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1. Sounding an Alarm over Spatial Biology

Author

CMM USEQ Facility, Orr, Miranda E., Kulasinghe, Arutha, Kolar, Grant R., Heyn, Holger, Plummer, Jasmine, Sommer Kristensen, Lasse, Kjems, Jorgen, Mills, Gordon, Garcia-Vallejo, Juan J., Nijman, I. J., West, Nicholas P., Cox, Amanda, CMM USEQ Facility, Orr, Miranda E., Kulasinghe, Arutha, Kolar, Grant R., Heyn, Holger, Plummer, Jasmine, Sommer Kristensen, Lasse, Kjems, Jorgen, Mills, Gordon, Garcia-Vallejo, Juan J., Nijman, I. J., West, Nicholas P., and Cox, Amanda

Published
2024

2. Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

Author

Nijman, I. J., Rosen, B. D., Bardou, P., Faraut, T., Cumer, T., Daly, K. G., Zheng, Z., Cai, Y., Asadollahpour, H., Kul, B. C., Zhang, W. -Y., Guangxin, E., Ayin, A., Baird, H., Bakhtin, M., Balteanu, V. A., Barfield, D., Berger, B., Blichfeldt, T., Boink, G., Bugiwati, S. R. A., Cai, Z., Carolan, S., Clark, E., Cubric-Curik, V., Dagong, M. I. A., Dorji, T., Drew, L., Guo, J., Hallsson, J., Horvat, S., Kantanen, J., Kawaguchi, F., Kazymbet, P., Khayatzadeh, N., Kim, N., Shah, M. K., Liao, Y., Martinez, A., Masangkay, J., Masaoka, M., Mazza, Raffaele, Mcewan, J., Milanesi, Marco, Omar, F. M., Nomura, Y., Ouchene-Khelifi, N. -A., Pereira, F., Sahana, G., Salavati, M., Sasazaki, S., Da Silva, A., Simcic, M., Solkner, J., Sutherland, A., Tigchelaar, J., Zhang, H., Ajmone Marsan, Paolo, Bradley, D. G., Colli, Licia, Drogemuller, C., Jiang, Y., Lei, C., Mannen, H., Pompanon, F., Tosser-Klopp, G., Lenstra, J. A., Kijas, J., Guldbrandtsen, B., Denoyelle, L., Sarry, J., le Talouarn, E., Alberti, A., Orvain, C., Engelen, S., Duby, D., Martin, P., Danchin, C., Duclos, D., Allain, D., Arquet, R., Mandonnet, N., Naves, M., Palhiere, I., Rupp, R., Rezaei, H. R., Foran, M., Stella, A., Del Corvo, Marcello, Crisa, A., Marletta, D., Crepaldi, P., Ottino, M., Randi, E., Mujibi, D. F., Gondwe, T., Benjelloun, B., Taela, M. D. G., Nash, O., Moaeen-ud-Din, M., Visser, C., Goyache, F., Alvarez, I., Amills, M., Sanchez, A., Capote, J., Jordana, J., Pons, A., Balears, I., Molina, A., Mruttu, H. A., Masiga, C. W., Van Tassell, C. P., Reecy, J., Luikart, G., Sikosana, J., Anila, H., Petrit, D., Roswitha, B., Philippe, B., Aziz, F., Christos, P., El-Barody, M. A. A., Pierre, T., Phillip, E., Gordon, L., Albano, B. -P., Stephanie, Z., Michel, T., Georg, E., Horst, B., Eveline, I. -A., Luhken, G., Krugmann, D., Eva-Maria, P., Shirin, L., Katja, G., Christina, P., Jutta, R., Marco, B., Andreas, G., Al Tarrayrah, J., Georgios, K., Olga, K., Katerina, K., Christina, L., Anton, I., Lazlo, F., Gabriele, C., Elisabetta, M., Marco, P., Antonello, C., Tiziana, S., Mario, C., Francesca, F., Stefano, G., Marta, M., Bordonaro, S., Giuseppe, D. U., Fabio, P., Mariasilvia, D. A., Alessio, V., Irene, C., Lorraine, P., Mahamoud, A. -S., Van Cann, L. M., Roman, N., Popielarczyk, D., Ewa, S., Augustin, V., Susana, D., Javier, C., Oscar, C., David, G., Regis, C., Gabriela, O. -R., Glowatzki, M. -L., Okan, E., Inci, T., Evren, K., Mike, B., Trinidad, P., Gabriela, J., Godfrey, H., Stella, D., Louise, W., Martin, T., Sam, J., Riccardo, S., Mazza R., Milanesi M., Ajmone-Marsan P. (ORCID:0000-0003-3165-4579), Colli L. (ORCID:0000-0002-7221-2905), Del Corvo M., Nijman, I. J., Rosen, B. D., Bardou, P., Faraut, T., Cumer, T., Daly, K. G., Zheng, Z., Cai, Y., Asadollahpour, H., Kul, B. C., Zhang, W. -Y., Guangxin, E., Ayin, A., Baird, H., Bakhtin, M., Balteanu, V. A., Barfield, D., Berger, B., Blichfeldt, T., Boink, G., Bugiwati, S. R. A., Cai, Z., Carolan, S., Clark, E., Cubric-Curik, V., Dagong, M. I. A., Dorji, T., Drew, L., Guo, J., Hallsson, J., Horvat, S., Kantanen, J., Kawaguchi, F., Kazymbet, P., Khayatzadeh, N., Kim, N., Shah, M. K., Liao, Y., Martinez, A., Masangkay, J., Masaoka, M., Mazza, Raffaele, Mcewan, J., Milanesi, Marco, Omar, F. M., Nomura, Y., Ouchene-Khelifi, N. -A., Pereira, F., Sahana, G., Salavati, M., Sasazaki, S., Da Silva, A., Simcic, M., Solkner, J., Sutherland, A., Tigchelaar, J., Zhang, H., Ajmone Marsan, Paolo, Bradley, D. G., Colli, Licia, Drogemuller, C., Jiang, Y., Lei, C., Mannen, H., Pompanon, F., Tosser-Klopp, G., Lenstra, J. A., Kijas, J., Guldbrandtsen, B., Denoyelle, L., Sarry, J., le Talouarn, E., Alberti, A., Orvain, C., Engelen, S., Duby, D., Martin, P., Danchin, C., Duclos, D., Allain, D., Arquet, R., Mandonnet, N., Naves, M., Palhiere, I., Rupp, R., Rezaei, H. R., Foran, M., Stella, A., Del Corvo, Marcello, Crisa, A., Marletta, D., Crepaldi, P., Ottino, M., Randi, E., Mujibi, D. F., Gondwe, T., Benjelloun, B., Taela, M. D. G., Nash, O., Moaeen-ud-Din, M., Visser, C., Goyache, F., Alvarez, I., Amills, M., Sanchez, A., Capote, J., Jordana, J., Pons, A., Balears, I., Molina, A., Mruttu, H. A., Masiga, C. W., Van Tassell, C. P., Reecy, J., Luikart, G., Sikosana, J., Anila, H., Petrit, D., Roswitha, B., Philippe, B., Aziz, F., Christos, P., El-Barody, M. A. A., Pierre, T., Phillip, E., Gordon, L., Albano, B. -P., Stephanie, Z., Michel, T., Georg, E., Horst, B., Eveline, I. -A., Luhken, G., Krugmann, D., Eva-Maria, P., Shirin, L., Katja, G., Christina, P., Jutta, R., Marco, B., Andreas, G., Al Tarrayrah, J., Georgios, K., Olga, K., Katerina, K., Christina, L., Anton, I., Lazlo, F., Gabriele, C., Elisabetta, M., Marco, P., Antonello, C., Tiziana, S., Mario, C., Francesca, F., Stefano, G., Marta, M., Bordonaro, S., Giuseppe, D. U., Fabio, P., Mariasilvia, D. A., Alessio, V., Irene, C., Lorraine, P., Mahamoud, A. -S., Van Cann, L. M., Roman, N., Popielarczyk, D., Ewa, S., Augustin, V., Susana, D., Javier, C., Oscar, C., David, G., Regis, C., Gabriela, O. -R., Glowatzki, M. -L., Okan, E., Inci, T., Evren, K., Mike, B., Trinidad, P., Gabriela, J., Godfrey, H., Stella, D., Louise, W., Martin, T., Sam, J., Riccardo, S., Mazza R., Milanesi M., Ajmone-Marsan P. (ORCID:0000-0003-3165-4579), Colli L. (ORCID:0000-0002-7221-2905), and Del Corvo M.

Abstract

By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographical range.

Published
2022

5. Cosmid-derived markers anchoring the bovine genetic map to the physical map

Author

Ferretti, L., Urquhart, B. G. D., Eggen, A., Olsaker, I., Harlizius, B., Castiglioni, B., Mezzelani, A., Toldo, S. Solinas, Thieven, U., Zhang, Y., Morgan, A. L. G., Teres, V. M., Schwerin, M., Martin-Burriel, I., Chowdhary, B. P., Erhardt, G., Nijman, I. J., Cribiu, E. P., Barendse, W., Leveziel, H., Fries, R., and Williams, J. L.

Published
1997
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6. A medium-density genetic linkage map of the bovine genome

Author

Barendse, W., Vaiman, D., Kemp, S. J., Sugimoto, Y., Armitage, S. M., Williams, J. L., Sun, H. S., Eggen, A., Agaba, M., Aleyasin, S. A., Band, M., Bishop, M. D., Buitkamp, J., Byrne, K., Collins, F., Cooper, L., Coppettiers, W., Denys, B., Drinkwater, R. D., Easterday, K., Elduque, C., Ennis, S., Erhardt, G., Ferretti, L., Flavin, N., Gao, Q., Georges, M., Gurung, R., Harlizius, B., Hawkins, G., Hetzel, J., Hirano, T., Hulme, D., Jorgensen, C., Kessler, M., Kirkpatrick, B. W., Konfortov, B., Kostia, S., Kuhn, C., Lenstra, J. A., Leveziel, H., Lewin, H. A., Leyhe, B., Lil, L., Burriel, I. Martin, McGraw, R. A., Miller, J. R., Moody, D. E., Moore, S. S., Nakane, S., Nijman, I. J., Olsaker, I., Pomp, D., Rando, A., Ron, M., Shalom, A., Teale, A. J., Thieven, U., Urquhart, B. G. D., Vage, D. -I., Van de Weghe, A., Varvio, S., Velmala, R., Vilkki, J., Weikard, R., Woodside, C., Womack, J. E., Zanotti, M., and Zaragoza, P.

Published
1997
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7. Differentiation of European cattle by AFLP fingerprinting

Author

Negrini, R., Nijman, I. J., Milanesi, E., Moazami-Goudarzi, K., Williams, J. L., Erhardt, G., Dunner, S., Rodellar, C., Valentini, A., Bradley, D. G., Olsaker, I., Kantanen, J., Ajmone-Marsan, P., and Lenstra, J. A.

Published
2007

14. Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

Author

Lenstra, J. A., Tigchelaar, J., Biebach, I., Econogene, Consortiumn, Hallsson, J. H., Kantanen, J., Nielsen, V. H., Pompanon, F., Naderi, S., Rezaei, H. R., Sæther, N., Ertugrul, O., Grossen, C., Camenisch, G., Vos, Loohuis, Van, Straten, Poel, De, E. A., Windig, Oldenbroek, J., Abo, Shehada, Marsan, M., P. A., Tarrayrah, J. A., Angiolillo, Baret, A., Baumung, P., Beja, Pereira, Bertaglia, A., Bordonaro, Salvatore, Brandt, H., Bruford, M., Caloz, R., Canali, G., Canon, J., Cappuccio, I., Carta, A., Cicogna, M., Crepaldi, P., Dalamitra, S., Dobi, P., Dunner, S., D'Urso, G., Barody, El, M. A. A., England, Erhardt, P., Ertuğrul, G., Glowatzki, O., M. L., Ibeagha, Awemu, Strzelec, E., Fadlaoui, E., Fornarelli, A., Garcia, F., Georgoudis, D., Giovenzana, A., Gutscher, S., Hewitt, K., Hoda, G., Istvan, A., Jones, A., Joost, S., Juma, S., Karetsou, G., Kliambas, K., Koban, G., Krugmann, E., Kutita, D., Lazlo, O., Ligda, F., Lipsky, C., Luikart, S., Lühken, G., Marilli, G., Marletta, Donata, Milanesi, E., Negrini, R., Nijman, I. J., Niznikowski, R., Obexer, Ruff, Papachristoforou, G., Pariset, C., Peter, L., M. P., Christinan, Perez, T., Pietrolà, E., Pilla, F., Popielarczyk, D., Prinzenberg, M. E., Roosen, J., Scarpa, R., Sechi, T., Taberlet, P., Taylor, M., Togan, I., Trommetter, M., Valentini, A., Van, Cann, L. M., Vlaic, Wiskin, A., Zundel, L., Auðlinda- og umhverfisdeild (LBHÍ), and Landbúnaðarháskóli Íslands

Subjects
0301 basic medicine, Male, microsatellite, Conservation of Natural Resources, goats, Endangered species, Zoology, Conservation, Biology, Geitur, diversity, Animals, Female, Goats, Phylogeography, Microsatellite Repeats, Food Animals, Animal Science and Zoology, 03 medical and health sciences, 14. Life underwater, Fokkerij & Genomica, Domestication, Genetics, Genetic diversity, Diversity, Settore AGR/17 - ZOOTECNICA GENERALE E MIGLIORAMENTO GENETICO, Detacheringen, business.industry, 0402 animal and dairy science, Búfjárrækt, Microsatellite, 04 agricultural and veterinary sciences, General Medicine, Cline (biology), 040201 dairy & animal science, Breed, 030104 developmental biology, Population bottleneck, WIAS, Livestock, business, Purebred, Animal Breeding & Genomics
Abstract

In the last decades, several endangered breeds of livestock species have been re-established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO-recommended microsatellites of these landraces and three phenotypically similar Nordic-type landraces and compared these breeds with central European, Mediterranean and south-west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south-west Asian domestication site with a south-east-to-north-west cline that is clearly steeper than the Mediterranean east-to-west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land-races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long-horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately., Stichting Zeldzame Huisdierassen

Published
2017
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15. Signatures of selection? Patterns of microsatellite diversity of a chromosome containing a selected locus

Author

Wiener, P., Burton, D., Ajmone-Marsan, P., Dunner, S., Mommens, G., Nijman, I. J., Rodellar, C., Valentini, A., and Williams, J. L.

Subjects
Heredity -- Research, Heredity -- Genetic aspects, Biological diversity -- Genetic aspects, Genetic research -- Analysis, Phenotype -- Genetic aspects, Cattle -- Genetic aspects, Population genetics -- Research, Breeding -- Genetic aspects, Natural selection -- Genetic aspects, Biological sciences
Abstract

Research has been conducted on cattle breeds' genetic diversity. The authors have analyzed population genetic parameters for the microsatellite loci in double-muscled and non-double-muscled cattle breeds in investigating genetic diversity petterns, and they present the results.

Published
2003

16. Hybridization of banteng (Bos javanicus) and zebu (Bos indicus) revealed by mitochondrial DNA, satellite DNA, AFLP and microsatellites

Author

Nijman, I. J., Otsen, M., Verkaar, E. L. C., Ruijter, C. de, Hanekamp, E., Ochieng, J. W., Shamshad, S., Rege, J. E. O., Hanotte, O., Barwegen, M. W., Sulawati, T., and Lenstra, J. A.

Subjects
Heredity -- Research, Heredity -- Genetic aspects, Mitochondrial DNA -- Genetic aspects, Hybridization -- Research, Hybridization -- Genetic aspects, Cattle -- Genetic aspects, Cattle -- Demographic aspects, Genotype -- Physiological aspects, Biological sciences
Abstract

Research has been conducted on (Bos javanicus) and zebu (Bos indicus) hybridization. The authors have investigated this hybridization in south-east Asian cattle via the use of microsatellite genotyping, satellite fragment length polymorphism, AFLP and mitochondrial DNA, and they report the results.

Published
2003

17. Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

Author

Utsunomiya, Yuri T., Bomba, Lorenzo, Lucente, Giordana, Colli, Licia, Negrini, Riccardo, Lenstra, Johannes A., Erhardt, Georg, Garcia, José F., Ajmone-Marsan, Paolo, Moazami-Goudarzi, K., Williams, J., Wiener, P., Olsaker, I., Kantanen, J., Dunner, S., Cañón, J., Rodellar, C., Martín-Burriel, I., Valentini, A., Zanotti, M., Holm, L. E., Eythorsdottir, E., Mommens, G., Polygen, Van Haeringen, Nijman, I. J., Dolf, G., Bradley, D. G., Algemeen Onderzoek DGK, LS IRAS Tox Algemeen, Dep Natuurkunde, Faculty of Veterinary Medicine Research Groups, Algemeen Onderzoek DGK, LS IRAS Tox Algemeen, Dep Natuurkunde, Faculty of Veterinary Medicine Research Groups, Universidade Estadual Paulista (Unesp), Univ Cattol Sacro Cuore, Univ Utrecht, and Univ Giessen

Subjects
Genetic Markers, Conservation of Natural Resources, AFLP, Genotype, ved/biology.organism_classification_rank.species, Introgression, Breeding, Genetic differentiation, Revisiting AFLP, Ascertainment bias, Genetic variation, genetic structure, Genetics, Animals, Cluster Analysis, Genetics(clinical), Amplified Fragment Length Polymorphism Analysis, Genetics (clinical), Models, Genetic, Settore AGR/17 - ZOOTECNICA GENERALE E MIGLIORAMENTO GENETICO, biology, ved/biology, Taurine cattle, Genetic Variation, Aurochs, Zebu, biology.organism_classification, humanities, Genetics, Population, Genetic marker, Genetic structure, Amplified fragment length polymorphism, Cattle, Research Article
Abstract

Made available in DSpace on 2014-12-03T13:07:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-04-17Bitstream added on 2014-12-03T13:24:33Z : No. of bitstreams: 1 WOS000335177200001.pdf: 750548 bytes, checksum: 075b52b143f984a79a48dec1b9a68ce6 (MD5) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Background: Descendants from the extinct aurochs (Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in particular genome-wide single nucleotide polymorphism (SNP) markers, can complement historic and archaeological records to elucidate these past events. However, SNP ascertainment in cattle has been optimized for taurine breeds, imposing limitations to the study of diversity in zebu cattle. As amplified fragment length polymorphism (AFLP) markers are discovered and genotyped as the samples are assayed, this type of marker is free of ascertainment bias. In order to obtain unbiased assessments of genetic differentiation and structure in taurine and zebu cattle, we analyzed a dataset of 135 AFLP markers in 1,593 samples from 13 zebu and 58 taurine breeds, representing nine continental areas.Results: We found a geographical pattern of expected heterozygosity in European taurine breeds decreasing with the distance from the domestication centre, arguing against a large-scale introgression from European or African aurochs. Zebu cattle were found to be at least as diverse as taurine cattle. Western African zebu cattle were found to have diverged more from Indian zebu than South American zebu. Model-based clustering and ancestry informative markers analyses suggested that this is due to taurine introgression. Although a large part of South American zebu cattle also descend from taurine cows, we did not detect significant levels of taurine ancestry in these breeds, probably because of systematic backcrossing with zebu bulls. Furthermore, limited zebu introgression was found in Podolian taurine breeds in Italy.Conclusions: The assessment of cattle diversity reported here contributes an unbiased global view to genetic differentiation and structure of taurine and zebu cattle populations, which is essential for an effective conservation of the bovine genetic resources. Univ Estadual Paulista, Fac Ciencias Agr & Vet, BR-14884900 Jaboticabal, SP, Brazil Univ Cattol Sacro Cuore, Inst Zootech, Piacenza, Italy Univ Cattol Sacro Cuore, BioDNA Biodivers & Ancient DNA Res Ctr, Piacenza, Italy Univ Utrecht, Fac Vet Med, Utrecht, Netherlands Univ Giessen, Inst Anim Breeding & Genet, D-35390 Giessen, Germany Univ Estadual Paulista, Fac Med Vet Aracatuba, BR-16050680 Aracatuba, SP, Brazil Univ Estadual Paulista, Fac Ciencias Agr & Vet, BR-14884900 Jaboticabal, SP, Brazil Univ Estadual Paulista, Fac Med Vet Aracatuba, BR-16050680 Aracatuba, SP, Brazil FAPESP: 11/16643-2 FAPESP: 13/12829-0

Published
2014
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18. Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

Author

Algemeen Onderzoek DGK, LS IRAS Tox Algemeen, Dep Natuurkunde, Faculty of Veterinary Medicine Research Groups, Utsunomiya, Yuri T., Bomba, Lorenzo, Lucente, Giordana, Colli, Licia, Negrini, Riccardo, Lenstra, Johannes A., Erhardt, Georg, Garcia, José F., Ajmone-Marsan, Paolo, Moazami-Goudarzi, K., Williams, J., Wiener, P., Olsaker, I., Kantanen, J., Dunner, S., Cañón, J., Rodellar, C., Martín-Burriel, I., Valentini, A., Zanotti, M., Holm, L. E., Eythorsdottir, E., Mommens, G., Polygen, Van Haeringen, Nijman, I. J., Dolf, G., Bradley, D. G., Algemeen Onderzoek DGK, LS IRAS Tox Algemeen, Dep Natuurkunde, Faculty of Veterinary Medicine Research Groups, Utsunomiya, Yuri T., Bomba, Lorenzo, Lucente, Giordana, Colli, Licia, Negrini, Riccardo, Lenstra, Johannes A., Erhardt, Georg, Garcia, José F., Ajmone-Marsan, Paolo, Moazami-Goudarzi, K., Williams, J., Wiener, P., Olsaker, I., Kantanen, J., Dunner, S., Cañón, J., Rodellar, C., Martín-Burriel, I., Valentini, A., Zanotti, M., Holm, L. E., Eythorsdottir, E., Mommens, G., Polygen, Van Haeringen, Nijman, I. J., Dolf, G., and Bradley, D. G.

Published
2014

19. Geographic Patterns of Molecular Diversity and Paternal Lineages of European cattle

Author

Lenstra, J A, Nijman, I J, Eding, H, Engelsma, K A, Bijma, P, Garcia, D, Cañón, J, Dunner, S, Moazami-Goudarzi, K, Laloe, D, Williams, J L, Wiener, P, Burton, D, Erhardt, G, Jann, O, Weimann, C, Prinzenberg, E M, Harlizius, B, Barre-Dirie, B, Mengers, A, Looft, C, Kalm, E, Rodellar, C, Zaragoza, P, Martin-Burriel, I, Sanchez, A, Ajmone-Marsan, P, Negrini, R, Milanesi, E, Valentini, A, Savarese, M C, Marchitelli, C, Zanotti, M, Ceriotti, G, Pilla, F, Bruzzone, A, Iamartino, D, Olsaker, I, Holm, Lars-Erik, Mommens, G, Dolf, G, Hiemstra, S J, and Winding, J J

Published
2009

20. Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity

Author

Naderi, S., Rezaei, H. R., Taberlet, P., Zundel, S., Rafat, S. A., Naghash, H. R., Barody, El, M. A. A., Ertugrul, Pompanon, O., Abo, Shehada, Ajmone, M., P. M., Tarrayrah, Al, Angiolillo, J., Baret, A., Baumung, P., Beja, Pereira, Bertaglia, A., Bordonaro, Salvatore, Bruford, M., Caloz, R., Canali, G., Canon, J., Cappuccio, I., Carta, A., Cicogna, M., Crepaldi, P. v, Dalamitra, S., Krugmann, D., Dobi, P., Popielarczyk, D., Dunner, S., D'Urso, G., M. A. A., England, Erhardt, P., Ertugrul, G., Prinzenberg, O., E. M., Ibeagha, Awemu, Strzelec, E., Aziz, E., Fornarelli, F., Garcia, F., Georgoudis, D., Gesine, A., Giovenzana, L., Gutscher, S., Hewitt, K., Hoda, G., Horst, A., Istvan, B., Juma, A., G. p, Joost, Jones, S., Karetsou, S., Kliambas, K., Koban, G., Kutita, E., Lazlo, O., Lenstra, F., J. A., Ligda, Lipsky, C., Luikart, S., Glowatzki, G., M. L., Marilli, Marletta, Donata, Milanesi, E., Negrini, R., Nijman, I. J., Obexer, Ruff, Papachristoforou, G., Pariset, C., Pellecchia, L., Peter, M., Perez, C., Pietrolà, T., Pilla, E., Niznikowski, F., Roosen, R., Scarpa, J., Sechi, R., Taberlet, T., Taylor, P., Togan, M., Trommetter, I., Valentini, M., Van, Cann, L. M., Vlaic, Wiskin, A., Zundel, L., Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Natural Resources Faculty, University of Guilan, Environmental Sciences Department, Gorgan University of Agriculture and Natural Resources, Animal Science Department, University of Tabriz [Tabriz], Animal Production Department, Minia University, Department of Genetics, and Ankara University

Subjects
Haplogroup, Evolutionary Biology/Animal Genetics, Phylogeny, 2. Zero hunger, Genetics, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, education.field_of_study, Multidisciplinary, Goats, 04 agricultural and veterinary sciences, Mitochondria, Mitochondrial, Genetic structure, Medicine, Research Article, Mitochondrial DNA, Evolution, Science, Population, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, DNA, Mitochondrial, Models, Biological, Evolution, Molecular, 03 medical and health sciences, Species Specificity, Animals, Genetics, Population, Genetics and Genomics/Population Genetics, Domestication, education, 030304 developmental biology, Genetic diversity, Evolutionary Biology, Polymorphism, Genetic, Models, Genetic, Haplotype, 0402 animal and dairy science, Genetic Variation, Molecular, DNA, 040201 dairy & animal science, Haplotypes, Evolutionary biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Haplogroup A
Abstract

International audience; BACKGROUND: From the beginning of domestication, the transportation of domestic animals resulted in genetic and demographic processes that explain their present distribution and genetic structure. Thus studying the present genetic diversity helps to better understand the history of domestic species. METHODOLOGY/PRINCIPAL FINDINGS: The genetic diversity of domestic goats has been characterized with 2430 individuals from all over the old world, including 946 new individuals from regions poorly studied until now (mainly the Fertile Crescent). These individuals represented 1540 haplotypes for the HVI segment of the mitochondrial DNA (mtDNA) control region. This large-scale study allowed the establishment of a clear nomenclature of the goat maternal haplogroups. Only five of the six previously defined groups of haplotypes were divergent enough to be considered as different haplogroups. Moreover a new mitochondrial group has been localized around the Fertile Crescent. All groups showed very high haplotype diversity. Most of this diversity was distributed among groups and within geographic regions. The weak geographic structure may result from the worldwide distribution of the dominant A haplogroup (more than 90% of the individuals). The large-scale distribution of other haplogroups (except one), may be related to human migration. The recent fragmentation of local goat populations into discrete breeds is not detectable with mitochondrial markers. The estimation of demographic parameters from mismatch analyses showed that all groups had a recent demographic expansion corresponding roughly to the period when domestication took place. But even with a large data set it remains difficult to give relative dates of expansion for different haplogroups because of large confidence intervals. CONCLUSIONS/SIGNIFICANCE: We propose standard criteria for the definition of the different haplogroups based on the result of mismatch analysis and on the use of sequences of reference. Such a method could be also applied for clarifying the nomenclature of mitochondrial haplogroups in other domestic species.

Published
2007
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27. Allele frequencies and diversity parameters of 27 single nucleotide polymorphisms within and across goat breeds

Author

CAPPUCCIO, I., primary, PARISET, L., additional, AJMONE‐MARSAN, P., additional, DUNNER, S., additional, CORTES, O., additional, ERHARDT, G., additional, LÜHKEN, G., additional, GUTSCHER, K., additional, JOOST, S., additional, NIJMAN, I. J., additional, LENSTRA, J. A., additional, ENGLAND, P. R., additional, ZUNDEL, S., additional, OBEXER‐RUFF, G., additional, BEJA‐PEREIRA, A., additional, VALENTINI, A., additional, and CONSORTIUM, THE ECONOGENE, additional

Published
2006
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33. Differentiation of cattle species in beef by PCR-RFLP of mitochondrial and satellite DNA.

Author

Verkaar EL, Nijman IJ, Boutaga K, and Lenstra JA

Abstract

Methods currently used for the identification of the species origin of meat or tissue samples have not been validated for other bovine species than taurine cattle or water buffalo. These methods also do not discriminate between the different bovine species that are used as source of beef. Here, we describe two complementary methods for detection and differentiation of bovine species, which are based on mutations in mitochondrial DNA and centromeric satellite DNA, respectively. The analysis of satellite DNA is especially relevant for the identification of animals that are of hybrid origin.

Published
2002
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34. Mutation and recombination in cattle satellite DNA: a feedback model for the evolution of satellite DNA repeats.

Author

Nijman IJ and Lenstra JA

Subjects
Animals, Base Sequence, Cattle classification, Evolution, Molecular, Genetic Variation, Molecular Sequence Data, Mutation, Phylogeny, Polymerase Chain Reaction, Recombination, Genetic, Sequence Alignment, Short Interspersed Nucleotide Elements, Time Factors, Cattle genetics, DNA, Satellite, Models, Genetic
Abstract

The cattle genome contains several distinct centromeric satellites with interrelated evolutionary histories. We compared these satellites in Bovini species that diverged 0.2 to about 5 Myr ago. Quantification of hybridization signals by phosphor imaging revealed a large variation in the relative amounts of the major satellites. In the genome of water buffalo this has led to the complete deletion of satellite III. Comparative sequencing and PCR-RFLP analysis of satellites IV, 1.711a, and 1.711b from the related Bos and Bison species revealed heterogeneities in 0.5 to 2% of the positions, again with variations in the relative amounts of sequence variants. Restriction patterns generated by double digestions suggested a recombination of sequence variants. Our results are compatible with a model of the life history of satellites during which homogeneity of interacting repeat units is both cause and consequence of the rapid turnover of satellite DNA. Initially, a positive feedback loop leads to a rapid saltatory amplification of homogeneous repeat units. In the second phase, mutations inhibit the interaction of repeat units and coexisting sequence variants amplify independently. Homogenization by the spreading of one of the variants is prevented by recombination and the satellite is eventually outcompeted by another, more homogeneous tandem repeat sequence.

Published
2001
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35. Llama heavy-chain V regions consist of at least four distinct subfamilies revealing novel sequence features.

Author

Harmsen MM, Ruuls RC, Nijman IJ, Niewold TA, Frenken LG, and de Geus B

Subjects
Amino Acid Sequence, Animals, Antigen-Antibody Reactions, Cloning, Molecular, Escherichia coli, Immunoglobulin Heavy Chains classification, Immunoglobulin Heavy Chains genetics, Immunoglobulin Variable Region classification, Immunoglobulin Variable Region genetics, Models, Molecular, Molecular Sequence Data, Protein Conformation, Recombinant Proteins, Sequence Alignment, Sequence Analysis, DNA, Camelids, New World immunology, Immunoglobulin Heavy Chains chemistry, Immunoglobulin Variable Region chemistry
Abstract

In addition to conventional antibodies (Abs), camelids possess Abs consisting of only heavy chains. The variable domain of such a heavy-chain Ab (VHH) is fully capable of antigen (Ag) binding. Earlier analysis of 47 VHHs showed sequence features unique to VHH domains. These include the presence of characteristic amino acid substitutions in positions which, in conventional VH domains are involved in interdomain interactions, and the presence of a long third complementarity-determining region (CDR3) which is frequently constrained by an interloop disulphide bond. Here, we describe a large (152) set of Lama glama VHH cDNAs. Based on amino acid sequence similarity, these and other published camelid VHHs were classified into four subfamilies. Three subfamilies are absent in dromedaries, which have been the primary source of VHHs thus far. Comparison of these subfamilies to conventional VH regions reveals new features characteristic of VHHs and shows that many features earlier regarded as characteristic of VHHs in general are actually subfamily specific. A long CDR3 with a concomitant putative additional disulphide bond is only observed in two VHH subfamilies. Furthermore, we identified new VHH-characteristic residues at positions forming interdomain sites in conventional VH domains. The VHH subfamilies also differ from each other and conventional VH domains in the canonical structure of CDR1 and CDR2, mean CDR3 length, and amino acid residue variability. Since different VHH-characteristic residues are observed in all four subfamilies, these subfamilies must have evolved independently from classical VH domains.

Published
2000
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36. Species origin of milk in Italian mozzarella and Greek feta cheese.

Author

Branciari R, Nijman IJ, Plas ME, Di Antonio E, and Lenstra JA

Subjects
Animals, Cattle, Cytochrome b Group genetics, DNA analysis, DNA isolation & purification, Food Handling standards, Goats, Polymerase Chain Reaction methods, Polymorphism, Restriction Fragment Length, Sheep, Species Specificity, Cheese, Food Contamination, Food Inspection methods, Milk
Abstract

Several animal species such as cattle, goats, sheep, and water buffalo provide milk for dairy products. We describe a simple procedure for detecting the species origin of milk used for cheese production. DNA was isolated from Italian mozzarella or Greek feta by sequential organic extractions and resin purification. This DNA was analyzed by polymerase chain reaction-restriction fragment length polymorphism as described previously for meat samples. This procedure differentiated mozzarella made from water buffalo milk and from less expensive bovine milk and also feta cheeses made from bovine, ovine, and caprine milk.

Published
2000
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37. A satellite DNA element specific for roe deer (Capreolus capreolus).

Author

Buntjer JB, Nijman IJ, Zijlstra C, and Lenstra JA

Subjects
Animals, Base Sequence, Cattle, Centromere genetics, Chromosome Mapping, Cloning, Molecular, DNA Primers genetics, Genomic Library, In Situ Hybridization, Fluorescence, Molecular Sequence Data, Polymerase Chain Reaction, Sequence Analysis, DNA, Species Specificity, DNA, Satellite genetics, Deer genetics
Abstract

An abundant tandem repetitive DNA segment (CCsatIII) with a repeat unit of 2.2 kb has been found in the genome of roe deer (Capreolus capreolus). It accounts for approximately 5%-10% of the genome and is only present in the two species of the genus Capreolus. The sequence has no similarity or common motives with other deer satellite DNAs and there is no internal repeat structure. A 93 bp fragment is homologous to a bovine repeat. Fluorescent in situ hybridisation showed a predominant centromeric staining of most chromosomes accompanied by a weak interstitial staining of the same chromosomes. On Southern blots, CCsatIII probes do not discriminate between the closely related Capreolus species.

Published
1998
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