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Pokharel K, Weldenegodguad M, Dudeck S, Honkatukia M, Lindeberg H, Mazzullo N, Paasivaara A, Peippo J, Soppela P, Stammler F, Kantanen J. Whole-genome sequencing provides novel insights into the evolutionary history and genetic adaptation of reindeer populations in northern Eurasia. Sci Rep 2023; 13:23019. [PMID: 38155192 PMCID: PMC10754820 DOI: 10.1038/s41598-023-50253-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023] Open
Abstract
Domestic reindeer (Rangifer tarandus) play a vital role in the culture and livelihoods of indigenous people across northern Eurasia. These animals are well adapted to harsh environmental conditions, such as extreme cold, limited feed availability and long migration distances. Therefore, understanding the genomics of reindeer is crucial for improving their management, conservation and utilisation. In this study, we have generated a new genome assembly for the Fennoscandian domestic reindeer with high contiguity, making it the most complete reference genome for reindeer to date. The new genome assembly was utilised to explore genetic diversity, population structure and selective sweeps in Eurasian Rangifer tarandus populations which was based on the largest population genomic dataset for reindeer, encompassing 58 individuals from diverse populations. Phylogenetic analyses revealed distinct genetic clusters, with the Finnish wild forest reindeer (Rangifer tarandus fennicus) standing out as a unique subspecies. Divergence time estimates suggested a separation of ~ 52 thousand years ago (Kya) between the northern European Rangifer tarandus fennicus and Rangifer tarandus tarandus. Our study identified four main genetic clusters: Fennoscandian, the eastern/northern Russian and Alaskan group, the Finnish forest reindeer, and the Svalbard reindeer. Furthermore, two independent reindeer domestication processes were inferred, suggesting separate origins for the domestic Fennoscandian and eastern/northern Russian reindeer. Notably, shared genes under selection, including retroviral genes, point towards molecular domestication processes that aided adaptation of this species to diverse environments.
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Affiliation(s)
- Kisun Pokharel
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Melak Weldenegodguad
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Stephan Dudeck
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | | | - Heli Lindeberg
- Natural Resources Institute Finland (Luke), 71750, Maaninka, Finland
| | - Nuccio Mazzullo
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | - Antti Paasivaara
- Natural Resources Institute Finland (Luke), Paavo Havaksentie 3, 90570, Oulu, Finland
| | - Jaana Peippo
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
- NordGen-Nordic Genetic Resource Center, 1432, Ås, Norway
| | - Päivi Soppela
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | | | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland.
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2
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Marzanov NS, Devrishov DA, Ozerov MY, Maluchenko OP, Marzanova SN, Shukurova EB, Koreckaya EA, Kantanen J, Petit D. The Significance of a Multilocus Analysis for Assessing the Biodiversity of the Romanov Sheep Breed in a Comparative Aspect. Animals (Basel) 2023; 13:ani13081320. [PMID: 37106883 PMCID: PMC10135317 DOI: 10.3390/ani13081320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The Romanov breed was evaluated using immunological and genetic markers. The seven blood group systems were characterized with a greater accuracy than in previous works on sheep in the Russian Federation, and were compared to eight ruminant species. Unlike other breeds, Romanov sheep shows a higher frequency of HBA than HBB alleles. There are 3-4 genotypes at the transferrin locus whereas in other breeds 6-11 genotypes have been found. At the albumin locus, the majority of the identified genotypes were heterozygotes, unlike in the other breeds studied. In the prealbumin locus, the Romanov breed was the only one where all the genotypes were heterozygous. We speculate that polymorphism at two loci (BMP-15 and BMPR1B) could effect on the high ovulation rates of Romanov sheep. Based on different genetic markers, the prevalence of heterozygotes in the Romanov sheep could determine their higher viability. A cluster analysis showed the close proximity of 12 populations of the Romanov breed, as the breeding stock come from the Yaroslavl region.
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Affiliation(s)
- Nurbiy S Marzanov
- Center for Animal Husbandry Named after Academy Member L.K. Ernst, Podolsk-Dubrovitsy, 60, Moscow Region 142132, Russia
| | - Davud A Devrishov
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after K.I. Skryabin, Federal State Budgetary Educational Institution of Higher Education, ul. Akademika Skryabina, 23, Moscow 109472, Russia
| | | | - Oleg P Maluchenko
- State Scientific Institution All-Russian Scientific Research Institute of Agricultural Biotechnology, UL Timiriazevskaya, 42, Moscow 127550, Russia
| | - Saida N Marzanova
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after K.I. Skryabin, Federal State Budgetary Educational Institution of Higher Education, ul. Akademika Skryabina, 23, Moscow 109472, Russia
| | - Elena B Shukurova
- Federal State Budgetary Institution "Far Eastern Scientific Research Institute of Agriculture", s. Vostochnoe, UL Clubnaya, 13, Khabarovsk 680521, Russia
| | - Elena A Koreckaya
- Tver State Agricultural Academy, Federal State Budgetary Educational Institution of Higher Education, UL Marshala Vasilevskogo, 7, Sakharovo, Tver 170904, Russia
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Daniel Petit
- LABCiS, University of Limoges, UR 22722, F-87000 Limoges, France
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3
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Rannamäe E, Saarma U, Kantanen J, Bläuer A. Maternal genetic diversity of ancient goats in Finland and Estonia and comparison with extant northern European goat breeds. Anim Genet 2023; 54:177-188. [PMID: 36514938 DOI: 10.1111/age.13281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/24/2022] [Accepted: 11/24/2022] [Indexed: 12/15/2022]
Abstract
Countries in the northern Baltic Sea region have been historically linked for thousands of years, and animal husbandry is one of the many information sources that enables the study of historical connections. Although goat husbandry in this part of Europe has been evidenced by scant archaeological materials, zooarchaeological and historical evidence has revealed its continuity, at least since the Late Iron Age. To explore the historical relationship between goat lineages and investigate affinities between the past and present-day populations in the Baltic Sea region, we analysed a 476-bp fragment of the mitochondrial DNA control region in 14 ancient goats from Finland and Estonia and 10 extant goats from Finland. The results revealed high mitochondrial diversity among the ancient goats. Two maternal lineages were shared between the Late Iron Age and medieval individuals from Finland and Estonia. Moreover, ancient Finnish and Estonian goats showed maternal affinity to extant Finngoat and Swedish Landrace breeds. Overall, the analysis of maternal goat lineages confirmed tight historical connections in the region.
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Affiliation(s)
- Eve Rannamäe
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu, Estonia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Juha Kantanen
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Auli Bläuer
- Archaeology, University of Turku, Turku, Finland
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Strandén I, Kantanen J, Lidauer MH, Mehtiö T, Negussie E. Animal board invited review: Genomic-based improvement of cattle in response to climate change. Animal 2022; 16:100673. [PMID: 36402112 DOI: 10.1016/j.animal.2022.100673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 12/24/2022] Open
Abstract
Climate change brings challenges to cattle production, such as the need to adapt to new climates and pressure to reduce greenhouse emissions (GHG). In general, the improvement of traits in current breeding goals is favourably correlated with the reduction of GHG. Current breeding goals and tools for increasing cattle production efficiency have reduced GHG. The same amount of production can be achieved by a much smaller number of animals. Genomic selection (GS) may offer a cost-effective way of using an efficient breeding approach, even in low- and middle-income countries. As climate change increases the intensity of heatwaves, adaptation to heat stress leads to lower efficiency of production and, thus, is unfavourable to the goal of reducing GHG. Furthermore, there is evidence that heat stress during cow pregnancy can have many generation-long lowering effects on milk production. Both adaptation and reduction of GHG are among the difficult-to-measure traits for which GS is more efficient and suitable than the traditional non-genomic breeding evaluation approach. Nevertheless, the commonly used within-breed selection may be insufficient to meet the new challenges; thus, cross-breeding based on selecting highly efficient and highly adaptive breeds may be needed. Genomic introgression offers an efficient approach for cross-breeding that is expected to provide high genetic progress with a low rate of inbreeding. However, well-adapted breeds may have a small number of animals, which is a source of concern from a genetic biodiversity point of view. Furthermore, low animal numbers also limit the efficiency of genomic introgression. Sustainable cattle production in countries that have already intensified production is likely to emphasise better health, reproduction, feed efficiency, heat stress and other adaptation traits instead of higher production. This may require the application of innovative technologies for phenotyping and further use of new big data techniques to extract information for breeding.
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Affiliation(s)
- I Strandén
- Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland.
| | - J Kantanen
- Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - M H Lidauer
- Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - T Mehtiö
- Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - E Negussie
- Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
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Carrier A, Prunier J, Poisson W, Trottier-Lavoie M, Gilbert I, Cavedon M, Pokharel K, Kantanen J, Musiani M, Côté SD, Albert V, Taillon J, Bourret V, Droit A, Robert C. Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus). BMC Genomics 2022; 23:687. [PMID: 36199020 PMCID: PMC9533608 DOI: 10.1186/s12864-022-08899-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Development of large single nucleotide polymorphism (SNP) arrays can make genomic data promptly available for conservation problematic. Medium and high-density panels can be designed with sufficient coverage to offer a genome-wide perspective and the generated genotypes can be used to assess different genetic metrics related to population structure, relatedness, or inbreeding. SNP genotyping could also permit sexing samples with unknown associated metadata as it is often the case when using non-invasive sampling methods favored for endangered species. Genome sequencing of wild species provides the necessary information to design such SNP arrays. We report here the development of a SNP-array for endangered Rangifer tarandus using a multi-platform sequencing approach from animals found in diverse populations representing the entire circumpolar distribution of the species. RESULTS From a very large comprehensive catalog of SNPs detected over the entire sample set (N = 894), a total of 63,336 SNPs were selected. SNP selection accounted for SNPs evenly distributed across the entire genome (~ every 50Kb) with known minor alleles across populations world-wide. In addition, a subset of SNPs was selected to represent rare and local alleles found in Eastern Canada which could be used for ecotype and population assignments - information urgently needed for conservation planning. In addition, heterozygosity from SNPs located in the X-chromosome and genotyping call-rate of SNPs located into the SRY gene of the Y-chromosome yielded an accurate and robust sexing assessment. All SNPs were validated using a high-throughput SNP-genotyping chip. CONCLUSION This design is now integrated into the first genome-wide commercially available genotyping platform for Rangifer tarandus. This platform would pave the way to future genomic investigation of populations for this endangered species, including estimation of genetic diversity parameters, population assignments, as well as animal sexing from genetic SNP data for non-invasive samples.
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Affiliation(s)
- Alexandra Carrier
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Julien Prunier
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Quebec City, Québec, Canada
| | - William Poisson
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Mallorie Trottier-Lavoie
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Isabelle Gilbert
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Maria Cavedon
- Department of biological sciences, Faculty of Science, University of Calgary, Calgary, Canada
| | | | - Juha Kantanen
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Marco Musiani
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Steeve D Côté
- Département de biologie - Faculté de sciences et génie, Caribou Ungava, Université Laval, Quebec City, Québec, Canada
| | - Vicky Albert
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Quebec City, Québec, Canada
| | - Joëlle Taillon
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Quebec City, Québec, Canada
| | - Vincent Bourret
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Quebec City, Québec, Canada
| | - Arnaud Droit
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Quebec City, Québec, Canada
| | - Claude Robert
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada. .,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada. .,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada.
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6
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Drzaic I, Curik I, Lukic B, Shihabi M, Li MH, Kantanen J, Mastrangelo S, Ciani E, Lenstra JA, Cubric-Curik V. High-Density Genomic Characterization of Native Croatian Sheep Breeds. Front Genet 2022; 13:940736. [PMID: 35910220 PMCID: PMC9337876 DOI: 10.3389/fgene.2022.940736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
A recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Balkan sheep populations have considerable genetic overlap but are distinctly different from surrounding breeds. All eight Croatian sheep breeds were represented by a small number of individuals per breed. Here, we genotyped 220 individuals representing the native Croatian sheep breeds (Istrian Sheep, Krk Island Sheep, Cres Island Sheep, Rab Island Sheep, Lika Pramenka, Pag Island Sheep, Dalmatian Pramenka, Dubrovnik Sheep) and mouflon using the Ovine Infinium® HD SNP BeadChip (606,006 SNPs). In addition, we included publicly available Balkan Pramenka and other Mediterranean sheep breeds. Our analyses revealed the complex population structure of Croatian sheep breeds and their origin and geographic barriers (island versus mainland). Migration patterns confirmed the historical establishment of breeds and the pathways of gene flow. Inbreeding coefficients (FROH>2 Mb) between sheep populations ranged from 0.025 to 0.070, with lower inbreeding coefficients observed in Dalmatian Pramenka and Pag Island Sheep and higher inbreeding in Dubrovnik sheep. The estimated effective population size ranged from 61 to 1039 for Krk Island Sheep and Dalmatian Pramenka, respectively. Higher inbreeding levels and lower effective population size indicate the need for improved conservation management to maintain genetic diversity in some breeds. Our results will contribute to breeding and conservation strategies of native Croatian sheep breeds.
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Affiliation(s)
- Ivana Drzaic
- Department of Animal Science, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
- *Correspondence: Ivana Drzaic, ; Vlatka Cubric-Curik,
| | - Ino Curik
- Department of Animal Science, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
| | - Boris Lukic
- Department of Animal Production and Biotechnology, Faculty of Agrobiotechnical Sciences Osijek, Chair for Domestic Animal Breeding and Genetics, J. J. Strossmayer University of Osijek, Osijek, Croatia
| | - Mario Shihabi
- Department of Animal Science, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Universita Degli Studi di Bari “Aldo Moro”, Bari, Italy
| | | | - Vlatka Cubric-Curik
- Department of Animal Science, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
- *Correspondence: Ivana Drzaic, ; Vlatka Cubric-Curik,
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Consortium VG, Nijman IJ, Rosen BD, Bardou P, Faraut T, Cumer T, Daly KG, Zheng Z, Cai Y, Asadollahpour H, Kul BÇ, Zhang WY, Guangxin E, Ayin A, Baird H, Bakhtin M, Bâlteanu VA, Barfield D, Berger B, Blichfeldt T, Boink G, Bugiwati SRA, Cai Z, Carolan S, Clark E, Cubric-Curik V, Dagong MIA, Dorji T, Drew L, Guo J, Hallsson J, Horvat S, Kantanen J, Kawaguchi F, Kazymbet P, Khayatzadeh N, Kim N, Shah MK, Liao Y, Martínez A, Masangkay JS, Masaoka M, Mazza R, McEwan J, Milanesi M, Faruque MO, Nomura Y, Ouchene-Khelifi NA, Pereira F, Sahana G, Salavati M, Sasazaki S, Da Silva A, Simčič M, Sölkner J, Sutherland A, Tigchelaar J, Zhang H, Consortium E, Ajmone-Marsan P, Bradley DG, Colli L, Drögemüller C, Jiang Y, Lei C, Mannen H, Pompanon F, Tosser-Klopp G, Lenstra JA. Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions. Mol Ecol 2022; 31:4364-4380. [PMID: 35751552 DOI: 10.1111/mec.16579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/12/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022]
Abstract
By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and 7 wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during the migrations into northern Europe, eastern and southern Asia and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographic range.
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Affiliation(s)
| | - Isaäc J Nijman
- Utrecht Univ., Netherlands.,Univ. Medical Center Utrecht, Utrecht Univ, The Netherlands
| | | | - Philippe Bardou
- GenPhySE, Univ. Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Thomas Faraut
- GenPhySE, Univ. Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Tristan Cumer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | | | - Zhuqing Zheng
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | - Yudong Cai
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | | | | | | | | | | | - Hayley Baird
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | - Valentin A Bâlteanu
- Inst. of Life SciencesUniv. Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | | | - Beate Berger
- Univ. Natural Resources and Life Sciences Vienna (BOKU)
| | - Thor Blichfeldt
- Norwegian Association of Sheep and Goat Breeders, Aas, Norway
| | - Geert Boink
- Stichting Zeldzame Huisdierrassen, Wageningen, The Netherlands
| | | | | | | | | | | | | | - Tashi Dorji
- International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | | | | | | | - Simon Horvat
- Univ. Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | | | | | | | - Namshin Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | | | - Yuying Liao
- Guangxi Key Laboratory of Livestock Genetic Improvement, Guangxi, China
| | | | | | | | - Raffaele Mazza
- Laboratorio Genetica e Servizi, Agrotis srl, Cremona, Italy
| | - John McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | | | | | | | - Filipe Pereira
- IDENTIFICA Genetic Testing Maia & Centre for Functional Ecology, Porto, Portugal
| | | | | | | | | | - Mojca Simčič
- Univ. Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | | | | | | | | | | | - Paolo Ajmone-Marsan
- Univ. Cattolica del S. Cuore di Piacenza and BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy.,UCSC PRONUTRIGEN Nutrigenomics Res. Centre, Piacenza, Italy
| | | | - Licia Colli
- Univ. Cattolica del S. Cuore di Piacenza and BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy.,UCSC BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy
| | | | - Yu Jiang
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | - Chuzhao Lei
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | | | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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8
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Ang L, Vinderola G, Endo A, Kantanen J, Jingfeng C, Binetti A, Burns P, Qingmiao S, Suying D, Zujiang Y, Rios-Covian D, Mantziari A, Beasley S, Gomez-Gallego C, Gueimonde M, Salminen S. Gut Microbiome Characteristics in feral and domesticated horses from different geographic locations. Commun Biol 2022; 5:172. [PMID: 35217713 PMCID: PMC8881449 DOI: 10.1038/s42003-022-03116-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/01/2022] [Indexed: 12/12/2022] Open
Abstract
Domesticated horses live under different conditions compared with their extinct wild ancestors. While housed, medicated and kept on a restricted source of feed, the microbiota of domesticated horses is hypothesized to be altered. We assessed the fecal microbiome of 57 domestic and feral horses from different locations on three continents, observing geographical differences. A higher abundance of eukaryota (p < 0.05) and viruses (p < 0.05) and lower of archaea (p < 0.05) were found in feral animals when compared with domestic ones. The abundance of genes coding for microbe-produced enzymes involved in the metabolism of carbohydrates was significantly higher (p < 0.05) in feral animals regardless of the geographic origin. Differences in the fecal resistomes between both groups of animals were also noted. The domestic/captive horse microbiomes were enriched in genes conferring resistance to tetracycline, likely reflecting the use of this antibiotic in the management of these animals. Our data showed an impoverishment of the fecal microbiome in domestic horses with diet, antibiotic exposure and hygiene being likely drivers. The results offer a view of the intestinal microbiome of horses and the impact of domestication or captivity, which may uncover novel targets for modulating the microbiome of horses to enhance animal health and well-being. Li Ang et al. present an investigation of feral and domesticated horse gut microbiomes across three continents. Their results provide new insight into how changes in horse lifestyle are reflected in the resident gut microbiome.
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Affiliation(s)
- Li Ang
- Health Management Centre, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Henan Gene Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Infection Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Gabriel Vinderola
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland, Jokioinen, Finland
| | - Chen Jingfeng
- Health Management Centre, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ana Binetti
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Patricia Burns
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Shi Qingmiao
- Department of Henan Gene Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Infection Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ding Suying
- Health Management Centre, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Zujiang
- Department of Henan Gene Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Infection Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - David Rios-Covian
- Department and Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Asturias, Spain
| | - Anastasia Mantziari
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Shea Beasley
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Carlos Gomez-Gallego
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland.,Institute of Public Health and Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Miguel Gueimonde
- Department and Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Asturias, Spain.
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland.
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9
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Lv FH, Cao YH, Liu GJ, Luo LY, Lu R, Liu MJ, Li WR, Zhou P, Wang XH, Shen M, Gao L, Yang JQ, Yang H, Yang YL, Liu CB, Wan PC, Zhang YS, Pi WH, Ren YL, Shen ZQ, Wang F, Wang YT, Li JQ, Salehian-Dehkordi H, Hehua E, Liu YG, Chen JF, Wang JK, Deng XM, Esmailizadeh A, Dehghani-Qanatqestani M, Charati H, Nosrati M, Štěpánek O, Rushdi HE, Olsaker I, Curik I, Gorkhali NA, Paiva SR, Caetano AR, Ciani E, Amills M, Weimann C, Erhardt G, Amane A, Mwacharo JM, Han JL, Hanotte O, Periasamy K, Johansson AM, Hallsson JH, Kantanen J, Coltman DW, Bruford MW, Lenstra JA, Li MH. Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci. Mol Biol Evol 2021; 39:6459180. [PMID: 34893856 PMCID: PMC8826587 DOI: 10.1093/molbev/msab353] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3′-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.
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Affiliation(s)
- Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yin-Hong Cao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | | | - Ling-Yun Luo
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ran Lu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Xin-Hua Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Yong-Lin Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Chang-Bin Liu
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Peng-Cheng Wan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Yun-Sheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Wen-Hui Pi
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Yu-Tao Wang
- College of Life and Geographic Sciences, Kashi University, Kashi, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Eer Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Jian-Fei Chen
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Kui Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xue-Mei Deng
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Hadi Charati
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Ondřej Štěpánek
- Department of Virology, State Veterinary Institute Jihlava, Jihlava, Czech Republic
| | - Hossam E Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Ingrid Olsaker
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Neena A Gorkhali
- Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council (NARC), Kathmandu, Nepal
| | - Samuel R Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, DF, Brazil
| | - Alexandre R Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, DF, Brazil
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo 24 Moro, Bari, Italy
| | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
- Department of Animal Sciences, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Christina Weimann
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Georg Erhardt
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Agraw Amane
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
- CTLGH and SRUC, The Roslin Institute Building, Easter Bush Campus, Edinburgh, Scotland
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jón H Hallsson
- Faculty of Natural Resources and Environmental Sciences, Agricultural University of Iceland, Borgarnes, Iceland
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, Wales, United Kingdom
- Sustainable Places Research Institute, Cardiff University, Wales, United Kingdom
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- Corresponding author: E-mail:
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10
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Chen ZH, Xu YX, Xie XL, Wang DF, Aguilar-Gómez D, Liu GJ, Li X, Esmailizadeh A, Rezaei V, Kantanen J, Ammosov I, Nosrati M, Periasamy K, Coltman DW, Lenstra JA, Nielsen R, Li MH. Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep. Commun Biol 2021; 4:1307. [PMID: 34795381 PMCID: PMC8602413 DOI: 10.1038/s42003-021-02817-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
The domestication and subsequent development of sheep are crucial events in the history of human civilization and the agricultural revolution. However, the impact of interspecific introgression on the genomic regions under domestication and subsequent selection remains unclear. Here, we analyze the whole genomes of domestic sheep and their wild relative species. We found introgression from wild sheep such as the snow sheep and its American relatives (bighorn and thinhorn sheep) into urial, Asiatic and European mouflons. We observed independent events of adaptive introgression from wild sheep into the Asiatic and European mouflons, as well as shared introgressed regions from both snow sheep and argali into Asiatic mouflon before or during the domestication process. We revealed European mouflons might arise through hybridization events between a now extinct sheep in Europe and feral domesticated sheep around 6000-5000 years BP. We also unveiled later introgressions from wild sheep to their sympatric domestic sheep after domestication. Several of the introgression events contain loci with candidate domestication genes (e.g., PAPPA2, NR6A1, SH3GL3, RFX3 and CAMK4), associated with morphological, immune, reproduction or production traits (wool/meat/milk). We also detected introgression events that introduced genes related to nervous response (NEURL1), neurogenesis (PRUNE2), hearing ability (USH2A), and placental viability (PAG11 and PAG3) into domestic sheep and their ancestral wild species from other wild species.
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Affiliation(s)
- Ze-Hui Chen
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China ,grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ya-Xi Xu
- grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xing-Long Xie
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Dong-Feng Wang
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Diana Aguilar-Gómez
- grid.47840.3f0000 0001 2181 7878Center for Computational Biology, University of California at Berkeley, Berkeley, CA 94720 USA
| | | | - Xin Li
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ali Esmailizadeh
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Vahideh Rezaei
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Juha Kantanen
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Innokentyi Ammosov
- grid.495192.2Laboratory of Reindeer Husbandry and Traditional Industries, Yakut Scientific Research Institute of Agriculture, The Sakha Republic (Yakutia), Yakutsk, Russia
| | - Maryam Nosrati
- grid.412462.70000 0000 8810 3346Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Kathiravan Periasamy
- grid.420221.70000 0004 0403 8399Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - David W. Coltman
- grid.17089.37Department of Biological Sciences, University of Alberta, Edmonton, AB T6G2E9 Canada
| | - Johannes A. Lenstra
- grid.5477.10000000120346234Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California at Berkeley, Berkeley, CA, 94720, USA. .,Department of Statistics, UC Berkeley, Berkeley, CA, 94707, USA. .,Globe Institute, University of Copenhagen, 1350, København K, Denmark.
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China.
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11
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Weldenegodguad M, Pokharel K, Niiranen L, Soppela P, Ammosov I, Honkatukia M, Lindeberg H, Peippo J, Reilas T, Mazzullo N, Mäkelä KA, Nyman T, Tervahauta A, Herzig KH, Stammler F, Kantanen J. Adipose gene expression profiles reveal insights into the adaptation of northern Eurasian semi-domestic reindeer (Rangifer tarandus). Commun Biol 2021; 4:1170. [PMID: 34620965 PMCID: PMC8497613 DOI: 10.1038/s42003-021-02703-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/21/2021] [Indexed: 02/08/2023] Open
Abstract
Reindeer (Rangifer tarandus) are semi-domesticated animals adapted to the challenging conditions of northern Eurasia. Adipose tissues play a crucial role in northern animals by altering gene expression in their tissues to regulate energy homoeostasis and thermogenic activity. Here, we perform transcriptome profiling by RNA sequencing of adipose tissues from three different anatomical depots: metacarpal (bone marrow), perirenal, and prescapular fat in Finnish and Even reindeer (in Sakha) during spring and winter. A total of 16,212 genes are expressed in our data. Gene expression profiles in metacarpal tissue are distinct from perirenal and prescapular adipose tissues. Notably, metacarpal adipose tissue appears to have a significant role in the regulation of the energy metabolism of reindeer in spring when their nutritional condition is poor after winter. During spring, genes associated with the immune system are upregulated in the perirenal and prescapular adipose tissue. Blood and tissue parameters reflecting general physiological and metabolic status show less seasonal variation in Even reindeer than in Finnish reindeer. This study identifies candidate genes potentially involved in immune response, fat deposition, and energy metabolism and provides new information on the mechanisms by which reindeer adapt to harsh arctic conditions.
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Affiliation(s)
- Melak Weldenegodguad
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland ,grid.9668.10000 0001 0726 2490Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Kisun Pokharel
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Laura Niiranen
- grid.10858.340000 0001 0941 4873Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Päivi Soppela
- grid.37430.330000 0001 0744 995XArctic Centre, University of Lapland, Rovaniemi, Finland
| | - Innokentyi Ammosov
- grid.495192.2Laboratory of Reindeer Husbandry and Traditional Industries, Yakut Scientific Research Institute of Agriculture, Yakutsk, The Sakha Republic (Yakutia) Russia
| | | | - Heli Lindeberg
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Maaninka, Finland
| | - Jaana Peippo
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland ,NordGen—Nordic Genetic Resource Center, Ås, Norway
| | - Tiina Reilas
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Nuccio Mazzullo
- grid.37430.330000 0001 0744 995XArctic Centre, University of Lapland, Rovaniemi, Finland
| | - Kari A. Mäkelä
- grid.10858.340000 0001 0941 4873Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Tommi Nyman
- grid.454322.60000 0004 4910 9859Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
| | - Arja Tervahauta
- grid.9668.10000 0001 0726 2490Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Karl-Heinz Herzig
- grid.10858.340000 0001 0941 4873Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland ,grid.10858.340000 0001 0941 4873Medical Research Center, Faculty of Medicine, University of Oulu, Oulu, Finland ,grid.412326.00000 0004 4685 4917Oulu University Hospital, Oulu, Finland ,grid.22254.330000 0001 2205 0971Institute of Pediatrics, Poznań University of Medical Sciences, Poznań, Poland
| | - Florian Stammler
- grid.37430.330000 0001 0744 995XArctic Centre, University of Lapland, Rovaniemi, Finland
| | - Juha Kantanen
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
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12
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Ovaska U, Bläuer A, Kroløkke C, Kjetså M, Kantanen J, Honkatukia M. The Conservation of Native Domestic Animal Breeds in Nordic Countries: From Genetic Resources to Cultural Heritage and Good Governance. Animals (Basel) 2021; 11:ani11092730. [PMID: 34573696 PMCID: PMC8464703 DOI: 10.3390/ani11092730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Native breeds are domestic animals that have adapted to local conditions. Their genetic and cultural values are high. The conservation of these breeds is maintained by national conservation programmes and agricultural support schemes in Nordic countries. In addition to financial support, the conservation of native breeds requires that their importance in society be widely understood and recognised. This is especially crucial in the local communities in which such breeds are kept. Farmers raising native breeds should be highly motivated to utilise these breeds in animal production. This article examines the extent to which farmers and stakeholders recognise the genetic and cultural significance of conservation, and how the requirements of good governance are met in current conservation arrangements. Moreover, we contemplate the potential to amalgamate the management of animal genetic resources and their cultural environment. Abstract Native breeds are domestic animal populations that have adapted to their habitats. The genetic value of breeds has been known for a long time, and recently more attention has been paid to their cultural value. Due to both ecological and cultural significance, it is important that native breeds continue to be bred in their native environments. This is supported by various financial support schemes. Support schemes rarely cover the financial gap in output compared to commercial breeds. A solution to this has been sought in special products, such as cheese or wool, and other businesses, such as animal-assisted care and tourism. Less attention has been paid to the role of administration and good governance in the maintenance of native breeds. In this study, a questionnaire was sent to all registered keepers of native breeds in Finland. This survey clarified their reasons for keeping native breeds and their ideas for improving governance structures and practices. The results were discussed in stakeholder workshops, and in a Nordic context. The results show that genetic and cultural values are recognised in several documents and programmes, but farmers need to be engaged more in the design of support schemes and practices.
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Affiliation(s)
- Ulla Ovaska
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland;
| | - Auli Bläuer
- School of History, Culture and Arts Studies, University of Turku, 20014 Turku, Finland;
| | - Charlotte Kroløkke
- Department for the Study of Culture, University of Southern Denmark, 5230 Odense, Denmark;
| | - Maria Kjetså
- Nordic Genetic Resource Center, NMBU, P.O. Box 5003, 1432 Ås, Norway;
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600 Jokioinen, Finland;
| | - Mervi Honkatukia
- Nordic Genetic Resource Center, NMBU, P.O. Box 5003, 1432 Ås, Norway;
- Correspondence:
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13
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Cao YH, Xu SS, Shen M, Chen ZH, Gao L, Lv FH, Xie XL, Wang XH, Yang H, Liu CB, Zhou P, Wan PC, Zhang YS, Yang JQ, Pi WH, Hehua EE, Berry DP, Barbato M, Esmailizadeh A, Nosrati M, Salehian-Dehkordi H, Dehghani-Qanatqestani M, Dotsev AV, Deniskova TE, Zinovieva NA, Brem G, Štěpánek O, Ciani E, Weimann C, Erhardt G, Mwacharo JM, Ahbara A, Han JL, Hanotte O, Miller JM, Sim Z, Coltman D, Kantanen J, Bruford MW, Lenstra JA, Kijas J, Li MH. Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep. Mol Biol Evol 2021; 38:838-855. [PMID: 32941615 PMCID: PMC7947771 DOI: 10.1093/molbev/msaa236] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667-248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.
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Affiliation(s)
- Yin-Hong Cao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xin-Hua Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Chang-Bin Liu
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Peng-Cheng Wan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Yun-Sheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Wen-Hui Pi
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - EEr Hehua
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Hui Autonomous Region, Yinchuan, Ningxia, China
| | - Donagh P Berry
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
| | - Mario Barbato
- Department of Animal Sciences, Food and Nutrition, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | | | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Ondřej Štěpánek
- Department of Virology, State Veterinary Institute Jihlava, Jihlava, Czech Republic
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo 24, Moro, Bari, Italy
| | - Christina Weimann
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Georg Erhardt
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Addis Abeba, Ethiopia
- Center for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Zijian Sim
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Fish and Wildlife Enforcement Branch Forensic Unit, Government of Alberta, Edmonton, AB, Canada
| | - David Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, United Kingdom
- Sustainable Places Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - James Kijas
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Brisbane, QLD, Australia
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
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14
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Deng J, Xie XL, Wang DF, Zhao C, Lv FH, Li X, Yang J, Yu JL, Shen M, Gao L, Yang JQ, Liu MJ, Li WR, Wang YT, Wang F, Li JQ, Hehua EE, Liu YG, Shen ZQ, Ren YL, Liu GJ, Chen ZH, Gorkhali NA, Rushdi HE, Salehian-Dehkordi H, Esmailizadeh A, Nosrati M, Paiva SR, Caetano AR, Štěpánek O, Olsaker I, Weimann C, Erhardt G, Curik I, Kantanen J, Mwacharo JM, Hanotte O, Bruford MW, Ciani E, Periasamy K, Amills M, Lenstra JA, Han JL, Zhang HP, Li L, Li MH. Paternal Origins and Migratory Episodes of Domestic Sheep. Curr Biol 2020; 30:4085-4095.e6. [PMID: 32822607 DOI: 10.1016/j.cub.2020.07.077] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/14/2020] [Accepted: 07/27/2020] [Indexed: 01/22/2023]
Abstract
The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred ∼11,800-9,000 years BP and ∼5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution.
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Affiliation(s)
- Juan Deng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Life Science, Hebei University, Baoding 071002, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xin Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jia-Lin Yu
- Station for Breeding and Improvement of Animal and Poultry of Changshou District, Chongqing 401220, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China; State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China; State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China; State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi 830001, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi 830001, China
| | - Yu-Tao Wang
- College of Life and Geographic Sciences, Kashi University, Kashi 844000, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010000, China
| | - EEr Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750000, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650000, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou 256600, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou 256600, China
| | - Guang-Jian Liu
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Neena A Gorkhali
- Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council (NARC), Kathmandu, Nepal
| | - Hossam E Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Samuel R Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Avenida W5 Norte (Final), Caixa Postal 02372, CEP 70770-917 Brasília, DF, Brazil
| | - Alexandre R Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Avenida W5 Norte (Final), Caixa Postal 02372, CEP 70770-917 Brasília, DF, Brazil
| | - Ondřej Štěpánek
- Department of Virology, State Veterinary Institute Jihlava, Rantirovska 93, 58601, Jihlava, Czech Republic
| | - Ingrid Olsaker
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Christina Weimann
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Georg Erhardt
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - Joram M Mwacharo
- International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia; CTLGH and SRUC, the Roslin Institute Building, Easter Bush Campus, Edinburgh EH25 9RG, UK
| | - Olivier Hanotte
- LiveGene, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia; School of Life Sciences, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff CF10 3AX, Wales, United Kingdom; Sustainable Places Research Institute, Cardiff University CF10 3BA, Wales, United Kingdom
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo 24 Moro, Bari, Italy
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Hong-Ping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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15
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Pokharel K, Peippo J, Li MH, Kantanen J. Identification and characterization of miRNAs during early pregnancy in domestic sheep. Anim Genet 2020; 51:833-836. [PMID: 32794198 PMCID: PMC7540487 DOI: 10.1111/age.12992] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/14/2022]
Abstract
MicroRNA resources in sheep are limited compared with those in other domesticated mammalian species. By sequencing small RNAs of sheep corpus luteum and endometrium, we have generated the largest amount of miRNA‐seq data and compiled the most comprehensive list thus far of miRNAs (n = 599) in sheep. Additionally, we observed a highly conserved maternally imprinted cluster of miRNAs on chromosome 18 homologous to that found on chromosome 14 in human and several other eutherian mammals.
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Affiliation(s)
- Kisun Pokharel
- Natural Resources Institute of Finland (Luke), Jokioinen, Finland
| | - Jaana Peippo
- Natural Resources Institute of Finland (Luke), Jokioinen, Finland
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Juha Kantanen
- Natural Resources Institute of Finland (Luke), Jokioinen, Finland
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16
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Li X, Yang J, Shen M, Xie XL, Liu GJ, Xu YX, Lv FH, Yang H, Yang YL, Liu CB, Zhou P, Wan PC, Zhang YS, Gao L, Yang JQ, Pi WH, Ren YL, Shen ZQ, Wang F, Deng J, Xu SS, Salehian-Dehkordi H, Hehua E, Esmailizadeh A, Dehghani-Qanatqestani M, Štěpánek O, Weimann C, Erhardt G, Amane A, Mwacharo JM, Han JL, Hanotte O, Lenstra JA, Kantanen J, Coltman DW, Kijas JW, Bruford MW, Periasamy K, Wang XH, Li MH. Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits. Nat Commun 2020; 11:2815. [PMID: 32499537 PMCID: PMC7272655 DOI: 10.1038/s41467-020-16485-1] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/04/2020] [Indexed: 01/15/2023] Open
Abstract
Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals.
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Affiliation(s)
- Xin Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Guang-Jian Liu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Ya-Xi Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Yong-Lin Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Chang-Bin Liu
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Peng-Cheng Wan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Yun-Sheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Wen-Hui Pi
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, 256600, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, 256600, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juan Deng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Eer Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Ondřej Štěpánek
- Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Christina Weimann
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen, Germany
| | - Georg Erhardt
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen, Germany
| | - Agraw Amane
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
- Center for Tropical Livestock Genetics and Health (CTLGH), the Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600, Jokioinen, Finland
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - James W Kijas
- CSIRO Livestock Industries, St Lucia, Brisbane, QLD, Australia
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, CF10 3AX, Wales, UK
- Sustainable Places Research Institute, Cardiff University, CF10 3BA, Cardiff, Wales, UK
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - Xin-Hua Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China.
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China.
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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17
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Weldenegodguad M, Pokharel K, Ming Y, Honkatukia M, Peippo J, Reilas T, Røed KH, Kantanen J. Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia. Sci Rep 2020; 10:8980. [PMID: 32488117 PMCID: PMC7265531 DOI: 10.1038/s41598-020-65487-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/05/2020] [Indexed: 12/24/2022] Open
Abstract
Reindeer are semi-domesticated ruminants that have adapted to the challenging northern Eurasian environment characterized by long winters and marked annual fluctuations in daylight. We explored the genetic makeup behind their unique characteristics by de novo sequencing the genome of a male reindeer and conducted gene family analyses with nine other mammalian species. We performed a population genomics study of 23 additional reindeer representing both domestic and wild populations and several ecotypes from various geographic locations. We assembled 2.66 Gb (N50 scaffold of 5 Mb) of the estimated 2.92 Gb reindeer genome, comprising 27,332 genes. The results from the demographic history analysis suggested marked changes in the effective population size of reindeer during the Pleistocene period. We detected 160 reindeer-specific and expanded genes, of which zinc finger proteins (n = 42) and olfactory receptors (n = 13) were the most abundant. Comparative genome analyses revealed several genes that may have promoted the adaptation of reindeer, such as those involved in recombination and speciation (PRDM9), vitamin D metabolism (TRPV5, TRPV6), retinal development (PRDM1, OPN4B), circadian rhythm (GRIA1), immunity (CXCR1, CXCR2, CXCR4, IFNW1), tolerance to cold-triggered pain (SCN11A) and antler development (SILT2). The majority of these characteristic reindeer genes have been reported for the first time here. Moreover, our population genomics analysis suggested at least two independent reindeer domestication events with genetic lineages originating from different refugial regions after the Last Glacial Maximum. Taken together, our study has provided new insights into the domestication, evolution and adaptation of reindeer and has promoted novel genomic research of reindeer.
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Affiliation(s)
- Melak Weldenegodguad
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70201, Kuopio, Finland
| | - Kisun Pokharel
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Yao Ming
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Mervi Honkatukia
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
- Nordic Genetic Resource Centre - NordGen, c/o NMBU - Biovit Box 5003, Ås, NO-1432, Norway
| | - Jaana Peippo
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Tiina Reilas
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Knut H Røed
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, P.O.Box 369 Centrum, 0102, Oslo, Norway
| | - Juha Kantanen
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland.
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18
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Pokharel K, Peippo J, Weldenegodguad M, Honkatukia M, Li MH, Kantanen J. Gene Expression Profiling of Corpus luteum Reveals Important Insights about Early Pregnancy in Domestic Sheep. Genes (Basel) 2020; 11:genes11040415. [PMID: 32290341 PMCID: PMC7231023 DOI: 10.3390/genes11040415] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 01/10/2023] Open
Abstract
The majority of pregnancy loss in ruminants occurs during the preimplantation stage, which is thus the most critical period determining reproductive success. Here, we performed a comparative transcriptome study by sequencing total mRNA from corpus luteum (CL) collected during the preimplantation stage of pregnancy in Finnsheep, Texel and F1 crosses. A total of 21,287 genes were expressed in our data. Highly expressed autosomal genes in the CL were associated with biological processes such as progesterone formation (STAR, CYP11A1, and HSD3B1) and embryo implantation (e.g., TIMP1, TIMP2 and TCTP). Among the list of differentially expressed genes, sialic acid-binding immunoglobulin (Ig)-like lectins (SIGLEC3, SIGLEC14, SIGLEC8), ribosomal proteins (RPL17, RPL34, RPS3A, MRPS33) and chemokines (CCL5, CCL24, CXCL13, CXCL9) were upregulated in Finnsheep, while four multidrug resistance-associated proteins (MRPs) were upregulated in Texel ewes. A total of 17 known genes and two uncharacterized non-coding RNAs (ncRNAs) were differentially expressed in breed-wise comparisons owing to the flushing diet effect. The significantly upregulated TXNL1 gene indicated potential for embryonic diapause in Finnsheep and F1. Moreover, we report, for the first time in any species, several genes that are active in the CL during early pregnancy (including TXNL1, SIGLEC14, SIGLEC8, MRP4, and CA5A).
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Affiliation(s)
- Kisun Pokharel
- Natural Resources, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland; (K.P.); (M.W.)
| | - Jaana Peippo
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland;
| | - Melak Weldenegodguad
- Natural Resources, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland; (K.P.); (M.W.)
| | | | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Correspondence: (M.-H.L.); (J.K.); Tel.: +358-295-326-210 (J.K.)
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland;
- Correspondence: (M.-H.L.); (J.K.); Tel.: +358-295-326-210 (J.K.)
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19
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Berres ME, Kantanen J, Honkatukia M, Wolc A, Fulton JE. Heritage Finnish Landrace chickens are genetically diverse and geographically structured. ACTA AGR SCAND A-AN 2020. [DOI: 10.1080/09064702.2020.1727561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- M. E. Berres
- Biotechnology Center, University of Wisconsin, Madison, WI, USA
| | - J. Kantanen
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - M. Honkatukia
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
- Nordic Genetic Resource Centre (NordGen), Ås, Norway
| | - A. Wolc
- Iowa State University, Ames, IA, USA
- Hy-Line International, Dallas Center, IA, USA
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20
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Omazic A, Aurosell C, Fedorov V, Hagström Å, Kantanen J, Leijon M, Mørk T, Nordtun CS, Nymo IH, Þórisson SG, Reilas T, Rockström U, Sánchez Romano J, Thorarinsdottir R, Tryland M, Johansson Wensman J, Albihn A. Seroprevalence of pestivirus in Eurasian tundra reindeer in Finland, Sweden, Norway, Iceland and Russian Federation. Infect Ecol Epidemiol 2019; 9:1682223. [PMID: 31700582 PMCID: PMC6830247 DOI: 10.1080/20008686.2019.1682223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/09/2019] [Indexed: 11/16/2022] Open
Abstract
Reindeer herding is of great importance for the indigenous people of the Fennoscandia peninsula and northern Russia. There are also free-ranging feral populations of reindeer in Finland, Iceland, Norway and Russian Federation. The genus Pestivirus contains several viral species that infect ungulates and often show capacity to transmit between different host species. Sera from 520 Eurasian tundra reindeer (Rangifer tarandus tarandus) from Finland, Sweden, Norway, Iceland and Russian Federation were analysed and the prevalence of pestivirus-specific antibodies was determined. Seropositivity proportion was 48.5% for Sweden and 41.2% for Norway, but only 1.6% for Iceland and 2.5% for Finland. All Russian reindeer investigated were seronegative. Pan-pestivirus RT-PCR of seronegative animals (n = 156) from seropositive herds confirmed their negative status. These results indicate unexpectedly non-uniform circulation of an as yet uncharacterised pestivirus in Eurasian reindeer populations. The high seroprevalence in some regions warrants further studies of pestivirus infection dynamics, effects on reindeer health and population dynamics.
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Affiliation(s)
- Anna Omazic
- National Veterinary Institute, Uppsala, Sweden
| | | | - Valery Fedorov
- Yakutian Research Institute of Agriculture, Yakutsk, Russia
| | | | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | | | - Torill Mørk
- Section for Pathology, The Norwegian Veterinary Institute, Tromsø, Norway
| | - Christine S Nordtun
- Department of Arctic and Marine Biology, Arctic Infection Biology, UiT- The Arctic University of Norway, Tromsø, Norway
| | | | | | - Tiina Reilas
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | | | - Javier Sánchez Romano
- Department of Arctic and Marine Biology, Arctic Infection Biology, UiT- The Arctic University of Norway, Tromsø, Norway
| | | | - Morten Tryland
- Department of Arctic and Marine Biology, Arctic Infection Biology, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Jonas Johansson Wensman
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ann Albihn
- National Veterinary Institute, Uppsala, Sweden.,Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
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21
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Sild E, Värv S, Kaart T, Kantanen J, Popov R, Viinalass H. Maternal and paternal genetic variation in Estonian local horse breeds in the context of geographically adjacent and distant Eurasian breeds. Anim Genet 2019; 50:757-760. [PMID: 31475379 PMCID: PMC6899971 DOI: 10.1111/age.12835] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2019] [Indexed: 11/29/2022]
Abstract
The maternal and paternal genetic variation of horse breeds from the Baltic Sea region, including three local Estonian breeds, was assessed and compared with that of Altai and Yakutian horses. In the mtDNA D‐loop region, 72 haplotypes assigned to 20 haplogroups in the nine breeds were detected. In Estonian local breeds, 38 mtDNA haplotypes were found, and five of them were shared by the three breeds. More than 60% of all identified haplotypes were rare. Compared with the Estonian Native and Estonian Heavy Draught breeds, a higher haplotypic diversity was found in the Tori breed (h = 0.969). Moreover, four haplotypes shared among Finnish and Estonian local horse breeds indicated ancient ancestry, and of these, H30 (haplogroup D3) showed global sharing and genetic links between modern Baltic Sea region and Siberian horses, specifically. The studied breed set showed high variability in maternal inheritance and mixed patterns of the international and native breeds of the Siberian and Baltic regions. No variation was found in paternally inherited markers among horse breeds in the Baltic Sea region.
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Affiliation(s)
- E Sild
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu, 51014, Estonia
| | - S Värv
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu, 51014, Estonia
| | - T Kaart
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu, 51014, Estonia
| | - J Kantanen
- Natural Resources Institute Finland (Luke), Myllytie 1, Alimentum, Jokioinen, FI-31600, Finland
| | - R Popov
- Yakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), ul. Bestyzhevo-Marlinskogo 23/1, Yakutsk, 677001, The Sakha Republic (Yakutia), Russia
| | - H Viinalass
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu, 51014, Estonia
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22
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Pokharel K, Weldenegodguad M, Popov R, Honkatukia M, Huuki H, Lindeberg H, Peippo J, Reilas T, Zarovnyaev S, Kantanen J. Whole blood transcriptome analysis reveals footprints of cattle adaptation to sub-arctic conditions. Anim Genet 2019; 50:217-227. [PMID: 30957254 PMCID: PMC6593690 DOI: 10.1111/age.12783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2019] [Indexed: 12/17/2022]
Abstract
Indigenous cattle breeds in northern Eurasia have adapted to harsh climate conditions. The local breeds are important genetic resources with cultural and historical heritages, and therefore, their preservation and genetic characterization are important. In this study, we profiled the whole‐blood transcriptome of two native breeds (Northern Finncattle and Yakutian cattle) and one commercial breed (Holstein) using high‐throughput RNA sequencing. More than 15 000 genes were identified, of which two, 89 and 162 genes were significantly upregulated exclusively in Northern Finncattle, Yakutian cattle and Holstein cattle respectively. The functional classification of these significantly differentially expressed genes identified several biological processes and pathways related to signalling mechanisms, cell differentiation and host–pathogen interactions that, in general, point towards immunity and disease resistance mechanisms. The gene expression pattern observed in Northern Finncattle was more similar to that of Yakutian cattle, despite sharing similar living conditions with the Holstein cattle included in our study. In conclusion, our study identified unique biological processes in these breeds that may have helped them to adapt and survive in northern and sub‐arctic environments.
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Affiliation(s)
- K Pokharel
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
| | - M Weldenegodguad
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, Kuopio, FI-70311, Finland
| | - R Popov
- Yakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), ul. Bestyzhevo-Marlinskogo 23/1, Yakutsk, 67001, The Sakha Republic (Yakutia), Russia
| | - M Honkatukia
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland.,The Nordic Genetic Resources Center (Nordgen), P.O. Box 115, Ås, NO-1431, Norway
| | - H Huuki
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
| | - H Lindeberg
- Production Systems, Natural Resources Institute Finland (Luke), Halolantie 31A, Maaninka, FI-71750, Finland
| | - J Peippo
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
| | - T Reilas
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
| | - S Zarovnyaev
- GBU Saha Agroplem, ul. Ordzhonkidze 20/204, Yakutsk, 67700, The Sakha Republic (Yakutia), Russia
| | - J Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen, FI-31600, Finland
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23
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Weldenegodguad M, Popov R, Pokharel K, Ammosov I, Ming Y, Ivanova Z, Kantanen J. Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions. Front Genet 2019; 9:728. [PMID: 30687392 PMCID: PMC6336893 DOI: 10.3389/fgene.2018.00728] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/22/2018] [Indexed: 12/30/2022] Open
Abstract
Northern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where cattle farming has been traditionally practiced. In this study, we performed whole-genome sequencing to genetically characterize three rare native breeds Eastern Finncattle, Western Finncattle and Yakutian cattle adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian taurine cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European taurine breeds. This result is in contrast to the results of marker-based cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic taurine cattle may have been higher than that of the European cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on cattle genomes and on the value of the adapted breeds for the conservation of cattle genetic resources.
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Affiliation(s)
- Melak Weldenegodguad
- Department of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ruslan Popov
- Yakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), Yakutsk, Russia
| | - Kisun Pokharel
- Department of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Innokentyi Ammosov
- Board of Agricultural Office of Eveno-Bytantaj Region, Batagay-Alyta, Russia
| | - Yao Ming
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | - Zoya Ivanova
- Yakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), Yakutsk, Russia
| | - Juha Kantanen
- Department of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, Finland
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24
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Cardoso TF, Amills M, Bertolini F, Rothschild M, Marras G, Boink G, Jordana J, Capote J, Carolan S, Hallsson JH, Kantanen J, Pons A, Lenstra JA. Patterns of homozygosity in insular and continental goat breeds. Genet Sel Evol 2018; 50:56. [PMID: 30449277 PMCID: PMC6241035 DOI: 10.1186/s12711-018-0425-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 10/15/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Genetic isolation of breeds may result in a significant loss of diversity and have consequences on health and performance. In this study, we examined the effect of geographic isolation on caprine genetic diversity patterns by genotyping 480 individuals from 25 European and African breeds with the Goat SNP50 BeadChip and comparing patterns of homozygosity of insular and nearby continental breeds. RESULTS Among the breeds analysed, number and total length of ROH varied considerably and depending on breeds, ROH could cover a substantial fraction of the genome (up to 1.6 Gb in Icelandic goats). When compared with their continental counterparts, goats from Iceland, Madagascar, La Palma and Ireland (Bilberry and Arran) displayed a significant increase in ROH coverage, ROH number and FROH values (P value < 0.05). Goats from Mediterranean islands represent a more complex case because certain populations displayed a significantly increased level of homozygosity (e.g. Girgentana) and others did not (e.g. Corse and Sarda). Correlations of number and total length of ROH for insular goat populations with the distance between islands and the nearest continental locations revealed an effect of extremely long distances on the patterns of homozygosity. CONCLUSIONS These results indicate that the effects of insularization on the patterns of homozygosity are variable. Goats raised in Madagascar, Iceland, Ireland (Bilberry and Arran) and La Palma, show high levels of homozygosity, whereas those bred in Mediterranean islands display patterns of homozygosity that are similar to those found in continental populations. These results indicate that the diversity of insular goat populations is modulated by multiple factors such as geographic distribution, population size, demographic history, trading and breed management.
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Affiliation(s)
- Taina F. Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona Spain
- CAPES Foundation, Ministry of Education of Brazil, Brasília, DF 70.040-020 Brazil
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150 USA
| | - Max Rothschild
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150 USA
| | - Gabriele Marras
- Bioinformatics Core Facility, Fondazione Parco Tecnologico Padano, Loc. Cascina Codazza, 26900 Lodi, LO Italy
| | - Geert Boink
- Stichting Zeldzame Huisdierrassen, De Drieslag 30, 8251 JZ Dronten, The Netherlands
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Juan Capote
- Instituto Canario de Investigaciones Agrarias, 38108 La Laguna, Tenerife Spain
| | - Sean Carolan
- The Old Irish Goat Society, Mulranny, Co Mayo Ireland
| | - Jón H. Hallsson
- Faculty of Land and Animal Resources, Agricultural University of Iceland, Reykjavík, Iceland
| | - Juha Kantanen
- Department of Production Systems, Natural Resources Institute Finland, 31600 Jokioinen, Finland
| | - Agueda Pons
- Unitat de Races Autòctones, Servei de Millora Agrària i Pesquera (SEMILLA), 07198 Son Ferriol, Spain
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - The AdaptMap Consortium
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona Spain
- CAPES Foundation, Ministry of Education of Brazil, Brasília, DF 70.040-020 Brazil
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150 USA
- Bioinformatics Core Facility, Fondazione Parco Tecnologico Padano, Loc. Cascina Codazza, 26900 Lodi, LO Italy
- Stichting Zeldzame Huisdierrassen, De Drieslag 30, 8251 JZ Dronten, The Netherlands
- Instituto Canario de Investigaciones Agrarias, 38108 La Laguna, Tenerife Spain
- The Old Irish Goat Society, Mulranny, Co Mayo Ireland
- Faculty of Land and Animal Resources, Agricultural University of Iceland, Reykjavík, Iceland
- Department of Production Systems, Natural Resources Institute Finland, 31600 Jokioinen, Finland
- Unitat de Races Autòctones, Servei de Millora Agrària i Pesquera (SEMILLA), 07198 Son Ferriol, Spain
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Fulton JE, Berres ME, Kantanen J, Honkatukia M. MHC-B variability within the Finnish Landrace chicken conservation program. Poult Sci 2018; 96:3026-3030. [PMID: 28453652 DOI: 10.3382/ps/pex102] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/05/2017] [Indexed: 11/20/2022] Open
Abstract
The major histocompatibility complex (MHC) is a cluster of genes involved with immune responses. The chicken MHC has been shown to influence resistance to viruses, bacteria, and infections from both internal and external parasites. The highly variable chicken MHC haplotypes were initially identified by the use of haplotype-specific serological reagents. A novel SNP-based panel encompassing 210,000 bp of the MHC-B locus was developed to allow fine scale genetic analyses including rapid identification of novel haplotypes for which serological reagents are not available. The Finnish Landrace breed of chickens traces its origins to almost 1,000 years ago, with multiple lineages maintained as small populations in isolated villages. The breed is well adapted to the cooler Finnish climate and is considered to be an infrequent egg layer. Conservation efforts to protect this endangered breed were initiated by a hobby breeder in the 1960s. An official conservation program was established in 1998 and now 12 different populations are currently maintained by a network of volunteer hobbyist breeders. Variation in the MHC-B region in these populations was examined using a panel of 90 selected SNP. A total of 195 samples from 12 distinct populations (average of 15 individuals sampled per population) were genotyped with the 90 SNP panel specific for the MHC-B region, spanning 210,000 bp. There were 36 haplotypes found, 16 of which are a subset of 78 that had been previously identified in either commercially utilized or heritage breeds from North America with the remaining 20 haplotypes being novel. The average number of MHC-B haplotypes found within each Finnish Landrace population was 5.9, and ranged from one to 13. While haplotypes common to multiple populations were found, population-specific haplotypes were also identified. This study shows that substantial MHC-B region diversity exists in the Finnish Landrace breed and exemplifies the significance tied to conserving multiple populations of rare breeds.
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Affiliation(s)
- J E Fulton
- Hy-Line International, Dallas Center, IA.
| | | | - J Kantanen
- Green Technology, Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland; Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland
| | - M Honkatukia
- Green Technology, Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
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26
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Xu SS, Gao L, Xie XL, Ren YL, Shen ZQ, Wang F, Shen M, Eyϸórsdóttir E, Hallsson JH, Kiseleva T, Kantanen J, Li MH. Genome-Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds. Front Genet 2018; 9:118. [PMID: 29692799 PMCID: PMC5902979 DOI: 10.3389/fgene.2018.00118] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/23/2018] [Indexed: 12/11/2022] Open
Abstract
Reproduction is an important trait in sheep breeding as well as in other livestock. However, despite its importance the genetic mechanisms of litter size in domestic sheep (Ovis aries) are still poorly understood. To explore genetic mechanisms underlying the variation in litter size, we conducted multiple independent genome-wide association studies in five sheep breeds of high prolificacy (Wadi, Hu, Icelandic, Finnsheep, and Romanov) and one low prolificacy (Texel) using the Ovine Infinium HD BeadChip, respectively. We identified different sets of candidate genes associated with litter size in different breeds: BMPR1B, FBN1, and MMP2 in Wadi; GRIA2, SMAD1, and CTNNB1 in Hu; NCOA1 in Icelandic; INHBB, NF1, FLT1, PTGS2, and PLCB3 in Finnsheep; ESR2 in Romanov and ESR1, GHR, ETS1, MMP15, FLI1, and SPP1 in Texel. Further annotation of genes and bioinformatics analyses revealed that different biological pathways could be involved in the variation in litter size of females: hormone secretion (FSH and LH) in Wadi and Hu, placenta and embryonic lethality in Icelandic, folliculogenesis and LH signaling in Finnsheep, ovulation and preovulatory follicle maturation in Romanov, and estrogen and follicular growth in Texel. Taken together, our results provide new insights into the genetic mechanisms underlying the prolificacy trait in sheep and other mammals, suggesting targets for selection where the aim is to increase prolificacy in breeding projects.
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Affiliation(s)
- Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Emma Eyϸórsdóttir
- Faculty of Natural Resources and Environmental Sciences, Agricultural University of Iceland, Borgarnes, Iceland
| | - Jón H. Hallsson
- Faculty of Natural Resources and Environmental Sciences, Agricultural University of Iceland, Borgarnes, Iceland
| | - Tatyana Kiseleva
- All-Russian Research Institute of Genetics and Farm Animal Breeding, Russian Academy of Sciences, Moscow, Russia
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland, Jokioinen, Finland
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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27
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Pokharel K, Peippo J, Honkatukia M, Seppälä A, Rautiainen J, Ghanem N, Hamama TM, Crowe MA, Andersson M, Li MH, Kantanen J. Integrated ovarian mRNA and miRNA transcriptome profiling characterizes the genetic basis of prolificacy traits in sheep (Ovis aries). BMC Genomics 2018; 19:104. [PMID: 29378514 PMCID: PMC5789708 DOI: 10.1186/s12864-017-4400-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 12/19/2017] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The highly prolific breeds of domestic sheep (Ovis aries) are globally valuable genetic resources for sheep industry. Genetic, nutritional and other environmental factors affect prolificacy traits in sheep. To improve our knowledge of the sheep prolificacy traits, we conducted mRNA-miRNA integrated profiling of ovarian tissues from two pure breeds with large (Finnsheep) vs. small (Texel) litter sizes and their F1 crosses, half of which were fed a flushing diet. RESULTS Among the samples, 16,402 genes (60.6% known ovine genes) were expressed, 79 novel miRNAs were found, and a cluster of miRNAs on chromosome 18 was detected. The majority of the differentially expressed genes between breeds were upregulated in the Texel with low prolificacy, owing to the flushing diet effect, whereas a similar pattern was not detected in the Finnsheep. F1 ewes responded similarly to Finnsheep rather than displaying a performance intermediate between the two pure breeds. CONCLUSIONS The identification and characterization of differentially expressed genes and miRNAs in the ovaries of sheep provided insights into genetic and environmental factors affecting prolificacy traits. The three genes (CST6, MEPE and HBB) that were differentially expressed between the group of Finnsheep and Texel ewes kept in normal diet appeared to be candidate genes of prolificacy traits and will require further validation.
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Affiliation(s)
- Kisun Pokharel
- Green Technology, Natural Resources Institute of Finland (Luke), Myllytie 1, Jokioinen, Finland
| | - Jaana Peippo
- Green Technology, Natural Resources Institute of Finland (Luke), Myllytie 1, Jokioinen, Finland
| | - Mervi Honkatukia
- Green Technology, Natural Resources Institute of Finland (Luke), Myllytie 1, Jokioinen, Finland
| | - Arja Seppälä
- Eastman Chemical Company, Tammasaarenkatu 1, Helsinki, Finland
| | | | - Nasser Ghanem
- Green Technology, Natural Resources Institute of Finland (Luke), Myllytie 1, Jokioinen, Finland
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Tuula-Marjatta Hamama
- Green Technology, Natural Resources Institute of Finland (Luke), Myllytie 1, Jokioinen, Finland
| | - Mark A. Crowe
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Magnus Andersson
- Department of Production Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Juha Kantanen
- Green Technology, Natural Resources Institute of Finland (Luke), Myllytie 1, Jokioinen, Finland
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28
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Zhao YX, Yang J, Lv FH, Hu XJ, Xie XL, Zhang M, Li WR, Liu MJ, Wang YT, Li JQ, Liu YG, Ren YL, Wang F, Hehua EE, Kantanen J, Arjen Lenstra J, Han JL, Li MH. Genomic Reconstruction of the History of Native Sheep Reveals the Peopling Patterns of Nomads and the Expansion of Early Pastoralism in East Asia. Mol Biol Evol 2017. [PMID: 28645168 PMCID: PMC5850515 DOI: 10.1093/molbev/msx181] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
China has a rich resource of native sheep (Ovis aries) breeds associated with historical movements of several nomadic societies. However, the history of sheep and the associated nomadic societies in ancient China remains poorly understood. Here, we studied the genomic diversity of Chinese sheep using genome-wide SNPs, mitochondrial and Y-chromosomal variations in > 1,000 modern samples. Population genomic analyses combined with archeological records and historical ethnic demographics data revealed genetic signatures of the origins, secondary expansions and admixtures, of Chinese sheep thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia. Originating from the Mongolian Plateau ∼5,000‒5,700 years ago, Chinese sheep were inferred to spread in the upper and middle reaches of the Yellow River ∼3,000‒5,000 years ago following the expansions of the Di-Qiang people. Afterwards, sheep were then inferred to reach the Qinghai-Tibetan and Yunnan-Kweichow plateaus ∼2,000‒2,600 years ago by following the north-to-southwest routes of the Di-Qiang migration. We also unveiled two subsequent waves of migrations of fat-tailed sheep into northern China, which were largely commensurate with the migrations of ancestors of Hui Muslims eastward and Mongols southward during the 12th‒13th centuries. Furthermore, we revealed signs of argali introgression into domestic sheep, extensive historical mixtures among domestic populations and strong artificial selection for tail type and other traits, reflecting various breeding strategies by nomadic societies in ancient China.
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Affiliation(s)
- Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xiao-Ju Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Min Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Yu-Tao Wang
- College of Life and Geographic Sciences, Kashgar University, Kashgar, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - EEr Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
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29
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Upadhyay M, da Silva VH, Megens HJ, Visker MHPW, Ajmone-Marsan P, Bâlteanu VA, Dunner S, Garcia JF, Ginja C, Kantanen J, Groenen MAM, Crooijmans RPMA. Distribution and Functionality of Copy Number Variation across European Cattle Populations. Front Genet 2017; 8:108. [PMID: 28878807 PMCID: PMC5572341 DOI: 10.3389/fgene.2017.00108] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/02/2017] [Indexed: 12/27/2022] Open
Abstract
Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations.
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Affiliation(s)
- Maulik Upadhyay
- Animal Breeding and Genomics, Wageningen University and ResearchWageningen, Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural SciencesUppsala, Sweden
| | - Vinicus H da Silva
- Animal Breeding and Genomics, Wageningen University and ResearchWageningen, Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural SciencesUppsala, Sweden
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University and ResearchWageningen, Netherlands
| | - Marleen H P W Visker
- Animal Breeding and Genomics, Wageningen University and ResearchWageningen, Netherlands
| | - Paolo Ajmone-Marsan
- Institute of Zootechnics and Nutrigenomics and Proteomics Research Center, Università Cattolica del Sacro CuorePiacenza, Italy
| | - Valentin A Bâlteanu
- Institute of Life Sciences, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine of Cluj-NapocaCluj-Napoca, Romania
| | - Susana Dunner
- Department of Animal Production, Veterinary Faculty, Universidad Complutense de MadridMadrid, Spain
| | - Jose F Garcia
- Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, Universidade Estadual PaulistaAraçatuba, Brazil.,IAEA Collaborating Centre on Animal Genomics and BioinformaticsAraçatuba, Brazil
| | - Catarina Ginja
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do PortoVairao, Portugal
| | - Juha Kantanen
- Green Technology, Natural Resources Institute FinlandJokioinen, Finland.,Department of Environmental and Biological Sciences, University of Eastern FinlandKuopio, Finland
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and ResearchWageningen, Netherlands
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30
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Peng WF, Xu SS, Ren X, Lv FH, Xie XL, Zhao YX, Zhang M, Shen ZQ, Ren YL, Gao L, Shen M, Kantanen J, Li MH. A genome-wide association study reveals candidate genes for the supernumerary nipple phenotype in sheep (Ovis aries). Anim Genet 2017; 48:570-579. [PMID: 28703336 DOI: 10.1111/age.12575] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2017] [Indexed: 01/20/2023]
Abstract
Genome-wide association studies (GWASs) have been widely applied in livestock to identify genes associated with traits of economic interest. Here, we conducted the first GWAS of the supernumerary nipple phenotype in Wadi sheep, a native Chinese sheep breed, based on Ovine Infinium HD SNP BeadChip genotypes in a total of 144 ewes (75 cases with four teats, including two normal and two supernumerary teats, and 69 control cases with two teats). We detected 63 significant SNPs at the chromosome-wise threshold. Additionally, one candidate region (chr1: 170.723-170.734 Mb) was identified by haplotype-based association tests, with one SNP (rs413490006) surrounding functional genes BBX and CD47 on chromosome 1 being commonly identified as significant by the two mentioned analyses. Moreover, Gene Ontology enrichment for the significant SNPs identified by the GWAS analysis was functionally clustered into the categories of receptor activity and synaptic membrane. In addition, pathway mapping revealed four promising pathways (Wnt, oxytocin, MAPK and axon guidance) involved in the development of the supernumerary nipple phenotype. Our results provide novel and important insights into the genetic mechanisms underlying the phenotype of supernumerary nipples in mammals, including humans. These findings may be useful for future breeding and genetics in sheep and other livestock.
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Affiliation(s)
- W-F Peng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - S-S Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - X Ren
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - F-H Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - X-L Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Y-X Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - M Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Z-Q Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, 256600, China
| | - Y-L Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, 256600, China
| | - L Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - M Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - J Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, 31600, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - M-H Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
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31
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Xu SS, Ren X, Yang GL, Xie XL, Zhao YX, Zhang M, Shen ZQ, Ren YL, Gao L, Shen M, Kantanen J, Li MH. Genome-wide association analysis identifies the genetic basis of fat deposition in the tails of sheep (Ovis aries). Anim Genet 2017; 48:560-569. [PMID: 28677334 DOI: 10.1111/age.12572] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2017] [Indexed: 12/13/2022]
Abstract
Fat-tailed sheep (Ovis aries) can survive in harsh environments and satisfy human's intake of dietary fat. However, the animals require more feed, which increases the cost of farming. Thus, most farmers currently prefer thin-tailed, short-tailed or docked sheep. To date, the molecular mechanism of the formation of fat tails in sheep has not been completely elucidated. Here, we conducted a genome-wide association study using phenotypes and genotypes (the Ovine Infinium HD SNP BeadChip genotype data) of two breeds of contrasting tail types (78 Small-tailed and 78 Large-tailed Han sheep breeds) to identify functional genes and variants associated with fat deposition. We identified four significantly (rs416433540, rs409848439, rs408118325 and rs402128848) and three approximately associated autosomal SNPs (rs401248376, rs402445895 and rs416201901). Gene annotation indicated that the surrounding genes (CREB1, STEAP4, CTBP1 and RIP140, also known as NRIP1) function in lipid storage or fat cell regulation. Furthermore, through an X-chromosome-wide association analysis, we detected significantly associated SNPs in the OARX: 88-89 Mb region, which could be a strong candidate genomic region for fat deposition in tails of sheep. Our results represent a new genomic resource for sheep genetics and breeding. In addition, the findings provide novel insights into genetic mechanisms of fat deposition in the tail of sheep and other mammals.
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Affiliation(s)
- S-S Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - X Ren
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - G-L Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,Department of Life Sciences, Shangqiu Normal University, Shangqiu, 476000, China
| | - X-L Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Y-X Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - M Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Z-Q Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, 256600, China
| | - Y-L Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, 256600, China
| | - L Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - M Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - J Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, 31600, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - M-H Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
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32
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Macneil MD, Alexander LJ, Kantanen J, Ammosov IA, Ivanova ZI, Popov RG, Ozerov M, Millbrooke A, Cronin MA. Potential emigration of Siberian cattle germplasm on Chirikof Island, Alaska. J Genet 2017; 96:47-51. [PMID: 28360389 DOI: 10.1007/s12041-016-0739-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Feral cattle residing in Chirikof Island, Alaska, are relatively distinct from breeds used in commercial production in North America. However, preliminary evidence suggested that they exhibit substantial genetic relationship with cattle from Yakutian region of Siberia. Thus, our objective was to further elucidate quantify the origins, admixture and divergence of the Chirikof Island cattle relative to cattle from Siberia and USA. Subject animals were genotyped at 15 microsatellite loci. Compared with Turano-Mongolian and North American cattle, Chirikof Island cattle had similar variation, with slightly less observed heterozygosity, fewer alleles per locus and a positive fixation index. Analysis of the genetic distances revealed two primary clusters; one that contained the North American breeds and the Kazakh White head, and a second that contained the Yakutian and Kalmyk breeds, and the Chirikof population. Thus, it is suggested that Chirikof Island cattle may be a composite of British breeds emanating from North America and Turano-Mongolian cattle. A potential founder effect, consistent with historical records of the Russian-American period, may contribute to the adaptation of the Chirikof Island cattle to their harsh high-latitude environment. Further study of adaptive mechanisms manifest by these cattle is warranted.
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Affiliation(s)
- M D Macneil
- Delta G, 145 Ice Cave Rd, Miles City, MT 59301, USA.
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33
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Iso-Touru T, Tapio M, Vilkki J, Kiseleva T, Ammosov I, Ivanova Z, Popov R, Ozerov M, Kantanen J. Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe. Anim Genet 2016; 47:647-657. [DOI: 10.1111/age.12473] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2016] [Indexed: 12/31/2022]
Affiliation(s)
- T. Iso-Touru
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
| | - M. Tapio
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
| | - J. Vilkki
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
| | - T. Kiseleva
- All-Russian Research Institute for Farm Animal Genetics and Breeding; Russian Academy of Sciences; 55-a Moskovskoe Shosse St. Petersburg-Pushkin 199601 Russia
| | - I. Ammosov
- Board of Agricultural Office of Eveno-Bytantaj Region; Batagay-Alyta 678580 The Sakha Republic (Yakutsk) Russia
| | - Z. Ivanova
- Yakutian Research Institute of Agriculture; Yakutsk Sakha 677007 Russia
| | - R. Popov
- Yakutian Research Institute of Agriculture; Yakutsk Sakha 677007 Russia
| | - M. Ozerov
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
- Department of Biology; University of Turku; Turku 20014 Finland
| | - J. Kantanen
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
- Department of Environmental and Biological Sciences; University of Eastern Finland; PO Box 1627 Kuopio 70211 Finland
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34
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Pokharel K, Hamama TM, Honkatukia M, Peippo J, Rautiainen J, Seppälä A, Li MH, Kantanen J. P3008 Transcriptome profiling of reproductive tissues characterizes genetic basis of the prolificacy traits in sheep (ovis aries). J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement455x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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35
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Weldenegodguad MB, Sarkissian CD, Bläuer A, Pokharel K, Taavitsainen JP, Orlando L, Kantanen J. P4053 Prospects for whole genome sequencing of ancient Finnish cattle. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4105x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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36
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Kantanen J. S0123 The adaptation of farm animals to northern and arctic environments. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement412x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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37
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Groeneveld LF, Gregusson S, Guldbrandtsen B, Hiemstra SJ, Hveem K, Kantanen J, Lohi H, Stroemstedt L, Berg P. Domesticated Animal Biobanking: Land of Opportunity. PLoS Biol 2016; 14:e1002523. [PMID: 27467395 PMCID: PMC4965055 DOI: 10.1371/journal.pbio.1002523] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In the past decade, biobanking has fuelled great scientific advances in the human medical sector. Well-established domesticated animal biobanks and integrated networks likewise harbour immense potential for great scientific advances with broad societal impacts, which are currently not being fully realised. Political and scientific leaders as well as journals and ethics committees should help to ensure that we are well equipped to meet future demands in livestock production, animal models, and veterinary care of companion animals.
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Affiliation(s)
| | | | | | - Sipke J. Hiemstra
- Centre for Genetic Resources, the Netherlands (CGN), Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Kristian Hveem
- Department of Public Health, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Helsinki, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Hannes Lohi
- Research Programs Unit, Molecular Neurology, and Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Lina Stroemstedt
- SLU Biobank, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Peer Berg
- NordGen—the Nordic Genetic Resource Center, Ås, Norway
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38
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Yang J, Li WR, Lv FH, He SG, Tian SL, Peng WF, Sun YW, Zhao YX, Tu XL, Zhang M, Xie XL, Wang YT, Li JQ, Liu YG, Shen ZQ, Wang F, Liu GJ, Lu HF, Kantanen J, Han JL, Li MH, Liu MJ. Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments. Mol Biol Evol 2016; 33:2576-92. [PMID: 27401233 PMCID: PMC5026255 DOI: 10.1093/molbev/msw129] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Global climate change has a significant effect on extreme environments and a profound influence on species survival. However, little is known of the genome-wide pattern of livestock adaptations to extreme environments over a short time frame following domestication. Sheep (Ovis aries) have become well adapted to a diverse range of agroecological zones, including certain extreme environments (e.g., plateaus and deserts), during their post-domestication (approximately 8–9 kya) migration and differentiation. Here, we generated whole-genome sequences from 77 native sheep, with an average effective sequencing depth of ∼5× for 75 samples and ∼42× for 2 samples. Comparative genomic analyses among sheep in contrasting environments, that is, plateau (>4,000 m above sea level) versus lowland (<100 m), high-altitude region (>1500 m) versus low-altitude region (<1300 m), desert (<10 mm average annual precipitation) versus highly humid region (>600 mm), and arid zone (<400 mm) versus humid zone (>400 mm), detected a novel set of candidate genes as well as pathways and GO categories that are putatively associated with hypoxia responses at high altitudes and water reabsorption in arid environments. In addition, candidate genes and GO terms functionally related to energy metabolism and body size variations were identified. This study offers novel insights into rapid genomic adaptations to extreme environments in sheep and other animals, and provides a valuable resource for future research on livestock breeding in response to climate change.
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Affiliation(s)
- Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wen-Rong Li
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - San-Gang He
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Shi-Lin Tian
- Novogene Bioinformatics Institute, Beijing, China
| | - Wei-Feng Peng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ya-Wei Sun
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xiao-Long Tu
- Novogene Bioinformatics Institute, Beijing, China
| | - Min Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Yu-Tao Wang
- College of Biological and Geographic Sciences, Kashgar University, Kashgar, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | | | - Hong-Feng Lu
- Novogene Bioinformatics Institute, Beijing, China
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Ming-Jun Liu
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
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39
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Lenstra JA, Tigchelaar J, Biebach I, Hallsson JH, Kantanen J, Nielsen VH, Pompanon F, Naderi S, Rezaei HR, Saether N, Ertugrul O, Grossen C, Camenisch G, Vos-Loohuis M, van Straten M, de Poel EA, Windig J, Oldenbroek K. Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry? J Anim Breed Genet 2016; 134:78-84. [PMID: 27339108 DOI: 10.1111/jbg.12226] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/24/2016] [Indexed: 11/25/2022]
Abstract
In the last decades, several endangered breeds of livestock species have been re-established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO-recommended microsatellites of these landraces and three phenotypically similar Nordic-type landraces and compared these breeds with central European, Mediterranean and south-west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south-west Asian domestication site with a south-east-to-north-west cline that is clearly steeper than the Mediterranean east-to-west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land-races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long-horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately.
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Affiliation(s)
- J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - J Tigchelaar
- Stichting Zeldzame Huisdierrassen, Wageningen, The Netherlands
| | - I Biebach
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | | | - J H Hallsson
- Faculty of Land and Animal Resources, Agricultural University of Iceland, Reykjavik, Iceland
| | - J Kantanen
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - V H Nielsen
- Research Centre Foulum, Aarhus University, Tjele, Denmark
| | - F Pompanon
- Université Grenoble Alpes, Grenoble, France
| | - S Naderi
- Environmental Sciences Department, Natural Resources Faculty, University of Guilan, Guilan, Iran
| | - H-R Rezaei
- Environmental Sciences Department, Gorgan University of Agriculture and Natural Resources, Gorgan, Iran
| | - N Saether
- Norwegian Genetic Resource Centre, Ås, Norway
| | - O Ertugrul
- Veterinary Faculty, Ankara University, Ankara, Turkey
| | - C Grossen
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - G Camenisch
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - M Vos-Loohuis
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - M van Straten
- Stichting Zeldzame Huisdierrassen, Wageningen, The Netherlands
| | - E A de Poel
- Stichting Zeldzame Huisdierrassen, Wageningen, The Netherlands
| | - J Windig
- Animal Sciences Group and Centre for Genetic Resources-Wageningen UR, Lelystad, The Netherlands
| | - K Oldenbroek
- Stichting Zeldzame Huisdierrassen, Wageningen, The Netherlands.,Animal Sciences Group and Centre for Genetic Resources-Wageningen UR, Lelystad, The Netherlands
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40
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Ren X, Yang GL, Peng WF, Zhao YX, Zhang M, Chen ZH, Wu FA, Kantanen J, Shen M, Li MH. Erratum: A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries). Sci Rep 2016; 7:25322. [PMID: 27203473 PMCID: PMC4874237 DOI: 10.1038/srep25322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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41
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Ren X, Yang GL, Peng WF, Zhao YX, Zhang M, Chen ZH, Wu FA, Kantanen J, Shen M, Li MH. A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries). Sci Rep 2016; 6:21111. [PMID: 26883901 PMCID: PMC4756668 DOI: 10.1038/srep21111] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/18/2016] [Indexed: 01/06/2023] Open
Abstract
Horns are a cranial appendage found exclusively in Bovidae, and play important roles in accessing resources and mates. In sheep (Ovies aries), horns vary from polled to six-horned, and human have been selecting polled animals in farming and breeding. Here, we conducted a genome-wide association study on 24 two-horned versus 22 four-horned phenotypes in a native Chinese breed of Sishui Fur sheep. Together with linkage disequilibrium (LD) analyses and haplotype-based association tests, we identified a genomic region comprising 132.0–133.1 Mb on chromosome 2 that contained the top 10 SNPs (including 4 significant SNPs) and 5 most significant haplotypes associated with the polycerate phenotype. In humans and mice, this genomic region contains the HOXD gene cluster and adjacent functional genes EVX2 and KIAA1715, which have a close association with the formation of limbs and genital buds. Our results provide new insights into the genetic basis underlying variable numbers of horns and represent a new resource for use in sheep genetics and breeding.
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Affiliation(s)
- Xue Ren
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Guang-Li Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,Department of Life Sciences, Shangqiu Normal University, Shangqiu 476000, China
| | - Wei-Feng Peng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Min Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Fu-An Wu
- Bureau of Animal Husbandry and Veterinary Medicine, Sishui County, Jining 273200, China
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen 31600, Finland.,Department of Biology, University of Eastern Finland, Kuopio 70211, Finland
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China.,Key Laboratory of Sheep Breeding and Development Technology of Xinjiang Production and Construction Crops (XPCC), Shihezi 832000, China
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
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42
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Rannamäe E, Lõugas L, Niemi M, Kantanen J, Maldre L, Kadõrova N, Saarma U. Maternal and paternal genetic diversity of ancient sheep in Estonia from the Late Bronze Age to the post-medieval period and comparison with other regions in Eurasia. Anim Genet 2016; 47:208-18. [PMID: 26805771 DOI: 10.1111/age.12407] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2015] [Indexed: 12/01/2022]
Abstract
Sheep were among the first domesticated animals to appear in Estonia in the late Neolithic and became one of the most widespread livestock species in the region from the Late Bronze Age onwards. However, the origin and historical expansion of local sheep populations in Estonia remain poorly understood. Here, we analysed fragments of the hypervariable D-loop of mitochondrial DNA (mtDNA; 213 bp) and the Y-chromosome SRY gene (130 bp) extracted from 31 archaeological sheep bones dated from approximately 800 BC to 1700 AD. The ancient DNA data of sheep from Estonia were compared with ancient sheep from Finland as well as a set of contemporary sheep breeds from across Eurasia in order to place them in a wider phylogeographical context. The analysis shows that: (i) 24 successfully amplified and analysed mtDNA sequences of ancient sheep cluster into two haplogroups, A and B, of which B is predominant; (ii) four of the ancient mtDNA haplotypes are novel; (iii) higher mtDNA haplotype diversity occurred during the Middle Ages as compared to other periods, a fact concordant with the historical context of expanding international trade during the Middle Ages; (iv) the proportion of rarer haplotypes declined during the expansion of sheep from the Near Eastern domestication centre to the northern European region; (v) three male samples showed the presence of the characteristic northern European haplotype, SNP G-oY1 of the Y-chromosome, and represent the earliest occurrence of this haplotype. Our results provide the first insight into the genetic diversity and phylogeographical background of ancient sheep in Estonia and provide basis for further studies on the temporal fluctuations of ancient sheep populations.
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Affiliation(s)
- E Rannamäe
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Jakobi 2, 51014, Tartu, Estonia
| | - L Lõugas
- Department of Archaeobiology, Institute of History, Tallinn University, Rüütli 6, 10130, Tallinn, Estonia
| | - M Niemi
- Department of Forensic Medicine, University of Helsinki, FI-00014, Helsinki, Finland.,Green Technology, Natural Resources Institute Finland, Myllytie 1, FI-31600, Jokioinen, Finland
| | - J Kantanen
- Green Technology, Natural Resources Institute Finland, Myllytie 1, FI-31600, Jokioinen, Finland.,Department of Biology, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - L Maldre
- Department of Archaeobiology, Institute of History, Tallinn University, Rüütli 6, 10130, Tallinn, Estonia
| | - N Kadõrova
- Department of Natural Sciences, Institute of Mathematics and Natural Sciences, Tallinn University, Narva Rd 25, 10120, Tallinn, Estonia
| | - U Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
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43
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Kantanen J. [Horse, cow and reindeer were converted into arctic domestic animals]. Duodecim 2016; 132:1231-1236. [PMID: 27522831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Domestic animal production in the arctic region is often thought to be based exclusively on reindeer herding. There are, however, regions in Northern Europe and Siberia having a long tradition in rearing breeds of cattle and horse adapted to the northers conditions also. The development of these arctic animal breeds has been largely founded on old tradition rather than on the programs of breeding organizations. As a result of the selection carried out by nature and man, the domestic animals of arctic regions express characteristics that are metabolic, structural, associated with reproductive physiology and conducive to the adaptation to arctic conditions.
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44
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Hu X, Pokharel K, Peippo J, Ghanem N, Zhaboyev I, Kantanen J, Li MH. Identification and characterization of miRNAs in the ovaries of a highly prolific sheep breed. Anim Genet 2015; 47:234-9. [PMID: 26582387 DOI: 10.1111/age.12385] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2015] [Indexed: 12/22/2022]
Abstract
Until recently, there have been few studies concerning miRNAs or miRNA-mediated biological processes in sheep (Ovis aries). In the present study, we used a deep-sequencing approach to examine ovarian miRNAs and the mRNA transcriptomes in two ewes of a highly prolific breed, Finnsheep. We identified 113 known sheep miRNAs, 131 miRNAs conserved in other mammals and 60 novel miRNAs, the expression levels of which accounted for 78.22%, 21.73% and 0.05% of the total respectively. Furthermore, the 10 most abundantly expressed miRNAs in the two libraries were characterized in detail, and the putative target genes of these miRNAs were annotated using GO annotation and KEGG pathway enrichment analyses. Among the target genes, intracellular transducers (SMAD1, SMAD4, SMAD5 and SMAD9) and bone morphogenetic protein (BMP) receptors (BMPR1B and BMPR2) were involved in the transforming growth factor β (TGFβ) signaling pathway in the reproductive axis, and the most significant GO terms were intracellular part (GO:0044424), binding (GO:0005488) and biological_process (GO:0008150) for cellular component, molecular function and biological process respectively. Thus, these results expanded the sheep miRNA database and provided additional information on the prolificacy trait regulated through specific miRNAs in sheep and other mammals.
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Affiliation(s)
- Xiaoju Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Kisun Pokharel
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, 31600, Finland.,Department of Biology, University of Eastern Finland, Kuopio, 70211, Finland
| | - Jaana Peippo
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, 31600, Finland
| | - Nasser Ghanem
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, 31600, Finland.,Animal Production Department, Faculty of Agriculture, Cairo University, Cairo, Giza, 12613
| | - Ismail Zhaboyev
- Department of Biology, University of Eastern Finland, Kuopio, 70211, Finland.,Faculty of Veterinary Medicine, Kazakh National Agrarian University, Almaty, 050010, Kazakhstan
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, 31600, Finland.,Department of Biology, University of Eastern Finland, Kuopio, 70211, Finland
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
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45
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Bruford MW, Ginja C, Hoffmann I, Joost S, Orozco-terWengel P, Alberto FJ, Amaral AJ, Barbato M, Biscarini F, Colli L, Costa M, Curik I, Duruz S, Ferenčaković M, Fischer D, Fitak R, Groeneveld LF, Hall SJG, Hanotte O, Hassan FU, Helsen P, Iacolina L, Kantanen J, Leempoel K, Lenstra JA, Ajmone-Marsan P, Masembe C, Megens HJ, Miele M, Neuditschko M, Nicolazzi EL, Pompanon F, Roosen J, Sevane N, Smetko A, Štambuk A, Streeter I, Stucki S, Supakorn C, Telo Da Gama L, Tixier-Boichard M, Wegmann D, Zhan X. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025. Front Genet 2015; 6:314. [PMID: 26539210 PMCID: PMC4612686 DOI: 10.3389/fgene.2015.00314] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/05/2015] [Indexed: 12/20/2022] Open
Abstract
Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that “…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.
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Affiliation(s)
- Michael W Bruford
- School of Biosciences, Cardiff University Cardiff, UK ; Sustainable Places Research Institute, Cardiff University Cardiff, UK
| | - Catarina Ginja
- Faculdade de Ciências, Centro de Ecologia, Evolução e Alterações Ambientais (CE3C), Universidade de Lisboa Lisboa, Portugal ; Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Campus Agrário de Vairão Portugal
| | - Irene Hoffmann
- Food and Agriculture Organization of the United Nations, Animal Genetic Resources Branch, Animal Production and Health Division Rome, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Florian J Alberto
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes Grenoble, France
| | - Andreia J Amaral
- Faculty of Sciences, BioISI- Biosystems and Integrative Sciences Institute, University of Lisbon Campo Grande, Portugal
| | - Mario Barbato
- School of Biosciences, Cardiff University Cardiff, UK
| | | | - Licia Colli
- BioDNA Centro di Ricerca sulla Biodiversità a sul DNA Antico, Istituto di Zootecnica, Università Cattolica del Sacro Cuore di Piacenza Italy
| | - Mafalda Costa
- School of Biosciences, Cardiff University Cardiff, UK
| | - Ino Curik
- Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - Solange Duruz
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Daniel Fischer
- Natural Resources Institute Finland (Luke), Green Technology Jokioinen, Finland
| | - Robert Fitak
- Institut für Populationsgenetik Vetmeduni, Vienna, Austria
| | | | | | - Olivier Hanotte
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Faiz-Ul Hassan
- School of Life Sciences, University of Nottingham Nottingham, UK ; Department of Animal Breeding and Genetics, University of Agriculture Faisalabad, Pakistan
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp Antwerp, Belgium
| | - Laura Iacolina
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Green Technology Jokioinen, Finland ; Department of Biology, University of Eastern Finland Kuopio, Finland
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Paolo Ajmone-Marsan
- BioDNA Centro di Ricerca sulla Biodiversità a sul DNA Antico, Istituto di Zootecnica, Università Cattolica del Sacro Cuore di Piacenza Italy
| | - Charles Masembe
- Institute of the Environment and Natural Resources, Makerere University Kampala, Uganda
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands
| | - Mara Miele
- School of Planning and Geography, Cardiff University Cardiff, UK
| | | | | | - François Pompanon
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes Grenoble, France
| | - Jutta Roosen
- TUM School of Management, Technische Universität München Munich, Germany
| | - Natalia Sevane
- Department of Animal Production, Veterinary Faculty, Universidad Complutense de Madrid Madrid, Spain
| | | | - Anamaria Štambuk
- Department of Biology, Faculty of Science, University of Zagreb Zagreb, Croatia
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, UK
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - China Supakorn
- School of Life Sciences, University of Nottingham Nottingham, UK ; School of Agricultural Technology, Walailak University Tha Sala, Thailand
| | - Luis Telo Da Gama
- Centre of Research in Animal Health (CIISA) - Faculty of Veterinary Medicine, University of Lisbon Lisbon, Portugal
| | | | - Daniel Wegmann
- Department of Biology, University of Fribourg Fribourg, Switzerland
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Beijing, China ; Cardiff University - Institute of Zoology, Joint Laboratory for Biocomplexity Research Beijing, China
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Lv FH, Peng WF, Yang J, Zhao YX, Li WR, Liu MJ, Ma YH, Zhao QJ, Yang GL, Wang F, Li JQ, Liu YG, Shen ZQ, Zhao SG, Hehua E, Gorkhali NA, Farhad Vahidi SM, Muladno M, Naqvi AN, Tabell J, Iso-Touru T, Bruford MW, Kantanen J, Han JL, Li MH. Mitogenomic Meta-Analysis Identifies Two Phases of Migration in the History of Eastern Eurasian Sheep. Mol Biol Evol 2015; 32:2515-33. [PMID: 26085518 PMCID: PMC4576706 DOI: 10.1093/molbev/msv139] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Despite much attention, history of sheep (Ovis aries) evolution, including its dating, demographic trajectory and geographic spread, remains controversial. To address these questions, we generated 45 complete and 875 partial mitogenomic sequences, and performed a meta-analysis of these and published ovine mitochondrial DNA sequences (n = 3,229) across Eurasia. We inferred that O. orientalis and O. musimon share the most recent female ancestor with O. aries at approximately 0.790 Ma (95% CI: 0.637-0.934 Ma) during the Middle Pleistocene, substantially predating the domestication event (∼8-11 ka). By reconstructing historical variations in effective population size, we found evidence of a rapid population increase approximately 20-60 ka, immediately before the Last Glacial Maximum. Analyses of lineage expansions showed two sheep migratory waves at approximately 4.5-6.8 ka (lineages A and B: ∼6.4-6.8 ka; C: ∼4.5 ka) across eastern Eurasia, which could have been influenced by prehistoric West-East commercial trade and deliberate mating of domestic and wild sheep, respectively. A continent-scale examination of lineage diversity and approximate Bayesian computation analyses indicated that the Mongolian Plateau region was a secondary center of dispersal, acting as a "transportation hub" in eastern Eurasia: Sheep from the Middle Eastern domestication center were inferred to have migrated through the Caucasus and Central Asia, and arrived in North and Southwest China (lineages A, B, and C) and the Indian subcontinent (lineages B and C) through this region. Our results provide new insights into sheep domestication, particularly with respect to origins and migrations to and from eastern Eurasia.
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Affiliation(s)
- Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wei-Feng Peng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Wen-Rong Li
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ming-Jun Liu
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Yue-Hui Ma
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Qian-Jun Zhao
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Guang-Li Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China College of Life Sciences, Shangqiu Normal University, Shangqiu, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Sheng-Guo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Eer Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Neena A Gorkhali
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council, Kathmandu, Nepal
| | - S M Farhad Vahidi
- Agricultural Biotechnology Research Institute of Iran-North Branch (ABRII), Rasht, Iran
| | - Muhammad Muladno
- Department of Animal Technology and Production Science, Bogor Agricultural University, Darmaga Campus, Bogor, Indonesia
| | - Arifa N Naqvi
- Faculty of Life Sciences, Karakoram International University, Gilgit, Baltistan, Pakistan
| | - Jonna Tabell
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland
| | - Terhi Iso-Touru
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland
| | - Michael W Bruford
- School of Biosciences and Sustainable Places Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland Department of Biology, University of Eastern Finland, Kuopio, Finland
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
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Kantanen J, Løvendahl P, Strandberg E, Eythorsdottir E, Li MH, Kettunen-Præbel A, Berg P, Meuwissen T. Utilization of farm animal genetic resources in a changing agro-ecological environment in the Nordic countries. Front Genet 2015; 6:52. [PMID: 25767477 PMCID: PMC4341116 DOI: 10.3389/fgene.2015.00052] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 02/05/2015] [Indexed: 12/16/2022] Open
Abstract
Livestock production is the most important component of northern European agriculture and contributes to and will be affected by climate change. Nevertheless, the role of farm animal genetic resources in the adaptation to new agro-ecological conditions and mitigation of animal production’s effects on climate change has been inadequately discussed despite there being several important associations between animal genetic resources and climate change issues. The sustainability of animal production systems and future food security require access to a wide diversity of animal genetic resources. There are several genetic questions that should be considered in strategies promoting adaptation to climate change and mitigation of environmental effects of livestock production. For example, it may become important to choose among breeds and even among farm animal species according to their suitability to a future with altered production systems. Some animals with useful phenotypes and genotypes may be more useful than others in the changing environment. Robust animal breeds with the potential to adapt to new agro-ecological conditions and tolerate new diseases will be needed. The key issue in mitigation of harmful greenhouse gas effects induced by livestock production is the reduction of methane (CH4) emissions from ruminants. There are differences in CH4 emissions among breeds and among individual animals within breeds that suggest a potential for improvement in the trait through genetic selection. Characterization of breeds and individuals with modern genomic tools should be applied to identify breeds that have genetically adapted to marginal conditions and to get critical information for breeding and conservation programs for farm animal genetic resources. We conclude that phenotyping and genomic technologies and adoption of new breeding approaches, such as genomic selection introgression, will promote breeding for useful characters in livestock species.
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Affiliation(s)
- Juha Kantanen
- Green Technology, Natural Resources Institute Finland , Jokioinen, Finland ; Department of Biology, University of Eastern Finland , Kuopio, Finland
| | - Peter Løvendahl
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University , Tjele, Denmark
| | - Erling Strandberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences , Uppsala, Sweden
| | - Emma Eythorsdottir
- Faculty of Land and Animal Resources, Agricultural University of Iceland , Reykjavik, Iceland
| | - Meng-Hua Li
- Green Technology, Natural Resources Institute Finland , Jokioinen, Finland ; Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing, China
| | | | - Peer Berg
- NordGen - Nordic Genetic Resource Center , Aas, Norway
| | - Theo Meuwissen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences , Aas, Norway
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48
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Abstract
Following domestication, sheep (Ovis aries) have become essential farmed animals across the world through adaptation to a diverse range of environments and varied production systems. Climate-mediated selective pressure has shaped phenotypic variation and has left genetic "footprints" in the genome of breeds raised in different agroecological zones. Unlike numerous studies that have searched for evidence of selection using only population genetics data, here, we conducted an integrated coanalysis of environmental data with single nucleotide polymorphism (SNP) variation. By examining 49,034 SNPs from 32 old, autochthonous sheep breeds that are adapted to a spectrum of different regional climates, we identified 230 SNPs with evidence for selection that is likely due to climate-mediated pressure. Among them, 189 (82%) showed significant correlation (P ≤ 0.05) between allele frequency and climatic variables in a larger set of native populations from a worldwide range of geographic areas and climates. Gene ontology analysis of genes colocated with significant SNPs identified 17 candidates related to GTPase regulator and peptide receptor activities in the biological processes of energy metabolism and endocrine and autoimmune regulation. We also observed high linkage disequilibrium and significant extended haplotype homozygosity for the core haplotype TBC1D12-CH1 of TBC1D12. The global frequency distribution of the core haplotype and allele OAR22_18929579-A showed an apparent geographic pattern and significant (P ≤ 0.05) correlations with climatic variation. Our results imply that adaptations to local climates have shaped the spatial distribution of some variants that are candidates to underpin adaptive variation in sheep.
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Affiliation(s)
- Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Saif Agha
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland Department of Animal Science, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Juha Kantanen
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland Department of Biology, University of Eastern Finland, Kuopio, Finland
| | - Licia Colli
- Istituto di Zootecnica, Facoltà di Agraria, Università Cattolica del Sacro Cuore, Piacenza, Italy Biodiversity and Ancient DNA Research Center-BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - James W Kijas
- CSIRO Livestock Industries, St Lucia, Brisbane, Qld, Australia
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Paolo Ajmone Marsan
- Istituto di Zootecnica, Facoltà di Agraria, Università Cattolica del Sacro Cuore, Piacenza, Italy Biodiversity and Ancient DNA Research Center-BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
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49
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Zhang M, Peng WF, Yang GL, Lv FH, Liu MJ, Li WR, Liu YG, Li JQ, Wang F, Shen ZQ, Zhao SG, Hehua EE, Marzanov N, Murawski M, Kantanen J, Li MH. Y chromosome haplotype diversity of domestic sheep (Ovis aries) in northern Eurasia. Anim Genet 2014; 45:903-7. [DOI: 10.1111/age.12214] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Min Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; Chinese Academy of Sciences (CAS); Beijing 100101 China
- School of Life Sciences; University of Science and Technology of China; Hefei 230027 China
| | - Wei-Feng Peng
- CAS Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; Chinese Academy of Sciences (CAS); Beijing 100101 China
- College of Life Sciences; University of Chinese Academy of Sciences; Beijing 100049 China
| | - Guang-Li Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; Chinese Academy of Sciences (CAS); Beijing 100101 China
- College of Life Sciences; Shangqiu Normal University; Shangqiu 476000 China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; Chinese Academy of Sciences (CAS); Beijing 100101 China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center; Xinjiang Academy of Animal Science; Urumqi 830000 China
| | - Wen-Rong Li
- Animal Biotechnological Research Center; Xinjiang Academy of Animal Science; Urumqi 830000 China
| | - Yong-Gang Liu
- College of Animal Science and Technology; Yunnan Agricultural University; Kunming 640201 China
| | - Jin-Quan Li
- College of Animal Science; Inner Mongolia Agricultural University; Hohhot 010018 China
| | - Feng Wang
- Institute of Sheep & Goat Science; Nanjing Agricultural University; Nanjing 210095 China
| | - Zhi-Qiang Shen
- Binzhou Academy of Animal Science and Veterinary Medicine; Binzhou 256600 China
| | - Sheng-Guo Zhao
- College of Animal Science and Technology; Gansu Agricultural University; Lanzhou 730070 China
| | - EEr Hehua
- Grass-feeding Livestock Engineering Technology Research Center; Ningxia Academy of Agriculture and Forestry Sciences; Yinchuan 750002 China
| | - Nurbiy Marzanov
- All-Russian Research Institute of Animal Husbandry; Russian Academy of Agricultural Sciences; 142132 Moscow Region Dubrovitsy Russia
| | - Maziek Murawski
- Department of Sheep and Goat Breeding; Agricultural University of Cracow; Cracow 31059 Poland
| | - Juha Kantanen
- Biotechnology and Food Research; MTT Agrifood Research Finland; Jokioinen 31600 Finland
- Department of Biology; University of Eastern Finland; Kuopio 70211 Finland
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; Chinese Academy of Sciences (CAS); Beijing 100101 China
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50
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Åby BA, Kantanen J, Aass L, Meuwissen T. Current status of livestock production in the Nordic countries and future challenges with a changing climate and human population growth. ACTA AGR SCAND A-AN 2014. [DOI: 10.1080/09064702.2014.950321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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