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Jourdan J, Bundschuh M, Copilaș-Ciocianu D, Fišer C, Grabowski M, Hupało K, Jemec Kokalj A, Kabus J, Römbke J, Soose LJ, Oehlmann J. Cryptic Species in Ecotoxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1889-1914. [PMID: 37314101 DOI: 10.1002/etc.5696] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/20/2023] [Accepted: 06/12/2023] [Indexed: 06/15/2023]
Abstract
The advent of genetic methods has led to the discovery of an increasing number of species that previously could not be distinguished from each other on the basis of morphological characteristics. Even though there has been an exponential growth of publications on cryptic species, such species are rarely considered in ecotoxicology. Thus, the particular question of ecological differentiation and the sensitivity of closely related cryptic species is rarely addressed. Tackling this question, however, is of key importance for evolutionary ecology, conservation biology, and, in particular, regulatory ecotoxicology. At the same time, the use of species with (known or unknown) cryptic diversity might be a reason for the lack of reproducibility of ecotoxicological experiments and implies a false extrapolation of the findings. Our critical review includes a database and literature search through which we investigated how many of the species most frequently used in ecotoxicological assessments show evidence of cryptic diversity. We found a high proportion of reports indicating overlooked species diversity, especially in invertebrates. In terrestrial and aquatic realms, at least 67% and 54% of commonly used species, respectively, were identified as cryptic species complexes. The issue is less prominent in vertebrates, in which we found evidence for cryptic species complexes in 27% of aquatic and 6.7% of terrestrial vertebrates. We further exemplified why different evolutionary histories may significantly determine cryptic species' ecology and sensitivity to pollutants. This in turn may have a major impact on the results of ecotoxicological tests and, consequently, the outcome of environmental risk assessments. Finally, we provide a brief guideline on how to deal practically with cryptic diversity in ecotoxicological studies in general and its implementation in risk assessment procedures in particular. Environ Toxicol Chem 2023;42:1889-1914. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Jonas Jourdan
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Mirco Bundschuh
- iES Landau, Institute for Environmental Sciences, University of Kaiserslautern-Landau, Landau, Germany
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Denis Copilaș-Ciocianu
- Laboratory of Evolutionary Ecology of Hydrobionts, Nature Research Centre, Vilnius, Lithuania
| | - Cene Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michał Grabowski
- Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - Kamil Hupało
- Department of Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Anita Jemec Kokalj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Kabus
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Römbke
- ECT Oekotoxikologie, Flörsheim am Main, Germany
| | - Laura J Soose
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Oehlmann
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
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Buryakov NP, Sycheva LV, Trukhachev VI, Zaikina AS, Buryakova MA, Nikonov IN, Petrov AS, Kravchenko AV, Fathala MM, Medvedev IK, Aleshin DE. Role of Dietary Inclusion of Phytobiotics and Mineral Adsorbent Combination on Dairy Cows' Milk Production, Nutrient Digestibility, Nitrogen Utilization, and Biochemical Parameters. Vet Sci 2023; 10:vetsci10030238. [PMID: 36977277 PMCID: PMC10058306 DOI: 10.3390/vetsci10030238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Our research purpose was to study the effect of the inclusion of a combination of phytobiotics in the form of dry Fucus vesiculosus grits (FG) and a mineral adsorbent from the heat-treated mineral shungite (TMS) on milk productivity, nutrient digestibility, and biochemical parameters of the Suksun dairy cows. A total of 80 dry-hardy cows of the Suksun breed were divided into four groups (20 heads each), balanced primarily by breed, age, body weight, body condition score, and indicators of milk yield for the previous lactation. The selected cows were with an average live body weight of 512.0 ± 1.28 kg, BCS 3.0-3.5, and parities of 6250 kg milk. The control group (CON) were fed the basic ration only; the second (TMS), third (FG), and fourth (TMS + FG) groups were fed the basic ration provided by 50 g of the mineral adsorbent from heat-treated shungite, 100 g of Fucus grits (Fucus vesiculosus), 50 g of the mineral adsorbent from heat-treated shungite, and 100 g of dry grits from Fucus vesiculosus, respectively. The total protein content in milk was significantly higher in the group receiving Fucus vesiculosus by 0.05% and the group receiving a combination of mineral adsorbent and Fucus vesiculosus by 0.03%. The percentage of milk fat content recorded the highest significant value in (TMS) group when compared to the control and represented (4.37 vs. 3.95). The group of cows that received (TMS + FG) revealed a significant difference in the digestibility of both ether extract and crude fiber when compared to the control group and represented (54.74 vs. 51.71 and 60.68 vs. 55.15%), respectively. The cows supplemented with a mineral adsorbent or a combination of mineral adsorbent and Fucus vesiculosus revealed a significant difference in the digestibility of ether extract and crude fiber in the group receiving TMS + FG by 3.0% (p < 0.05) and 5.5% (p < 0.05), respectively. The intake of nitrogen with the diet increased in (FG) and (TMS + FG) groups by 11.3 g (p < 0.05) and 13.4 g (p < 0.05) of nitrogen. There was an increase (p < 0.05) in the concentration of rumen ammonia in the control group compared to the other groups. The glucose content of those cows that received FG and TMS + FG combination increased (p < 0.05) by 0.76 mmol/L and 0.90 mmol/l in relation to the control group. The globulin, albumin/globulin ratio, and the level of triglycerides revealed a significant difference between the different experimental groups. In brief, the inclusion of a combination of phytobiotics in the form of dry Fucus vesiculosus grits and a mineral adsorbent from the heat-treated mineral shungite in Suksun dairy cows' diets improved milk composition, digestibility of nutrients, utilization of nitrogen, and did not cause deleterious effects on blood biochemical indicators.
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Affiliation(s)
- Nikolai P Buryakov
- Department of Feeding Animals, Institute of Animal Science and Biology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow 125493, Russia
| | - Larisa V Sycheva
- Department of Animal Husbandry, Faculty of Veterinary Medicine and Animal Science, Perm State Agro-Technological University, Perm 614990, Russia
| | - Vladimir I Trukhachev
- Department of Feeding Animals, Institute of Animal Science and Biology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow 125493, Russia
| | - Anastasiya S Zaikina
- Department of Feeding Animals, Institute of Animal Science and Biology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow 125493, Russia
| | - Maria A Buryakova
- Department of Feeding Animals, Institute of Animal Science and Biology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow 125493, Russia
| | - Ilia N Nikonov
- Department of Animal Hygiene and Poultry Breeding Named after A.K. Danilova, Faculty of Animal Technologies and Agribusiness, Moscow State Academy of Veterinary Medicine and Biotechnology-MVA Named after K.I. Skryabin, Moscow 109472, Russia
| | - Alexander S Petrov
- Department of Feeding Animals, Institute of Animal Science and Biology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow 125493, Russia
| | - Andrey V Kravchenko
- Department of Animal Husbandry, Faculty of Veterinary Medicine and Animal Science, Perm State Agro-Technological University, Perm 614990, Russia
| | - Mohamed M Fathala
- Department of Feeding Animals, Institute of Animal Science and Biology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow 125493, Russia
- Animal Husbandry and Wealth Development Department, Faculty of Veterinary Medicine, Alexandria University, Alexandria 5424041, Egypt
| | - Ivan K Medvedev
- Department of Feeding Animals, Institute of Animal Science and Biology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow 125493, Russia
| | - Dmitrii E Aleshin
- Department of Feeding Animals, Institute of Animal Science and Biology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow 125493, Russia
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Solodneva E, Svishcheva G, Smolnikov R, Bazhenov S, Konorov E, Mukhina V, Stolpovsky Y. Genetic Structure Analysis of 155 Transboundary and Local Populations of Cattle ( Bos taurus, Bos indicus and Bos grunniens) Based on STR Markers. Int J Mol Sci 2023; 24:5061. [PMID: 36902492 PMCID: PMC10003406 DOI: 10.3390/ijms24055061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/09/2023] Open
Abstract
Every week, 1-2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study. In order to determine the population genetic characteristics, and clarify the phylogenetic relationships of modern representatives of 155 cattle populations from different regions of the world, we collected a large set of STR data (10,250 individuals), including unique native cattle, 12 yak populations from Russia, Mongolia and Kyrgyzstan, as well as zebu breeds. Estimation of main population genetic parameters, phylogenetic analysis, principal component analysis and Bayesian cluster analysis allowed us to refine genetic structure and provided insights in relationships of native populations, transboundary breeds and populations of domestic yak. Our results can find practical application in conservation programs of endangered breeds, as well as become the basis for future fundamental research.
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Affiliation(s)
- Evgenia Solodneva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Gulnara Svishcheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Rodion Smolnikov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Sergey Bazhenov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Evgenii Konorov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Gorbatov Federal Research Center for Food Systems, Russian Academy of Sciences, 109316 Moscow, Russia
| | - Vera Mukhina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Yurii Stolpovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
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Hall SJG. Genetic Differentiation among Livestock Breeds-Values for F st. Animals (Basel) 2022; 12:1115. [PMID: 35565543 PMCID: PMC9103131 DOI: 10.3390/ani12091115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 12/02/2022] Open
Abstract
(1) Background: The Fst statistic is widely used to characterize between-breed relationships. Fst = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding Fst values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed Fst were as follows, cattle: microsatellite 0.06-0.12, SNP 0.08-0.15; sheep: microsatellite 0.06-0.10, SNP 0.06-0.17; horses: microsatellite 0.04-0.11, SNP 0.08-0.12; goats: microsatellite 0.04-0.14, SNP 0.08-0.16; pigs: microsatellite 0.06-0.27, SNP 0.15-0.22; chickens: microsatellite 0.05-0.28, SNP 0.08-0.26. (4) Conclusions: (1) Large amounts of Fst data are available for a substantial proportion of the world's livestock breeds, (2) the value for between-breed Fst of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated Fst data may have value for interdisciplinary research.
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Affiliation(s)
- Stephen J G Hall
- Department of Environmental Protection and Landscape, Estonian University of Life Sciences, Kreutzwaldi 5, 51014 Tartu, Estonia
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5
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Yudin NS, Yurchenko AA, Larkin DM. [Signatures of selection and candidate genes for adaptation to extreme environmental factors in the genomes of Turano-Mongolian cattle breeds]. Vavilovskii Zhurnal Genet Selektsii 2021; 25:190-201. [PMID: 34901717 PMCID: PMC8627871 DOI: 10.18699/vj21.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022] Open
Abstract
Changes in the environment force populations of organisms to adapt to new conditions, either through phenotypic plasticity or through genetic or epigenetic changes. Signatures of selection, such as specific changes in the frequency of alleles and haplotypes, as well as the reduction or increase in genetic diversity, help to identify changes in the cattle genome in response to natural and artificial selection, as well as loci and genetic variants directly affecting adaptive and economically important traits. Advances in genetics and biotechnology enable a rapid transfer of unique genetic variants that have originated in local cattle breeds in the process of adaptation to local environments into the genomes of cosmopolitan high-performance breeds, in order to preserve their outstanding performance in new environments. It is also possible to use genomic selection approach to increase the frequency of already present adaptive alleles in cosmopolitan breeds. The review examines recent work on the origin and evolution of Turano-Mongolian cattle breeds, adaptation of Turano-Mongolian cattle to extreme environments, and summarizes available information on potential candidate genes for climate adaptation of Turano-Mongolian breeds, including cold resistance genes, immune response genes, and high-altitude adaptation genes. The authors conclude that the current literature data do not provide preference to one of the two possible scenarios of Turano-Mongolian breed origins: as a result of the domestication of a wild aurochs at East Asia or as a result of the migration of taurine proto-population from the Middle East. Turano-Mongolian breeds show a high degree of adaptation to extreme climatic conditions (cold, heat, lack of oxygen in the highlands) and parasites (mosquitoes, ticks, bacterial and viral infections). As a result of high-density genotyping and sequencing of genomes and transcriptomes, prospective candidate genes and genetic variants involved in adaptation to environmental factors have recently been identified.
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Affiliation(s)
- N S Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Yurchenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D M Larkin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia The Royal Veterinary College, University of London, London, United Kingdom
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Buggiotti L, Yurchenko AA, Yudin NS, Vander Jagt CJ, Vorobieva NV, Kusliy MA, Vasiliev SK, Rodionov AN, Boronetskaya OI, Zinovieva NA, Graphodatsky AS, Daetwyler HD, Larkin DM. Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia. Mol Biol Evol 2021; 38:3093-3110. [PMID: 33784744 PMCID: PMC8321547 DOI: 10.1093/molbev/msab078] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Native cattle breeds represent an important cultural heritage. They are a reservoir of genetic variation useful for properly responding to agriculture needs in the light of ongoing climate changes. Evolutionary processes that occur in response to extreme environmental conditions could also be better understood using adapted local populations. Herein, different evolutionary histories of the world northernmost native cattle breeds from Russia were investigated. They highlighted Kholmogory as a typical taurine cattle, whereas Yakut cattle separated from European taurines approximately 5,000 years ago and contain numerous ancestral and some novel genetic variants allowing their adaptation to harsh conditions of living above the Polar Circle. Scans for selection signatures pointed to several common gene pathways related to adaptation to harsh climates in both breeds. But genes affected by selection from these pathways were mostly different. A Yakut cattle breed-specific missense mutation in a highly conserved NRAP gene represents a unique example of a young amino acid residue convergent change shared with at least 16 species of hibernating/cold-adapted mammals from six distinct phylogenetic orders. This suggests a convergent evolution event along the mammalian phylogenetic tree and fast fixation in a single isolated cattle population exposed to a harsh climate.
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Affiliation(s)
- Laura Buggiotti
- Royal Veterinary College, University of London, London, United Kingdom
| | - Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | | | - Nadezhda V Vorobieva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Mariya A Kusliy
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Sergei K Vasiliev
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Russia
| | - Andrey N Rodionov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Podolsk, Russia
| | - Oksana I Boronetskaya
- Moscow Agrarian Academy, Timiryazev Russian State Agrarian University, Moscow, Russia
| | | | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Denis M Larkin
- Royal Veterinary College, University of London, London, United Kingdom
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
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Zinovieva NA, Sheiko IP, Dotsev AV, Sheiko RI, Mikhailova ME, Sermyagin AA, Abdelmanova AS, Kharzinova VR, Reyer H, Wimmers K, Sölkner J, Pleshanov NV, Brem G. Genome-wide SNP analysis clearly distinguished the Belarusian Red cattle from other European cattle breeds. Anim Genet 2021; 52:720-724. [PMID: 34131930 DOI: 10.1111/age.13102] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 01/06/2023]
Abstract
Local breeds can serve as an important source of genetic variability in domestic animal species. This study aimed to assess the genetic diversity and population structure of Belarusian Red cattle and their differentiation from other European cattle populations based on genome-wide SNP genotypes. Twenty pedigree-recorded non-closely related cows of Belarusian Red cattle were genotyped using the Illumina BovineHD BeadChip. Genotypes of 22 other European cattle breeds were included in the study for comparison. A total of 28 562 SNPs passed through the quality control checks and were selected for analysis. The Belarusian Red cattle displayed a moderate level of genetic variability (U HE = 0.341, HO = 0.368), and the highest heterozygote excess (U FIS = -0.066), among the studied breeds; this reflects the contribution of multiple breeds to their formation. The principal component analysis, FST -based Neighbor-Net tree and Admixture clustering, clearly distinguished the Belarusian Red cattle from the other European cattle breeds. Moreover, the presence of ancestral genomic components of Danish Red and Brown Swiss breeds were clearly visible, which agrees with the breed's history and its recent development. Our study highlights the importance of maintaining the specific genomic components, which makes a significant contribution to the global genetic diversity in the modern population of Belarusian Red cattle, allowing us to consider them a valuable national genetic resource. Our research results will be useful for the development of conservation programs for this local cattle breed.
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Affiliation(s)
- N A Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - I P Sheiko
- Scientific and Practical Center of the National Academy of Sciences of Belarus for Animal Husbandry, Zhodino, 222160, Belarus
| | - A V Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - R I Sheiko
- Institute of Genetics and Cytology of the National Academy of Science of Belarus, Minsk, 220072, Belarus
| | - M E Mikhailova
- Institute of Genetics and Cytology of the National Academy of Science of Belarus, Minsk, 220072, Belarus
| | - A A Sermyagin
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - A S Abdelmanova
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - V R Kharzinova
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - H Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, 18196, Germany
| | - K Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, 18196, Germany
| | - J Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, 1180, Austria
| | - N V Pleshanov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, St. Petersburg - Pushkin, 196601, Russia
| | - G Brem
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, 1210, Austria
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Islam S, Reddy UK, Natarajan P, Abburi VL, Bajwa AA, Imran M, Zahoor MY, Abdullah M, Bukhari AM, Iqbal S, Ashraf K, Nadeem A, Rehman H, Rashid I, Shehzad W. Population demographic history and population structure for Pakistani Nili-Ravi breeding bulls based on SNP genotyping to identify genomic regions associated with male effects for milk yield and body weight. PLoS One 2020; 15:e0242500. [PMID: 33232358 PMCID: PMC7685427 DOI: 10.1371/journal.pone.0242500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 11/03/2020] [Indexed: 11/20/2022] Open
Abstract
The domestic Nili-Ravi water buffalo (Bubalus bubalis) is the best dairy animal contributing 68% to total milk production in Pakistan. In this study, we identified genome-wide single nucleotide polymorphisms (SNPs) to estimate various population genetic parameters such as diversity, pairwise population differentiation, linkage disequilibrium (LD) distribution and for genome-wide association study for milk yield and body weight traits in the Nili-Ravi dairy bulls that they may pass on to their daughters who are retained for milking purposes. The genotyping by sequencing approach revealed 13,039 reference genome-anchored SNPs with minor allele frequency of 0.05 among 167 buffalos. Population structure analysis revealed that the bulls were grouped into two clusters (K = 2), which indicates the presence of two different lineages in the Pakistani Nili-Ravi water buffalo population, and we showed the extent of admixture of these two lineages in our bull collection. LD analysis revealed 4169 significant SNP associations, with an average LD decay of 90 kb for these buffalo genome. Genome-wide association study involved a multi-locus mixed linear model for milk yield and body weight to identify genome-wide male effects. Our study further illustrates the utility of the genotyping by sequencing approach for identifying genomic regions to uncover additional demographic complexity and to improve the complex dairy traits of the Pakistani Nili-Ravi water buffalo population that would provide the lot of economic benefits to dairy industry.
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Affiliation(s)
- Saher Islam
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Umesh K. Reddy
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Purushothaman Natarajan
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Venkata Lakshmi Abburi
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Amna Arshad Bajwa
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Imran
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Yasir Zahoor
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Abdullah
- Department of Livestock Production, University of Veterinary and Animal Sciences, Pattoki, Pakistan
| | - Aamir Mehmood Bukhari
- Semen Production Unit, Qadirabad, District Sahiwal, Pakistan
- Livestock and Dairy Development Department, Government of the Punjab, Lahore, Pakistan
| | - Sajid Iqbal
- Semen Production Unit, Qadirabad, District Sahiwal, Pakistan
- Livestock and Dairy Development Department, Government of the Punjab, Lahore, Pakistan
| | - Kamran Ashraf
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Asif Nadeem
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Habibur Rehman
- Department of Physiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Imran Rashid
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Wasim Shehzad
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
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9
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Kierkegaard LS, Groeneveld LF, Kettunen A, Berg P. The status and need for characterization of Nordic animal genetic resources. ACTA AGR SCAND A-AN 2020. [DOI: 10.1080/09064702.2020.1722216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | | | - Anne Kettunen
- Farm Animal Section, NordGen – The Nordic Genetic Resource Center, Ås, Norway
- Nofima AS, Ås, Norway
| | - Peer Berg
- Farm Animal Section, NordGen – The Nordic Genetic Resource Center, Ås, Norway
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
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10
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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] [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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11
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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: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [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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12
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Sermyagin AA, Dotsev AV, Gladyr EA, Traspov AA, Deniskova TE, Kostyunina OV, Reyer H, Wimmers K, Barbato M, Paronyan IA, Plemyashov KV, Sölkner J, Popov RG, Brem G, Zinovieva NA. Whole-genome SNP analysis elucidates the genetic structure of Russian cattle and its relationship with Eurasian taurine breeds. Genet Sel Evol 2018; 50:37. [PMID: 29996786 PMCID: PMC6042431 DOI: 10.1186/s12711-018-0408-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/01/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The origin of native and locally developed Russian cattle breeds is linked to the historical, social, cultural, and climatic features of the diverse geographical regions of Russia. In the present study, we investigated the population structure of nine Russian cattle breeds and their relations to the cattle breeds from around the world to elucidate their origin. Genotyping of single nucleotide polymorphisms (SNPs) in Bestuzhev (n = 26), Russian Black-and-White (n = 21), Kalmyk (n = 14), Kholmogor (n = 25), Kostromsky (n = 20), Red Gorbatov (n = 23), Suksun (n = 20), Yakut (n = 25), and Yaroslavl cattle breeds (n = 21) was done using the Bovine SNP50 BeadChip. SNP profiles from an additional 70 breeds were included in the analysis as references. RESULTS The observed heterozygosity levels were quite similar in eight of the nine studied breeds (HO = 0.337-0.363) except for Yakut (Ho = 0.279). The inbreeding coefficients FIS ranged from -0.028 for Kalmyk to 0.036 for Russian Black-and-White and were comparable to those of the European breeds. The nine studied Russian breeds exhibited taurine ancestry along the C1 axis of the multidimensional scaling (MDS)-plot, but Yakut was clearly separated from the European taurine breeds on the C2 axis. Neighbor-Net and admixture analyses, discriminated three groups among the studied Russian breeds. Yakut and Kalmyk were assigned to a separate group because of their Turano-Mongolian origin. Russian Black-and-White, Kostromsky and Suksun showed transboundary European ancestry, which originated from the Holstein, Brown Swiss, and Danish Red breeds, respectively. The lowest level of introgression of transboundary breeds was recorded for the Kholmogor, Yaroslavl, Red Gorbatov and Bestuzhev breeds, which can be considered as an authentic genetic resource. CONCLUSIONS Whole-genome SNP analysis revealed that Russian native and locally developed breeds have conserved authentic genetic patterns in spite of the considerable influence of Eurasian taurine cattle. In this paper, we provide fundamental genomic information that will contribute to the development of more accurate breed conservation programs and genetic improvement strategies.
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Affiliation(s)
- Alexander A Sermyagin
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Elena A Gladyr
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Alexey A Traspov
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Olga V Kostyunina
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Mecklenburg-Vorpommern, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Mecklenburg-Vorpommern, Germany
| | - Mario Barbato
- Department of Animal Sciences, Food and Nutrition, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, Piacenza, Italy
| | - Ivan A Paronyan
- Russian Research Institute of Farm Animal Genetics and Breeding, Moskovskoe shosse 55a, St. Petersburg-Pushkin, Russia, 196601
| | - Kirill V Plemyashov
- Russian Research Institute of Farm Animal Genetics and Breeding, Moskovskoe shosse 55a, St. Petersburg-Pushkin, Russia, 196601
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Ruslan G Popov
- Yakut Scientific Research Institute of Agriculture, 23/1, ul. Bestuzheva-Marlynskogo, Yakutsk, Sakha Republic, Russia, 677001
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132.
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13
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Xu L, Haasl RJ, Sun J, Zhou Y, Bickhart DM, Li J, Song J, Sonstegard TS, Van Tassell CP, Lewin HA, Liu GE. Systematic Profiling of Short Tandem Repeats in the Cattle Genome. Genome Biol Evol 2018; 9:20-31. [PMID: 28172841 PMCID: PMC5381564 DOI: 10.1093/gbe/evw256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2016] [Indexed: 12/13/2022] Open
Abstract
Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive 2–6 base pair motifs in many mammalian genomes. Using high-throughput sequencing and experimental validations, we systematically profiled STRs in five Holsteins. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map, representing a substantial pool of polymorphism in dairy cattle. We observed significant STRs overlap with functional genes and quantitative trait loci (QTL). We performed evolutionary and population genetic analyses using over 20,000 common dinucleotide STRs. Besides corroborating the well-established positive correlation between allele size and variance in allele size, these analyses also identified dozens of outlier STRs based on two anomalous relationships that counter expected characteristics of neutral evolution. And one STR locus overlaps with a significant region of a summary statistic designed to detect STR-related selection. Additionally, our results showed that only 57.1% of STRs located within SNP-based linkage disequilibrium (LD) blocks whereas the other 42.9% were out of blocks. Therefore, a substantial number of STRs are not tagged by SNPs in the cattle genome, likely due to STR's distinct mutation mechanism and elevated polymorphism. This study provides the foundation for future STR-based studies of cattle genome evolution and selection.
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Affiliation(s)
- Lingyang Xu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, Beltsville, MD.,Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Department of Animal and Avian Sciences, University of Maryland, College Park, MD
| | - Ryan J Haasl
- Department of Biology, University of Wisconsin - Platteville, WI
| | - Jiajie Sun
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yang Zhou
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, Beltsville, MD.,College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shannxi, China
| | - Derek M Bickhart
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, Beltsville, MD
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, Beltsville, MD
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, Beltsville, MD
| | - Harris A Lewin
- Department of Evolution and Ecology, University of California, Davis, CA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, Beltsville, MD
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14
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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] [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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15
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Wang MD, Dzama K, Rees DJG, Muchadeyi FC. Tropically adapted cattle of Africa: perspectives on potential role of copy number variations. Anim Genet 2015; 47:154-64. [DOI: 10.1111/age.12391] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2015] [Indexed: 12/12/2022]
Affiliation(s)
- M. D. Wang
- Department of Animal Sciences; University of Stellenbosch; Private Bag X1 Matieland 7602 South Africa
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
| | - K. Dzama
- Department of Animal Sciences; University of Stellenbosch; Private Bag X1 Matieland 7602 South Africa
| | - D. J. G. Rees
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
| | - F. C. Muchadeyi
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
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16
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Dyer RJ. Population Graphs and Landscape Genetics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054150] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rodney J. Dyer
- Department of Biology and Center for Environmental Studies, Virginia Commonwealth University, Richmond, Virginia 23284-2012;
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17
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Wang Y, Xu L, Yan W, Li S, Wang J, Liu X, Hu J, Luo Y. Y chromosomal haplotype characteristics of domestic sheep (Ovis aries) in China. Gene 2015; 565:242-5. [PMID: 25865303 DOI: 10.1016/j.gene.2015.04.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 02/11/2015] [Accepted: 04/07/2015] [Indexed: 11/16/2022]
Abstract
Investigations on the variation present at the male-specific Y chromosome region provide strong information to understand the origin and evolution of domestic sheep. One SNP OY1 (g.88A>G) in the upstream region of SRY gene, and the microsatellite SRYM18 locus within ovine Y chromosome were analyzed in one hundred and forty five samples collected from eleven breeds in China. SNP OY1 was analyzed using PCR-SSCP method and sequencing. Two different PCR-SSCP patterns represented two specific sequences with sequence analysis revealing SNP-OY1 (g.88A>G) were observed, while SNP A-OY1 showed the most common frequency (82.8%). Sequencing of the SRYM18 region revealed one novel size fragment (A2) with different repetitive units. Seven haplotypes (H4, H5, H6, H7, H8, H9 and H12) and two novel haplotypes (Ha and Hb) were established using combined genotype analysis. H6 showed the highest frequency (43.4%) across all breeds, and H8 showed the second frequency (24.1%). Ha was only found in one breed (Tan), while Hb was present in three breeds (Gansu alpine, White Suffolk and Duolang). Our findings reveal one novel allele in SRYM18 region and two novel male haplotypes of domestic sheep in China.
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Affiliation(s)
- Yutao Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; The Key Laboratory of Ecology and Biological Resources in Yarkand Oasis at Colleges & Universities under the Department of Education of Xinjiang Uygur Autonomous Region, Kashgar Teachers College, Kashgar 844000, China
| | - Lei Xu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Wei Yan
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
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18
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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] [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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19
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Herrera-Arroyo ML, Sork VL, González-Rodríguez A, Rocha-Ramírez V, Vega E, Oyama K. Seed-mediated connectivity among fragmented populations of Quercus castanea (Fagaceae) in a Mexican landscape. AMERICAN JOURNAL OF BOTANY 2013; 100:1663-1671. [PMID: 23942083 DOI: 10.3732/ajb.1200396] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF STUDY Anthropogenic fragmentation is an ongoing process in many forested areas that may create loss of connectivity among tree populations and constitutes a serious threat to ecological and genetic processes. We tested the central hypothesis that seed dispersal mitigates the impact of fragmentation by comparing connectivity and genetic diversity of adult vs. seedling populations in recently fragmented populations of the Mexican red oak Quercus castanea. METHODS Adult individuals, established before fragmentation, and seedlings, established after fragmentation, were sampled at 33 forest fragments of variable size (0.2 to 294 ha) within the Cuitzeo basin, Michoacán state, and genotyped using seven highly polymorphic chloroplast microsatellite markers (cpSSRs). To test whether seed dispersal retains connectivity among fragmented populations, we compared genetic diversity and connectivity networks between adults and progeny and determined the effect of fragment size on these values. KEY RESULTS Seventy haplotypes were identified, 63 in the adults and 60 in the seedlings, with average within-population diversity (hS) values of 0.624 in the adults and 0.630 in the seedlings. A positive correlation of genetic diversity values with fragment size was found in the seedling populations but not in the adult populations. The network connectivity analysis revealed lower connectivity among seedling populations than among adults. The number of connections (edges) as well as other network properties, such as betweenness centrality, node degree and closeness, were significantly lower in the seedlings network. CONCLUSIONS Habitat fragmentation in this landscape is disrupting seed-dispersal-mediated genetic connectivity among extant populations.
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Affiliation(s)
- M Luisa Herrera-Arroyo
- Centro de Investigaciones en Ecosistemas. Universidad Nacional Autónoma de México UNAM, Antigua carretera a Pátzcuaro no. 8701, Col. Ex-hacienda San José de la Huerta, Morelia 58190 Michoacán, México
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20
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Gómez YM, Fernández M, Rivera D, Gómez G, Bernal JE. Genetic characterization of Colombian Brahman cattle using microsatellites markers. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413070041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Pham LD, Do DN, Binh NT, Nam LQ, Van Ba N, Thuy TTT, Hoan TX, Cuong VC, Kadarmideen HN. Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites. Livest Sci 2013. [DOI: 10.1016/j.livsci.2013.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Lenstra JA, Groeneveld LF, Eding H, Kantanen J, Williams JL, Taberlet P, Nicolazzi EL, Sölkner J, Simianer H, Ciani E, Garcia JF, Bruford MW, Ajmone-Marsan P, Weigend S. Molecular tools and analytical approaches for the characterization of farm animal genetic diversity. Anim Genet 2012; 43:483-502. [DOI: 10.1111/j.1365-2052.2011.02309.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2011] [Indexed: 12/30/2022]
Affiliation(s)
- J. A. Lenstra
- Faculty of Veterinary Medicine; Utrecht University; Utrecht; The Netherlands
| | - L. F. Groeneveld
- Institute of Farm Animal Genetics; Friedrich-Loeffler-Institut; Hoeltystr. 10; 31535; Neustadt; Germany
| | - H. Eding
- Animal Evaluations Unit; CRV; Arnhem; The Netherlands
| | - J. Kantanen
- Biotechnology and Food Research; MTT Agrifood Research Finland; FI-31600; Jokioinen; Finland
| | - J. L. Williams
- Parco Tecnologico Padano; via Einstein; 2600; Lodi; Italy
| | - P. Taberlet
- Laboratoire d'Ecologie Alpine; Université Joseph Fourier; BP 53; Grenoble; France
| | - E. L. Nicolazzi
- Istituto di Zootecnica and BioDNA Research Centre; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | - J. Sölkner
- Department of Sustainable Agricultural Systems; Animal Breeding Group; BOKU - University of Natural Resources and Life Sciences; Vienna; Austria
| | - H. Simianer
- Department of Animal Sciences; Animal Breeding and Genetics Group; Georg-August-University Göttingen; 37075; Göttingen; Germany
| | - E. Ciani
- Department of General and Environmental Physiology; University of Bari “Aldo Moro”; Bari; Italy
| | - J. F. Garcia
- Universidade Estadual Paulista; Araçatuba; Brazil
| | - M. W. Bruford
- Organisms and Environment Division; School of Biosciences; Cardiff University; Cardiff; UK
| | - P. Ajmone-Marsan
- Istituto di Zootecnica and BioDNA Research Centre; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | - S. Weigend
- Institute of Farm Animal Genetics; Friedrich-Loeffler-Institut; Hoeltystr. 10; 31535; Neustadt; Germany
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Wilkinson S, Wiener P, Teverson D, Haley CS, Hocking PM. Characterization of the genetic diversity, structure and admixture of British chicken breeds. Anim Genet 2011; 43:552-63. [DOI: 10.1111/j.1365-2052.2011.02296.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zerabruk M, Li MH, Kantanen J, Olsaker I, Ibeagha-Awemu EM, Erhardt G, Vangen O. Genetic diversity and admixture of indigenous cattle from North Ethiopia: implications of historical introgressions in the gateway region to Africa. Anim Genet 2011; 43:257-66. [PMID: 22486496 DOI: 10.1111/j.1365-2052.2011.02245.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microsatellite variation was surveyed to determine the genetic diversity, population structure and admixture of seven North Ethiopian cattle breeds by combining multiple microsatellite data sets of Indian and West African zebu, and European, African and Near-Eastern taurine in genetic analyses. Based on allelic distribution, we identified four diagnostic alleles (HEL1-123 bp, CSSM66-201 bp, BM2113-150 bp and ILSTS6-285 bp) specific to the Near-Eastern taurine. Results of genetic relationship and population structure analyses confirmed the previously established marked genetic distinction between taurine and zebu, and indicated further divergence among the bio-geographical groupings of breeds such as North Ethiopian, Indian and West African zebu, and African, European and Near-Eastern taurine. Using the diagnostic alleles for bio-geographical groupings and a Bayesian method for population structure inference, we estimated the genetic influences of major historical introgressions in North Ethiopian cattle. The breeds have been heavily (>90%) influenced by zebu, followed by African, European and the Near-Eastern taurine. Overall, North Ethiopian cattle show a high level of within-population genetic variation (e.g. observed heterozygosity = 0.659-0.687), which is in the upper range of that reported for domestic cattle and indicates their potential for future breeding applications, even in a global context. Rather low but significant population differentiation (F(ST) = 1.1%, P < 0.05) was recorded as a result of multiple introgression events and strong genetic exchanges among the North Ethiopian breeds.
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Affiliation(s)
- M Zerabruk
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Aas, Norway
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Li MH, Kantanen J, Michelson A, Saarma U. Genetic components of grey cattle in Estonia as revealed by microsatellite analysis using two Bayesian clustering methods. BMC Res Notes 2011; 4:37. [PMID: 21314923 PMCID: PMC3045957 DOI: 10.1186/1756-0500-4-37] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 02/11/2011] [Indexed: 11/17/2022] Open
Abstract
Background It was recently postulated that a few individual grey cattle still found in Estonia might be a relict of the old native cattle stock. Genotypes at 17 microsatellite loci from a total of 243 cattle from North European breeds and 11 grey cattle in Estonia were used in an attempt to clarify the genetic composition of the grey cattle. Findings We characterize the genetic components of 11 examples of the grey cattle in Estonia at the population and individual levels. Our results show that the grey cattle in Estonia are most genetically similar to the Holstein-Friesian breed and secondarily to the Estonian Red cattle. Conclusions Both Bayesian approaches gave similar results in terms of the identification of numbers of clusters and the estimation of proportions of genetic components. This study suggested that the Estonian grey cattle included in the analysis are a genetic composite resulting from cross-breeding of European dairy breeds.
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Affiliation(s)
- Meng-Hua Li
- Biotechnology and Food Research, MTT Agrifood Research Finland, FI-31600 Jokioinen, Finland.
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Amigues Y, Boitard S, Bertrand C, SanCristobal M, Rocha D. Genetic characterization of the Blonde d’Aquitaine cattle breed using microsatellite markers and relationship with three other French cattle populations. J Anim Breed Genet 2011; 128:201-8. [DOI: 10.1111/j.1439-0388.2010.00890.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Edwards CJ, Ginja C, Kantanen J, Pérez-Pardal L, Tresset A, Stock F, Gama LT, Penedo MCT, Bradley DG, Lenstra JA, Nijman IJ. Dual origins of dairy cattle farming--evidence from a comprehensive survey of European Y-chromosomal variation. PLoS One 2011; 6:e15922. [PMID: 21253012 PMCID: PMC3016991 DOI: 10.1371/journal.pone.0015922] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 11/29/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Diversity patterns of livestock species are informative to the history of agriculture and indicate uniqueness of breeds as relevant for conservation. So far, most studies on cattle have focused on mitochondrial and autosomal DNA variation. Previous studies of Y-chromosomal variation, with limited breed panels, identified two Bos taurus (taurine) haplogroups (Y1 and Y2; both composed of several haplotypes) and one Bos indicus (indicine/zebu) haplogroup (Y3), as well as a strong phylogeographic structuring of paternal lineages. METHODOLOGY AND PRINCIPAL FINDINGS Haplogroup data were collected for 2087 animals from 138 breeds. For 111 breeds, these were resolved further by genotyping microsatellites INRA189 (10 alleles) and BM861 (2 alleles). European cattle carry exclusively taurine haplotypes, with the zebu Y-chromosomes having appreciable frequencies in Southwest Asian populations. Y1 is predominant in northern and north-western Europe, but is also observed in several Iberian breeds, as well as in Southwest Asia. A single Y1 haplotype is predominant in north-central Europe and a single Y2 haplotype in central Europe. In contrast, we found both Y1 and Y2 haplotypes in Britain, the Nordic region and Russia, with the highest Y-chromosomal diversity seen in the Iberian Peninsula. CONCLUSIONS We propose that the homogeneous Y1 and Y2 regions reflect founder effects associated with the development and expansion of two groups of dairy cattle, the pied or red breeds from the North Sea and Baltic coasts and the spotted, yellow or brown breeds from Switzerland, respectively. The present Y1-Y2 contrast in central Europe coincides with historic, linguistic, religious and cultural boundaries.
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Affiliation(s)
- Ceiridwen J. Edwards
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Research Laboratory for Archaeology, University of Oxford, Oxford, United Kingdom
| | - Catarina Ginja
- Veterinary Genetics Laboratory, University of California Davis, Davis, California, United States of America
- Departamento de Genética, Melhoramento Animal e Reprodução, Instituto Nacional dos Recursos Biológicos, Fonte Boa, Vale de Santarém, Portugal
| | - Juha Kantanen
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
| | | | - Anne Tresset
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, CNRS Muséum National d'Histoire Naturelle, Paris, France
| | - Frauke Stock
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Luis T. Gama
- Departamento de Genética, Melhoramento Animal e Reprodução, Instituto Nacional dos Recursos Biológicos, Fonte Boa, Vale de Santarém, Portugal
| | - M. Cecilia T. Penedo
- Veterinary Genetics Laboratory, University of California Davis, Davis, California, United States of America
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Isaäc J. Nijman
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Tapio M, Ozerov M, Tapio I, Toro MA, Marzanov N, Cinkulov M, Goncharenko G, Kiselyova T, Murawski M, Kantanen J. Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia. BMC Genet 2010; 11:76. [PMID: 20698974 PMCID: PMC2931448 DOI: 10.1186/1471-2156-11-76] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 08/10/2010] [Indexed: 11/19/2022] Open
Abstract
Background Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation. Results Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity. Conclusions During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success.
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Affiliation(s)
- Miika Tapio
- Biotechnology and Food Research, MTT Agrifood Research Finland, 31600 Jokioinen, Finland
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A microsatellite-based analysis for the detection of selection on BTA1 and BTA20 in northern Eurasian cattle (Bos taurus) populations. Genet Sel Evol 2010; 42:32. [PMID: 20691068 PMCID: PMC2928188 DOI: 10.1186/1297-9686-42-32] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 08/06/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microsatellites surrounding functionally important candidate genes or quantitative trait loci have received attention as proxy measures of polymorphism level at the candidate loci themselves. In cattle, selection for economically important traits is a long-term strategy and it has been reported that microsatellites are linked to these important loci. METHODS We have investigated the variation of seven microsatellites on BTA1 (Bos taurus autosome 1) and 16 on BTA20, using bovine populations of typical production types and horn status in northern Eurasia. Genetic variability of these loci and linkage disequilibrium among these loci were compared with those of 28 microsatellites on other bovine chromosomes. Four different tests were applied to detect molecular signatures of selection. RESULTS No marked difference in locus variability was found between microsatellites on BTA1, BTA20 and the other chromosomes in terms of different diversity indices. Average D' values of pairwise syntenic markers (0.32 and 0.28 across BTA 1 and BTA20 respectively) were significantly (P < 0.05) higher than for non-syntenic markers (0.15). The Ewens-Watterson test, the Beaumont and Nichol's modified frequentist test and the Bayesian FST-test indicated elevated or decreased genetic differentiation, at SOD1 and AGLA17 markers respectively, deviating significantly (P < 0.05) from neutral expectations. Furthermore, lnRV, lnRH and lnRtheta' statistics were used for the pairwise population comparison tests and were significantly less variable in one population relative to the other, providing additional evidence of selection signatures for two of the 51 loci. Moreover, the three Finnish native populations showed evidence of subpopulation divergence at SOD1 and AGLA17. Our data also indicate significant intergenic linkage disequilibrium around the candidate loci and suggest that hitchhiking selection has played a role in shaping the pattern of observed linkage disequilibrium. CONCLUSION Hitchhiking due to tight linkage with alleles at candidate genes, e.g. the POLL gene, is a possible explanation for this pattern. The potential impact of selective breeding by man on cattle populations is discussed in the context of selection effects. Our results also suggest that a practical approach to detect loci under selection is to simultaneously apply multiple neutrality tests based on different assumptions and estimations.
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Tapio I, Tapio M, Li MH, Popov R, Ivanova Z, Kantanen J. Estimation of relatedness among non-pedigreed Yakutian cryo-bank bulls using molecular data: implications for conservation and breed management. Genet Sel Evol 2010; 42:28. [PMID: 20626845 PMCID: PMC2909159 DOI: 10.1186/1297-9686-42-28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 07/13/2010] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Yakutian cattle, the last remaining native cattle breed in Siberia, are well adapted to the extreme sub-arctic conditions. Nowadays only ca. 1200 purebred animals are left in Yakutia. The semen of six Yakutian bulls was stored in a cryo-bank without any pedigree documentation because of the traditional free herding style of the population. METHODS To clarify the genetic relatedness between these bulls and to provide recommendations to use their semen in future conservation and breed management programs, we have analysed 30 autosomal microsatellites and mitochondrial DNA sequences in 60 individuals including the six for which semen has been stored. Four relatedness estimators were calculated. In addition, we assessed the value of the cryo-bank bulls for the preservation of genetic variation of the contemporary Yakutian cattle by calculating allelic and gene diversity estimates and mean molecular coancestries. RESULTS On the basis of microsatellite variability, including the Yakutian cryo-bank bulls increases the allelic variation in the contemporary population by 3% and in the male subpopulation by 13%. In terms of the mean molecular coancestries, they are less related to the contemporary cow population than the breeding bulls and therefore could be used to reduce inbreeding in the living population. Although 30 loci are insufficient to resolve definitely their relatedness categories, the data suggest four pairs of cryo-bank bulls as possible half-sibs. CONCLUSIONS Our results show that even relatively limited cryo-bank storage of semen can carry allelic variation through a bottleneck. We propose a breeding scheme based on the rotation of breeding females and the division of cryo-bank bulls into three groups. Thus, if molecular data (e.g. autosomal microsatellite genotypes) for the contemporary population are available and based on relatively small-scale laboratory analyses, it is possible to avoid serious mistakes in their use for breeding applications. The approach suggested here based on the use of Yakutian cryo-bank semen can be easily extended to cryo-bank materials of other animals in future breeding programs.
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Affiliation(s)
- Ilma Tapio
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, FI-31600 Finland
| | - Miika Tapio
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, FI-31600 Finland
| | - Meng-Hua Li
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, FI-31600 Finland
| | - Ruslan Popov
- Yakutian Research Institute of Agriculture, 677002 Yakutsk, Sakha, Russia
| | - Zoya Ivanova
- Yakutian Research Institute of Agriculture, 677002 Yakutsk, Sakha, Russia
| | - Juha Kantanen
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, FI-31600 Finland
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Spatial Trends of Genetic Variation of Domestic Ruminants in Europe. DIVERSITY-BASEL 2010. [DOI: 10.3390/d2060932] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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An empirical assessment of individual-based population genetic statistical techniques: application to British pig breeds. Heredity (Edinb) 2010; 106:261-9. [PMID: 20551978 DOI: 10.1038/hdy.2010.80] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Recently developed Bayesian genotypic clustering methods for analysing genetic data offer a powerful tool to evaluate the genetic structure of domestic farm animal breeds. The unit of study with these approaches is the individual instead of the population. We aimed to empirically evaluate various individual-based population genetic statistical methods for characterization of genetic diversity and structure of livestock breeds. Eighteen British pig populations, comprising 819 individuals, were genotyped at 46 microsatellite markers. Three Bayesian genotypic clustering approaches, principle component analysis (PCA) and phylogenetic reconstruction were applied to individual multilocus genotypes to infer the genetic structure and diversity of the British pig breeds. Comparisons of the three Bayesian genotypic clustering methods (STRUCTURE, BAPS and STRUCTURAMA) revealed some broad similarities but also some notable differences. Overall, the methods agreed that majority of the British pig breeds are independent genetic units with little evidence of admixture. The three Bayesian genotypic clustering methods provided complementary, biologically credible clustering solutions but at different levels of resolution. BAPS detected finer genetic differentiation and in some cases, populations within breeds. Consequently, it estimated a greater number of underlying genetic populations (K, in the notation of Bayesian clustering methods). Two of the Bayesian methods (STRUCTURE and BAPS) and phylogenetic reconstruction provided similar success in assignment of individuals, supporting the use of these methods for breed assignment.
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Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S. Genetic diversity in farm animals--a review. Anim Genet 2010; 41 Suppl 1:6-31. [PMID: 20500753 DOI: 10.1111/j.1365-2052.2010.02038.x] [Citation(s) in RCA: 293] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.
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Affiliation(s)
- L F Groeneveld
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Hoeltystr. 10, 31535 Neustadt, Germany
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Revealing fine scale subpopulation structure in the Vietnamese H'Mong cattle breed for conservation purposes. BMC Genet 2010; 11:45. [PMID: 20525403 PMCID: PMC2889845 DOI: 10.1186/1471-2156-11-45] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 06/07/2010] [Indexed: 11/21/2022] Open
Abstract
Background During the last decades, there has been an acceleration of the loss of domestic animal biodiversity. For conservation purposes, the genetic diversity of the H'Mong cattle, an indigenous local breed was studied. Single-nucleotide polymorphisms (SNP) of the SRY gene and mtDNA D-Loop sequence were analysed to clarify the origin of the breed. The genetic diversity was assessed through genetic data with twenty-five FAO microsatellites, and morphometric data with five body measurements from 408 animals sampled from eight districts of the Ha Giang province. Results The SRY genes were all of the zebu type. Among the 27 mtDNA haplotypes, 12 haplotypes were of the taurine type and the remaining 15 of the zebu type. This indicates female taurine introgression in the zebu H'Mong. The observed and expected heterozygosity ranged from 0.616 to 0.673 and from 0.681 to 0.729 respectively according to district, with low genetic differentiation (FST = 0.0076). Multivariate analysis on morphometric and genetic data shows a separation of districts into two groups following a south-west/north-east cline and admixture analysis confirmed the two clusters, but no differentiation of taurine introgression between clusters was observed. A possible admixture with the Yellow cattle breed from a neighbouring province was suggested through genetic data and householder interviews. Conclusions In this study we demonstrate the interest of fine-scale sampling for the study of genetic structure of local breeds. Such a study allows avoiding erroneous conservation policies and on the contrary, proposes measures for conserving and limiting crossbreeding between the H'Mong and the Yellow cattle breeds.
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Li MH, Kantanen J. Genetic structure of Eurasian cattle (Bos taurus) based on microsatellites: clarification for their breed classification. Anim Genet 2009; 41:150-8. [PMID: 19845598 DOI: 10.1111/j.1365-2052.2009.01980.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We pool three previously published data sets and present population genetic analyses of microsatellite variation in 48 Bos taurus cattle breeds from a wide range of geographical origins in Eurasia, mostly its northern territory. Bayesian model-based clustering reveals six distinct clusters: besides a single-population cluster of the Yakutian Cattle from Far Eastern Siberia and a cluster of breeds characteristic of an early origin, the other four major clusters largely correspond to previously defined morphological subgroups of Red Lowland, Lowland Black-Pied, Longhorned Dairy and North European Polled cattle breeds. The results highlighted past expansion events of the productive breeds such as Danish Red, Angeln, Holstein-Friesian and Ayrshire in northern and Eastern Europe. Based on genetic assignment of the breeds and the availability of breed information, we provide a preliminary classification of the five breeds that were to date undefined. Furthermore, in the analysis of molecular variance, despite some correspondence between geographical proximity and genetic similarity, the breed classification appears to be a better predictor of genetic structure in the cattle populations (the among-group variance component: breed classification, 2.47%, P < 0.001; geographical division, 0.77%, P < 0.001).
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Affiliation(s)
- M-H Li
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
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36
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Heller R, Siegismund HR. Relationship between three measures of genetic differentiation G(ST), D(EST) and G'(ST): how wrong have we been? Mol Ecol 2009; 18:2080-3; discussion 2088-91. [PMID: 19645078 DOI: 10.1111/j.1365-294x.2009.04185.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R Heller
- Department of Biology, University of Copenhagen, Copenhagen Ø, Denmark.
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MEDUGORAC IVICA, MEDUGORAC ANA, RUSS INGOLF, VEIT-KENSCH CLAUDIAE, TABERLET PIERRE, LUNTZ BERNHARD, MIX HENRYM, FÖRSTER MARTIN. Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size. Mol Ecol 2009; 18:3394-410. [DOI: 10.1111/j.1365-294x.2009.04286.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Kantanen J, Edwards CJ, Bradley DG, Viinalass H, Thessler S, Ivanova Z, Kiselyova T, Cinkulov M, Popov R, Stojanović S, Ammosov I, Vilkki J. Maternal and paternal genealogy of Eurasian taurine cattle (Bos taurus). Heredity (Edinb) 2009; 103:404-15. [PMID: 19603063 DOI: 10.1038/hdy.2009.68] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Maternally inherited mitochondrial DNA (mtDNA) has been used extensively to determine origin and diversity of taurine cattle (Bos taurus) but global surveys of paternally inherited Y-chromosome diversity are lacking. Here, we provide mtDNA information on previously uncharacterised Eurasian breeds and present the most comprehensive Y-chromosomal microsatellite data on domestic cattle to date. The mitochondrial haplogroup T3 was the most frequent, whereas T4 was detected only in the Yakutian cattle from Siberia. The mtDNA data indicates that the Ukrainian and Central Asian regions are zones where hybrids between taurine and zebu (B. indicus) cattle have existed. This zebu influence appears to have subsequently spread into southern and southeastern European breeds. The most common Y-chromosomal microsatellite haplotype, termed here as H11, showed an elevated frequency in the Eurasian sample set compared with that detected in Near Eastern and Anatolian breeds. The taurine Y-chromosomal microsatellite haplotypes were found to be structured in a network according to the Y-haplogroups Y1 and Y2. These data do not support the recent hypothesis on the origin of Y1 from the local European hybridization of cattle with male aurochsen. Compared with mtDNA, the intensive culling of breeding males and male-mediated crossbreeding of locally raised native breeds has accelerated loss of Y-chromosomal variation in domestic cattle, and affected the contribution of genetic drift to diversity. In conclusion, to maintain diversity, breeds showing rare Y-haplotypes should be prioritised in the conservation of cattle genetic resources.
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Affiliation(s)
- J Kantanen
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland.
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Svensson E, Götherström A. Temporal fluctuations of Y-chromosomal variation in Bos taurus. Biol Lett 2009; 4:752-4. [PMID: 18713712 DOI: 10.1098/rsbl.2008.0342] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phylogeography has recently become more abundant in studies of demographic history of both wild and domestic species. A single nucleotide polymorphism (SNP) in the intron of the Y-chromosomal gene UTY19 displays a north-south gradient in modern cattle. Support for this geographical distribution of haplogroups has previously also been seen in ancient cattle from Germany. However, when analysing 38 historic remains of domestic bulls and three aurochs from northern Europe for this SNP we found no such association. Instead, we noted extensive amounts of temporal variation that can be attributed to transportation of cattle and late breed formation.
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Affiliation(s)
- Emma Svensson
- Department of Evolution, Genomics and Systematics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
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