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Perfilyeva A, Bespalova K, Kuzovleva Y, Mussabayev R, Begmanova М, Amirgalyeva A, Vishnyakova O, Nazarenko I, Zhaxsylykova A, Yerzhan A, Perfilyeva Y, Dzhaembaeva T, Khamchukova A, Plakhov K, Torekhanov A, Djansugurova L, Zhunussova G, Bekmanov B. Genetic diversity and origin of Kazakh Tobet Dogs. Sci Rep 2024; 14:23137. [PMID: 39367220 DOI: 10.1038/s41598-024-74061-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 09/23/2024] [Indexed: 10/06/2024] Open
Abstract
The Kazakh Tobet is an indigenous Kazakh dog breed that has been used to guard livestock since ancient times. To understand the genetic structure and phylogenetic relationship of the Kazakh Tobet breed with other herding and livestock guarding dog breeds, we analysed short tandem repeat data of 107 Kazakh Tobet dogs from different regions of Kazakhstan and Mongolia, as well as whole genome sequencing data from two Kazakh Tobet dogs and 43 dogs from 24 working breeds. Our results indicate a high genetic diversity of the Kazakh Tobet, with the average number of alleles per locus ranging from 6.00 to 10.22 and observed heterozygosity ranging from 76 to 78%. The breed has a complex genetic structure characterised by seven different clusters. The neighbour-joining tree constructed based on 14,668,406 autosomal and the maximum likelihood tree based on mitochondrial D-loop sequences indicate a common genetic heritage between the Kazakh Tobet, the Central Asian Shepherd Dog and the Turkish Akbash. The presence of haplotype A18 in the Kazakh Tobets supports the hypothesis of the ancient origin of the breed, which was previously suggested by archaeological finds and written sources. These results provide an important genetic basis for the ongoing efforts to improve the Kazakh Tobet breed, to ensure its preservation as an independent genetic lineage and to recognise a breed on an international level.
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Affiliation(s)
- Anastassiya Perfilyeva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Kira Bespalova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan.
| | - Yelena Kuzovleva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Rustam Mussabayev
- Laboratory of Informational Processes Analysis and Modelling, Institute of Information and Computational Technologies, Almaty, 050000, Kazakhstan
| | - Мamura Begmanova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Almira Amirgalyeva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Olga Vishnyakova
- Department of Сynology, Republican Federation of Public Associations of Hunters and Hunting Societies "Kansonar", Almaty, 050008, Kazakhstan
| | - Inna Nazarenko
- Department of Сynology, Republican Federation of Public Associations of Hunters and Hunting Societies "Kansonar", Astana, 020000, Kazakhstan
| | - Assel Zhaxsylykova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Arailym Yerzhan
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Yuliya Perfilyeva
- Laboratory of Molecular Immunology and Immunobiotechnology, M.A. Aitkhozhin's Institute of Molecular Biology and Biochemistry, Almaty, 050012, Kazakhstan
| | | | - Anna Khamchukova
- Laboratory of Biocenology and Hunting management, Institute of Zoology, Almaty, 050060, Kazakhstan
| | - Konstantin Plakhov
- Laboratory of Biocenology and Hunting management, Institute of Zoology, Almaty, 050060, Kazakhstan
| | - Aibyn Torekhanov
- Kazakh Research Institute of Livestock and Fodder Production, Almaty, 050071, Kazakhstan
| | - Leyla Djansugurova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Gulnur Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
| | - Bakhytzhan Bekmanov
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty, 050060, Kazakhstan
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Ahn B, Kang M, Jeon H, Kim JS, Jiang H, Ha J, Park C. Origin and population structure of native dog breeds in the Korean peninsula and East Asia. iScience 2023; 26:106982. [PMID: 37378348 PMCID: PMC10291505 DOI: 10.1016/j.isci.2023.106982] [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: 09/01/2022] [Revised: 01/13/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
To study the ancestry and phylogenetic relationships of native Korean dog breeds to other Asian dog populations, we analyzed nucleotide variations in whole-genome sequences of 205 canid individuals. Sapsaree, Northern Chinese indigenous dog, and Tibetan Mastiff were largely related to West Eurasian ancestry. Jindo, Donggyeongi, Shiba, Southern Chinese indigenous (SCHI), Vietnamese indigenous dogs (VIET), and Indonesian indigenous dogs were related to Southeast and East Asian ancestry. Among East Asian dog breeds, Sapsaree presented the highest haplotype sharing with German Shepherds, indicating ancient admixture of European ancestry to modern East Asian dog breeds. SCHI showed greater haplotype sharing with New Guinea singing dogs, VIET, and Jindo than with other Asian breeds. The predicted divergence time of East Asian populations from their common ancestor was approximately 2,000 to 11,000 years ago. Our results expand understanding of the genetic history of dogs in the Korean peninsula to the Asian continent and Oceanic region.
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Affiliation(s)
- Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Hyoim Jeon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jong-Seok Kim
- Department of Korean Jindo and Domestic Animal, Jindo 58927, Republic of Korea
| | - Hao Jiang
- College of Animal Science, Jilin University, Changchun, Jilin 130119, China
| | - Jihong Ha
- Korean Sapsaree Foundation, Gyeongsan 38412, Republic of Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
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Zhang S, Xu Z, Luo L, Gu S, Hu Z, Wan S, Gao Z. Genetic Diversity and Population Structure of Coilia nasus Revealed by 2b-RAD Sequencing. BIOLOGY 2023; 12:biology12040600. [PMID: 37106800 PMCID: PMC10135584 DOI: 10.3390/biology12040600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023]
Abstract
Coilia nasus is a threatened migratory species in the Yangtze River Basin. To reveal the genetic diversity of natural and farmed populations of C. nasus and the status of germplasm resources in the Yangtze River, the genetic diversity and structure of two wild populations (Yezhi Lake: YZ; Poyang Lake: PY) and two farmed populations (Zhenjiang: ZJ; Wuhan: WH) of C. nasus were analyzed using 44,718 SNPs obtained via 2b-RAD sequencing. The results indicate that both the wild and farmed populations had low genetic diversity, and germplasm resources have undergone varying degrees of degradation. Population genetic structure analyses indicated that the four populations may have come from two ancestral groups. Different amounts of gene flow were identified among WH, ZJ, and PY populations, but gene flow among YZ and other populations was low. It is speculated that the river-lake isolation of Yezhi Lake is the main cause of this phenomenon. In conclusion, this study revealed that genetic diversity reduction and germplasm resource degradation had occurred in both wild and farmed C. nasus, suggesting that conservation of its resources is of great urgency. This study provides a theoretical basis for the conservation and rational exploitation of germplasm resources for C. nasus.
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Affiliation(s)
- Shuangmeng Zhang
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zisheng Xu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Lifei Luo
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Shuxin Gu
- Zhenjiang Jiangzhiyuan Fishery Technology Co., Ltd., Zhenjiang 212213, China
| | - Zhen Hu
- Hubei Provincial Aquatic Technology Promotion Station, Wuhan 430060, China
| | - Shiming Wan
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zexia Gao
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Perfilyeva A, Bespalova K, Bespalov S, Begmanova М, Kuzovleva Y, Zhaniyazov Z, Vishnyakova O, Nazarenko I, Perfilyeva Y, Khamdiyeva O, Bekmanov B. Kazakh national dog breed Tazy: What do we know? PLoS One 2023; 18:e0282041. [PMID: 36888576 PMCID: PMC9994743 DOI: 10.1371/journal.pone.0282041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/07/2023] [Indexed: 03/09/2023] Open
Abstract
The Tazy or Kazakh National sighthound has been officially recognized as the national heritage of Kazakhstan. Comprehensive genetic studies of genetic diversity and population structure that could be used for selection and conservation of this unique dog breed have not been conducted so far. The aim of this study was to determine the genetic structure of the Tazy using microsatellite and SNP markers and to place the breed in the context of the world sighthound breeds. Our results showed that all 19 microsatellite loci examined were polymorphic. The observed number of alleles in the Tazy population varied from 6 (INU030 locus) to 12 (AHT137, REN169D01, AHTh260, AHT121, and FH2054 loci) with a mean of 9.778 alleles per locus. The mean number of effective alleles was 4.869 and ranged from 3.349 f to 4.841. All markers were highly informative (PIC values greater than 0.5) and ranged from 0.543 (REN247M23 locus) to 0.865 (AHT121 locus). The observed and expected heterozygosities in a total population were 0.748 and 0.769 and ranged from 0.746 to 0.750 and 0.656 to 0.769, respectively. Overall, the results confirmed that the Tazy breed has a high level of genetic diversity, no significant inbreeding, and a specific genetic structure. Three gene pools underlie the genetic diversity of the Tazy breed. SNP analysis using the CanineHD SNP array, which contains more than 170,000 SNP markers, showed that the Tazy breed is distinct from other sighthound breeds and genetically related to ancient eastern sighthound breeds sharing the same branch with the Afghan Hound and the Saluki. The results, together with archeological findings, confirm the ancient origin of the breed. The findings can be used for the conservation and international registration of the Tazy dog breed.
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Affiliation(s)
- Anastassiya Perfilyeva
- Department of Molecular Genetics, Institute of Genetics and Physiology, Almaty, Kazakhstan
| | - Kira Bespalova
- Department of Molecular Genetics, Institute of Genetics and Physiology, Almaty, Kazakhstan.,Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Sergey Bespalov
- Department of Theriology, Institute of Zoology, Almaty, Kazakhstan
| | - Мamura Begmanova
- Department of Molecular Genetics, Institute of Genetics and Physiology, Almaty, Kazakhstan
| | - Yelena Kuzovleva
- Department of Molecular Genetics, Institute of Genetics and Physiology, Almaty, Kazakhstan
| | - Zhassulan Zhaniyazov
- Department of Molecular Genetics, Institute of Genetics and Physiology, Almaty, Kazakhstan.,Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Olga Vishnyakova
- Department of Сynology, Republican Federation of Public Associations of Hunters and Hunting Societies "Kansonar", Almaty, Kazakhstan
| | - Inna Nazarenko
- Department of Сynology, Republican Federation of Public Associations of Hunters and Hunting Societies "Kansonar", Astana, Kazakhstan
| | - Yuliya Perfilyeva
- Department of Immunology, M.A. Aitkhozhin's Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Ozada Khamdiyeva
- Department of Molecular Genetics, Institute of Genetics and Physiology, Almaty, Kazakhstan
| | - Bakhytzhan Bekmanov
- Department of Molecular Genetics, Institute of Genetics and Physiology, Almaty, Kazakhstan.,Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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Evaluation of Genetic Diversity in Dog Breeds Using Pedigree and Molecular Analysis: A Review. DIVERSITY 2022. [DOI: 10.3390/d14121054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Domestic dogs are important for many economic and social reasons, and they have become a well-known model species for human disease. According to research, dog breeds exhibit significant levels of inbreeding and genetic diversity loss, decreasing the population’s ability to adapt in certain conditions, and indicating the need of conservation strategies. Before the development of molecular markers, pedigree information was used for genetic diversity management. In recent years, genomic tools are frequently applied for accurate estimation of genetic diversity and improved genetic conservation due to incomplete pedigrees and pedigree errors. The most frequently used molecular markers include PCR-based microsatellite markers (STRs) and DNA sequencing-based single-nucleotide polymorphism markers (SNP). The aim of this review was to highlight genetic diversity studies on dog breeds conducted using pedigree and molecular markers, as well as the importance of genetic diversity conservation in increasing the adaptability and survival of dog breed populations.
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Barrios N, González-Lagos C, Dreger DL, Parker HG, Nourdin-Galindo G, Hogan AN, Gómez MA, Ostrander EA. Patagonian sheepdog: Genomic analyses trace the footprints of extinct UK herding dogs to South America. PLoS Genet 2022; 18:e1010160. [PMID: 35482674 PMCID: PMC9049511 DOI: 10.1371/journal.pgen.1010160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/21/2022] [Indexed: 11/26/2022] Open
Abstract
Most modern dog breeds were developed within the last two hundred years, following strong and recent human selection based predominantly on aesthetics, with few modern breeds constructed solely to maximize their work potential. In many cases, these working breeds represent the last remnants of now lost populations. The Patagonian sheepdog (PGOD), a rare herding breed, is a remarkable example of such a population. Maintained as an isolated population for over 130 years, the PGOD offers a unique opportunity to understand the genetic relationship amongst modern herding breeds, determine key genomic structure of the founder PGOD populations, and investigate how canine genomic data can mirror human migration patterns. We thus analyzed the population structure of 159 PGOD, comparing them with 1514 dogs representing 175 established breeds. Using 150,069 SNPs from a high-density SNP genotyping array, we establish the genomic composition, ancestry, and genetic diversity of the population, complementing genomic data with the PGOD's migratory history to South America. Our phylogenetic analysis reveals that PGODs are most closely related to modern herding breeds hailing from the United Kingdom. Admixture models illustrate a greater degree of diversity and genetic heterogeneity within the very small PGOD population than in Western European herding breeds, suggesting the PGOD predates the 200-year-old construction of most pure breeds known today. We thus propose that PGODs originated from the foundational herding dogs of the UK, prior to the Victorian explosion of breeds, and that they are the closest link to a now-extinct population of herding dogs from which modern herding breeds descended.
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Grants
- Agencia Nacional de Investigación y Desarrollo, FONDECYT, Chile.
- Agencia Nacional de Investigación y Desarrollo, Beca Doctorado Nacional, 2018, Chile.
- Agencia Nacional de Investigación y Desarrollo, REDI, Chile.
- Agencia Nacional de Investigación y Desarrollo, PIA/BASAL, Chile.
- Intramural Program of the National Human Genome Research Institute of the National Institute of Health, Bethesda MD, USA.
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Affiliation(s)
- Natasha Barrios
- Instituto de Farmacología y Morfofisiología, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
- Escuela de Graduados, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - César González-Lagos
- Departamento de Ciencias, Facultad de Artes Liberales, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Dayna L. Dreger
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Heidi G. Parker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - Andrew N. Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marcelo A. Gómez
- Instituto de Farmacología y Morfofisiología, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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Kang M, Ahn B, Youk S, Lee YM, Kim JJ, Ha JH, Park C. Tracing the Origin of the RSPO2 Long-Hair Allele and Epistatic Interaction between FGF5 and RSPO2 in Sapsaree Dog. Genes (Basel) 2022; 13:genes13010102. [PMID: 35052442 PMCID: PMC8775186 DOI: 10.3390/genes13010102] [Citation(s) in RCA: 1] [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: 12/02/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 02/04/2023] Open
Abstract
Genetic analysis of the hair-length of Sapsaree dogs, a Korean native dog breed, showed a dominant mode of inheritance for long hair. Genome-Wide Association Study (GWAS) analysis and subsequent Mendelian segregation analysis revealed an association between OXR1, RSPO2, and PKHD1L1 on chromosome 13 (CFA13). We identified the previously reported 167 bp insertion in RSPO2 3’ untranslated region as a causative mutation for hair length variations. The analysis of 118 dog breeds and wolves revealed the selection signature on CFA13 in long-haired breeds. Haplotype analysis showed the association of only a few specific haplotypes to the breeds carrying the 167 bp insertion. The genetic diversity in the neighboring region linked to the insertion was higher in Sapsarees than in other Asian and European dog breeds carrying the same variation, suggesting an older history of its insertion in the Sapsaree genome than in that of the other breeds analyzed in this study. Our results show that the RSPO2 3’ UTR insertion is responsible for not only the furnishing phenotype but also determining the hair length of the entire body depending on the genetic background, suggesting an epistatic interaction between FGF5 and RSPO2 influencing the hair-length phenotype in dogs.
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Affiliation(s)
- Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (B.A.); (S.Y.)
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (B.A.); (S.Y.)
| | - Seungyeon Youk
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (B.A.); (S.Y.)
| | - Yun-Mi Lee
- Department of Biotechnology, Yeungnam University, Gyeongsan 36461, Korea; (Y.-M.L.); (J.-J.K.)
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 36461, Korea; (Y.-M.L.); (J.-J.K.)
| | - Ji-Hong Ha
- Korean Sapsaree Foundation, Gyeongsan 38412, Korea;
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (B.A.); (S.Y.)
- Correspondence: ; Tel.: +82-10-8826-1363
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Kang M, Ahn B, Youk S, Cho HS, Choi M, Hong K, Do JT, Song H, Jiang H, Kennedy LJ, Park C. High Allelic Diversity of Dog Leukocyte Antigen Class II in East Asian Dogs: Identification of New Alleles and Haplotypes. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09560-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Soh PXY, Hsu WT, Khatkar MS, Williamson P. Evaluation of genetic diversity and management of disease in Border Collie dogs. Sci Rep 2021; 11:6243. [PMID: 33737533 PMCID: PMC7973533 DOI: 10.1038/s41598-021-85262-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/28/2021] [Indexed: 01/31/2023] Open
Abstract
Maintaining genetic diversity in dog breeds is an important consideration for the management of inherited diseases. We evaluated genetic diversity in Border Collies using molecular and genealogical methods, and examined changes to genetic diversity when carriers for Trapped Neutrophil Syndrome (TNS) and Neuronal Ceroid Lipofuscinosis (NCL) are removed from the genotyped population. Genotype data for 255 Border Collies and a pedigree database of 83,996 Border Collies were used for analysis. Molecular estimates revealed a mean multi-locus heterozygosity (MLH) of 0.311 (SD 0.027), 20.79% of the genome consisted of runs of homozygosity (ROH ) > 1 Mb, effective population size (Ne) was 84.7, and mean inbreeding (F) was 0.052 (SD 0.083). For 227 genotyped Border Collies that had available pedigree information (GenoPed), molecular and pedigree estimates of diversity were compared. A reference population (dogs born between 2005 and 2015, inclusive; N = 13,523; RefPop) and their ancestors (N = 12,478) were used to evaluate the diversity of the population that are contributing to the current generation. The reference population had a Ne of 123.5, a mean F of 0.095 (SD 0.082), 2276 founders (f), 205.5 effective founders (fe), 28 effective ancestors (fa) and 10.65 (SD 2.82) founder genomes (Ng). Removing TNS and NCL carriers from the genotyped population had a small impact on diversity measures (ROH > 1 Mb, MLH, heterozygosity), however, there was a loss of > 10% minor allele frequency for 89 SNPs around the TNS mutation (maximum loss of 12.7%), and a loss of > 5% for 5 SNPs around the NCL mutation (maximum 5.18%). A common ancestor was identified for 38 TNS-affected dogs and 64 TNS carriers, and a different common ancestor was identified for 33 NCL-affected dogs and 28 carriers, with some overlap of prominent individuals between both pedigrees. Overall, Border Collies have a high level of genetic diversity compared to other breeds.
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Affiliation(s)
- Pamela Xing Yi Soh
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Wei Tse Hsu
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Mehar Singh Khatkar
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Peter Williamson
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW 2006 Australia
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Letko A, Minor KM, Jagannathan V, Seefried FR, Mickelson JR, Oliehoek P, Drögemüller C. Genomic diversity and population structure of the Leonberger dog breed. Genet Sel Evol 2020; 52:61. [PMID: 33054768 PMCID: PMC7557023 DOI: 10.1186/s12711-020-00581-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/02/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Leonberger is a giant dog breed formed in the 1850s in Germany. Its post-World War II popularity has resulted in a current global population of ~ 30,000 dogs. The breed has predispositions to neurodegenerative disorders and cancer, which is likely due in large part to limited genetic diversity. However, to date there is no scientific literature on the overall demography and genomic architecture of this breed. RESULTS We assessed extensive pedigree records, SNP array genotype data, and whole-genome sequences (WGS) on 142,072, 1203 and 39 Leonberger dogs, respectively. Pedigree analyses identified 22 founder animals and revealed an apparent popular sire effect. The average pedigree-based inbreeding coefficient of 0.29 and average kinship of 0.31 show a dramatic loss of genetic diversity. The observed average life span decreased over time from 9.4 years in 1989 to 7.7 years in 2004. A global health survey confirmed a high prevalence of cancer and neurological disorders. Analysis of SNP-based runs of homozygosity (ROH) identified 125,653 ROH with an average length of 5.88 Mb, and confirmed an average inbreeding coefficient of 0.28. Genome-wide filtering of the WGS data revealed 28 non-protein-changing variants that were present in all Leonberger individuals and a list of 22 potentially pathogenic variants for neurological disorders of which 50% occurred only in Leonbergers and 50% occurred rarely in other breeds. Furthermore, one of the two mtDNA haplogroups detected was present in one dog only. CONCLUSIONS The increasing size of the Leonberger population has been accompanied by a considerable loss of genetic diversity after the bottleneck that occurred in the 1940s due to the intensive use of popular sires resulting in high levels of inbreeding. This might explain the high prevalence of certain disorders; however, genomic data provide no evidence for fixed coding variants that explain these predispositions. The list of candidate causative variants for polyneuropathy needs to be further evaluated. Preserving the current genetic diversity is possible by increasing the number of individuals for breeding while restricting the number of litters per sire/dam. In addition, outcrossing would help optimize long-term genetic diversity and contribute to the sustainability and health of the population.
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Affiliation(s)
- Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Katie M. Minor
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota 55108 USA
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | | | - James R. Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota 55108 USA
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
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