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2. Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

Author

Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, Wade, C. M., Giulotto, E., Sigurdsson, S., Zoli, M., Gnerre, S., Imsland, F., Lear, T. L., Adelson, D. L., Bailey, E., Bellone, R. R., Blöcker, H., Distl, O., Edgar, R. C., Garber, M., Leeb, T., Mauceli, E., MacLeod, J. N., Penedo, M. C. T., Raison, J. M., Sharpe, T., Vogel, J., Andersson, L., Antczak, D. F., Biagi, T., Binns, M. M., Chowdhary, B. P., Coleman, S. J., Valle, G. Delia, Fryc, S., Guérin, G., Hasegawa, T., Hill, E. W., Jurka, J., Kiialainen, A., Lindgren, G., Liu, J., Magnani, E., Mickelson, J. R., Murray, J., Nergadze, S. G., Onofrio, R., Pedroni, S., Piras, M. F., Raudsepp, T., Rocchi, M., Røed, K. H., Ryder, O. A., Searle, S., Skow, L., Swinburne, J. E., Syvänen, A. C., Tozaki, T., Valberg, S. J., Vaudin, M., White, J. R., Zody, M. C., Lander, E. S., and Lindblad-Toh, K.

Published
2009
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6. Genetic characterization of Latin-American Creole cattle using microsatellite markers

Author

Delgado, J. V., Martínez, A. M., Acosta, A., Álvarez, L. A., Armstrong, E., Camacho, E., Cañón, J., Cortés, O., Dunner, S., Landi, V., Marques, J. R., Martín-Burriel, I., Martínez, O. R., Martínez, R. D., Melucci, L., Muñoz, J. E., Penedo, M. C. T., Postiglioni, A., Quiróz, J., Rodellar, C., Sponenberg, P., Uffo, O., Ulloa-Arvizu, R., Vega-Pla, J. L., Villalobos, A., Zambrano, D., Zaragoza, P., Gama, L. T., and Ginja, C.

Published
2012
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25. Warmblood fragile foal syndrome type 1 mutation (PLOD1 c.2032G>A) is not associated with catastrophic breakdown and has a low allele frequency in the Thoroughbred breed.

Author

Bellone, R. R., Ocampo, N. R., Hughes, S. S., Le, V., Arthur, R., Finno, C. J., and Penedo, M. C. T.

Abstract

Summary: Background: Catastrophic fractures are among the most common cause of fatalities in racehorses. Several factors, including genetics, likely contribute to increased risk for fatal injuries. A variant in the procollagen‐lysine, 2‐oxoglutarate 5‐dioxygenase1 gene (PLOD1 c.2032G>A) was shown to cause Warmblood fragile foal syndrome type 1 (WFFS), a fatal recessive defect of the connective tissue. Screening of multiple horse breeds identified the presence of the WFFS allele in the Thoroughbred. PLOD1 is involved in cross‐linking of collagen fibrils and thus could potentially increase the risk of catastrophic breakdown. Objectives: Estimate the frequency of the WFFS allele (PLOD1 c.2032G>A) and determine if it is a risk factor for catastrophic breakdown in the Thoroughbred. Study design: Case–control genetic study. Methods: Genomic DNA from hair and/or tissue samples was genotyped for the WFFS allele. Fisher's Exact tests were performed to compare allele and carrier frequencies between the case cohort (catastrophic breakdown, n = 22) and several cohorts with no record of injury (n = 138 raced/trained at same track and season and n = 185 older than 7 years and raced during same season), nonracers (n = 92), and a random sample without consideration for racing history (n = 279). Results: The frequency of the PLOD1 c.2032G>A variant in the Thoroughbred breed is low (1.2%). Seventeen of 716 Thoroughbreds tested were carriers (2.4%) and no WFFS homozygotes were detected. Only one catastrophic breakdown case carried the WFFS allele. No statistically significant difference in allele or carrier frequency was identified between case and control cohorts (P>0.05 in all comparisons performed). Main limitations: This study evaluated cases from one single track. Conclusions: This study demonstrated that the PLOD1 c.2032G>A associated with WFFS is present at very low frequency in Thoroughbreds and is not a genetic risk factor for catastrophic breakdown. [ABSTRACT FROM AUTHOR]

Published
2020
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31. Investigation of Known Genetic Mutations of Arabian Horses in Egyptian Arabian Foals with Juvenile Idiopathic Epilepsy.

Author

Aleman, M., Weich, K., Finno, C. J., and Penedo, M. C. T.

Subjects
GENETIC mutation, GENETICS of epilepsy, HORSES, ARABIAN horses, DNA analysis, GENETICS
Abstract

Background: The carrier status of lavender foal syndrome (LFS), cerebellar abiotrophy (CA), severe combined immunodeficiency (SCID), and occipitoatlantoaxial malformation (OAAM1) in foals with juvenile idiopathic epilepsy (JIE) is unknown. Hypothesis/Objectives: To determine the carrier status of LFS, CA, SCID, and OAAM1 in foals with JIE. Animals: Ten foals with JIE. Materials and Methods: Archived DNA samples were tested for known genetic mutations causing LFS, CA, SCID, and OAAM1. The inclusion criteria consisted of having been diagnosed with JIE by ruling out other causes of seizures in foals and supported by electroencephalographic examination. Results: Ten Egyptian Arabian horses (5 females and 5 males) were phenotyped as foals with JIE by electroencephalography (EEG). All foals were negative for the genetic mutations that cause LFS, CA, SCID, and OAAM1 except for 1 foal that was a carrier of CA. Conclusions and Clinical Importance: Juvenile idiopathic epilepsy of Egyptian Arabian foals and LFS appear to be phenotypically and genetically distinct disorders. There was no apparent association between JIE and LFS, CA, SCID, and OAAM1. [ABSTRACT FROM AUTHOR]

Published
2018
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32. Identification of Ancestry Informative Markers in the Domestic Horse

Author

Petersen, J. L., Mickelson, J. R., Andersson, L. S., Bailey, E., Bannasch, D. L., Binns, M. M., Borges, A. S., Cothran, E. G., Câmara Machado, A., Distl, O., Felicetti, Michela, Graves, K. T., Guérin, G., Hasegawa, T., Haase, B., Hill, E. W., Leeb, T., Lopes, M. S., Lindgren, G., Lohi, H., Penedo, M. C. T., Piercy, R., Røed, K. H., Ryder, O. A., Silvestrelli, Maurizio, Swinburne, J. E., Tozaki, T., Vaudin, M., Wade, C. M., and Mccue, M. E.

Published
2012

33. The Equine Genetic Diversity Consortium: an international collaboration to describe genetic variation in modern horse breeds

Author

Petersen, J. L., Mickelson, J. R., Andersson, L. S., Bailey, E., Bannasch, D. L., Binns, M. M., Borges, A. S., Cothran, E. G., Câmara Machado, A., Distl, O., Felicetti, Michela, Graves, K. T., Guérin, G., Hasegawa, T., Haase, B., Hill, E. W., Leeb, T., Lopes, M. S., Lindgren, G., Lohi, H., Penedo, M. C. T., Piercy, R., Røed, K. H., Ryder, O. A., Silvestrelli, Maurizio, Swinburne, J. E., Tozaki, T., Vaudin, M., Wade, C. M., and Mccue, M. E.

Published
2011

34. On the breeds of cattle-Historic and current classifications

Author

Felius, M., Koolmees, Peter A., Theunissen, B., Baumung, R., Manatrinon, S., Mommens, G., Holm, L. -E., Withen, K. B., Pedersen, B. V., Gravlund, P., Viinalass, H., Kantanen, J., Tapio, I., M. H., Li, Moazami-Goudarzi, K., Gautier, M., Denis, Laloë, Oulmouden, A., Levéziel, H., Taberlet, P., Harlizius, B., Simianer, H., Täubert, H., Erhardt, G., Jann, O., Weimann, C., Prinzenberg, E. -M., Medugorac, I., Medugorac, A., Förster, M., Mix, H. M., Looft, C., Kalm, E., Bradley, D. G., Edwards, C. J., Machugh, D. E., Freeman, A. R., Ajmone Marsan, P., Negrini, R., Longeri, M., Ceriotti, G., Zanotti, M., Marletta, D., Criscione, A., Valentini, A., Marchitelli, C., Pariset, L., Savarese, M. C., Pilla, F., Grislis, Z., Miceikienė, I., Nijman, I. J., van Haeringen, W., van de Goor, L., Olsaker, I., Ginja, C., Gama, L. T., Mateus, J. C., Beja-Pereira, A., Ferrand, N., Ivanova, Z., Popov, R., Ammosov, I., Kiselyova, T., Marzanov, N., Stojanovic, S., Simčič, M., Dovč, P., Kompan, D., Dunner, S., Rodellar, C., Martín-Burriel, I., Sánchez, A., Piedrafita, J., Azor, P. J., Delgado, J. V., Martínez-Martínez, A., Molina, A., Rodero, E., Dolf, G., Williams, J. L., Wiener, P., Bruford, M. W., Bray, T. C., Alderson, L., Penedo, M. C. T., Lenstra, J. A., Lenstra, Johannes A., Utrecht University [Utrecht], and European Cattle Genetic Diversity Consortium

Subjects
breeds, breed, [SDV]Life Sciences [q-bio], Ecology (disciplines), Breeds, Zoology, Ethnic origin, Subspecies, Q1, Crossbreed, 03 medical and health sciences, symbols.namesake, QH301, aurochs, auroch, lcsh:QH301-705.5, 030304 developmental biology, Nature and Landscape Conservation, 2. Zero hunger, 0303 health sciences, Genetic diversity, biology, Ecology, Ecological Modeling, Linnaean taxonomy, 0402 animal and dairy science, 04 agricultural and veterinary sciences, Aurochs, biology.organism_classification, cattle, classification, Classification, 040201 dairy & animal science, Agricultural and Biological Sciences (miscellaneous), Breed, Ecological Modelling, lcsh:Biology (General), Evolutionary biology, symbols, Cattle
Abstract

Chantier qualité GA Liste des auteurs de l'European Cattle Genetic Consortium, classés par pays : Austria: R. Baumung, S. Manatrinon, BOKU University, Vienna; Belgium: G. Mommens, University of Ghent, Merelbeke; Denmark: L.-E. Holm, Aarhus University, Tjele; K.B. Withen, B.V. Pedersen, P. Gravlund, University of Copenhagen, Copenhagen; Estonia: H. Viinalass, Estonian University of Life Sciences, Tartu; Finland: J. Kantanen, I. Tapio, M.H. Li, MTT, Jokioinen; France: K. Moazami-Goudarzi, M. Gautier, Denis Laloë, INRA, Jouy-en-Josas; A. Oulmouden, H. Levéziel, INRA, Limoges; P. Taberlet, Université Joseph Fourier et CNRS, Grenoble; Germany: B. Harlizius, School of Veterinary Medicine, Hannover; H. Simianer, H. Täubert, Georg-August-Universität, Göttingen; G. Erhardt, O. Jann, C. Weimann, E.-M. Prinzenberg, Justus-Liebig Universität, Giessen; I. Medugorac, A. Medugorac, M. Förster, Ludwig-Maximilians Universität, Munich; H.M. Mix, Naturschutz International, Grünheide; C. Looft, E. Kalm, Christian-Albrechts-Universität, Kiel; Ireland: D.G. Bradley, C.J. Edwards, D.E. MacHugh, A.R. Freeman, Trinity College, Dublin; Italy: P. Ajmone Marsan, R. Negrini, Università Cattolica del S. Cuore, Piacenza; M. Longeri, G. Ceriotti, M. Zanotti, Università degli Studi di Milano; D. Marletta, A. Criscione, Universita degli Studi di Catania, Catania; A. Valentini, C. Marchitelli, L. Pariset, M.C. Savarese, Università della Tuscia, Viterbo; F. Pilla, Università del Molise, Campobasso; Latvia: Z. Grislis, Latvia University of Agriculture, Jelgava; Lithuania: I. Miceikienė, Lithuanian Veterinary Academy, Kaunas; Netherlands: I.J. Nijman, Utrecht University; W. van Haeringen, L. van de Goor, Van Haeringen Laboratory, Wageningen; Norway: I. Olsaker, Norwegian School of Veterinary Science, Oslo; Portugal: C. Ginja, L.T.Gama, Instituto Nacional de Recursos Biológicos—INIA, Lisbon University, Lisboa; L.T. Gama, Instituto Nacional de Recursos Biológicos-INIA, I.P., Vale de Santarem; J.C. Mateus, Universidade de Trás-os-Montes e Alto Douro, Vila Real; A. Beja-Pereira, N. Ferrand, Oporto University; Russia: Z. Ivanova, R. Popov, I. Ammosov, Yakutian Research Institute of Agricultural Sciences, Yakutsk, Sakha; T. Kiselyova, All-Russian Research Institute for Farm Animals and Breeding, St. Petersburgh-Pushkin; N. Marzanov, All-Russian Research Institute of Animal Husbandry, Dubrovitsy; Serbia: S. Stojanovic, Ministry of Agriculture and Water Management, Belgrade; Slovenia: M. Simčič, P. Dovč, D.Kompan, University of Ljubljana, Domzale; Spain: S. Dunner, Universidad Complutense de Madrid; C. Rodellar, I. Martín-Burriel, Veterinary Faculty, Zaragoza; A. Sánchez, J. Piedrafita, Universitat Autònoma de Barcelona; P.J. Azor, J.V. Delgado, A. Martínez-Martínez, A. Molina, E. Rodero, University of Córdoba; Switzerland: G. Dolf, University of Berne; UK: J.L. Williams, P. Wiener, Roslin Institute; M.W. Bruford, T.C. Bray, Cardiff University, Cardiff; L. Alderson, Countrywide Livestock Ltd, Shrewsbury; USA: M.C.T. Penedo. University of California, Davis, CA; International audience; Classification of cattle breeds contributes to our understanding of the history of cattle and is essential for an effective conservation of genetic diversity. Here we review the various classifications over the last two centuries and compare the most recent classifications with genetic data. The classifications devised during the 19th to the late 20th century were in line with the Linnaean taxonomy and emphasized cranial or horn morphology. Subsequent classifications were based on coat color, geographic origin or molecular markers. Several theories were developed that linked breed characteristics either to a supposed ancestral aurochs subspecies or to a presumed ethnic origin. Most of the older classifications have now been discarded, but have introduced several Latin terms that are still in use. The most consistent classification was proposed in 1995 by Felius and emphasizes the geographic origin of breeds. This is largely in agreement with the breed clusters indicated by a biochemical and molecular genetic analysis, which reflect either groups of breeds with a common geographic origin or single breeds that have expanded by export and/or crossbreeding. We propose that this information is also relevant for managing the genetic diversity of cattle.

Published
2011

36. Worldwide frequency distribution of the 'Gait keeper' mutation in the DMRT3 gene

Author

Promerová, Marta, Andersson, L. S., Juras, R., Penedo, M. C. T., Reissmann, M., Tozaki, T., Bellone, R., Dunner, S., Horin, P., Imsland, Freyja, Imsland, P., Mikko, S., Modry, D., Roed, K. H., Schwochow, D., Vega-Pla, J. L., Mehrabani-Yeganeh, H., Yousefi-Mashouf, N., Cothran, E. G., Lindgren, G., Andersson, Leif, Promerová, Marta, Andersson, L. S., Juras, R., Penedo, M. C. T., Reissmann, M., Tozaki, T., Bellone, R., Dunner, S., Horin, P., Imsland, Freyja, Imsland, P., Mikko, S., Modry, D., Roed, K. H., Schwochow, D., Vega-Pla, J. L., Mehrabani-Yeganeh, H., Yousefi-Mashouf, N., Cothran, E. G., Lindgren, G., and Andersson, Leif

Abstract

For centuries, domestic horses have represented an important means of transport and served as working and companion animals. Although their role in transportation is less important today, many horse breeds are still subject to intense selection based on their pattern of locomotion. A striking example of such a selected trait is the ability of a horse to perform additional gaits other than the common walk, trot and gallop. Those could be four-beat ambling gaits, which are particularly smooth and comfortable for the rider, or pace, used mainly in racing. Gaited horse breeds occur around the globe, suggesting that gaitedness is an old trait, selected for in many breeds. A recent study discovered that a nonsense mutation in DMRT3 has a major impact on gaitedness in horses and is present at a high frequency in gaited breeds and in horses bred for harness racing. Here, we report a study of the worldwide distribution of this mutation. We genotyped 4396 horses representing 141 horse breeds for the DMRT3 stop mutation. More than half (2749) of these horses also were genotyped for a SNP situated 32kb upstream of the DMRT3 nonsense mutation because these two SNPs are in very strong linkage disequilibrium. We show that the DMRT3 mutation is present in 68 of the 141 genotyped horse breeds at a frequency ranging from 1% to 100%. We also show that the mutation is not limited to a geographical area, but is found worldwide. The breeds with a high frequency of the stop mutation (>50%) are either classified as gaited or bred for harness racing., De två första författarna delar första författarskapet.

Published
2014
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37. Deletion of 2.7 kb near HOXD3 in an Arabian horse with occipitoatlantoaxial malformation.

Author

Bordbari, M. H., Penedo, M. C. T., Aleman, M., Valberg, S. J., Mickelson, J., and Finno, C. J.

Subjects
*HORSE breeds, *HOMEOBOX genes, *NUCLEOTIDE sequencing, *DELETION mutation, CERVICAL vertebrae abnormalities
Abstract

In the horse, the term occipitoatlantoaxial malformation ( OAAM) is used to describe a developmental defect in which the first cervical vertebra (atlas) resembles the base of the skull (occiput) and the second cervical vertebra (axis) resembles the atlas. Affected individuals demonstrate an abnormal posture and varying degrees of ataxia. The homeobox ( HOX) gene cluster is involved in the development of both the axial and appendicular skeleton. Hoxd3-null mice demonstrate a strikingly similar phenotype to Arabian foals with OAAM. Whole-genome sequencing was performed in an OAAM-affected horse ( OAAM1) and seven unaffected Arabian horses. Visual inspection of the raw reads within the region of HOXD3 identified a 2.7-kb deletion located 4.4 kb downstream of the end of HOXD4 and 8.2 kb upstream of the start of HOXD3. A genotyping assay revealed that both parents of OAAM1 were heterozygous for the deletion. Additional genotyping identified two of 162 heterozygote Arabians, and the deletion was not present in 371 horses of other breeds. Comparative genomics studies have revealed that this region is highly conserved across species and that the entire genomic region between Hoxd4 and Hoxd3 is transcribed in mice. Two additional Arabian foals diagnosed with OAAM ( OAAM 2 and 3) were genotyped and did not have the 2.7-kb deletion. Closer examination of the phenotype in these cases revealed notable variation. OAAM3 also had facial malformations and a patent ductus arteriosus, and the actual malformation at the craniocervical junction differed. Genetic heterogeneity may exist across the HOXD locus in Arabian foals with OAAM. [ABSTRACT FROM AUTHOR]

Published
2017
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38. Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

Author

Wade, C. M., Giulotto, E., Sigurdsson, Snaevar, Zoli, M., Gnerre, S., Imsland, Freyja, Lear, T. L., Adelson, D. L., Bailey, E., Bellone, R. R., Bloecker, H., Distl, O., Edgar, R. C., Garber, M., Leeb, T., Mauceli, E., MacLeod, J. N., Penedo, M. C. T., Raison, J. M., Sharpe, T., Vogel, J., Andersson, Leif, Antczak, D. F., Biagi, T., Binns, M. M., Chowdhary, B. P., Coleman, S. J., Della Valle, G., Fryc, S., Guerin, G., Hasegawa, T., Hill, E. W., Jurka, J., Kiialainen, A., Lindgren, G., Liu, J., Magnani, E., Mickelson, J. R., Murray, J., Nergadze, S. G., Onofrio, R., Pedroni, S., Piras, M. F., Raudsepp, T., Rocchi, M., Roed, K. H., Ryder, O. A., Searle, S., Skow, L., Swinburne, J. E., Syvänen, A. C., Tozaki, T., Valberg, S. J., Vaudin, M., White, J. R., Zody, Michael C., Lander, E. S., Lindblad-Toh, Kerstin, Wade, C. M., Giulotto, E., Sigurdsson, Snaevar, Zoli, M., Gnerre, S., Imsland, Freyja, Lear, T. L., Adelson, D. L., Bailey, E., Bellone, R. R., Bloecker, H., Distl, O., Edgar, R. C., Garber, M., Leeb, T., Mauceli, E., MacLeod, J. N., Penedo, M. C. T., Raison, J. M., Sharpe, T., Vogel, J., Andersson, Leif, Antczak, D. F., Biagi, T., Binns, M. M., Chowdhary, B. P., Coleman, S. J., Della Valle, G., Fryc, S., Guerin, G., Hasegawa, T., Hill, E. W., Jurka, J., Kiialainen, A., Lindgren, G., Liu, J., Magnani, E., Mickelson, J. R., Murray, J., Nergadze, S. G., Onofrio, R., Pedroni, S., Piras, M. F., Raudsepp, T., Rocchi, M., Roed, K. H., Ryder, O. A., Searle, S., Skow, L., Swinburne, J. E., Syvänen, A. C., Tozaki, T., Valberg, S. J., Vaudin, M., White, J. R., Zody, Michael C., Lander, E. S., and Lindblad-Toh, Kerstin

Abstract

We report a high-quality draft sequence of the genome of the horse ( Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.

Published
2009
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40. International Equine Gene Mapping Workshop Report : a comprehensive linkage map constructed with data from new markers and by merging four mapping resources.

Author

Penedo, M C T, Millon, L V, Bernoco, D, Bailey, E, Binns, M, Cholewinski, G, Ellis, N, Flynn, J, Gralak, B, Guthrie, A, Hasegawa, T, Lindgren, G, Lyons, L A, Røed, K H, Swinburne, J E, Tozaki, T, Penedo, M C T, Millon, L V, Bernoco, D, Bailey, E, Binns, M, Cholewinski, G, Ellis, N, Flynn, J, Gralak, B, Guthrie, A, Hasegawa, T, Lindgren, G, Lyons, L A, Røed, K H, Swinburne, J E, and Tozaki, T

Published
2005

43. Genetic characterization of Latin-American Creole cattle using microsatellite markers

Author

Delgado, J. V., primary, Martínez, A. M., additional, Acosta, A., additional, Álvarez, L. A., additional, Armstrong, E., additional, Camacho, E., additional, Cañón, J., additional, Cortés, O., additional, Dunner, S., additional, Landi, V., additional, Marques, J. R., additional, Martín-Burriel, I., additional, Martínez, O. R., additional, Martínez, R. D., additional, Melucci, L., additional, Muñoz, J. E., additional, Penedo, M. C. T., additional, Postiglioni, A., additional, Quiróz, J., additional, Rodellar, C., additional, Sponenberg, P., additional, Uffo, O., additional, Ulloa-Arvizu, R., additional, Vega-Pla, J. L., additional, Villalobos, A., additional, Zambrano, D., additional, Zaragoza, P., additional, Gama, L. T., additional, and Ginja, C., additional

Published
2011
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44. Genetic diversity, structure, and breed relationships in Iberian cattle1

Author

Martín-Burriel, I., primary, Rodellar, C., additional, Cañón, J., additional, Cortés, O., additional, Dunner, S., additional, Landi, V., additional, Martínez-Martínez, A., additional, Gama, L. T., additional, Ginja, C., additional, Penedo, M. C. T., additional, Sanz, A., additional, Zaragoza, P., additional, and Delgado, J. V., additional

Published
2011
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48. Linkage of bovine erythrocyte antigen loci B, C, L, S, Z, R‘ and T’ and the serum protein loci post-transferrin 2 (PTF 2), vitamin D binding protein (GC) and albumin (ALB) to DNA microsatellite markers

Author

Kappes, S M, primary, Bishop, M D, additional, Keele, J W, additional, Penedo, M C T, additional, Hines, H C, additional, Grosz, M D, additional, Hawkins, G A, additional, Stone, R T, additional, Sunden, S L F, additional, and Beattie, C W, additional

Published
2009
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