1,622 results on '"Crooijmans, R."'
Search Results
2. Genetic characterization of cashmere goat ( Capra hircus ) populations in Mongolia.
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Baldan S, Sölkner J, Gebre KT, Mészáros G, Crooijmans R, Periasamy K, Pichler R, Manaljav B, Baatar N, and Purevdorj M
- Abstract
Objective: Characterization studies of the phenotypic and genetic diversity of Mongolian goats are limited, despite several goat breeds being registered in the country. This study aimed to evaluate the phenotypic and genetic diversity of 14 cashmere goat populations in Mongolia, consisting largely of identified goat breeds., Methods: Body weight, cashmere quality, and coat color were the phenotypic traits considered in this study. A linear model was used to fit body weight and cashmere traits, and least squares means ( LSMs ) were estimated for the region and location classes. Genetic diversity and structure were assessed using a goat 50K SNP array., Results: The studied populations exhibited greater phenotypic diversity at the regional level. A very small overall differentiation index ( Fst : 0.017) was revealed by Wright's Fst and a very small overall inbreeding index ( F
ROH1 :0.019) was revealed based on runs of homozygosity. Genetic clustering of populations by principal components showed large variances for the two goat populations of the Russian admixture (Gobi Gurvan Saikhan and Uuliin Bor), and smaller but differentiated clusters for the remaining populations. Similar results were observed in the admixture analysis, which identified populations with the highest (Govi Gurvan Saikhan and Uuliin Bor) and lowest (Tsagaan Ovoo Khar) exotic admixtures. A genomewide association study (GWAS) of body weight and cashmere traits identified a few significant variants on chromosomes 2, 4, 5, 9, and 15, with the strongest variant for cashmere yield on chromosome 4. The GWAS on coat color yielded nine significant variants, with the strongest variants located on chromosomes 6, 13, and 18 and potential associations with KIT , ASIP , and MC1R genes. These signals were also found in other studies on coat color and patterns in goats., Conclusion: Mongolian cashmere goats showed relatively low genetic differentiation and low inbreeding levels, possibly caused by the traditional pastoral livestock management system and the practice of trading breeding bucks across provinces, along with a recent increase in the goat population. Further investigation of cashmere traits using larger samples and alternative methods may help identify the genes or genomic regions underlying cashmere quality in goats., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Baldan, Sölkner, Gebre, Mészáros, Crooijmans, Periasamy, Pichler, Manaljav, Baatar and Purevdorj.)- Published
- 2024
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3. Additional file 2 of Identification and characterisation of de novo germline structural variants in two commercial pig lines using trio-based whole genome sequencing
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Steensma, Marije J., Lee, Y. L., Bouwman, A. C., Pita Barros, C., Derks, M. F.L., Bink, M. C.A.M., Harlizius, B., Huisman, A. E., Crooijmans, R. P.M.A., Groenen, M. A.M., Mulder, H. A., and Rochus, C. M.
- Abstract
Supplementary Material 2
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- 2023
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4. Genome‐wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds
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Onzima, R. B., Upadhyay, M. R., Mukiibi, R., Kanis, E., Groenen, M. A. M., and Crooijmans, R. P. M. A.
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- 2018
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5. Editorial: Global green strategies and capacities to manage a sustainable animal biodiversity.
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Perini, F., Ceccobelli, S., Crooijmans, R. P. M. A., Tiambo, C. K., and Lasagna, E.
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ANIMAL diversity ,GERMPLASM ,BIODIVERSITY - Published
- 2023
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6. Exploiting phenotypic plasticity in animal breeding
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Kebede, F.G., Komen, H., Dessie, T., Hanotte, O., Kemp, S., Pita Barros, C., Crooijmans, R., Derks, M., Alemu, S.W., Bastiaansen, J.W.M., Kebede, F.G., Komen, H., Dessie, T., Hanotte, O., Kemp, S., Pita Barros, C., Crooijmans, R., Derks, M., Alemu, S.W., and Bastiaansen, J.W.M.
- Abstract
Livestock populations can have different genetic backgrounds and may vary in their capacity to respond to environmental changes. Our findings suggest that improved chicken breeds differ in growth performance and phenotypic plasticity (yield stability) when they are introduced into new tropical environments. Dual consideration of productivity and phenotypic plasticity gives opportunities to select or recommend genotypes with optimal performance and wider adaptability for smallholder farmers raising livestock in different agroecologies.
- Published
- 2022
7. Mapping genetic diversity in European gene banks: preliminary results on chickens for the validation of IMAGE001 array
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Tixier-Boichard, M., Peynot, N., Duclos, D., Weigend, S., Monteagudo, L., Martinez Martinez, A., Delgado, J.V., Gonzalez Prendes, R., Crooijmans, R., Restoux, G., Tixier-Boichard, M., Peynot, N., Duclos, D., Weigend, S., Monteagudo, L., Martinez Martinez, A., Delgado, J.V., Gonzalez Prendes, R., Crooijmans, R., and Restoux, G.
- Abstract
Gene banks are a component of a national strategy for the preservation of genetic diversity. Gene bank managers need to have a global and comparable picture of the diversity in their collections in order to rationalize them. Facing a diversity of molecular tools is a difficulty. The IMAGE H2020 project aimed at developing a low cost 60k SNP array to facilitate the mapping of diversity in gene banks. The first test of this array was performed for chicken with 204 samples from 18 local breeds and nine experimental lines provided by Germany, France and Spain. The MAF across population was 0.34, showing that this tool is useful over a range of populations. The principal component analysis and the Neighbor-joining tree showed that local breeds did not cluster according to country and were generally homogenous. Comparison with on-farm populations remains to be done to assess the value of the gene bank collections.
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- 2022
8. Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization
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Abernathy, J., Li, X., Jia, X., Chou, W., Lamont, S. J., Crooijmans, R., and Zhou, H.
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- 2014
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9. Maximum longevity and juvenile mortality in zoo-housed mangabeys.
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de Visser M, Prins E, Bosse M, Crooijmans R, and Ter Meulen T
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- Animals, Cercocebus, Animals, Zoo
- Abstract
Little is known about the biology of grey-cheeked and black crested mangabeys (Lophocebus albigena and Lophocebus aterrimus, respectively). As these primates face threats in the wild, well-monitored zoo-housed populations with up to date registries are becoming increasingly valuable to acquire species knowledge and to support conservation efforts. We used international studbooks to extract demographic and genetic information on 519 mangabeys to investigate how life history and parent-related variables influence maximum longevity and juvenile mortality. Generalized linear mixed models, as well as survival analyses, were applied. Results showed that females lived significantly longer than males, which is not uncommon in primates. Furthermore, our results indicated that the maximum longevity is lower for individuals living in European zoos versus individuals from North American zoos, which may be due to a combination of environmental differences and potential founder effects. We also show that the maternal maximum longevity is positively related to the maximum longevity of the offspring, which may be explained by the inheritance of "good genes". However, the age of the mother at the moment of birth was negatively related to the maximum longevity of the offspring, which contradicts literature that states that, in primates, more experienced and thus older mothers will raise their offspring better than less experienced mothers. Instead, it is more likely that an "optimal age range" exists for breeding mothers. Our study provides insights into the population biology of captive mangabeys and may be helpful for identifying future research priorities to optimize primate health and welfare directly ex situ, and indirectly in situ., (© 2022 The Authors. Zoo Biology published by Wiley Periodicals LLC.)
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- 2022
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10. Identification of QTLs Involved in Open-Field Behavior in Young and Adult Laying Hens
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Buitenhuis, A. J., Rodenburg, T. B., Siwek, M., Cornelissen, S. J. B., Nieuwland, M. G. B., Crooijmans, R. P. M. A., Groenen, M. A. M., Koene, P., Bovenhuis, H., and van der Poel, J. J.
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- 2004
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11. Genetic diversity of Vietnamese domestic chicken populations as decision-making support for conservation strategies
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Pham, M. H., Berthouly-Salazar, C., Tran, X. H., Chang, W. H., Crooijmans, R. P. M. A., Lin, D. Y., Hoang, V. T., Lee, Y. P., Tixier-Boichard, M., and Chen, C. F.
- Published
- 2013
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12. Farm-by-farm analysis of microsatellite, mtDNA and SNP genotype data reveals inbreeding and crossbreeding as threats to the survival of a native Spanish pig breed
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Herrero-Medrano, J. M., Megens, H. J., Crooijmans, R. P., Abellaneda, J. M., and Ramis, G.
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- 2013
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13. Identification of high utility SNPs for population assignment and traceability purposes in the pig using high-throughput sequencing
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Ramos, A. M., Megens, H. J., Crooijmans, R. P. M. A., Schook, L. B., and Groenen, M. A. M.
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- 2011
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14. East Asian contributions to Dutch traditional and western commercial chickens inferred from mtDNA analysis
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Dana, N., Megens, H.-J., Crooijmans, R. P. M. A., Hanotte, O., Mwacharo, J., Groenen, M. A. M., and van Arendonk, J. A. M.
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- 2011
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15. FISH mapping of 57 BAC clones reveals strong conservation of synteny between Galliformes and Anseriformes
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Fillon, V., Vignoles, M., Crooijmans, R. P. M. A., Groenen, M. A. M., Zoorob, R., and Vignal, A.
- Published
- 2007
16. Genetic mapping of quantitative trait loci affecting susceptibility in chicken to develop pulmonary hypertension syndrome
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Rabie, T. S. K. M., Crooijmans, R. P. M. A., Bovenhuis, H., Vereijken, A. L. J., Veenendaal, T., van der Poel, J. J., Van Arendonk, J. A. M., Pakdel, A., and Groenen, M. A. M.
- Published
- 2005
17. Chromosomal assignment of chicken clone contigs by extending the consensus linkage map
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Aerts, J. A., Veenendaal, T., van der Poel, J. J., Crooijmans, R. P. M. A., and Groenen, M. A. M.
- Published
- 2005
18. Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs
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Upadhyay, M., Bortoluzzi, C., Barbato, Mario, Ajmone Marsan, Paolo, Colli, Licia, Ginja, C., Sonstegard, T. S., Bosse, M., Lenstra, J. A., Groenen, M. A. M., Crooijmans, R. P. M. A., Barbato M. (ORCID:0000-0002-7203-1549), Ajmone Marsan P. (ORCID:0000-0003-3165-4579), Colli L. (ORCID:0000-0002-7221-2905), Upadhyay, M., Bortoluzzi, C., Barbato, Mario, Ajmone Marsan, Paolo, Colli, Licia, Ginja, C., Sonstegard, T. S., Bosse, M., Lenstra, J. A., Groenen, M. A. M., Crooijmans, R. P. M. A., Barbato M. (ORCID:0000-0002-7203-1549), Ajmone Marsan P. (ORCID:0000-0003-3165-4579), and Colli L. (ORCID:0000-0002-7221-2905)
- Abstract
The divergence between indicine cattle (Bos indicus) and taurine cattle (Bos taurus) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non-European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole-genome sequencing data. Additionally, we also employed unlinked and phased SNP-based approaches on high-density SNP array data to characterize non-European cattle ancestry in several southern European cattle breeds. Using heterozygosity-based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross-bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non-European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might ac
- Published
- 2019
19. A radiation hybrid map of chicken chromosome 15
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Jennen, D. G. J., Crooijmans, R. P. M. A., Morisson, M., Grootemaat, A. E., van der der Poel, J. J., Vignal, A., and Groenen, M. A. M.
- Published
- 2004
20. Detection of QTL for immune response to sheep red blood cells in laying hens
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Siwek, M., Cornelissen, S. J. B., Nieuwland, M. G. B., Buitenhuis, A. J., Bovenhuis, H., Crooijmans, R. P. M. A., Groenen, M. A. M., de Vries-Reilingh, G., Parmentier, H. K., and van der Poel, J. J.
- Published
- 2003
21. Development of a single nucleotide polymorphism map of porcine chromosome 2
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Jungerius, B. J., Rattink, A. P., Crooijmans, R. P. M. A., van der Poel, J. J., van Oost, B. A., te Pas, M. F. W., and Groenen, M. A. M.
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- 2003
22. Improvement of the comparative map of chicken chromosome 13
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Buitenhuis, A. J., Crooijmans, R. P. M. A., van Coppenraet, E. S. Bruijnesteijn, Veenendaal, A., Groenen, M. A. M., and van der Poel, J. J.
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- 2002
23. A comparative map of chicken chromosome 24 and human chromosome 11
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Jennen, D. G. J., Crooijmans, R. P. M. A., Kamps, B., Açar, R., Veenendaal, A., van der Poel, J. J., and Groenen, M. A. M.
- Published
- 2002
24. Porcine BAC derived microsatellites linked to ADRBK1, CNTF and GAL on SSC2
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Faivre, M., Rattink, A. P., Harlizius, B., Crooijmans, R. P. M. A., and Groenen, M. A. M.
- Published
- 2002
25. Development of 112 unique expressed sequence tags from chicken liver using an arbitrarily primed reverse transcriptase–polymerase chain reaction and single strand conformation gel purification method
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Carré, W., Diot, C., Fillon, V., Crooijmans, R. P. M. A., Lagarrigue, S., Morrisson, M., Vignal, A., Groenen, M. A. M., and Douaire, M.
- Published
- 2001
26. The influence of facies heterogeneity on the doublet performance in low-enthalpy geothermal sedimentary reservoirs
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Crooijmans, R. A., Willems, C. J L, Nick, Hamid, Bruhn, D. F., Crooijmans, R. A., Willems, C. J L, Nick, Hamid, and Bruhn, D. F.
- Abstract
A three-dimensional model is used to study the influence of facies heterogeneity on energy production under different operational conditions of low-enthalpy geothermal doublet systems. Process-based facies modelling is utilised for the Nieuwerkerk sedimentary formation in the West Netherlands Basin to construct realistic reservoir models honouring geological heterogeneity. A finite element based reservoir simulator is used to model the fluid flow and heat transfer over time. A series of simulations is carried out to examine the effects of reservoir heterogeneity (Net-to-Gross ratio, N/G) on the life time and the energy recovery rate for different discharge rates and the production temperature (Tmin) above which the doublet is working. With respect to the results, we propose a design model to estimate the life time and energy recovery rate of the geothermal doublet. The life time is estimated as a function of N/G, Tmin and discharge rate, while the design model for the energy recovery rate is only a function of N/G and Tmin. Both life time and recovery show a positive relation with an increasing N/G. Further our results suggest that neglecting details of process-based facies modelling may lead to significant errors in predicting the life time of low-enthalpy geothermal systems for N/G values below 70%.
- Published
- 2016
27. Extending the chicken-human comparative map by placing 15 genes on the chicken linkage map
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Groenen, M A M, Crooijmans, R P M A, Dijkhof, R J M, Acar, R, and van der Poel, J J
- Published
- 1999
28. Multicolour fluorescent detection and mapping of AFLP markers in chicken (Gallus domesticus)
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Herbergs, J, Siwek, M, Crooijmans, R P M A, Van der Poel, J J, and Groenen, M A M
- Published
- 1999
29. Developing microsatellite markers from cDNA: a tool for adding expressed sequence tags to the genetic linkage map of the chicken
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Ruyter-Spira, C P, de Koning, D J, van der Poel, J J, Crooijmans, R P M A, Dijkhof, R J M, and Groenen, M A M
- Published
- 1998
30. New microsatellite markers in chicken optimized for automated fluorescent genotyping
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Crooijmans, R P M A, Dijkhof, R J M, van der Poel, J J, and Groenen, M A M
- Published
- 1997
31. Fourth Report on Chicken Genes and Chromosomes 2022.
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Smith J, Alfieri JM, Anthony N, Arensburger P, Athrey GN, Balacco J, Balic A, Bardou P, Barela P, Bigot Y, Blackmon H, Borodin PM, Carroll R, Casono MC, Charles M, Cheng H, Chiodi M, Cigan L, Coghill LM, Crooijmans R, Das N, Davey S, Davidian A, Degalez F, Dekkers JM, Derks M, Diack AB, Djikeng A, Drechsler Y, Dyomin A, Fedrigo O, Fiddaman SR, Formenti G, Frantz LAF, Fulton JE, Gaginskaya E, Galkina S, Gallardo RA, Geibel J, Gheyas AA, Godinez CJP, Goodell A, Graves JAM, Griffin DK, Haase B, Han JL, Hanotte O, Henderson LJ, Hou ZC, Howe K, Huynh L, Ilatsia E, Jarvis ED, Johnson SM, Kaufman J, Kelly T, Kemp S, Kern C, Keroack JH, Klopp C, Lagarrigue S, Lamont SJ, Lange M, Lanke A, Larkin DM, Larson G, Layos JKN, Lebrasseur O, Malinovskaya LP, Martin RJ, Martin Cerezo ML, Mason AS, McCarthy FM, McGrew MJ, Mountcastle J, Muhonja CK, Muir W, Muret K, Murphy TD, Ng'ang'a I, Nishibori M, O'Connor RE, Ogugo M, Okimoto R, Ouko O, Patel HR, Perini F, Pigozzi MI, Potter KC, Price PD, Reimer C, Rice ES, Rocos N, Rogers TF, Saelao P, Schauer J, Schnabel RD, Schneider VA, Simianer H, Smith A, Stevens MP, Stiers K, Tiambo CK, Tixier-Boichard M, Torgasheva AA, Tracey A, Tregaskes CA, Vervelde L, Wang Y, Warren WC, Waters PD, Webb D, Weigend S, Wolc A, Wright AE, Wright D, Wu Z, Yamagata M, Yang C, Yin ZT, Young MC, Zhang G, Zhao B, and Zhou H
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- 2022
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32. RECON: Reef effect structures in the North Sea, islands or connections? : Summary report
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Coolen, J.W.P., Jak, R.G., van der Weide, B.E., Cuperus, J., Luttikhuizen, P., Schutter, M., Dorenbosch, M., Driessen, F., Lengkeek, W., Blomberg, M., van Moorsel, G., Faasse, M.A., Bos, O.G., Dias, I.M., Spierings, M., Glorius, S.G., Becking, L.E., Schol, T., Crooijmans, R., Boon, A.R., van Pelt, H., Kleissen, F., Gerla, D., Degraer, S., Lindeboom, H.J., Coolen, J.W.P., Jak, R.G., van der Weide, B.E., Cuperus, J., Luttikhuizen, P., Schutter, M., Dorenbosch, M., Driessen, F., Lengkeek, W., Blomberg, M., van Moorsel, G., Faasse, M.A., Bos, O.G., Dias, I.M., Spierings, M., Glorius, S.G., Becking, L.E., Schol, T., Crooijmans, R., Boon, A.R., van Pelt, H., Kleissen, F., Gerla, D., Degraer, S., and Lindeboom, H.J.
- Published
- 2018
33. Diversiteit en krielonderzoek : bij de traditionele Nederlandse hoenderrassen
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Bortoluzzi, C., Megens, H.J., Crooijmans, R., Boer, H. de, Taks, A., Kroon, P., Hoving, R., Bortoluzzi, C., Megens, H.J., Crooijmans, R., Boer, H. de, Taks, A., Kroon, P., and Hoving, R.
- Published
- 2018
34. Identification of QTLs involved in open-field behavior in young and adult laying hens
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Buitenhuis, A. J., Rodenburg, T. B., Siwek, M., Cornelissen, S. J. B., Nieuwland, M. G. B., Crooijmans, R. P. M. A., Groenen, M. A. M., Koene, P., Bovenhuis, H., and van der Poel, J. J.
- Published
- 2007
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35. Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos)
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Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, C-G, Champagnon, J, Guillemain, M, Kreisinger, J, Prins, H T, Crooijmans, R. P. M. A., R. H. S., Kraus, Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, C-G, Champagnon, J, Guillemain, M, Kreisinger, J, Prins, H T, Crooijmans, R. P. M. A., and R. H. S., Kraus
- Abstract
Disruption of naturally evolved spatial patterns of genetic variation and local adaptations is a growing concern in wildlife management and conservation. During the last decade, releases of native taxa with potentially non-native genotypes have received increased attention. This has mostly concerned conservation programs, but releases are also widely carried out to boost harvest opportunities. The mallard, Anas platyrhynchos, is one of few terrestrial migratory vertebrates subjected to large-scale releases for hunting purposes. It is the most numerous and widespread duck in the world, yet each year more than three million farmed mallard ducklings are released into the wild in the European Union alone to increase the harvestable population. This study aimed to determine the genetic effects of such large-scale releases of a native species, specifically if wild and released farmed mallards differ genetically among subpopulations in Europe, if there are signs of admixture between the two groups, if the genetic structure of the wild mallard population has changed since large-scale releases began in the 1970s, and if the current data matches global patterns across the Northern hemisphere. We used Bayesian clustering (Structure software) and Discriminant Analysis of Principal Components (DAPC) to analyze the genetic structure of historical and present-day wild (n = 171 and n = 209, respectively) as well as farmed (n = 211) mallards from six European countries as inferred by 360 single-nucleotide polymorphisms (SNPs). Both methods showed a clear genetic differentiation between wild and farmed mallards. Admixed individuals were found in the present-day wild population, implicating introgression of farmed genotypes into wild mallards despite low survival among released farmed mallards. Such cryptic introgression would alter the genetic composition of wild populations and may have unknown long-term consequences for conservation.
- Published
- 2017
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36. Design and characterization of a 52K SNP chip for goats
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Tosser-Klopp G., Bardou P., Bouchez O., Cabau C., Crooijmans R., Dong Y., Donnadieu-Tonon C., Eggen A., Heuven H.C.M., Jamli S., Jiken A.J., Klopp C., Lawley C.T., McEwan J., Martin P., Moreno C.R., Mulsant P., Nabihoudine I., Pailhoux E., Palhiere I., Rupp R., Sarry J., Sayre B.L., Tircazes A., Wang J., Wang W., Zhang W., Ajmone P., Amills M., Boitard S., Faraut T., San Cristobal M., Servin B., Chen W., Cheng S., Liu X., Pan S., Song C., Xu X., Ye C., Zhang B., Lv J., Li X., Ren L., Shi P., Yu J., Faruque O., Lenstra H., Poli M.A., Zhao J., Rui S., Zhang Y., Stella A., Valentini A., Zhao S., Ecole Nationale Vétérinaire de Toulouse - ENVT (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Animal Breeding and Genomics Centre, Wageningen University and Research Centre [Wageningen] (WUR), Kunming Institute of Zoology, State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences [Changchun Branch] (CAS), Faculty of Veterinary Medicine, Utrecht University [Utrecht], Strategic Livestock Research Centre, Malaysian Agricultural Research Development Institute, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Invermay Agricultural Center, AgResearch, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Station d'Amélioration Génétique des Animaux (SAGA), Biologie du Développement et Reproduction (BDR), Department of Biology, Virginia State University, Inner Mongolia Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, ANR-09-GENM-009-03 GENIDOV, ANR CHEST-454, CAPRISNIP programme: UNCEIA, CAPGENES and APIS-GENE French Breeding organizations, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Wageningen University and Research [Wageningen] (WUR), Biologie du développement et reproduction (BDR), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), and Amills i Eras, Marcel
- Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,Gene Identification and Analysis ,lcsh:Medicine ,Sequence assembly ,polledness ,Molecular Inversion Probe ,Genome ,Sequence alignment ,generation ,single-nucleotide polymorphisms ,lcsh:Science ,Génétique ,Animal Management ,Genetics ,0303 health sciences ,Multidisciplinary ,Goats ,Illumina 52K SNP Chip ,goat ,Agriculture ,Genomics ,04 agricultural and veterinary sciences ,Tag SNP ,SNP genotyping ,Grasslands ,Research Article ,dbSNP ,Animal Breeding and Genomics ,Biology ,Molecular Genetics ,03 medical and health sciences ,Genetic Mutation ,Biologie animale ,Genome-Wide Association Studies ,Fokkerij en Genomica ,BioNanoTechnology ,genome ,prp gene ,Alleles ,030304 developmental biology ,classical scrapie ,capra-hircus ,lcsh:R ,Sequence assembly tools ,0402 animal and dairy science ,association ,snp ,Genome analysis ,040201 dairy & animal science ,Sustainable Agriculture ,genotyping assay ,Genetic Polymorphism ,WIAS ,lcsh:Q ,Veterinary Science ,Cattle ,Animal Genetics ,Population Genetics ,Genomic databases ,discovery ,Reference genome - Abstract
The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50-60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years. Copyright: © 2014 Tosser-Klopp et al.
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- 2014
37. Segregation distortion in chicken and the evolutionary consequences of female meiotic drive in birds
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Axelsson, Erik Gunnar, Albrechtsen, Anders, Van, A. P., Li, L., Megens, H. J., Vereijken, A. L. J., Crooijmans, R. P. M. A., Groenen, M. A. M., Ellegren, H., Willerslev, Eske, Nielsen, R., Axelsson, Erik Gunnar, Albrechtsen, Anders, Van, A. P., Li, L., Megens, H. J., Vereijken, A. L. J., Crooijmans, R. P. M. A., Groenen, M. A. M., Ellegren, H., Willerslev, Eske, and Nielsen, R.
- Abstract
As all four meiotic products give rise to sperm in males, female meiosis result in a single egg in most eukaryotes. Any genetic element with the potential to influence chromosome segregation, so that it is preferentially included in the egg, should therefore gain a transmission advantage; a process termed female meiotic drive. We are aware of two chromosomal components, centromeres and telomeres, which share the potential to influence chromosome movement during meioses and make the following predictions based on the presence of female meiotic drive: (1) centromere-binding proteins should experience rapid evolution as a result of a conflict between driving centromeres and the rest of the genome; and (2) segregation patterns should be skewed near centromeres and telomeres. To test these predictions, we first analyze the molecular evolution of seven centromere-binding proteins in nine divergent bird species. We find strong evidence for positive selection in two genes, lending support to the genomic conflict hypothesis. Then, to directly test for the presence of segregation distortion, we also investigate the transmission of approximately 9000 single-nucleotide polymorphisms in 197 chicken families. By simulating fair Mendelian meioses, we locate chromosomal regions with statistically significant transmission ratio distortion. One region is located near the centromere on chromosome 1 and a second region is located near the telomere on the p-arm of chromosome 1. Although these observations do not provide conclusive evidence in favour of the meiotic drive/genome conflict hypothesis, they do lend support to the hypothesis that centromeres and telomeres drive during female meioses in chicken.
- Published
- 2010
38. Farmed European mallards are genetically different and cause introgression in the wild population following releases
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Elmberg, Johan, Söderquist, Pär, Gunnarsson, Gunnar, Thulin, Carl-Gustaf, Champagnon, Jocelyn, Guillemain, Matthieu, Kreisinger, Jakub, Prins, H. H. T., Crooijmans, R. P. M. A., Kraus, R. H. S., Elmberg, Johan, Söderquist, Pär, Gunnarsson, Gunnar, Thulin, Carl-Gustaf, Champagnon, Jocelyn, Guillemain, Matthieu, Kreisinger, Jakub, Prins, H. H. T., Crooijmans, R. P. M. A., and Kraus, R. H. S.
- Abstract
The practice of restocking already viable populations to increase harvest potential has since long been common in forestry, fisheries and wildlife management. The potential risks of restocking native species have long been overshadowed by the related issue of invasive alien species. However, during the last decade releases of native species with potentially non-native genome have received more attention. A suitable model to study genetic effects of large-scale releases of native species is the Mallard Anas platyrhynchos, being the most widespread duck in the world, largely migratory, and an important quarry species. More than 3 million unfledged hatchlings are released each year around Europe to increase local harvest. The aims of this study were to determine if wild and released farmed Mallards differ genetically, if there are signs of previous or ongoing introgression between wild and farmed birds, and if the genetic structure of the wild Mallard population has changed since large-scale releases started in Europe in the 1970s. Using 360 Single Nucleotide Polymorphisms (SNPs) we found that the genetic structure differed among historical wild, present-day wild, and farmed Mallards in Europe. We also found signs of introgression in the wild Mallard population, that is, individuals with a genetic background of farmed stock are part of the present free-living population. Although only a small proportion of the released Mallards appears to survive to merge with the free-living breeding population, their numbers are still so large that the genetic impact may have significance for the wild population in terms of individual survival and longterm fitness.
- Published
- 2016
39. Marine stepping-stones: Connectivity of Mytilus edulis populations between offshore energy installations.
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Coolen JWP, Boon AR, Crooijmans R, van Pelt H, Kleissen F, Gerla D, Beermann J, Birchenough SNR, Becking LE, and Luttikhuizen PC
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- Animals, North Sea, Aquatic Organisms growth & development, Genetics, Population, Marine Biology, Mytilus edulis growth & development
- Abstract
Recent papers have suggested that epifaunal organisms use artificial structures as stepping-stones to spread to areas that are too distant to reach in a single generation. With thousands of artificial structures present in the North Sea, we test the hypothesis that these structures are connected by water currents and act as an interconnected reef. Population genetic structure of the blue mussel, Mytilus edulis, was expected to follow a pattern predicted by a particle tracking model (PTM). Correlation between population genetic differentiation, based on microsatellite markers, and particle exchange was tested. Specimens of M. edulis were found at each location, although the PTM indicated that locations >85 km offshore were isolated from coastal subpopulations. The fixation coefficient F
ST correlated with the number of arrivals in the PTM. However, the number of effective migrants per generation as inferred from coalescent simulations did not show a strong correlation with the arriving particles. Isolation by distance analysis showed no increase in isolation with increasing distance and we did not find clear structure among the populations. The marine stepping-stone effect is obviously important for the distribution of M. edulis in the North Sea and it may influence ecologically comparable species in a similar way. In the absence of artificial shallow hard substrates, M. edulis would be unlikely to survive in offshore North Sea waters., (© 2020 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)- Published
- 2020
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40. CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes.
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da Silva V, Ramos M, Groenen M, Crooijmans R, Johansson A, Regitano L, Coutinho L, Zimmer R, Waldron L, and Geistlinger L
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- Computational Biology, Phenotype, Polymorphism, Single Nucleotide, DNA Copy Number Variations, Genome-Wide Association Study
- Abstract
Summary: Copy number variation (CNV) is a major type of structural genomic variation that is increasingly studied across different species for association with diseases and production traits. Established protocols for experimental detection and computational inference of CNVs from SNP array and next-generation sequencing data are available. We present the CNVRanger R/Bioconductor package which implements a comprehensive toolbox for structured downstream analysis of CNVs. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and genome-wide association analysis with gene expression and quantitative phenotypes., Availability and Implementation: http://bioconductor.org/packages/CNVRanger., (© The Author(s) 2019. Published by Oxford University Press.)
- Published
- 2020
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41. Genetic diversity, population structure and origin of the native goats in Central Laos.
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Le SV, de Las Heras-Saldana S, Alexandri P, Olmo L, Walkden-Brown SW, and van der Werf JHJ
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- Animals, Laos, Genetics, Population, Inbreeding, Polymorphism, Single Nucleotide, Breeding, Goats genetics, Goats classification, Genetic Variation
- Abstract
Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (F
ST : 0.011-0.043) and negligible inbreeding coefficients (FIS : -0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92-6.85 Mb, with short ROH segments (1-5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20-40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features., (© 2024 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd.)- Published
- 2024
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42. Freigelassenes Federwild führt zu kontinent-weiter genetischer Introgression : die sich ändernde genetische Landschaft der Stockente (Anas platyrhynchos) in Europa
- Author
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Kraus, R. H. S., Söderquist, Pär, Gunnarsson, Gunnar, Thulin, C.-G., Champagnon, Jocelyn, Guillemain, Matthieu, Kreisinger, Jakub, Prins, H. H. T., Crooijmans, R. P. M. A., Elmberg, Johan, Kraus, R. H. S., Söderquist, Pär, Gunnarsson, Gunnar, Thulin, C.-G., Champagnon, Jocelyn, Guillemain, Matthieu, Kreisinger, Jakub, Prins, H. H. T., Crooijmans, R. P. M. A., and Elmberg, Johan
- Published
- 2015
43. Released game birds cause introgression in European mallard
- Author
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Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, Carl-Gustaf, Champagnon, Jocelyn, Guillemain, Matthieu, Kreisinger, Jakub, Prins, Herbert, Crooijmans, R, Kraus, Robert, Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, Carl-Gustaf, Champagnon, Jocelyn, Guillemain, Matthieu, Kreisinger, Jakub, Prins, Herbert, Crooijmans, R, and Kraus, Robert
- Abstract
The practice of restocking already viable populations to improve harvest has since long been common in forestry, fisheries and wildlife management. The potential risks with restocking of native species has for a long time been overshadowed by the related issue of invasive species. However, during the last decade releases of native species with a potential non-native genome have attained more attention. A suitable model species for studying genetic effects of large-scale releases of a native species is the Mallard, Anas platyrhynchos; it is the most widespread duck in the world, it is a migrating species, and an important game bird. In several European countries it is also farmed and released to increase the harvestable population, and more than 3 million unfledged hatchlings are released each year around Europe. The aims of this study were to determine if wild and released farmed Mallards differed genetically among subpopulations in Europe, if there are signs of previous or ongoing introgression between wild and farmed Mallards, and if the genetic structure of the wild Mallard population has changed since large-scale releases started in the 1970s. We used 360 Single Nucleotide Polymorphisms (SNPs) to analyze the genetic structure of historical wild, present-day wild, and farmed Mallards. We found a clear genetic difference between wild and farmed Mallards in Europe. We also found signs of introgression of farmed genes in the wild Mallard population, however, the rate of hybridization is probably minor due to low survival of released farmed Mallards and a change of the wild population since the start of large-scale releases is therefore limited. A low level of hybridization between farmed and wild Mallard is desired as introgressed genes may be detrimental for wild Mallards, and efforts to increase survival of farmed Mallards should therefore not be encouraged.
- Published
- 2015
44. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.
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Frantz LAF, Haile J, Lin AT, Scheu A, Geörg C, Benecke N, Alexander M, Linderholm A, Mullin VE, Daly KG, Battista VM, Price M, Gron KJ, Alexandri P, Arbogast RM, Arbuckle B, Bӑlӑşescu A, Barnett R, Bartosiewicz L, Baryshnikov G, Bonsall C, Borić D, Boroneanţ A, Bulatović J, Çakirlar C, Carretero JM, Chapman J, Church M, Crooijmans R, De Cupere B, Detry C, Dimitrijevic V, Dumitraşcu V, du Plessis L, Edwards CJ, Erek CM, Erim-Özdoğan A, Ervynck A, Fulgione D, Gligor M, Götherström A, Gourichon L, Groenen MAM, Helmer D, Hongo H, Horwitz LK, Irving-Pease EK, Lebrasseur O, Lesur J, Malone C, Manaseryan N, Marciniak A, Martlew H, Mashkour M, Matthews R, Matuzeviciute GM, Maziar S, Meijaard E, McGovern T, Megens HJ, Miller R, Mohaseb AF, Orschiedt J, Orton D, Papathanasiou A, Pearson MP, Pinhasi R, Radmanović D, Ricaut FX, Richards M, Sabin R, Sarti L, Schier W, Sheikhi S, Stephan E, Stewart JR, Stoddart S, Tagliacozzo A, Tasić N, Trantalidou K, Tresset A, Valdiosera C, van den Hurk Y, Van Poucke S, Vigne JD, Yanevich A, Zeeb-Lanz A, Triantafyllidis A, Gilbert MTP, Schibler J, Rowley-Conwy P, Zeder M, Peters J, Cucchi T, Bradley DG, Dobney K, Burger J, Evin A, Girdland-Flink L, and Larson G
- Subjects
- Animals, Europe, History, Ancient, Middle East, Skin Pigmentation genetics, DNA, Ancient, DNA, Mitochondrial genetics, Domestication, Gene Flow, Phylogeny, Swine genetics
- Abstract
Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)
- Published
- 2019
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45. Genetic consequences of breaking migratory traditions in barnacle geese Branta leucopsis.
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Jonker, R. M., Kraus, R. H. S., Zhang, Q., Hooft, P., Larsson, K., Jeugd, H. P., Kurvers, R. H. J. M., Wieren, S. E., Loonen, M. J. J. E., Crooijmans, R. P. M. A., Ydenberg, R. C., Groenen, M. A. M., and Prins, H. H. T.
- Subjects
BARNACLE goose ,ANIMAL genetics ,SINGLE nucleotide polymorphisms ,BIOMARKERS ,PRINCIPAL components analysis - Abstract
Cultural transmission of migratory traditions enables species to deal with their environment based on experiences from earlier generations. Also, it allows a more adequate and rapid response to rapidly changing environments. When individuals break with their migratory traditions, new population structures can emerge that may affect gene flow. Recently, the migratory traditions of the Barnacle Goose Branta leucopsis changed, and new populations differing in migratory distance emerged. Here, we investigate the population genetic structure of the Barnacle Goose to evaluate the consequences of altered migratory traditions. We used a set of 358 single nucleotide polymorphism ( SNP) markers to genotype 418 individuals from breeding populations in Greenland, Spitsbergen, Russia, Sweden and the Netherlands, the latter two being newly emerged populations. We used discriminant analysis of principal components, F
ST , linkage disequilibrium and a comparison of geneflow models using migrate- n to show that there is significant population structure, but that relatively many pairs of SNPs are in linkage disequilibrium, suggesting recent admixture between these populations. Despite the assumed traditions of migration within populations, we also show that genetic exchange occurs between all populations. The newly established nonmigratory population in the Netherlands is characterized by high emigration into other populations, which suggests more exploratory behaviour, possibly as a result of shortened parental care. These results suggest that migratory traditions in populations are subject to change in geese and that such changes have population genetic consequences. We argue that the emergence of nonmigration probably resulted from developmental plasticity. [ABSTRACT FROM AUTHOR]- Published
- 2013
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46. Production of a comparative physical genome map of the turkey (Meleagris gallopavo)
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Robertson, L. B., Tempest, H. G., Patel, A. P., Alain Vignal, Valerie Fillon, Crooijmans, R. P. M. A., Groenen, M. A. M., Hillier, L. W., Morrice, D. R., Speed, D., Bentley, J., Masabanda, J. S., Burt, D. W., Griffin, D. K., Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Inconnu, and ProdInra, Migration
- Subjects
[SDV] Life Sciences [q-bio] ,HYSICAL MAPS ,COMPARATIVE MAPPING ,[SDV]Life Sciences [q-bio] ,TURKEYS ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2005
47. The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird.
- Author
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Spurgin LG, Bosse M, Adriaensen F, Albayrak T, Barboutis C, Belda E, Bushuev A, Cecere JG, Charmantier A, Cichon M, Dingemanse NJ, Doligez B, Eeva T, Erikstad KE, Fedorov V, Griggio M, Heylen D, Hille S, Hinde CA, Ivankina E, Kempenaers B, Kerimov A, Krist M, Kvist L, Laine VN, Mänd R, Matthysen E, Nager R, Nikolov BP, Norte AC, Orell M, Ouyang J, Petrova-Dinkova G, Richner H, Rubolini D, Slagsvold T, Tilgar V, Török J, Tschirren B, Vágási CI, Yuta T, Groenen MAM, Visser ME, van Oers K, Sheldon BC, and Slate J
- Subjects
- Animals, Genetics, Population methods, Europe, Passeriformes genetics, Passeriformes classification, Haplotypes genetics, Recombination, Genetic, Selection, Genetic, Genetic Variation, Polymorphism, Single Nucleotide, Songbirds genetics, Songbirds classification
- Abstract
A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (F
ST ), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics., (© 2024 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)- Published
- 2024
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48. Natural selection on feralization genes contributed to the invasive spread of wild pigs throughout the United States.
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Barmentlo NWG, Meirmans PG, Stiver WH, Yarkovich JG, McCann BE, Piaggio AJ, Wright D, Smyser TJ, and Bosse M
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- Animals, United States, Genotype, Hybridization, Genetic, Swine genetics, Animals, Wild genetics, Genetic Variation, Selection, Genetic, Introduced Species, Polymorphism, Single Nucleotide genetics, Sus scrofa genetics, Genetics, Population
- Abstract
Despite a long presence in the contiguous United States (US), the distribution of invasive wild pigs (Sus scrofa × domesticus) has expanded rapidly since the 1980s, suggesting a more recent evolutionary shift towards greater invasiveness. Contemporary populations of wild pigs represent exoferal hybrid descendants of domestic pigs and European wild boar, with such hybridization expected to enrich genetic diversity and increase the adaptive potential of populations. Our objective was to characterize how genetic enrichment through hybridization increases the invasiveness of populations by identifying signals of selection and the ancestral origins of selected loci. Our study focused on invasive wild pigs within Great Smoky Mountains National Park, which represents a hybrid population descendent from the admixture of established populations of feral pigs and an introduction of European wild boar to North America. Accordingly, we genotyped 881 wild pigs with multiple high-density single-nucleotide polymorphism (SNP) arrays. We found 233 markers under putative selection spread over 79 regions across 16 out of 18 autosomes, which contained genes involved in traits affecting feralization. Among these, genes were found to be related to skull formation and neurogenesis, with two genes, TYRP1 and TYR, also encoding for crucial melanogenesis enzymes. The most common haplotypes associated with regions under selection for the Great Smoky Mountains population were also common among other populations throughout the region, indicating a key role of putatively selective variants in the fitness of invasive populations. Interestingly, many of these haplotypes were absent among European wild boar reference genotypes, indicating feralization through genetic adaptation., (© 2024 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)
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- 2024
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49. How structural variants shape avian phenotypes: Lessons from model systems.
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Recuerda M and Campagna L
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- Animals, Birds genetics, Genomic Structural Variation, INDEL Mutation, Phenotype, Chickens genetics
- Abstract
Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although recent advances in long-read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review the role of SVs in shaping phenotypes in avian model systems, and identify some general patterns in SV type, length and their associated traits. We found that most of the avian SVs so far identified are short indels in chickens, which are frequently associated with changes in body weight and plumage colouration. Overall, we found that relatively short SVs are more frequently detected, likely due to a combination of their prevalence compared to large SVs, and a detection bias, stemming primarily from the widespread use of short-read sequencing and associated analytical methods. SVs most commonly involve non-coding regions, especially introns, and when patterns of inheritance were reported, SVs associated primarily with dominant discrete traits. We summarise several examples of phenotypic convergence across different species, mediated by different SVs in the same or different genes and different types of changes in the same gene that can lead to various phenotypes. Complex rearrangements and supergenes, which can simultaneously affect and link several genes, tend to have pleiotropic phenotypic effects. Additionally, SVs commonly co-occur with single-nucleotide polymorphisms, highlighting the need to consider all types of genetic changes to understand the basis of phenotypic traits. We end by summarising expectations for when long-read technologies become commonly implemented in non-model birds, likely leading to an increase in SV discovery and characterisation. The growing interest in this subject suggests an increase in our understanding of the phenotypic effects of SVs in upcoming years., (© 2024 John Wiley & Sons Ltd.)
- Published
- 2024
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50. Status of the chicken radiation hybrid map
- Author
-
Mireille Morisson, Frédérique Pitel, Sophie Leroux, Denis, M., Denis Milan, Jennen, D. G. J., Crooijmans, R. P. M. A., Morrice, D., Burt, D. W., Groenen, M. A. M., Alain Vignal, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and ProdInra, Migration
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2004
Catalog
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