-IVF embryos were produced after IVU oocytes were fertilized in vitro with domestic cat spermatozoa. To determine chromosome numbers, embryos (2-4-cell) or fibroblast cells were cultured in medium containing 0.28 microg/mL of Colcemid for 22-24 h or 15-24 h, respectively. Subsequently, embryos and cells were placed in hypotonic solution, fixed, and stained for analysis of chromosome spreads by bright field microscopy. Chromosomal abnormalities in AWC fibroblast cells increased progressively during culture in vitro: P1 (43%), P3 (46%), P4 (62%), and P9 (59%). In fibroblast cells, hypoploidy (94/202, 46%) was the major chromosomal abnormality, and it occurred more frequently than hyperploidy (14/202, 7%; p < 0.05). While the percentage of hyperploid cells remained stable during all passages, the proportion of hypoploidy in fibroblast cells increased significantly after P4. The overall incidence of chromosomal abnormalities in AWC-NT embryos at P1 (45%), P3 (60%), and P4 (50%) was similar to that of the fibroblast cells from which they were derived; however, the incidence was higher for embryos reconstructed with donor fibroblasts at P9 (89%). Hypoploidy was the most common chromosomal abnormality observed in either AWC-NT or DSH-IVF embryos. AWCNT embryos reconstructed with donor cells at early passages (P1, P3, and P4) had similar frequencies of chromosomal diploidy, as did DSH-IVF embryos. Accordingly, based on the present results, for NT we are currently using cat donor cells at early passages, when the percentage of cells with chromosomal abnormalities is low. It is recommended that the chromosomal stability of each cell line be analyzed before use as NT donor cells to reduce the incidence of chromosomal anomalies in reconstructed embryos and to possibly produce a subsequent increase in cloning efficiency.
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Affiliation(s)
- Martha C Gómez
- Audubon Center for Research of Endangered Species, 14001 River Road, New Orleans, LA 70131, USA.
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20
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Shi W, Dirim F, Wolf E, Zakhartchenko V, Haaf T. Methylation Reprogramming and Chromosomal Aneuploidy in In Vivo Fertilized and Cloned Rabbit Preimplantation Embryos1. Biol Reprod 2004; 71:340-7. [PMID: 15028628 DOI: 10.1095/biolreprod.103.024554] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Active demethylation of the paternal genome but not of the maternal genome occurs in fertilized mouse, rat, pig, and bovine zygotes. To study whether this early demethylation wave is important for embryonic development, we have analyzed the global methylation patterns of both in vivo-fertilized and cloned rabbit embryos. Anti-5-methylcytosine immunofluorescence of in vivo-fertilized rabbit embryos revealed that the equally high methylation levels of the paternal and maternal genomes are largely maintained from the zygote up to the 16-cell stage. The lack of detectable methylation changes in rabbit preimplantation embryos suggests that genome-wide demethylation is not an obligatory requirement for epigenetic reprogramming. The methylation patterns of embryos derived from fibroblast and cumulus cell nuclear transfer were similar to those of in vivo-fertilized rabbit embryos. Fluorescence in situ hybridization with chromosome-specific BACs demonstrated significantly increased chromosomal aneuploidy rates in cumulus cell nuclear transfer rabbit embryos and embryos derived from nuclear transfer of rabbit fibroblasts into bovine oocytes compared with in vivo-fertilized rabbit embryos. The incidence of chromosomal abnormalities was correlated with subsequent developmental failure. We propose that postzygotic mitotic errors are one important explanation of why mammalian cloning often fails.
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Affiliation(s)
- Wei Shi
- Department of Molecular Animal Breeding and Biotechnology, University of Munich, 85764 Oberschleissheim, Germany
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Gallagher DS, Lewis BC, De Donato M, Davis SK, Taylor JF, Edwards JF. Autosomal trisomy 20 (61,XX,+20) in a malformed bovine fetus. Vet Pathol 1999; 36:448-51. [PMID: 10490213 DOI: 10.1354/vp.36-5-448] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A 240-day-gestation female bovine fetus with severe anasarca, palatoschisis, cheiloschisis, mild cranioschisis, and a flattened facies was collected at a slaughterhouse, and a fibroblast line was established from the fetal skin. Chromosome preparations were Q-banded, and chromosome counts were taken that indicated the presence of 61 chromosomes in cells of the fetus (the normal diploid number for domestic cattle is 60). Q-band karyotypes were constructed, and Q-band analysis revealed the presence of three copies of chromosome 20. Trisomy 20 (61,XX,+20) was confirmed through the use of two-color fluorescence in situ hybridization of bovine bacterial artificial chromosome clones that were specific to chromosome 20 and the X chromosome.
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Abstract
Infertility and anatomic defects unique to breeding bulls can be influenced by genetics. Veterinarians and animal breeders need to report disorders that may be inherited to a central recording agent, usually the breed association or a veterinary specialist interested in characterizing the disease. Occurrence of these defects is rare, and a large population of animals should be studied to recognize patterns of inheritance early. Numbers of affected animals in a given practice area are often limited, leading to an underestimation of the condition's importance. Genetic defects occur regularly at low frequencies. New syndromes continually arise and most are silently eliminated. Cooperation between cattle breeders, veterinarians, breed associations, and the scientific community is essential in controlling these diseases.
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Affiliation(s)
- D Steffen
- Department of Veterinary and Biomedical Sciences, University of Nebraska, Lincoln, USA
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