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102. 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

107. The characterization of goat genetic diversity: Towards a genomic approach

Author

Algemeen Onderzoek DGK, LS IRAS Tox Algemeen, Ajmone-Marsan, P., Colli, L., Han, J. L., Achilli, A., Lancioni, H., Joost, S., Crepaldi, P., Pilla, F., Stella, A., Taberlet, P., Boettcher, P., Negrini, R., Lenstra, J. A., Algemeen Onderzoek DGK, LS IRAS Tox Algemeen, Ajmone-Marsan, P., Colli, L., Han, J. L., Achilli, A., Lancioni, H., Joost, S., Crepaldi, P., Pilla, F., Stella, A., Taberlet, P., Boettcher, P., Negrini, R., and Lenstra, J. A.

Published
2014

108. Advancing maternal age predisposes to mitochondrial damage and loss during maturation of equine oocytes invitro

Author

LS IRAS Tox Algemeen, LS Klinische Reproductie, LS Voortplanting Inwendige Ziekten, Afd Algemeen BC, ES/FAH BRC, IRAS RATIA1, Risk Assessment of Toxic and Immunomodulatory Agents, Rambags, B. P B, van Boxtel, D. C J, Tharasanit, T., Lenstra, J. A., Colenbrander, B., Stout, T. A E, LS IRAS Tox Algemeen, LS Klinische Reproductie, LS Voortplanting Inwendige Ziekten, Afd Algemeen BC, ES/FAH BRC, IRAS RATIA1, Risk Assessment of Toxic and Immunomodulatory Agents, Rambags, B. P B, van Boxtel, D. C J, Tharasanit, T., Lenstra, J. A., Colenbrander, B., and Stout, T. A E

Published
2014

109. The characterization of goat genetic diversity: Towards a genomic approach

Author

Ajmone Marsan, Paolo, Colli, Licia, Han, J, Achilli, A, Lancioni, H, Joost, Stephane, Crepaldi, Paola, Pilla, Fabio, Stella, A, Taberlet, P, Boettcher, Paul John, Negrini, Riccardo, Lenstra, J., Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Colli, Licia (ORCID:0000-0002-7221-2905), Negrini, Riccardo (ORCID:0000-0002-8735-0286), Ajmone Marsan, Paolo, Colli, Licia, Han, J, Achilli, A, Lancioni, H, Joost, Stephane, Crepaldi, Paola, Pilla, Fabio, Stella, A, Taberlet, P, Boettcher, Paul John, Negrini, Riccardo, Lenstra, J., Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Colli, Licia (ORCID:0000-0002-7221-2905), and Negrini, Riccardo (ORCID:0000-0002-8735-0286)

Abstract

The investigation of genetic diversity at molecular level has been proposed as a valuable complement and sometimes proxy to phenotypic diversity of local breeds and is presently considered as one of the FAO priorities for breed characterization. By recommending a set of selected molecular markers for each of the main livestock species, FAO has promoted the meta-analysis of local datasets, to achieve a global view of molecular genetic diversity. Analysis within the EU Globaldiv project of two large goat microsatellite datasets produced by the Econogene Consortium and the IAEA CRP-Asia Consortium, respectively, has generated a picture of goat diversity across continents. This indicates a gradient of decreasing diversity from the domestication centre towards Europe and Asia, a clear phylogeographic structure at the continental and regional levels, and in Asia a limited genetic differentiation among local breeds. The development of SNP panels that assay thousands of markers and the whole genome sequencing of livestock permit an affordable use of genomic technologies in all livestock species, goats included. Preliminary data from the Italian Goat Consortium indicate that the SNP panel developed for this species is highly informative. The existing panel can be improved by integrating additional SNPs identified from the whole genome sequence alignment of goats adapted to extreme climates. Part of this effort is being achieved by international projects (e.g. EU FP7 NextGen and 3SR projects), but a fair representation of the global diversity in goats requires a large panel of samples (i.e. as in the recently launched 1000 cattle genomes initiative). Genomic technologies offer new strategies to investigate complex traits difficult to measure. For example, the comparison of patterns of diversity among the genomes in selected groups of animals (e.g. adapted to different environments) and the integration of genome-wide diversity with new GIScience-based methods are able to ident

Published
2014

110. Meta-Analysis of Mitochondrial DNA Reveals Several Population Bottlenecks during Worldwide Migrations of Cattle

Author

Lenstra, J, Ajmone Marsan, Paolo, Beja Pereira, A, Bollongino, R, Bradley, D, Colli, Licia, De Gaetano, A, Edwards, C, Felius, M, Ferretti, L, Ginja, C, Hristov, P, Kantanen, J, Lirón, J, Magee, D, Negrini, Riccardo, Radoslavov, G., Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Colli, Licia (ORCID:0000-0002-7221-2905), Negrini, Riccardo (ORCID:0000-0002-8735-0286), Lenstra, J, Ajmone Marsan, Paolo, Beja Pereira, A, Bollongino, R, Bradley, D, Colli, Licia, De Gaetano, A, Edwards, C, Felius, M, Ferretti, L, Ginja, C, Hristov, P, Kantanen, J, Lirón, J, Magee, D, Negrini, Riccardo, Radoslavov, G., Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Colli, Licia (ORCID:0000-0002-7221-2905), and Negrini, Riccardo (ORCID:0000-0002-8735-0286)

Abstract

Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a role. © 2014 by the authors.

Published
2014

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

Author

Utsunomiya, Y, Bomba, Lorenzo, Lucente, Giordana, Colli, Licia, Negrini, Riccardo, Lenstra, J, Erhardt, G, Garcia, J, Ajmone Marsan, Paolo, Colli, Licia (ORCID:0000-0002-7221-2905), Negrini, Riccardo (ORCID:0000-0002-8735-0286), Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Utsunomiya, Y, Bomba, Lorenzo, Lucente, Giordana, Colli, Licia, Negrini, Riccardo, Lenstra, J, Erhardt, G, Garcia, J, Ajmone Marsan, Paolo, Colli, Licia (ORCID:0000-0002-7221-2905), Negrini, Riccardo (ORCID:0000-0002-8735-0286), and Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579)

Abstract

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 population

Published
2014

113. Molecular tools and analytical approaches for the characterization of farm animal genetic diversity

Author

LS IRAS Tox Algemeen, Faculty of Veterinary Medicine Research Groups, Dep Natuurkunde, Algemeen Onderzoek DGK, Lenstra, J. A., Groeneveld, L. F., Eding, H., Kantanen, J., Williams, J. L., Taberlet, P., Nicolazzi, E. L., Sölkner, J., Simianer, H., Ciani, E., Garcia, J. F., Bruford, M. W., Ajmone-Marsan, P., Weigend, S., LS IRAS Tox Algemeen, Faculty of Veterinary Medicine Research Groups, Dep Natuurkunde, Algemeen Onderzoek DGK, Lenstra, J. A., Groeneveld, L. F., Eding, H., Kantanen, J., Williams, J. L., Taberlet, P., Nicolazzi, E. L., Sölkner, J., Simianer, H., Ciani, E., Garcia, J. F., Bruford, M. W., Ajmone-Marsan, P., and Weigend, S.

Published
2012

114. The origin of Indonesian cattle and conservation genetics of the Bali cattle breed

Author

dES/dFAH FR, Faculty of Veterinary Medicine Research Groups, Sub Celbiologisch lab., LS IRAS Tox Algemeen, Mohamad, K., Olsson, M., Andersson, G., Purwantara, B., van Tol, H. T A, Rodriguez-Martinez, H., Colenbrander, B., Lenstra, J. A., dES/dFAH FR, Faculty of Veterinary Medicine Research Groups, Sub Celbiologisch lab., LS IRAS Tox Algemeen, Mohamad, K., Olsson, M., Andersson, G., Purwantara, B., van Tol, H. T A, Rodriguez-Martinez, H., Colenbrander, B., and Lenstra, J. A.

Published
2012

116. Y-chromosomal variation confirms independent domestications of swamp and river buffalo

Author

LS IRAS Tox Algemeen, Faculty of Veterinary Medicine Research Groups, Algemeen Onderzoek DGK, Yindee, M., Vlamings, B. H., Wajjwalku, W., Techakumphu, M., Lohachit, C., Sirivaidyapong, S., Thitaram, C., Amarasinghe, A. A A W K, Alexander, P. A B D A, Colenbrander, B., Lenstra, J. A., LS IRAS Tox Algemeen, Faculty of Veterinary Medicine Research Groups, Algemeen Onderzoek DGK, Yindee, M., Vlamings, B. H., Wajjwalku, W., Techakumphu, M., Lohachit, C., Sirivaidyapong, S., Thitaram, C., Amarasinghe, A. A A W K, Alexander, P. A B D A, Colenbrander, B., and Lenstra, J. A.

Published
2010

117. Genetic diversity in farm animals - A review

Author

LS IRAS Tox Algemeen, Faculty of Veterinary Medicine Research Groups, Sub Physical and Colloid Chemistry, Algemeen Onderzoek DGK, Groeneveld, L. F., Lenstra, J. A., Eding, H., Toro, M. A., Scherf, B., Pilling, D., Negrini, R., Finlay, E. K., Jianlin, H., Groeneveld, E., Weigend, S., LS IRAS Tox Algemeen, Faculty of Veterinary Medicine Research Groups, Sub Physical and Colloid Chemistry, Algemeen Onderzoek DGK, Groeneveld, L. F., Lenstra, J. A., Eding, H., Toro, M. A., Scherf, B., Pilling, D., Negrini, R., Finlay, E. K., Jianlin, H., Groeneveld, E., and Weigend, S.

Published
2010

118. Algorithms for the radio link frequency assignment problem

Author

Aardal, K. I., Cor Hurkens, Lenstra, J. K., Tiourine, S. R., Stochastic Operations Research, and Combinatorial Optimization 1

Abstract

The radio link frequency assignment problem occurs when a network of radio links has to be established. Each link must be assigned an operating frequency from a given domain. The assignment has to satisfy certain restrictions so as to limit the interference between links. The number of frequencies used is to be minimized. Problems of this type were investigated by a consortium consisting of research groups from Delft, Eindhoven, London, Maastricht, Norwich, and Toulouse. The participants developed optimization algorithms based on branch-and-cut and constraint satisfaction, and approximation techniques including a variety of local search methods, genetic algorithms, neural networks, and potential reduction. These algorithms were tested and compared on a set of real-life instances.

Published
1999

119. Algorithms for frequency assignment problems

Author

Aardal, K. I., Cor Hurkens, Lenstra, J. K., Tiourine, S. R., Stochastic Operations Research, and Combinatorial Optimization 1

Abstract

Frequency assignment problems occur when a network of radio links has to be established. Each link has to be assigned an operating frequency from a set of available frequencies. The assignment has to satisfy certain interference limiting restrictions defined on pairs of links. Moreover, the number of frequencies used is to be minimized. These problems have been investigated by a consortium consisting of research groups from Delft, Eindhoven, London, Maastricht, Norwich, and Toulouse. The participants developed optimization algorithms based on branch-and-cut and constraint satisfaction, as well as approximation techniques such as simulated annealing, taboo search, variable-depth search, genetic algorithms, and potential reduction methods. These algorithms were tested and compared on a set of real-life instances.

Published
1996

128. 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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129. Linear neutralizing epitopes on the peplomer protein of coronaviruses

Author

Posthumus, W. P A, Meloen, R. H., Enjuanes, L., Correa, I., van Nieuwstadt, A. P., Koch, G., de Groot, R. J., Kusters, J. G., Luytjes, W., Spaan, W. J., van der Zeijst, B. A M, Lenstra, J. A., LS IRAS Tox Algemeen, Sub ULS, and LS Virologie

Subjects
Mouse Hepatitis Virus, Biochemistry, Genetics and Molecular Biology(all), Infectious Bronchitis Virus, Linear Epitope, Antigenic Site, Hybrid Protein
Abstract

Three years ago, we reported a comparison of the primary structures of the S peplomer proteins of three coronaviruses - mouse hepatitis virus (MHV, strain A59), infectious bronchitis virus (IBV, strain M41), and feline infectious peritonitis virus (FIPV, strain 79-1146) - which represent the three antigenic clusters in the Coronavirus family (De Groot et al., 1987a, b). A periodicity in the C-terminal part of the S sequence indicated the presence of a coiled-coil structure, which forms the stalk of the peplomer. The nonconserved N-terminal sequence probably forms the bulbous part of the peplomer.

Published
1990

130. Analysis and simulation of a neutralizing epitope of transmissible gastroenteritis virus

Author

Posthumus, W. P A, Lenstra, J. A., Schaaper, W. M M, Van Nieuwstadt, A. P., Enjuanes, L., Meloen, R. H., LS IRAS Tox Algemeen, and Sub ULS

Subjects
Immunology
Abstract

The amino acid sequences recognized by monoclonal antibodies (MAbs) specific for the antigenic site IV of the spike protein S of transmissible gastroenteritis virus were analyzed by PEPSCAN. All MAbs of group IV recognized peptides from the S region consisting of residues 378 to 390. In addition, the neutralizing MAbs (subgroup IV-A) also bound to peptides from the region consisting of residues 1173 to 1184 and to several other peptides with a related amino acid composition. The contribution of the individual residues of both sequences to the binding of a MAb was determined by varying the length of the peptide and by a consecutive deletion or replacement of parental residues by the 19 other amino acids. The sequence consisting of residues 326 to 558, tested as part of a cro-β-galactosidase hybrid protein, was antigenic, but the sequence consisting of residues 1150 to 1239 was not. Furthermore, antibodies raised in rabbits against the peptide SDSSFFSYGEIPFGN (residues 377 to 391), but not those raised against the peptide VRASRQLAKDKVNEC (residues 1171 to 1185), recognized the virus and had neutralizing activity. We infer that the epitope of the neutralizing MAbs is composite and consists of the linear sequence SFFSYGEI (residues 380 to 387) with contributions of A, D, K, N, Q, or V residues from other parts of the S molecule. The complex epitope was simulated by sythesizing peptides in which the sequences consisting of residues 380 to 387 and 1176 to 1184 were combined. MAbs of subgroup IV-A recognized the combination peptides two to six times better than the individual sequences. These results may offer prospects for the development of an experimental vaccine.

Published
1990

134. Conservation of cattle genetic resources: the role of breeds.

Author

FELIUS, M., THEUNISSEN, B., and LENSTRA, J. A.

Abstract

Focusing on cattle (Bos taurus, Bos indicus), the present paper discusses the concept of the breed in the context of the dynamic history of livestock domestication. A breed categorization is proposed on the basis of how the breeds came into existence. The online Appendix (available at http://journals.cambridge.org/AGS) presents a survey of the cattle breeds of the world consisting of: (1) a list of breeds per country and then subdivided according to the proposed categories; (2) a list of breed names, including synonyms and translations, ordered according to a comprehensive breed classification; and (3) an alphabetical list of these names. The commonly accepted perceptions of breeds and how these are influenced by the nomenclature are described. Considering the history of breeds, it is argued that conservation of genetic diversity does not necessarily imply conservation of breeds. However, breeds are instrumental for the conservation of genetic diversity as independent genetic management units. These considerations may very well be extrapolated to other domestic species. [ABSTRACT FROM PUBLISHER]

Published
2015
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136. Localization of antigenic sites of the E2 glycoprotein of transmissible gastroenteritis coronavirus

Author

Correa, I., Gebauer, F., Bullido, M. J., Sune, C., Baay, M. F D, Zwaagstra, K. A., Posthumus, W. P A, Lenstra, J. A., Enjuanes, L., Correa, I., Gebauer, F., Bullido, M. J., Sune, C., Baay, M. F D, Zwaagstra, K. A., Posthumus, W. P A, Lenstra, J. A., and Enjuanes, L.

Abstract

Four antigenic sites of the E2 glycoprotein of transmissible gastroenteritis virus were defined by competitive radioimmunoassays of monoclonal antibodies (MAbs). Here, we describe the localization of these sites by testing the antigenicity of protein fragments and prokaryotic expression products of E2 gene fragments, and by sequencing of MAb-resistant (mar) mutants. Partial proteolysis of purified E2 protein allowed the isolation of a 28K fragment recognized by both site A- and site C-specific MAbs. An antiserum against this fragment bound to a synthetic peptide containing residues 1 to 18 and to an expression product containing residues 1 to 325. The same expression product was recognized by site C-specific MAbs. These data indicate that residues within the sequence 1 to 325 contribute to site C and possibly also to site A. Sequencing of mar mutants that escaped neutralization by site A-specific MAbs indicated that residues 538 and 543 also belong to site A. The binding of site-specific MAbs to expression products led directly to the localization of sites B and D, between residues 1 to 325 and 379 to 529, respectively. The first 37% of the polypeptide chain of E2 appears to be more immunogenic than the rest of the sequence.

Published
1990

138. Location of antigenic sites of the S-glycoprotein of transmissible gastroenteritis virus and their conservation in coronaviruses

Author

LS IRAS Tox Algemeen, Sub ULS, Enjuanes, L., Gebauer, F., Correa, I., Bullido, M. J., Sune, C., Smerdou, C., Sanchez, C., Lenstra, J. A., Posthumus, W. P A, Meloen, R. H., LS IRAS Tox Algemeen, Sub ULS, Enjuanes, L., Gebauer, F., Correa, I., Bullido, M. J., Sune, C., Smerdou, C., Sanchez, C., Lenstra, J. A., Posthumus, W. P A, and Meloen, R. H.

Published
1990

139. Linear neutralizing epitopes on the peplomer protein of coronaviruses

Author

LS IRAS Tox Algemeen, Sub ULS, LS Virologie, Posthumus, W. P A, Meloen, R. H., Enjuanes, L., Correa, I., van Nieuwstadt, A. P., Koch, G., de Groot, R. J., Kusters, J. G., Luytjes, W., Spaan, W. J., van der Zeijst, B. A M, Lenstra, J. A., LS IRAS Tox Algemeen, Sub ULS, LS Virologie, Posthumus, W. P A, Meloen, R. H., Enjuanes, L., Correa, I., van Nieuwstadt, A. P., Koch, G., de Groot, R. J., Kusters, J. G., Luytjes, W., Spaan, W. J., van der Zeijst, B. A M, and Lenstra, J. A.

Published
1990

142. Short Shop Schedules

Author

Williamson, D. P., primary, Hall, L. A., additional, Hoogeveen, J. A., additional, Hurkens, C. A. J., additional, Lenstra, J. K., additional, Sevast'janov, S. V., additional, and Shmoys, D. B., additional

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

Author

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

Published
1997
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147. Molecular tools and analytical approaches for the characterization of farm animal genetic diversity.

Author

Lenstra, J. A., Groeneveld, L. F., Eding, H., Kantanen, J., Williams, J. L., Taberlet, P., Nicolazzi, E. L., Sölkner, J., Simianer, H., Ciani, E., Garcia, J. F., Bruford, M. W., Ajmone-Marsan, P., and Weigend, S.

Subjects
*BAYESIAN analysis, *SINGLE nucleotide polymorphisms, *DOMESTICATION of animals, *POPULATION genetics, *GENOMICS
Abstract

Genetic studies of livestock populations focus on questions of domestication, within- and among-breed diversity, breed history and adaptive variation. In this review, we describe the use of different molecular markers and methods for data analysis used to address these questions. There is a clear trend towards the use of single nucleotide polymorphisms and whole-genome sequence information, the application of Bayesian or Approximate Bayesian analysis and the use of adaptive next to neutral diversity to support decisions on conservation. [ABSTRACT FROM AUTHOR]

Published
2012
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148. Population studies of 17 equine STR for forensic and phylogenetic analysis.

Author

van de Goor, L. H. P., van Haeringen, W. A., and Lenstra, J. A.

Subjects
PHYLOGENY, HORSE breeding, HORSE breeds, FORENSIC genetics, HETEROZYGOSITY
Abstract

Summary As a consequence of the close integration of horses into human society, equine DNA analysis has become relevant for forensic purposes. However, the information content of the equine Short Tandem Repeat (STR) loci commonly used for the identification or paternity testing has so far not been fully characterized. Population studies were performed for 17 polymorphic STR loci ( AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, HTG10, LEX3 and VHL20) including 8641 horses representing 35 populations. The power of parental exclusion, polymorphic information content, expected and observed heterozygosity and probability of identity were calculated, showing that the set of 17 STRs has sufficient discriminating power for forensic analysis in almost all breeds. We also explored the reliability of individual assignment tests in identifying the correct breeds of origin for unknown samples. The overall proportion of individuals correctly assigned to a population was 97.2%. Finally, we demonstrate the phylogenetic signal of the 17 STR. We found three clusters of related breeds: (i) the cold-blooded draught breeds Haflinger, Dutch draft and Friesian; (ii) the pony breeds Shetland and Miniature horse with the Falabella, Appaloosa and Icelandic; and (iii) The Warmblood riding breeds, together with the hot-blooded Standard-bred, Thoroughbred and Arabian. [ABSTRACT FROM AUTHOR]

Published
2011
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149. Genetic diversity in farm animals – a review.

Author

Groeneveld, L. F., Lenstra, J. A., Eding, H., Toro, M. A., Scherf, B., Pilling, D., Negrini, R., Finlay, E. K., Jianlin, H., Groeneveld, E., and Weigend, S.

Subjects
*DOMESTICATION of animals, *LIVESTOCK, *GERMPLASM of domestic animals, *LIVESTOCK breeds, *ANIMAL breeds, *DEMOGRAPHIC characteristics
Abstract

Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology. [ABSTRACT FROM AUTHOR]

Published
2010
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150. Breed assignment of Italian cattle using biallelic AFLP® markers.

Author

Negrini, R., Milanesi, E., Colli, L., Pellecchia, M., Nicoloso, L., Crepaldi, P., Lenstra, J. A., and Ajmone-Marsan, P.

Subjects
CATTLE, ANIMAL products, ANIMAL breeds, FOOD safety, GENETIC polymorphisms, BAYESIAN analysis
Abstract

The verification of the breed origin of animal products is relevant for food safety and authenticity. We assessed the suitability of AFLP molecular markers in the assignment of cattle individuals to their breed of origin. Three hundred and ninety-six animals belonging to 16 cattle breeds genotyped with 141 AFLP markers were used as reference data set. Assignment was performed with likelihood (aflpop) and Bayesian (structure) methods. The Bayesian approach was superior to the likelihood algorithm with respect to (i) the correct assignment of simulated individuals to their breed of origin (93% vs. 81% respectively), (ii) the correct assignment of 44 sampled Romagnola animals (91% vs. 45% respectively) and (iii) the correct classification of animals belonging to a breed that was not included within the reference dataset. Thus, AFLP profiling in combination with the Bayesian approach seems a useful tool for breed assignment. [ABSTRACT FROM AUTHOR]

Published
2007
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