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1. Genetic Eye Diseases in Animals: A Selected Review of Recent Advances.

Author

Komáromy, A. M. and Lenstra, J. A.

Subjects
*ANIMAL diseases, *RETINAL diseases, *GENETIC disorders, *EYE diseases, *ANIMAL genetics, *DOG breeds, *HORSE breeding, *CATTLE breeds
Abstract

The online collection 'Genetic Eye Diseases in Animals: A Review of Recent Advances' features 17 articles published in Veterinary Ophthalmology and Animal Genetics since 2021, focusing on inherited eye diseases in animals. The publications cover topics such as inherited retinal diseases, equine recurrent uveitis, ocular surface diseases, lens disorders, feline glaucoma, and hereditary eye diseases in the Lagotto Romagnolo dog. The collection aims to provide valuable insights into genetic eye diseases in animals for readers in veterinary medicine and animal genetics. [Extracted from the article]

Published
2024
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2. Short Shop Schedules

Author

Williamson, D. P., Hall, L. A., Hoogeveen, J. A., Hurkens, C. A. J., Lenstra, J. K., and Shmoys, D. B.

Published
1997

3. 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, R., Mcewan, J., Milanesi, M., 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, P., Bradley, D. G., Colli, L., 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, M., 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., and Riccardo, S.

Subjects
haplogroup, introgresija, domestication, goat, introgression, migration, phylogeography, Y-chromosome, Evolution, MITOCHONDRIAL-DNA, FLOW, Haplotypes/genetics, divje koze, DNA, Mitochondrial, DNA, Mitochondrial/genetics, Behavior and Systematics, BREEDS, Y Chromosome, Goats/genetics, Genetics, Animals, domače koze, Ecology, Evolution, Behavior and Systematics, Phylogeny, udc:575:636.39, kozorogi, Ecology, 630 Agriculture, Goats, Genetic Variation, NETWORKS, DIFFERENTIATION, genetika, Haplotypes, ORIGINS, GENETIC DIVERSITY, 590 Animals (Zoology), 570 Life sciences, biology, Y Chromosome/genetics
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
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4. Unraveling the genetic diversity of Belgian Milk Sheep using medium‐density SNP genotypes

Author

Meyermans, R, Gorssen, W, Wijnrocx, K, Lenstra, J A, Vellema, P, Buys, N, Janssens, S, One Health Toxicologie, LS IRAS Tox Algemeen, dIRAS RA-1, Sub Analysis begr. 01-01-2014, One Health Toxicologie, LS IRAS Tox Algemeen, dIRAS RA-1, and Sub Analysis begr. 01-01-2014

Subjects
0301 basic medicine, Veterinary medicine, animal diseases, Runs of Homozygosity, fluids and secretions, Belgium, single nucleotide polymorphism, HOMOZYGOSITY, health care economics and organizations, Genetics & Heredity, education.field_of_study, Full Paper, biology, ROH, food and beverages, East Friesian sheep, Agriculture, RUNS, Articles, 04 agricultural and veterinary sciences, General Medicine, Breed, Pedigree, Agriculture, Dairy & Animal Science, admixture, Livestock, Life Sciences & Biomedicine, Inbreeding, Flemish Sheep, Genotype, biology.animal_breed, Population, inbreeding, Polymorphism, Single Nucleotide, Crossbreed, 03 medical and health sciences, otorhinolaryngologic diseases, Genetics, Animals, Friesian Milk Sheep, education, Sheep, Domestic, runs of homozygosity, Genetic diversity, Science & Technology, business.industry, 0402 animal and dairy science, 040201 dairy & animal science, 030104 developmental biology, Sheep HapMap, Animal Science and Zoology, business, effective population size
Abstract

The present study focuses on the Belgian Milk Sheep in Flanders (Belgium) and compares its genetic diversity and relationship with the Flemish Sheep, the Friesian Milk Sheep, the French Lacaune dairy sheep and other Northern European breeds. For this study, 94 Belgian Milk Sheep, 23 Flemish Sheep and 22 Friesian Milk Sheep were genotyped with the OvineSNP50 array. In addition, 29 unregistered animals phenotypically similar to Belgian Milk Sheep were genotyped using the 15K ISGC chip. Both Belgian and Friesian Milk Sheep as well as the East Friesian Sheep were found to be less diverse than the other seven breeds included in this study. Genomic inbreeding coefficients based on runs of homozygosity (ROH) were estimated at 14.5, 12.4 and 10.2% for Belgian Milk Sheep, Flemish Sheep and Friesian Milk Sheep respectively. Out of 29 unregistered Belgian Milk Sheep, 28 mapped in the registered Belgian Milk Sheep population. Ancestry analysis, PCA and FST calculations showed that Belgian Milk Sheep are more related to Friesian Milk Sheep than to Flemish Sheep, which was contrary to the breeders' expectations. Consequently, breeders may prefer to crossbreed Belgian Milk Sheep with Friesian sheep populations (Friesian Milk Sheep or East Friesian Sheep) in order to increase diversity. This research underlines the usefulness of SNP chip genotyping and ROH analyses for monitoring genetic diversity and studying genetic links in small livestock populations, profiting from internationally available genotypes. As assessment of genetic diversity is vital for long-term breed survival, these results will aid flockbooks to preserve genetic diversity. ispartof: ANIMAL GENETICS vol:51 issue:2 pages:258-265 ispartof: location:England status: published

Published
2019
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26. 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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28. 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

45. Evolution and domestication of the Bovini species.

Author

Zhang, K., Lenstra, J. A., Zhang, S., Liu, W., and Liu, J.

Subjects
*AMERICAN bison, *MITOCHONDRIAL DNA, *YAK, *ZEBUS, *INTROGRESSION (Genetics), *CATTLE, *COWS
Abstract

Summary: Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species – taurine cattle, zebu and yak – and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y‐chromosomal DNA. The high diversity of European breeds has been shaped through isolation‐by‐distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation. [ABSTRACT FROM AUTHOR]

Published
2020
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46. Unraveling the genetic diversity of Belgian Milk Sheep using medium‐density SNP genotypes.

Author

Meyermans, R., Gorssen, W., Wijnrocx, K., Lenstra, J. A., Vellema, P., Buys, N., and Janssens, S.

Subjects
SHEEP milk, HOMOZYGOSITY, CATTLE genetics, GENOTYPES
Abstract

Summary: The present study focuses on the Belgian Milk Sheep in Flanders (Belgium) and compares its genetic diversity and relationship with the Flemish Sheep, the Friesian Milk Sheep, the French Lacaune dairy sheep and other Northern European breeds. For this study, 94 Belgian Milk Sheep, 23 Flemish Sheep and 22 Friesian Milk Sheep were genotyped with the OvineSNP50 array. In addition, 29 unregistered animals phenotypically similar to Belgian Milk Sheep were genotyped using the 15K ISGC chip. Both Belgian and Friesian Milk Sheep as well as the East Friesian Sheep were found to be less diverse than the other seven breeds included in this study. Genomic inbreeding coefficients based on runs of homozygosity (ROH) were estimated at 14.5, 12.4 and 10.2% for Belgian Milk Sheep, Flemish Sheep and Friesian Milk Sheep respectively. Out of 29 unregistered Belgian Milk Sheep, 28 mapped in the registered Belgian Milk Sheep population. Ancestry analysis, PCA and FST calculations showed that Belgian Milk Sheep are more related to Friesian Milk Sheep than to Flemish Sheep, which was contrary to the breeders' expectations. Consequently, breeders may prefer to crossbreed Belgian Milk Sheep with Friesian sheep populations (Friesian Milk Sheep or East Friesian Sheep) in order to increase diversity. This research underlines the usefulness of SNP chip genotyping and ROH analyses for monitoring genetic diversity and studying genetic links in small livestock populations, profiting from internationally available genotypes. As assessment of genetic diversity is vital for long‐term breed survival, these results will aid flockbooks to preserve genetic diversity. [ABSTRACT FROM AUTHOR]

Published
2020
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