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Elblinger E, Bokor J, Bokor Á, Altbäcker V, Nagy J, Szabó J, Sárdi B, Bâlteanu A, Rónai Z, Rózsa L, Rátky J, Anton I, Zsolnai A. Parentage testing and looking for single nucleotide markers associated with antler quality in deer ( Cervus elaphus). Arch Anim Breed 2022; 65:267-274. [PMID: 36035877 PMCID: PMC9399935 DOI: 10.5194/aab-65-267-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 07/12/2022] [Indexed: 11/22/2022] Open
Abstract
To provide a cost-efficient parentage testing kit for red deer (Cervus elaphus), a 63 SNP set has been developed from a high-density Illumina
BovineHD BeadChip containing 777 962 SNPs after filtering of genotypes of 50
stags. The successful genotyping rate was 38.6 % on the chip. The ratio
of polymorphic loci among effectively genotyped loci was 6.5 %. The
selected 63 SNPs have been applied to 960 animals to perform parentage
control. Thirty SNPs out of the 63 had worked on the OpenArray platform. Their
combined value of the probability of identity and exclusion probability was
4.9×10-11 and 0.99803, respectively. A search for loci linked with antler quality was also performed on the
genotypes of the above-mentioned stags. Association studies revealed 14 SNPs
associated with antler quality, where low-quality antlers with short and
thin main beam antlers had values from 1 to 2, while high-quality antlers
with long and strong main beams had values between 4 and 5. The chance for a
stag to be correctly identified as having high-value antlers is expected to
be over 88 %.
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Affiliation(s)
- Edith Elblinger
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Kaposvár, 7400, Hungary
| | - Julianna Bokor
- Game Management
Landscape Center, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Bőszénfa, 7475, Hungary
| | - Árpád Bokor
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Kaposvár, 7400, Hungary
| | - Vilmos Altbäcker
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Kaposvár, 7400, Hungary
| | - János Nagy
- Game Management
Landscape Center, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Bőszénfa, 7475, Hungary
| | - József Szabó
- Game Management
Landscape Center, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Bőszénfa, 7475, Hungary
| | - Bertalan Sárdi
- Game Management
Landscape Center, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Bőszénfa, 7475, Hungary
| | - Adrian Valentin Bâlteanu
- Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine,
Cluj-Napoca, Romania
| | - Zsolt Rónai
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Eötvös Loránd University, Budapest, 1053, Hungary
| | - László Rózsa
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Herceghalom, 2053, Hungary
| | - József Rátky
- Department of Obstetrics
and Food Animal Medicine Clinic, University of Veterinary Medicine Budapest, Budapest, 1078, Hungary
| | - István Anton
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Herceghalom, 2053, Hungary
| | - Attila Zsolnai
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Herceghalom, 2053, Hungary
- Institute for Farm Animal Gene Conservation, National Centre for
Biodiversity and Gene Conservation, Gödöllő, 2100, Hungary
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Gustine D, Barboza P, Adams L, Griffith B, Cameron R, Whitten K. Advancing the match-mismatch framework for large herbivores in the Arctic: Evaluating the evidence for a trophic mismatch in caribou. PLoS One 2017; 12:e0171807. [PMID: 28231256 PMCID: PMC5322966 DOI: 10.1371/journal.pone.0171807] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 01/26/2017] [Indexed: 11/17/2022] Open
Abstract
Climate-induced shifts in plant phenology may adversely affect animals that cannot or do not shift the timing of their reproductive cycle. The realized effect of potential trophic "mismatches" between a consumer and its food varies with the degree to which species rely on dietary income and stored capital. Large Arctic herbivores rely heavily on maternal capital to reproduce and give birth near the onset of the growing season but are they vulnerable to trophic mismatch? We evaluated the long-term changes in the temperatures and characteristics of the growing seasons (1970-2013), and compared growing conditions and dynamics of forage quality for caribou at peak parturition, peak lactation, and peak forage biomass, and plant senescence between two distinct time periods over 36 years (1977 and 2011-13). Despite advanced thaw dates (7-12 days earlier), increased growing season lengths (15-21 days longer), and consistent parturition dates, we found no decline in forage quality and therefore no evidence within this dataset for a trophic mismatch at peak parturition or peak lactation from 1977 to 2011-13. In Arctic ungulates that use stored capital for reproduction, reproductive demands are largely met by body stores deposited in the previous summer and autumn, which reduces potential adverse effects of any mismatch between food availability and timing of parturition. Climate-induced effects on forages growing in the summer and autumn ranges, however, do correspond with the demands of female caribou and their offspring to gain mass for the next reproductive cycle and winter. Therefore, we suggest the window of time to examine the match-mismatch framework in Arctic ungulates is not at parturition but in late summer-autumn, where the multiplier effects of small changes in forage quality are amplified by forage abundance, peak forage intake, and resultant mass gains in mother-offspring pairs.
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Affiliation(s)
- David Gustine
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America
| | - Perry Barboza
- Wildlife and Fisheries Science, Texas A&M University, College Station, Texas, United States of America
| | - Layne Adams
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America
| | - Brad Griffith
- U.S. Geological Survey, Alaska Cooperative Fish and Wildlife Research Unit, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Raymond Cameron
- Alaska Department of Fish and Game, Fairbanks, Alaska, United States of America
| | - Kenneth Whitten
- Alaska Department of Fish and Game, Fairbanks, Alaska, United States of America
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Chen M, Zheng Y, Hao Y, Mei Z, Wang K, Zhao Q, Zheng J, Wang D. Parentage-Based Group Composition and Dispersal Pattern Studies of the Yangtze Finless Porpoise Population in Poyang Lake. Int J Mol Sci 2016; 17:ijms17081268. [PMID: 27529217 PMCID: PMC5000666 DOI: 10.3390/ijms17081268] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/16/2016] [Accepted: 07/28/2016] [Indexed: 11/18/2022] Open
Abstract
Social behaviors are poorly known for the critically endangered Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis asiaeorientalis). Here, group composition and dispersal patterns of the YFP population living in the Poyang Lake were studied by parentage-based pedigree analyses using 21 microsatellite loci and a 597 bp segment of the mitochondrial DNA control region. In this study, 21 potential mother-offspring pairs and six potential father-offspring pairs (including two potential parents-offspring pairs) were determined, among which 12 natural mother-offspring groups and a maternal group of three generations were found. No genetically-determined fathers were found associated with their offspring. This study also found that maternally related porpoises at the reproductive state tend to group together. This suggest maternal relationship and reproductive state may be factors for grouping in the YFP population. In natural mother-offspring groups, male offspring were all younger than two years old, which suggest male offspring may leave their mothers at approximately two years of age, or at least they were not in tight association with their mothers as they may have been under two years old. However, female offspring can stay longer with their mothers and can reproduce in the natal group.
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Affiliation(s)
- Minmin Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology of the Chinese Academy of Sciences, Wuhan 430072, China.
- Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, School of Life Sciences, Anqing Normal University, Anqing 246133, China.
| | - Yang Zheng
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology of the Chinese Academy of Sciences, Wuhan 430072, China.
- University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Yujiang Hao
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology of the Chinese Academy of Sciences, Wuhan 430072, China.
| | - Zhigang Mei
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology of the Chinese Academy of Sciences, Wuhan 430072, China.
| | - Kexiong Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology of the Chinese Academy of Sciences, Wuhan 430072, China.
| | - Qingzhong Zhao
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology of the Chinese Academy of Sciences, Wuhan 430072, China.
| | - Jinsong Zheng
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology of the Chinese Academy of Sciences, Wuhan 430072, China.
| | - Ding Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology of the Chinese Academy of Sciences, Wuhan 430072, China.
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Radko A, Zalewski D, Rubiś D, Szumiec A. Genetic differentiation among 6 populations of red deer (Cervus elaphus L.) in Poland based on microsatellite DNA polymorphism. ACTA BIOLOGICA HUNGARICA 2014; 65:414-27. [PMID: 25475981 DOI: 10.1556/abiol.65.2014.4.6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recently, there has been considerable interest in genetic differentiation in the Cervidae family. A common tool used to determine genetic variation in different species, breeds and populations is DNA analysis, which allows for direct determination of the differences and changes within a group of animals. Because the analysis of microsatellite polymorphism in different Cervidae populations revealed considerable genetic variability in individual populations, it was important to test a set of markers in animals from these populations.The study was performed with muscle tissue and blood samples collected from a total of 793 red deer. Six groups (subpopulations) of red deer were defined according to region: Masurian (330 animals), Bieszczady (194 animals), Małopolska (80 animals), Sudety (76 animals), Lower Silesian (62 animals) and Lubusz (51 animals). The analysis involved 12 STR markers (BM1818, OarAE129, OarFCB5, OarFCB304, RM188, RT 1, RT 13, T26, T156, T193, T501, TGLA53), for which conditions for simultaneous amplification were established.Based on this study, it is concluded that the chosen set of 12 microsatellite markers could be used to evaluate the genetic structure and to monitor changes in Poland's red deer population.
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Affiliation(s)
- Anna Radko
- National Research Institute of Animal Production Department of Animal Cytogenetics and Molecular Genetics Krakowska 1 32-083 Balice Poland
| | - D Zalewski
- University of Warmia and Mazury in Olsztyn Department of Fur-bearing Animal Breeding and Game Management Oczapowskiego 5 10-719 Olsztyn Poland
| | - Dominika Rubiś
- National Research Institute of Animal Production Department of Animal Cytogenetics and Molecular Genetics Krakowska 1 32-083 Balice Poland
| | - Agnieszka Szumiec
- National Research Institute of Animal Production Department of Animal Cytogenetics and Molecular Genetics Krakowska 1 32-083 Balice Poland
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Haanes H, Rosvold J, Røed KH. Non-indigenous introgression into the Norwegian red deer population. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0431-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Haanes H, Røed KH, Mysterud A, Langvatn R, Rosef O. Consequences for genetic diversity and population performance of introducing continental red deer into the northern distribution range. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0048-1] [Citation(s) in RCA: 16] [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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Haanes H, Røed KH, Flagstad Ø, Rosef O. Genetic structure in an expanding cervid population after population reduction. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9781-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pérez-Espona S, Pérez-Barbería FJ, McLeod JE, Jiggins CD, Gordon IJ, Pemberton JM. Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus). Mol Ecol 2008; 17:981-96. [PMID: 18261043 DOI: 10.1111/j.1365-294x.2007.03629.x] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Landscape features have been shown to strongly influence dispersal and, consequently, the genetic population structure of organisms. Studies quantifying the effect of landscape features on gene flow of large mammals with high dispersal capabilities are rare and have mainly been focused at large geographical scales. In this study, we assessed the influence of several natural and human-made landscape features on red deer gene flow in the Scottish Highlands by analysing 695 individuals for 21 microsatellite markers. Despite the relatively small scale of the study area (115 x 87 km), significant population structure was found using F-statistics (F(ST) = 0.019) and the program structure, with major differentiation found between populations sampled on either side of the main geographical barrier (the Great Glen). To assess the effect of landscape features on red deer population structure, the ArcMap GIS was used to create cost-distance matrices for moving between populations, using a range of cost values for each of the landscape features under consideration. Landscape features were shown to significantly affect red deer gene flow as they explained a greater proportion of the genetic variation than the geographical distance between populations. Sea lochs were found to be the most important red deer gene flow barriers in our study area, followed by mountain slopes, roads and forests. Inland lochs and rivers were identified as landscape features that might facilitate gene flow of red deer. Additionally, we explored the effect of choosing arbitrary cell cost values to construct least cost-distance matrices and described a method for improving the selection of cell cost values for a particular landscape feature.
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Affiliation(s)
- S Pérez-Espona
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK.
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