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Ahozonlin MC, Dossa LH, Dahouda M, Gbangboche AB. Morphological divergence in the West African shorthorn Lagune cattle populations from Benin. Trop Anim Health Prod 2019; 52:803-814. [PMID: 31617051 DOI: 10.1007/s11250-019-02071-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/06/2019] [Indexed: 11/27/2022]
Abstract
This study explored the potential role of agro-ecology in shaping the morphology of Lagune cattle population of Benin. A total of 708 adult Lagune cattle were sampled randomly from nine provenances in two agro-ecological zones (AEZs) and were assessed for eight qualitative and twelve linear body measurements. Data were analyzed using generalized linear model procedures (PROC GLM) followed by the multiple comparison of least square means (LSMEAN) according to the Tukey-Kramer method and multivariate analytical methods, including canonical discrimination analysis (CDA) and hierarchical ascendant classification. Irrespective of AEZ and sex, the body length (102.3 ± 9.31 cm) was greater than the wither height (93.1 ± 7.39 cm) and the body index smaller than 0.85. However, there were significant differences between the two AEZs for most of the measured morphometric and qualitative traits. Moreover, a male-biased sexual size dimorphism was recorded. The CDA based on only four basic body measurements (rump height, body length, heart girth, and ear length) and the calculated Mahalanobis distances suggest that the populations from the two AEZs are distinct and could be further considered ecotypes. Nevertheless, the overall moderate classification rate (70%) of the individual animals into their group of origin indicates interbreeding between the two populations. The pairwise Mahalanobis distances between provenances in the same AEZ were also significant. Together, these results provide supporting evidence for the existence of subdivisions in the Lagune cattle populations from South Benin. The high morphological diversity in the Lagune cattle recorded in the present study could serve as a starting point for the development of efficient selection and sound subpopulation management strategies but also for further phenotypic and genetic characterizations.
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Affiliation(s)
- Maurice Cossi Ahozonlin
- Ecole des Sciences et Techniques de Production Animale, Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, 03 Boîte Postale 2819 Jericho, Cotonou, Benin
| | - Luc Hippolyte Dossa
- Ecole des Sciences et Techniques de Production Animale, Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, 03 Boîte Postale 2819 Jericho, Cotonou, Benin.
| | - Mahamadou Dahouda
- Ecole des Sciences et Techniques de Production Animale, Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, 03 Boîte Postale 2819 Jericho, Cotonou, Benin
| | - Armand Bienvenu Gbangboche
- Ecole de Gestion et d'Exploitation des Systèmes d'Elevage, Université Nationale d'Agriculture, Boîte Postale 43, Kétou, Benin
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52
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System-Level Testing and Evaluation Plan for Field Robots: A Tutorial with Test Course Layouts. ROBOTICS 2019. [DOI: 10.3390/robotics8040083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Field robotics is a very important sub-field of robotic systems, focusing on systems which need to navigate in open, unpredictable terrain and perform non-repetitive missions while monitoring and reacting to their surroundings. General testing and validation standards for larger robotic systems, including field robots, have not been developed yet due to a variety of factors including disagreement over terminology and functional/performance requirements. This tutorial presents a generalized, step-by-step system-level test plan for field robots under manual, semi-autonomous/tele-operated, and autonomous control schemes; this includes a discussion of the requirements and testing parameters, and a set of suggested safety, communications, and behavior evaluation test courses. The testing plan presented here is relevant to both commercial and academic research into field robotics, providing a standardized general testing procedure.
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Siripan S, Wonnapinij P, Auetrakulvit P, Wangthongchaicharoen N, Surat W. Origin of prehistoric cattle excavated from four archaeological sites in central and northeastern Thailand. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:609-617. [PMID: 30957607 DOI: 10.1080/24701394.2019.1597072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cattle have been domesticated in Southeast Asia, including Thailand, for thousands of years, but the history of cattle domestication in the region remains unclear. To date, only genetic studies of modern Thai cattle DNA have been reported. To gain some insight into cattle domestication in the country, a total of 56 cattle remains excavated from four archaeological sites (dated to between 3550 and 1700 years before present (YBP)) in northeastern and central Thailand were analysed in this study. Of 56, the 157-bp D-loop fragment was successfully generated from 26 samples, all of which belonged to Bos taurus in haplogroup T/T3. One haplotype contained 19 members from all four archaeological sites and clustered with the ancient B. taurus from Iran, Turkey and China. Other haplotypes have not shared haplotype with B. taurus from other countries but they showed close relationship to those from China. This represents the first genetic evidence that B. taurus was domesticated in Thailand between 3550 and 1700 YBP. In addition, the close relationship among ancient Thai, Iranian and Chinese taurines suggests that cattle from the Near East were introduced into North China, and were subsequently brought into Thailand thousands of years ago.
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Affiliation(s)
- Sirianong Siripan
- a Department of Genetics, Faculty of Science, Evolutionary Genetics and Computational Biology Research Unit , Kasetsart University , Bangkok , Thailand
| | - Passorn Wonnapinij
- a Department of Genetics, Faculty of Science, Evolutionary Genetics and Computational Biology Research Unit , Kasetsart University , Bangkok , Thailand.,b Centre for Advanced Studies in Tropical Natural Resources , National Research University-Kasetsart University, Kasetsart University (CASTNAR, NRU-KU) , Bangkok , Thailand
| | - Prasit Auetrakulvit
- c Department of Archaeology, Faculty of Archaeology , Silpakorn University , Bangkok , Thailand
| | | | - Wunrada Surat
- a Department of Genetics, Faculty of Science, Evolutionary Genetics and Computational Biology Research Unit , Kasetsart University , Bangkok , Thailand.,b Centre for Advanced Studies in Tropical Natural Resources , National Research University-Kasetsart University, Kasetsart University (CASTNAR, NRU-KU) , Bangkok , Thailand
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54
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Pitt D, Bruford MW, Barbato M, Orozco‐terWengel P, Martínez R, Sevane N. Demography and rapid local adaptation shape Creole cattle genome diversity in the tropics. Evol Appl 2019; 12:105-122. [PMID: 30622639 PMCID: PMC6304683 DOI: 10.1111/eva.12641] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 02/06/2023] Open
Abstract
The introduction of Iberian cattle in the Americas after Columbus' arrival imposed high selection pressures on a limited number of animals over a brief period of time. Knowledge of the genomic regions selected during this process may help in enhancing climatic resilience and sustainable animal production. We first determined taurine and indicine contributions to the genomic structure of modern Creole cattle. Second, we inferred their demographic history using approximate Bayesian computation (ABC), linkage disequilibrium (LD) and N e Slope (NeS) analysis. Third, we performed whole genome scans for selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) and population differentiation (F ST) to disentangle the genetic mechanisms involved in adaptation and phenotypic change by a rapid and major environmental transition. To tackle these questions, we combined SNP array data (~54,000 SNPs) in Creole breeds with their modern putative Iberian ancestors. Reconstruction of the population history of Creoles from the end of the 15th century indicated a major demographic expansion until the introduction of zebu and commercial breeds into the Americas ~180 years ago, coinciding with a drastic N e contraction. NeS analysis provided insights into short-term complexity in population change and depicted a decrease/expansion episode at the end of the ABC-inferred expansion, as well as several additional fluctuations in N e with the attainment of the current small N e only towards the end of the 20th century. Selection signatures for tropical adaptation pinpointed the thermoregulatory slick hair coat region, identifying a new candidate gene (GDNF), as well as novel candidate regions involved in immune function, behavioural processes, iron metabolism and adaptation to new feeding conditions. The outcomes from this study will help in future-proofing farm animal genetic resources (FAnGR) by providing molecular tools that allow selection for improved cattle performance, resilience and welfare under climate change.
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Affiliation(s)
- Daniel Pitt
- School of BiosciencesCardiff UniversityCardiffUK
| | - Michael W. Bruford
- School of BiosciencesCardiff UniversityCardiffUK
- Sustainable Places Research InstituteCardiff UniversityCardiffUK
| | - Mario Barbato
- Institute of ZootechnicsUniversità Cattolica del Sacro CuorePiacenzaItaly
| | | | - Rodrigo Martínez
- Centro de investigaciones TibaitatáCorporación Colombiana De Investigación Agropecuaria (Corpoica)BogotáColombia
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Cai Y, Jiao T, Lei Z, Liu L, Zhao S. Maternal genetic and phylogenetic characteristics of domesticated cattle in northwestern China. PLoS One 2018; 13:e0209645. [PMID: 30589861 PMCID: PMC6307701 DOI: 10.1371/journal.pone.0209645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 12/10/2018] [Indexed: 11/19/2022] Open
Abstract
Northwestern China, an important part of the Silk Road, was the birthplace of the Zhouzu farming culture. The domestication of cattle as an important aspect of farming culture has had a long history in northwestern China. In this study, we assessed the maternal structure and phylogeny of cattle by analyzing the mitochondrial DNA hypervariable segment I (HVS-I) in 698 native cattle from eight areas of northwestern China. The phylogenetic analyses revealed two highly divergent mtDNA clades: clade T, which had four sub-clades (Ta—Td), and clade I. The cattle domesticated from Bos taurus showed a clear dominant distribution pattern in northwestern China. The nucleotide diversity of the Bos indicus clade was lower than that of clades from Bos taurus. In summary, our results suggest that the native cattle of northwestern China were domesticated from two different maternal ancestors, Bos taurus and Bos indicus, which migrated to the central plains of China from the north and south, respectively, with Bos taurus remaining at the edges of the region. The population expansion of the cattle domesticated from Bos taurus occurred in the Longdong region of Gansu Province, and these cattle formed four relatively independent evolutionary branches. Subsequent to this expansion event, Bos indicus migrated from southern to northern China.
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Affiliation(s)
- Yuan Cai
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, PR China
| | - Ting Jiao
- College of Grassland, Gansu Agricultural University, Lanzhou, Gansu, PR China
| | - Zhaomin Lei
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, PR China
| | - Li Liu
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, PR China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, PR China
- * E-mail:
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56
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Valverde A, Areán H, Fernández A, Bompart D, García-Molina A, López-Viana J, Soler C. Combined effect of type and capture area of counting chamber and diluent on Holstein bull sperm kinematics. Andrologia 2018; 51:e13223. [PMID: 30588646 DOI: 10.1111/and.13223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 11/28/2022] Open
Abstract
The evaluation of sperm motion is crucial for processing of seminal doses for artificial insemination. Here, the combined effect of the type and capture area of three counting chambers, together with the type of diluent employed, on sperm motility was analysed. Ejaculates from thirteen Holstein bulls were used for sperm kinematic analysis with the ISAS® v1 CASA-Mot system, using two capillary-loaded counting chambers (Leja® and Cell-Vu® ) and one drop displacement chamber (Makler® ). Nine fixed positions were analysed per chamber type, considering central and lateral and three longitudinal fields. Independent of the diluent used, differences were found between the three chambers. Independent of the extender, no differences in x-axis were observed with Cell-Vu® , while using Leja® , some parameters showed lower values in the centre than in lateral areas. In both counting chambers, the lowest values were observed in the distal area. Results obtained with the two diluents were highly different with a very low correlation between them. In conclusion, the capture area inside the chambers leads to significant changes in sperm kinematic parameters and different dilution media introduce considerable differences in the motility patterns. It is necessary to optimise sampling methods and specific set-ups to be used with CASA-Mot technology.
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Affiliation(s)
- Anthony Valverde
- Costa Rica Institute of Technology, School of Agronomy, Alajuela, Costa Rica.,Departament de Biologia Cellular, Biologia Funcional i Antropologia Física, Universitat de València, Burjassot, Spain
| | | | | | - Daznia Bompart
- R+D Department, Projectes i Serveis R+D, S.L., Science Park of the València University, Paterna, Spain
| | - Almudena García-Molina
- R+D Department, Projectes i Serveis R+D, S.L., Science Park of the València University, Paterna, Spain
| | | | - Carles Soler
- Departament de Biologia Cellular, Biologia Funcional i Antropologia Física, Universitat de València, Burjassot, Spain.,R+D Department, Projectes i Serveis R+D, S.L., Science Park of the València University, Paterna, Spain
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57
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Sermyagin AA, Dotsev AV, Gladyr EA, Traspov AA, Deniskova TE, Kostyunina OV, Reyer H, Wimmers K, Barbato M, Paronyan IA, Plemyashov KV, Sölkner J, Popov RG, Brem G, Zinovieva NA. Whole-genome SNP analysis elucidates the genetic structure of Russian cattle and its relationship with Eurasian taurine breeds. Genet Sel Evol 2018; 50:37. [PMID: 29996786 PMCID: PMC6042431 DOI: 10.1186/s12711-018-0408-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/01/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The origin of native and locally developed Russian cattle breeds is linked to the historical, social, cultural, and climatic features of the diverse geographical regions of Russia. In the present study, we investigated the population structure of nine Russian cattle breeds and their relations to the cattle breeds from around the world to elucidate their origin. Genotyping of single nucleotide polymorphisms (SNPs) in Bestuzhev (n = 26), Russian Black-and-White (n = 21), Kalmyk (n = 14), Kholmogor (n = 25), Kostromsky (n = 20), Red Gorbatov (n = 23), Suksun (n = 20), Yakut (n = 25), and Yaroslavl cattle breeds (n = 21) was done using the Bovine SNP50 BeadChip. SNP profiles from an additional 70 breeds were included in the analysis as references. RESULTS The observed heterozygosity levels were quite similar in eight of the nine studied breeds (HO = 0.337-0.363) except for Yakut (Ho = 0.279). The inbreeding coefficients FIS ranged from -0.028 for Kalmyk to 0.036 for Russian Black-and-White and were comparable to those of the European breeds. The nine studied Russian breeds exhibited taurine ancestry along the C1 axis of the multidimensional scaling (MDS)-plot, but Yakut was clearly separated from the European taurine breeds on the C2 axis. Neighbor-Net and admixture analyses, discriminated three groups among the studied Russian breeds. Yakut and Kalmyk were assigned to a separate group because of their Turano-Mongolian origin. Russian Black-and-White, Kostromsky and Suksun showed transboundary European ancestry, which originated from the Holstein, Brown Swiss, and Danish Red breeds, respectively. The lowest level of introgression of transboundary breeds was recorded for the Kholmogor, Yaroslavl, Red Gorbatov and Bestuzhev breeds, which can be considered as an authentic genetic resource. CONCLUSIONS Whole-genome SNP analysis revealed that Russian native and locally developed breeds have conserved authentic genetic patterns in spite of the considerable influence of Eurasian taurine cattle. In this paper, we provide fundamental genomic information that will contribute to the development of more accurate breed conservation programs and genetic improvement strategies.
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Affiliation(s)
- Alexander A Sermyagin
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Elena A Gladyr
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Alexey A Traspov
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Olga V Kostyunina
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Mecklenburg-Vorpommern, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Mecklenburg-Vorpommern, Germany
| | - Mario Barbato
- Department of Animal Sciences, Food and Nutrition, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, Piacenza, Italy
| | - Ivan A Paronyan
- Russian Research Institute of Farm Animal Genetics and Breeding, Moskovskoe shosse 55a, St. Petersburg-Pushkin, Russia, 196601
| | - Kirill V Plemyashov
- Russian Research Institute of Farm Animal Genetics and Breeding, Moskovskoe shosse 55a, St. Petersburg-Pushkin, Russia, 196601
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Ruslan G Popov
- Yakut Scientific Research Institute of Agriculture, 23/1, ul. Bestuzheva-Marlynskogo, Yakutsk, Sakha Republic, Russia, 677001
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132.
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58
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Mastrangelo S, Ciani E, Ajmone Marsan P, Bagnato A, Battaglini L, Bozzi R, Carta A, Catillo G, Cassandro M, Casu S, Ciampolini R, Crepaldi P, D'Andrea M, Di Gerlando R, Fontanesi L, Longeri M, Macciotta NP, Mantovani R, Marletta D, Matassino D, Mele M, Pagnacco G, Pieramati C, Portolano B, Sarti FM, Tolone M, Pilla F. Conservation status and historical relatedness of Italian cattle breeds. Genet Sel Evol 2018; 50:35. [PMID: 29940848 PMCID: PMC6019226 DOI: 10.1186/s12711-018-0406-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 06/11/2018] [Indexed: 01/30/2023] Open
Abstract
Background In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. Results After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding. Conclusions This study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource. Electronic supplementary material The online version of this article (10.1186/s12711-018-0406-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy.
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, 70124, Bari, Italy
| | | | - Alessandro Bagnato
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | - Luca Battaglini
- Dipartimento di Scienze Agrarie Forestali e Alimentari, University of Torino, 10095, Grugliasco, Italy
| | - Riccardo Bozzi
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, University of Firenze, 50144, Florence, Italy
| | - Antonello Carta
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, 07100, Sassari, Italy
| | - Gennaro Catillo
- CREA Research Centre for Animal Production and Acquaculture, CREA, 00015, Monterotondo, Italy
| | - Martino Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020, Legnaro, Italy
| | - Sara Casu
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, 07100, Sassari, Italy
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie, University of Pisa, 56100, Pisa, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | | | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Luca Fontanesi
- Dipartimento di Scienze e tecnologie Agroalimentari, University of Bologna, 40127, Bologna, Italy
| | - Maria Longeri
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | | | - Roberto Mantovani
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020, Legnaro, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione, Ambiente, University of Catania, 95125, Catania, Italy
| | - Donato Matassino
- Divulgazione e Applicazione di Biotecniche Innovative, Consorzio per la Sperimentazione, 82100, Benevento, Italy
| | - Marcello Mele
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, 56124, Pisa, Italy
| | - Giulio Pagnacco
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | - Camillo Pieramati
- Dipartimento di Medicina Veterinaria, University of Perugia, 06126, Perugia, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Francesca M Sarti
- Dipartimento di Scienze Agrarie, Alimentari, Ambientali, University of Perugia, 06121, Perugia, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, University of Molise, 86100, Campobasso, Italy.,Centro Risorse Bio-Culturali e Sviluppo Locale, University of Molise, 86100, Campobasso, Italy
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Eusebi PG, Cortés O, Carleos C, Dunner S, Cañon J. Detection of selection signatures for agonistic behaviour in cattle. J Anim Breed Genet 2018; 135:170-177. [PMID: 29700853 DOI: 10.1111/jbg.12325] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/20/2018] [Indexed: 02/04/2023]
Abstract
The identification of genomic regions including signatures of selection produced by domestication and its subsequent artificial selection processes allows the understanding of the evolution of bovine breeds. Although several studies describe the genomic variability among meat or milk production cattle breeds, there are limited studies orientated towards bovine behavioural features. This study is focused on mapping genomic signatures of selection which may provide insights of differentiation between neutral and selected polymorphisms. Their effects are studied in the Lidia cattle traditionally selected for agonistic behaviour compared with Spanish breeds showing tamed behaviour. Two different approaches, BayeScan and SelEstim, were applied using genotypic 50K SNP BeadChip data. Both procedures detected two genomic regions bearing genes previously related to behavioural traits. The frequencies of the selected allele in these two regions in Lidia breed were opposite to those found in the tamed breeds. In these genomic regions, several putative genes associated with enriched metabolic pathways related to the behavioural development were identified, as neurochondrin gene (NCDN) or glutamate ionotropic receptor kainate type subunit 3 (GRIK3) both located at BTA3 or leucine-rich repeat and Ig domain containing 2 (LINGO2) and phospholipase A2-activating protein (PLAA) at BTA8.
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Affiliation(s)
- P G Eusebi
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - O Cortés
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - C Carleos
- Departamento de Estadística e Investigación Operativa, Universidad de Oviedo, Oviedo, Spain
| | - S Dunner
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - J Cañon
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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61
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Species composition and environmental adaptation of indigenous Chinese cattle. Sci Rep 2017; 7:16196. [PMID: 29170422 PMCID: PMC5700937 DOI: 10.1038/s41598-017-16438-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/13/2017] [Indexed: 12/13/2022] Open
Abstract
Indigenous Chinese cattle combine taurine and indicine origins and occupy a broad range of different environments. By 50 K SNP genotyping we found a discontinuous distribution of taurine and indicine cattle ancestries with extremes of less than 10% indicine cattle in the north and more than 90% in the far south and southwest China. Model-based clustering and f4-statistics indicate introgression of both banteng and gayal into southern Chinese cattle while the sporadic yak influence in cattle in or near Tibetan area validate earlier findings of mitochondrial DNA analysis. Geographic patterns of taurine and indicine mitochondrial and Y-chromosomal DNA diversity largely agree with the autosomal cline. The geographic distribution of the genomic admixture of different bovine species is proposed to be the combined effect of prehistoric immigrations, gene flow, major rivers acting as genetic barriers, local breeding objectives and environmental adaptation. Whole-genome scan for genetic differentiation and association analyses with both environmental and morphological covariables are remarkably consistent with previous studies and identify a number of genes implicated in adaptation, which include TNFRSF19, RFX4, SP4 and several coat color genes. We propose indigenous Chinese cattle as a unique and informative resource for gene-level studies of climate adaptation in mammals.
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62
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Affiliation(s)
- Antonella Dalle Zotte
- Department of Animal Medicine, Production and Health, University of Padova, Agripolis, Viale dell'Università 16, 35020 Legnaro, Padova, Italy
| | - Alberto Brugiapaglia
- Department of Agricultural, Forest and Food Sciences, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Torino, Italy
| | - Marco Cullere
- Department of Animal Medicine, Production and Health, University of Padova, Agripolis, Viale dell'Università 16, 35020 Legnaro, Padova, Italy
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63
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González-Rodríguez A, Munilla S, Mouresan EF, Cañas-Álvarez JJ, Díaz C, Piedrafita J, Altarriba J, Baro JÁ, Molina A, Varona L. On the performance of tests for the detection of signatures of selection: a case study with the Spanish autochthonous beef cattle populations. Genet Sel Evol 2016; 48:81. [PMID: 27793093 PMCID: PMC5084421 DOI: 10.1186/s12711-016-0258-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 10/18/2016] [Indexed: 01/05/2023] Open
Abstract
Background Procedures for the detection of signatures of selection can be classified according to the source of information they use to reject the null hypothesis of absence of selection. Three main groups of tests can be identified that are based on: (1) the analysis of the site frequency spectrum, (2) the study of the extension of the linkage disequilibrium across the length of the haplotypes that surround the polymorphism, and (3) the differentiation among populations. The aim of this study was to compare the performance of a subset of these procedures by using a dataset on seven Spanish autochthonous beef cattle populations. Results Analysis of the correlations between the logarithms of the statistics that were obtained by 11 tests for detecting signatures of selection at each single nucleotide polymorphism confirmed that they can be clustered into the three main groups mentioned above. A factor analysis summarized the results of the 11 tests into three canonical axes that were each associated with one of the three groups. Moreover, the signatures of selection identified with the first and second groups of tests were shared across populations, whereas those with the third group were more breed-specific. Nevertheless, an enrichment analysis identified the metabolic pathways that were associated with each group; they coincided with canonical axes and were related to immune response, muscle development, protein biosynthesis, skin and pigmentation, glucose metabolism, fat metabolism, embryogenesis and morphology, heart and uterine metabolism, regulation of the hypothalamic–pituitary–thyroid axis, hormonal, cellular cycle, cell signaling and extracellular receptors. Conclusions We show that the results of the procedures used to identify signals of selection differed substantially between the three groups of tests. However, they can be classified using a factor analysis. Moreover, each canonical factor that coincided with a group of tests identified different signals of selection, which could be attributed to processes of selection that occurred at different evolutionary times. Nevertheless, the metabolic pathways that were associated with each group of tests were similar, which suggests that the selection events that occurred during the evolutionary history of the populations probably affected the same group of traits. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0258-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Sebastián Munilla
- Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain.,Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, 1417, Buenos Aires, Argentina
| | - Elena F Mouresan
- Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain
| | - Jhon J Cañas-Álvarez
- Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Clara Díaz
- Departamento de Mejora Genética Animal, INIA, 28040, Madrid, Spain
| | - Jesús Piedrafita
- Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Juan Altarriba
- Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain.,Instituto Agroalimentario de Aragón (IA2), 50013, Saragossa, Spain
| | - Jesús Á Baro
- Departamento de Ciencias Agroforestales, Universidad de Valladolid, 34004, Palencia, Spain
| | | | - Luis Varona
- Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain. .,Instituto Agroalimentario de Aragón (IA2), 50013, Saragossa, Spain.
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64
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Upadhyay MR, Chen W, Lenstra JA, Goderie CRJ, MacHugh DE, Park SDE, Magee DA, Matassino D, Ciani F, Megens HJ, van Arendonk JAM, Groenen MAM. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle. Heredity (Edinb) 2016; 118:169-176. [PMID: 27677498 PMCID: PMC5234481 DOI: 10.1038/hdy.2016.79] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 01/10/2023] Open
Abstract
The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations.
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Affiliation(s)
- M R Upadhyay
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands.,Department of Animal Breeding and Genetics, Swedish Institute of Agricultural Sciences, Uppsala, Sweden
| | - W Chen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, CM Utrecht, The Netherlands
| | | | - D E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - S D E Park
- IdentiGEN Ltd, Unit 2, Trinity Enterprise Centre, Dublin 2, Ireland
| | - D A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - D Matassino
- Consortium for Experimentation, Dissemination and application of Innovative Biotechniques, ConSDABI NFP, I FAO-GS AnGR, Benevento, Italy
| | - F Ciani
- Consortium for Experimentation, Dissemination and application of Innovative Biotechniques, ConSDABI NFP, I FAO-GS AnGR, Benevento, Italy
| | - H-J Megens
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - J A M van Arendonk
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - M A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
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65
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Di Lorenzo P, Lancioni H, Ceccobelli S, Curcio L, Panella F, Lasagna E. Uniparental genetic systems: a male and a female perspective in the domestic cattle origin and evolution. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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66
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Boitard S, Rodríguez W, Jay F, Mona S, Austerlitz F. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach. PLoS Genet 2016; 12:e1005877. [PMID: 26943927 PMCID: PMC4778914 DOI: 10.1371/journal.pgen.1005877] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 01/27/2016] [Indexed: 12/02/2022] Open
Abstract
Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles. Molecular data sampled from extant individuals contains considerable information about their demographic history. In particular, one classical question in population genetics is to reconstruct past population size changes from such data. Relating these changes to various climatic, geological or anthropogenic events allows characterizing the main factors driving genetic diversity and can have major outcomes for conservation. Until recently, mostly very simple histories, including one or two population size changes, could be estimated from genetic data. This has changed with the sequencing of entire genomes in many species, and several methods allow now inferring complex histories consisting of several tens of population size changes. However, analyzing entire genomes, while accounting for recombination, remains a statistical and numerical challenge. These methods, therefore, can only be applied to small samples with a few diploid genomes. We overcome this limitation by using an approximate estimation approach, where observed genomes are summarized using a small number of statistics related to allele frequencies and linkage disequilibrium. In contrast to previous approaches, we show that our method allows us to reconstruct also the most recent part (the last 100 generations) of the population size history. As an illustration, we apply it to large samples of whole-genome sequences in four cattle breeds.
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Affiliation(s)
- Simon Boitard
- Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - CNRS & MNHN & UPMC & EPHE, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- * E-mail:
| | - Willy Rodríguez
- UMR CNRS 5219, Institut de Mathématiques de Toulouse, Université de Toulouse, Toulouse, France
| | - Flora Jay
- UMR 7206 Eco-anthropologie et Ethnobiologie, Muséum National d’Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France
- LRI, Paris-Sud University, CNRS UMR 8623, Orsay, France
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - CNRS & MNHN & UPMC & EPHE, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
| | - Frédéric Austerlitz
- UMR 7206 Eco-anthropologie et Ethnobiologie, Muséum National d’Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France
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67
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68
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Wang MD, Dzama K, Rees DJG, Muchadeyi FC. Tropically adapted cattle of Africa: perspectives on potential role of copy number variations. Anim Genet 2015; 47:154-64. [DOI: 10.1111/age.12391] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2015] [Indexed: 12/12/2022]
Affiliation(s)
- M. D. Wang
- Department of Animal Sciences; University of Stellenbosch; Private Bag X1 Matieland 7602 South Africa
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
| | - K. Dzama
- Department of Animal Sciences; University of Stellenbosch; Private Bag X1 Matieland 7602 South Africa
| | - D. J. G. Rees
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
| | - F. C. Muchadeyi
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
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69
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Berthier D, Brenière SF, Bras-Gonçalves R, Lemesre JL, Jamonneau V, Solano P, Lejon V, Thévenon S, Bucheton B. Tolerance to Trypanosomatids: A Threat, or a Key for Disease Elimination? Trends Parasitol 2015; 32:157-168. [PMID: 26643519 DOI: 10.1016/j.pt.2015.11.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/20/2015] [Accepted: 11/03/2015] [Indexed: 12/20/2022]
Abstract
So far, research on trypanosomatid infections has been driven by 'disease by disease' approaches, leading to different concepts and control strategies. It is, however, increasingly clear that they share common features such as the ability to generate long-lasting asymptomatic infections in their mammalian hosts. Trypanotolerance, long integrated in animal African trypanosomiasis control, historically refers to the ability of cattle breeds to limit Trypanosoma infection and pathology, but has only recently been recognized in humans. Whilst trypanotolerance is absent from the vocabulary on leishmaniasis and Chagas disease, asymptomatic infections also occur. We review the concept of trypanotolerance across the trypanosomatids and discuss the importance of asymptomatic carriage in the current context of elimination.
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Affiliation(s)
| | | | | | | | - Vincent Jamonneau
- CIRDES Bobo-Dioulasso 01 BP 454, Burkina Faso; IPR, 01 BP 1500 Bouaké 01, Côte d'Ivoire
| | | | - Veerle Lejon
- IRD, UMR INTERTRYP, Montpellier Cedex 5, 34398 France
| | | | - Bruno Bucheton
- IRD, UMR INTERTRYP, Montpellier Cedex 5, 34398 France; PNLTHA, Ministère de la Santé, BP 851 Conakry, République de Guinée
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70
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The indigenous Somba cattle of the hilly Atacora region in North-West Benin: threats and opportunities for its sustainable use. Trop Anim Health Prod 2015; 48:349-59. [DOI: 10.1007/s11250-015-0958-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/11/2015] [Indexed: 10/22/2022]
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71
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Williams JL, Hall SJ, Del Corvo M, Ballingall KT, Colli L, Ajmone Marsan P, Biscarini F. Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non-random SNP heterozygosity. Anim Genet 2015; 47:19-27. [DOI: 10.1111/age.12376] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2015] [Indexed: 11/29/2022]
Affiliation(s)
- J. L. Williams
- PTP Science Park; Via Einstein - Loc. Cascina Codazza 26900 Lodi Italy
| | - S. J.G. Hall
- School of Life Sciences; University of Lincoln; Brayford Pool Lincoln LN6 7TS UK
| | - M. Del Corvo
- PTP Science Park; Via Einstein - Loc. Cascina Codazza 26900 Lodi Italy
| | - K. T. Ballingall
- Moredun Research Institute; Pentlands Science Park; Bush Loan Penicuik Midlothian EH26 0PZ UK
| | - L. Colli
- Università Cattolica del Sacro Cuore; via Emilia Parmense 84 29122 Piacenza Italy
| | - P. Ajmone Marsan
- Università Cattolica del Sacro Cuore; via Emilia Parmense 84 29122 Piacenza Italy
| | - F. Biscarini
- PTP Science Park; Via Einstein - Loc. Cascina Codazza 26900 Lodi Italy
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72
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Orozco-terWengel P, Barbato M, Nicolazzi E, Biscarini F, Milanesi M, Davies W, Williams D, Stella A, Ajmone-Marsan P, Bruford MW. Revisiting demographic processes in cattle with genome-wide population genetic analysis. Front Genet 2015; 6:191. [PMID: 26082794 PMCID: PMC4451420 DOI: 10.3389/fgene.2015.00191] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/12/2015] [Indexed: 11/23/2022] Open
Abstract
The domestication of the aurochs took place approximately 10,000 years ago giving rise to the two main types of domestic cattle known today, taurine (Bos taurus) domesticated somewhere on or near the Fertile Crescent, and indicine (Bos indicus) domesticated in the Indus Valley. However, although cattle have historically played a prominent role in human society the exact origin of many extant breeds is not well known. Here we used a combination of medium and high-density Illumina Bovine SNP arrays (i.e., ~54,000 and ~770,000 SNPs, respectively), genotyped for over 1300 animals representing 56 cattle breeds, to describe the relationships among major European cattle breeds and detect patterns of admixture among them. Our results suggest modern cross-breeding and ancient hybridisation events have both played an important role, including with animals of indicine origin. We use these data to identify signatures of selection reflecting both domestication (hypothesized to produce a common signature across breeds) and local adaptation (predicted to exhibit a signature of selection unique to a single breed or group of related breeds with a common history) to uncover additional demographic complexity of modern European cattle.
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Affiliation(s)
| | - Mario Barbato
- School of Biosciences, Cardiff University Cardiff, UK
| | | | | | - Marco Milanesi
- Faculty of Agriculture, Università Cattolica del Sacro Cuore Piacenza, Italy
| | | | | | | | - Paolo Ajmone-Marsan
- Faculty of Agriculture, Università Cattolica del Sacro Cuore Piacenza, Italy
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73
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Gargani M, Pariset L, Lenstra JA, De Minicis E, Valentini A. Microsatellite genotyping of medieval cattle from central Italy suggests an old origin of Chianina and Romagnola cattle. Front Genet 2015; 6:68. [PMID: 25788902 PMCID: PMC4349168 DOI: 10.3389/fgene.2015.00068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/10/2015] [Indexed: 12/02/2022] Open
Abstract
Analysis of DNA from archeological remains is a valuable tool to interpret the history of ancient animal populations. So far most studies of ancient DNA target mitochondrial DNA (mtDNA), which reveals maternal lineages, but only partially the relationships of current breeds and ancient populations. In this study we explore the feasibility of nuclear DNA analysis. DNA was extracted from 1000-years old cattle bone collected from Ferento, an archeological site in central Italy. Amplification of 15 microsatellite FAO-recommended markers with PCR products yielded genotypes for four markers. Expected heterozygosity was comparable with values of modern breeds, but observed heterozygosity was underestimated due to allelic loss. Genetic distances suggested a position intermediate between (1) Anatolian, Balkan, Sicilian and South-Italian cattle and (2) the Iberian, North-European and Central-European cattle, but also a clear relationship with two central-Italian breeds, Chianina and Romagnola. This suggests that these breeds are derived from medieval cattle living in the same area. Our results illustrate the potential of ancient DNA for reconstructing the history of local cattle husbandry.
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Affiliation(s)
- Maria Gargani
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia Viterbo, Italy
| | - Lorraine Pariset
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia Viterbo, Italy
| | | | - Elisabetta De Minicis
- Department of Sciences of Cultural Heritage (DISBEC), University of Tuscia Viterbo, Italy
| | | | - Alessio Valentini
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia Viterbo, Italy
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