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Liu D, Yang Y, Chen Z, Fan Y, Liu J, Xu Y, Ahmed Z, Zhang J, Li F, Qi X, Song W, Zhu K, Gongque J, Li G, Huang B, Lei C. Temperature adaptation patterns in Chinese cattle revealed by TRPM2 gene mutation analysis. Anim Biotechnol 2024; 35:2299944. [PMID: 38164963 DOI: 10.1080/10495398.2023.2299944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Cattle are sensitive to temperature fluctuations but adapt well to inclement weather conditions. When environmental temperatures exceed specific thresholds, heat stress becomes a critical concern for cattle. The TRPM2 gene, which resides on cattle chromosome 1 encodes a TRP channel protein, holding a unique capacity to sense temperature changes and facilitate rapid response to avoid heat stress. Here, we utilized the Bovine Genome Variation Database (BGVD) (http://animal.omics.pro/code/index.php/BosVar), and identified a missense mutation site, c.805A > G: p. Met269Val (rs527146862), within the TRPM2 gene. To elucidate the functional assessment of this mutation in temperature adaptation attributes of Chinese cattle, we genotyped 407 samples from 20 distinct breeds representing diverse climatic zones across China. The association analysis incorporates three temperature parameters and revealed compelling insights in terms of allele frequency. Interestingly, the prevalence of the wild-type allele A was notably higher among northern cattle breeds and this trend diminished gradually as observed in southern cattle populations. Conversely, the mutant-type allele G demonstrated a contrasting trend. Moreover, southern cattle exhibited markedly higher frequencies of GG and GA genotypes (P < 0.01). The presence of heterozygous and homozygous mutations appears to confer an enhanced capacity for adaptation to elevated temperatures. These results provide unequivocal correlation evidence between TRPM2 genotypes (AA, GA, GG) and environmental temperature parameters and comprehend the genetic mechanisms governing temperature adaptation in cattle. This provides valuable insights for strategic breed selection across diverse climatic regions, thereby aiding livestock production amid evolving climate challenges.
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Affiliation(s)
- Dekai Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Yifan Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Zhefu Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Yijie Fan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Yibing Xu
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Zulfiqar Ahmed
- Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Jammu and Kashmir, Pakistan
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Fuqiang Li
- Hunan Tianhua Industrial Corporation Ltd, Lianyuan, China
| | - Xingshan Qi
- Biyang Xianan Cattle Technology and Development Company Ltd, Biyang, China
| | - Weiru Song
- Animal Disease Prevention and Control Center of Yushu Tibetan Autonomous Prefecture, Yushu, China
| | - Kaixia Zhu
- Animal Disease Prevention and Control Center of Yushu Tibetan Autonomous Prefecture, Yushu, China
| | - Jiangcai Gongque
- Animal Disease Prevention and Control Center of Yushu Tibetan Autonomous Prefecture, Yushu, China
| | - Guomei Li
- Forestry and Grassland Comprehensive Service Center of Yushu Prefecture, Qinghai, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A and F University, Yangling, China
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Masharing N, Sodhi M, Chanda D, Singh I, Vivek P, Tiwari M, Kumari P, Mukesh M. ddRAD sequencing based genotyping of six indigenous dairy cattle breeds of India to infer existing genetic diversity and population structure. Sci Rep 2023; 13:9379. [PMID: 37296129 PMCID: PMC10256769 DOI: 10.1038/s41598-023-32418-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/27/2023] [Indexed: 06/12/2023] Open
Abstract
The present investigation aimed to identify genome wide SNPs and to carry out diversity and population structure study using ddRAD-seq based genotyping of 58 individuals of six indigenous milch cattle breeds (Bos indicus) such as Sahiwal, Gir, Rathi, Tharparkar, Red Sindhi and Kankrej of India. A high percentage of reads (94.53%) were mapped to the Bos taurus (ARS-UCD1.2) reference genome assembly. Following filtration criteria, a total of 84,027 high quality SNPs were identified across the genome of 6 cattle breeds with the highest number of SNPs observed in Gir (34,743), followed by Red Sindhi (13,092), Kankrej (12,812), Sahiwal (8956), Tharparkar (7356) and Rathi (7068). Most of these SNPs were distributed in the intronic regions (53.87%) followed by intergenic regions (34.94%) while only 1.23% were located in the exonic regions. Together with analysis of nucleotide diversity (π = 0.373), Tajima's D (D value ranging from - 0.295 to 0.214), observed heterozygosity (HO ranging from 0.464 to 0.551), inbreeding coefficient (FIS ranging from - 0.253 to 0.0513) suggested for the presence of sufficient within breed diversity in the 6 major milch breeds of India. The phylogenetic based structuring, principal component and admixture analysis revealed genetic distinctness as well as purity of almost all of the 6 cattle breeds. Overall, our strategy has successfully identified thousands of high-quality genome wide SNPs that will further enrich the Bos indicus representation basic information about genetic diversity and structure of 6 major Indian milch cattle breeds which should have implications for better management and conservation of valuable indicine cattle diversity.
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Affiliation(s)
- Nampher Masharing
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
- Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Monika Sodhi
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Divya Chanda
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Inderpal Singh
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Prince Vivek
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Manish Tiwari
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
- Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Parvesh Kumari
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Manishi Mukesh
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India.
- ICAR-NBAGR, Karnal, Haryana, 132001, India.
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Liu H, Zhai J, Wu H, Wang J, Zhang S, Li J, Niu Z, Shen C, Zhang K, Liu Z, Jiang F, Song E, Sun X, Wang Y, Lan X. Diversity of Mitochondrial DNA Haplogroups and Their Association with Bovine Antral Follicle Count. Animals (Basel) 2022; 12:ani12182350. [PMID: 36139210 PMCID: PMC9495067 DOI: 10.3390/ani12182350] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/30/2022] [Accepted: 09/05/2022] [Indexed: 12/02/2022] Open
Abstract
Maternal origins based on the bovine mitochondrial D-loop region are proven to have two main origins: Bos taurus and Bos indicus. To examine the association between the maternal origins of bovine and reproductive traits, the complete mitochondrial D-loop region sequences from 501 Chinese Holstein cows and 94 individuals of other breeds were analyzed. Based on the results obtained from the haplotype analysis, 260 SNPs (single nucleotide polymorphism), 32 indels (insertion/deletion), and 219 haplotypes were identified. Moreover, the nucleotide diversity (π) and haplotype diversity (Hd) were 0.024 ± 0.001 and 0.9794 ± 0.003, respectively, indicating the abundance of genetic resources in Chinese Holstein cows. The results of the median-joining network analysis showed two haplogroups (HG, including HG1 and HG2) that diverged in genetic distance. Furthermore, the two haplogroups were significantly (p < 0.05) correlated with the antral follicle (diameter ≥ 8 mm) count, and HG1 individuals had more antral follicles than HG2 individuals, suggesting that these different genetic variants between HG1 and HG2 correlate with reproductive traits. The construction of a neighbor-joining phylogenetic tree and principal component analysis also revealed two main clades (HG1 and HG2) with different maternal origins: Bos indicus and Bos taurus, respectively. Therefore, HG1 originating from the maternal ancestors of Bos indicus may have a greater reproductive performance, and potential genetic variants discovered may promote the breeding process in the cattle industry.
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Affiliation(s)
- Hongfei Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Junjun Zhai
- College of Life Science, Yulin University, Yulin 719000, China
| | - Hui Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jingyi Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Shaowei Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Jie Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhihan Niu
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Chenglong Shen
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Kaijuan Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Zhengqing Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Fugui Jiang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250000, China
| | - Enliang Song
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250000, China
| | - Xiuzhu Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
| | - Yongsheng Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
- Correspondence: (Y.W.); (X.L.)
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Correspondence: (Y.W.); (X.L.)
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Petretto E, Dettori ML, Pazzola M, Manca F, Amills M, Vacca GM. Mitochondrial DNA diversity of the Sardinian local cattle stock. Sci Rep 2022; 12:2486. [PMID: 35169207 PMCID: PMC8847569 DOI: 10.1038/s41598-022-06420-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/25/2022] [Indexed: 12/14/2022] Open
Abstract
The aim of this research was to characterize the genetic diversity of the Sarda (Sa, n = 131), Sardo Bruna (SB, n = 44) and Sardo Modicana (SM, n = 26) cattle breeds, reared in the island of Sardinia (Italy). A portion of the mitochondrial DNA hypervariable region was sequenced, in order to identify a potential signature of African introgression. The FST coefficients among populations ranged between 0.056 for Sa vs SB and 0.167 for SB vs SM. AMOVA analysis indicated there was a significant differentiation of the three breeds, although most of diversity was gathered at the within-breed level. The Median Joining Network of the Sardinian sequences showed a potential founder effect signature. A MJ network including Sardinian cattle plus African, Italian, Iberian and Asian sequences, revealed the presence of haplogroup T3, already detected in Sa cattle, and the presence of Hg T1 and Hg T1′2′3, in Sa and SB. The presence of a private haplotype belonging to haplogroup T1, which is characteristic of African taurine breeds, may be due to the introgression of Sardinian breeds with African cattle, either directly (most probable source: North African cattle) or indirectly (through a Mediterranean intermediary already introgressed with African blood).
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Affiliation(s)
- Elena Petretto
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Maria Luisa Dettori
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy.
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Fabio Manca
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Marcel Amills
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Giuseppe Massimo Vacca
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
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Mannen H, Yonezawa T, Murata K, Noda A, Kawaguchi F, Sasazaki S, Olivieri A, Achilli A, Torroni A. Cattle mitogenome variation reveals a post-glacial expansion of haplogroup P and an early incorporation into northeast Asian domestic herds. Sci Rep 2020; 10:20842. [PMID: 33257722 PMCID: PMC7704668 DOI: 10.1038/s41598-020-78040-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022] Open
Abstract
Surveys of mitochondrial DNA (mtDNA) variation have shown that worldwide domestic cattle are characterized by just a few major haplogroups. Two, T and I, are common and characterize Bos taurus and Bos indicus, respectively, while the other three, P, Q and R, are rare and are found only in taurine breeds. Haplogroup P is typical of extinct European aurochs, while intriguingly modern P mtDNAs have only been found in northeast Asian cattle. These Asian P mtDNAs are extremely rare with the exception of the Japanese Shorthorn breed, where they reach a frequency of 45.9%. To shed light on the origin of this haplogroup in northeast Asian cattle, we completely sequenced 14 Japanese Shorthorn mitogenomes belonging to haplogroup P. Phylogenetic and Bayesian analyses revealed: (1) a post-glacial expansion of aurochs carrying haplogroup P from Europe to Asia; (2) that all Asian P mtDNAs belong to a single sub-haplogroup (P1a), so far never detected in either European or Asian aurochs remains, which was incorporated into domestic cattle of continental northeastern Asia possibly ~ 3700 years ago; and (3) that haplogroup P1a mtDNAs found in the Japanese Shorthorn breed probably reached Japan about 650 years ago from Mongolia/Russia, in agreement with historical evidence.
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Affiliation(s)
- Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan.
| | - Takahiro Yonezawa
- Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Japan
| | - Kako Murata
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Aoi Noda
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
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Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
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Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Xia X, Huang G, Wang Z, Sun J, Wu Z, Chen N, Lei C, Hanif Q. Mitogenome Diversity and Maternal Origins of Guangxi Cattle Breeds. Animals (Basel) 2019; 10:E19. [PMID: 31861849 PMCID: PMC7022393 DOI: 10.3390/ani10010019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/14/2019] [Accepted: 12/18/2019] [Indexed: 01/16/2023] Open
Abstract
Guangxi Province is located in the southernmost region of China, adjacent to the hotspot that is considered to be the putative migratory corridor or domestication area for Chinese indicine cattle. Here, we investigated the evolutionary status of Guangxi native breeds, Longlin (n = 21), Nandan (n = 18), and Weizhou cattle (n = 17) using mitogenome sequencing. Our results show that Bos indicus sub-haplogroup I1a predominates in Guangxi cattle breeds. Population structure by multidimensional-scaling analysis significantly differentiates Weizhou from the other two breeds (Longlin and Nandan). Moreover, the mtDNA haplotype composition and FST values indicate that the formation of Longlin and Nandan breeds may have been affected by Indian indicine, whereas, Weizhou island might have preserved pure Chinese indicine cattle due to its geographical isolation. We speculate that following the initial entry of zebu into southern China, the subsequent introgression of Indian indicine may have influenced the matrilineal origin of local breeds in southwestern China.
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Affiliation(s)
- Xiaoting Xia
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (X.X.); (G.H.); (Z.W.); (J.S.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (N.C.); (C.L.)
| | - Guangyun Huang
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (X.X.); (G.H.); (Z.W.); (J.S.)
| | - Zihao Wang
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (X.X.); (G.H.); (Z.W.); (J.S.)
| | - Junli Sun
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (X.X.); (G.H.); (Z.W.); (J.S.)
| | - Zhuyue Wu
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (X.X.); (G.H.); (Z.W.); (J.S.)
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (N.C.); (C.L.)
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (N.C.); (C.L.)
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad 577, Pakistan;
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Abundant Genetic Diversity of Yunling Cattle Based on Mitochondrial Genome. Animals (Basel) 2019; 9:ani9090641. [PMID: 31480663 PMCID: PMC6769864 DOI: 10.3390/ani9090641] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Mitochondrial DNA (mtDNA) analysis is a critical tool in assessing the maternal origin, phylogeny and population structure of domestic animals. Yunling cattle are a composite breed that was created by local Yunnan cattle breeds (as a maternal line) 30 years ago. It can be said that Yunling cattle represent important reservoirs of genetic diversity of local Yunnan cattle. Yunling cattle are characterized as a tropical/subtropical breed with fast growth, heat tolerance and parasite resistance, and can survive in a harsh environment and on low-quality roughage. Assessing the genetic characteristics of Yunling cattle is of particular importance for reasonable breeding strategies for Yunling cattle and the design of a local Yunnan cattle conservation program. Abstract Yunling cattle are a composite beef cattle breed, combining Brahman (1/2), Murray Grey (1/4) and Local Yunnan cattle (1/4), that was developed in Yunnan, China in the 1980s. Understanding the genetic information of Yunling cattle is of great significance to the development of reasonable breeding strategies for this breed. In the present study, we assessed the current genetic status of Yunling cattle in Yunnan Province (China) by analyzing the variability of the whole mitochondrial genome of 129 individuals. Altogether, 129 sequences displayed 47 different haplotypes. The haplotype diversity and the average number of nucleotide differences were 0.964 and 128.074, respectively. Phylogenetic analyses classified Yunling cattle into seven haplogroups: T1, T2, T3, T4, T6, I1 and I2. Haplogroup I1 was found to be predominant (41.86%), followed by T3 (28.68%). Furthermore, we also identified a novel haplogroup, T6, and defined the sub-haplogroup I1a in Yunling cattle. According to the formation process of Yunling cattle (local Yunnan cattle as the maternal line), the high genetic diversities in the mitochondria of Yunling cattle could be due to the complex maternal origin of local Yunnan cattle. Further studies about local Yunnan breeds are necessary to determine the exact source of haplogroup T6 in Yunling cattle. Our results will be useful for the evaluation and effective management of Yunling cattle.
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9
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Utsunomiya YT, Milanesi M, Fortes MRS, Porto-Neto LR, Utsunomiya ATH, Silva MVGB, Garcia JF, Ajmone-Marsan P. Genomic clues of the evolutionary history of Bos indicus cattle. Anim Genet 2019; 50:557-568. [PMID: 31475748 DOI: 10.1111/age.12836] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2019] [Indexed: 01/08/2023]
Abstract
Together with their sister subspecies Bos taurus, zebu cattle (Bos indicus) have contributed to important socioeconomic changes that have shaped modern civilizations. Zebu cattle were domesticated in the Indus Valley 8000 years before present (YBP). From the domestication site, they expanded to Africa, East Asia, southwestern Asia and Europe between 4000 and 1300 YBP, intercrossing with B. taurus to form clinal variations of zebu ancestry across the landmass of Afro-Eurasia. In the past 150 years, zebu cattle reached the Americas and Oceania, where they have contributed to the prosperity of emerging economies. The zebu genome is characterized by two mitochondrial haplogroups (I1 and I2), one Y chromosome haplogroup (Y3) and three major autosomal ancestral groups (Indian-Pakistani, African and Chinese). Phenotypically, zebu animals are recognized by their hump, large ears and excess skin. They are rustic, resilient to parasites and capable of bearing the hot and humid climates of the tropics. Many resources are available to study the zebu genome, including commercial arrays of SNP, reference assemblies and publicly available genotypes and whole-genome sequences. Nevertheless, many of these resources were initially developed to support research and subsidize industrial applications in B. taurus, and therefore they can produce bias in data analysis. The combination of genomics with precision agriculture holds great promise for the identification of genetic variants affecting economically important traits such as tick resistance and heat tolerance, which were naturally selected for millennia and played a major role in the evolution of B. indicus cattle.
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Affiliation(s)
- Y T Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M Milanesi
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Chemistry Bld, 68 Cooper Rd, Brisbane, 4072, Qld, Australia
| | - L R Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia QLD, Brisbane, 4067, Qld, Australia
| | - A T H Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M V G B Silva
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Gado de Leite, Juiz de Fora, MG, 360381330, Brazil
| | - J F Garcia
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900 Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, Brazil
| | - P Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA and BioDNA, Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, Piacenza, 29122, Italy
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10
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Siripan S, Wonnapinij P, Auetrakulvit P, Wangthongchaicharoen N, Surat W. Origin of prehistoric cattle excavated from four archaeological sites in central and northeastern Thailand. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:609-617. [PMID: 30957607 DOI: 10.1080/24701394.2019.1597072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cattle have been domesticated in Southeast Asia, including Thailand, for thousands of years, but the history of cattle domestication in the region remains unclear. To date, only genetic studies of modern Thai cattle DNA have been reported. To gain some insight into cattle domestication in the country, a total of 56 cattle remains excavated from four archaeological sites (dated to between 3550 and 1700 years before present (YBP)) in northeastern and central Thailand were analysed in this study. Of 56, the 157-bp D-loop fragment was successfully generated from 26 samples, all of which belonged to Bos taurus in haplogroup T/T3. One haplotype contained 19 members from all four archaeological sites and clustered with the ancient B. taurus from Iran, Turkey and China. Other haplotypes have not shared haplotype with B. taurus from other countries but they showed close relationship to those from China. This represents the first genetic evidence that B. taurus was domesticated in Thailand between 3550 and 1700 YBP. In addition, the close relationship among ancient Thai, Iranian and Chinese taurines suggests that cattle from the Near East were introduced into North China, and were subsequently brought into Thailand thousands of years ago.
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Affiliation(s)
- Sirianong Siripan
- a Department of Genetics, Faculty of Science, Evolutionary Genetics and Computational Biology Research Unit , Kasetsart University , Bangkok , Thailand
| | - Passorn Wonnapinij
- a Department of Genetics, Faculty of Science, Evolutionary Genetics and Computational Biology Research Unit , Kasetsart University , Bangkok , Thailand.,b Centre for Advanced Studies in Tropical Natural Resources , National Research University-Kasetsart University, Kasetsart University (CASTNAR, NRU-KU) , Bangkok , Thailand
| | - Prasit Auetrakulvit
- c Department of Archaeology, Faculty of Archaeology , Silpakorn University , Bangkok , Thailand
| | | | - Wunrada Surat
- a Department of Genetics, Faculty of Science, Evolutionary Genetics and Computational Biology Research Unit , Kasetsart University , Bangkok , Thailand.,b Centre for Advanced Studies in Tropical Natural Resources , National Research University-Kasetsart University, Kasetsart University (CASTNAR, NRU-KU) , Bangkok , Thailand
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11
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Cai Y, Jiao T, Lei Z, Liu L, Zhao S. Maternal genetic and phylogenetic characteristics of domesticated cattle in northwestern China. PLoS One 2018; 13:e0209645. [PMID: 30589861 PMCID: PMC6307701 DOI: 10.1371/journal.pone.0209645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 12/10/2018] [Indexed: 11/19/2022] Open
Abstract
Northwestern China, an important part of the Silk Road, was the birthplace of the Zhouzu farming culture. The domestication of cattle as an important aspect of farming culture has had a long history in northwestern China. In this study, we assessed the maternal structure and phylogeny of cattle by analyzing the mitochondrial DNA hypervariable segment I (HVS-I) in 698 native cattle from eight areas of northwestern China. The phylogenetic analyses revealed two highly divergent mtDNA clades: clade T, which had four sub-clades (Ta—Td), and clade I. The cattle domesticated from Bos taurus showed a clear dominant distribution pattern in northwestern China. The nucleotide diversity of the Bos indicus clade was lower than that of clades from Bos taurus. In summary, our results suggest that the native cattle of northwestern China were domesticated from two different maternal ancestors, Bos taurus and Bos indicus, which migrated to the central plains of China from the north and south, respectively, with Bos taurus remaining at the edges of the region. The population expansion of the cattle domesticated from Bos taurus occurred in the Longdong region of Gansu Province, and these cattle formed four relatively independent evolutionary branches. Subsequent to this expansion event, Bos indicus migrated from southern to northern China.
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Affiliation(s)
- Yuan Cai
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, PR China
| | - Ting Jiao
- College of Grassland, Gansu Agricultural University, Lanzhou, Gansu, PR China
| | - Zhaomin Lei
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, PR China
| | - Li Liu
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, PR China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, PR China
- * E-mail:
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12
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Xia X, Qu K, Zhang G, Jia Y, Ma Z, Zhao X, Huang Y, Chen H, Huang B, Lei C. Comprehensive analysis of the mitochondrial DNA diversity in Chinese cattle. Anim Genet 2018; 50:70-73. [PMID: 30421479 DOI: 10.1111/age.12749] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2018] [Indexed: 12/15/2022]
Abstract
Complete mitochondrial DNA D-loop sequences of 1105 individuals were used to assess the diversity of maternal lineages of cattle populations in China. In total, 250 taurine and 88 zebu haplotypes were identified. Five main haplogroups-T1a, T2, T3, T4 and T5-were identified in Bos taurus, whereas Bos indicus harbored two haplogroups-I1 and I2. Our results suggest that the distribution of T1a in Asia was concentrated mainly in the northeast region (northeast China, Korea and Japan); haplogroups T2, T3 and T4 were predominant in Chinese cattle; and T5 was sporadically detected in Mongolian and Pingwu cattle. In contrast to the widespread presence of I1, I2 was distributed only in southwestern China (Yunnan-Guizhou Plateau and the Tibet Autonomous Region) and Xinjiang Uygur Autonomous Region. This is the first time that all five taurine haplogroups and two zebu haplogroups have been found in Mongolian cattle. In addition, eight individuals in Tibetan cattle carried the Bos grunniens mtDNA type. The high mtDNA diversity (H = 0.904 ± 0.008) and the weak genetic structure among the 57 Chinese cattle breeds/populations are consistent with their complex historical background, migration route and ecological environment.
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Affiliation(s)
- X Xia
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - K Qu
- Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan, 650212, China
| | - G Zhang
- Branch of Animal Science, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin, 136100, China
| | - Y Jia
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Z Ma
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai, 810016, China
| | - X Zhao
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Y Huang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - H Chen
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - B Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan, 650212, China
| | - C Lei
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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13
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Elayadeth‐Meethal M, Thazhathu Veettil A, Maloney SK, Hawkins N, Misselbrook TH, Sejian V, Rivero MJ, Lee MRF. Size does matter: Parallel evolution of adaptive thermal tolerance and body size facilitates adaptation to climate change in domestic cattle. Ecol Evol 2018; 8:10608-10620. [PMID: 30464832 PMCID: PMC6238145 DOI: 10.1002/ece3.4550] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/01/2018] [Accepted: 08/04/2018] [Indexed: 01/18/2023] Open
Abstract
The adaptive potential of livestock under a warming climate is increasingly relevant in relation to the growing pressure of global food security. Studies on heat tolerance demonstrate the interplay of adaptation and acclimatization in functional traits, for example, a reduction in body size and enhanced tolerance in response to a warming climate. However, current lack of understanding of functional traits and phylogenetic history among phenotypically distinct populations constrains predictions of climate change impact. Here, we demonstrate evidence of parallel evolution in adaptive tolerance to heat stress in dwarf cattle breeds (DCB, Bos taurus indicus) and compare their thermoregulatory responses with those in standard size cattle breeds (SCB, crossbred, Bos taurus indicus × Bos taurus taurus). We measured vital physiological, hematological, biochemical, and gene expression changes in DCB and SCB and compared the molecular phylogeny using mitochondrial genome (mitogenome) analysis. Our results show that SCB can acclimatize in the short term to higher temperatures but reach their tolerance limit under prevailing tropical conditions, while DCB is adapted to the warmer climate. Increased hemoglobin concentration, reduced cellular size, and smaller body size enhance thermal tolerance. Mitogenome analysis revealed that different lineages of DCB have evolved reduced size independently, as a parallel adaptation to heat stress. The results illustrate mechanistic ways of dwarfing, body size-dependent tolerance, and differential fitness in a large mammal species under harsh field conditions, providing a background for comparing similar populations during global climate change. These demonstrate the value of studies combining functional, physiological, and evolutionary approaches to delineate adaptive potential and plasticity in domestic species. We thus highlight the value of locally adapted breeds as a reservoir of genetic variation contributing to the global domestic genetic resource pool that will become increasingly important for livestock production systems under a warming climate.
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Affiliation(s)
- Muhammed Elayadeth‐Meethal
- Kerala Veterinary and Animal Sciences UniversityWayanadIndia
- School of Human SciencesUniversity of Western AustraliaCrawleyAustralia
- Rothamsted ResearchNorth WykeUK
| | | | - Shane K. Maloney
- School of Human SciencesUniversity of Western AustraliaCrawleyAustralia
| | | | | | - Veerasamy Sejian
- ICAR‐National Institute of Animal Nutrition and PhysiologyBangaloreIndia
| | | | - Michael R. F. Lee
- Rothamsted ResearchNorth WykeUK
- Bristol Veterinary SchoolUniversity of BristolLangfordUK
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14
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Mitochondrial diversity and phylogeographic structure of native cattle breeds from Yunnan, Southwestern China. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Species composition and environmental adaptation of indigenous Chinese cattle. Sci Rep 2017; 7:16196. [PMID: 29170422 PMCID: PMC5700937 DOI: 10.1038/s41598-017-16438-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/13/2017] [Indexed: 12/13/2022] Open
Abstract
Indigenous Chinese cattle combine taurine and indicine origins and occupy a broad range of different environments. By 50 K SNP genotyping we found a discontinuous distribution of taurine and indicine cattle ancestries with extremes of less than 10% indicine cattle in the north and more than 90% in the far south and southwest China. Model-based clustering and f4-statistics indicate introgression of both banteng and gayal into southern Chinese cattle while the sporadic yak influence in cattle in or near Tibetan area validate earlier findings of mitochondrial DNA analysis. Geographic patterns of taurine and indicine mitochondrial and Y-chromosomal DNA diversity largely agree with the autosomal cline. The geographic distribution of the genomic admixture of different bovine species is proposed to be the combined effect of prehistoric immigrations, gene flow, major rivers acting as genetic barriers, local breeding objectives and environmental adaptation. Whole-genome scan for genetic differentiation and association analyses with both environmental and morphological covariables are remarkably consistent with previous studies and identify a number of genes implicated in adaptation, which include TNFRSF19, RFX4, SP4 and several coat color genes. We propose indigenous Chinese cattle as a unique and informative resource for gene-level studies of climate adaptation in mammals.
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16
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Di Lorenzo P, Lancioni H, Ceccobelli S, Curcio L, Panella F, Lasagna E. Uniparental genetic systems: a male and a female perspective in the domestic cattle origin and evolution. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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17
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Kim JH, Lee SS, Kim SC, Choi SB, Kim SH, Lee CW, Jung KS, Kim ES, Choi YS, Kim SB, Kim WH, Cho CY. Haplogroup Classification of Korean Cattle Breeds Based on Sequence Variations of mtDNA Control Region. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:624-30. [PMID: 26954229 PMCID: PMC4852222 DOI: 10.5713/ajas.15.0692] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/23/2015] [Accepted: 01/05/2016] [Indexed: 11/27/2022]
Abstract
Many studies have reported the frequency and distribution of haplogroups among various cattle breeds for verification of their origins and genetic diversity. In this study, 318 complete sequences of the mtDNA control region from four Korean cattle breeds were used for haplogroup classification. 71 polymorphic sites and 66 haplotypes were found in these sequences. Consistent with the genetic patterns in previous reports, four haplogroups (T1, T2, T3, and T4) were identified in Korean cattle breeds. In addition, T1a, T3a, and T3b sub-haplogroups were classified. In the phylogenetic tree, each haplogroup formed an independent cluster. The frequencies of T3, T4, T1 (containing T1a), and T2 were 66%, 16%, 10%, and 8%, respectively. Especially, the T1 haplogroup contained only one haplotype and a sample. All four haplogroups were found in Chikso, Jeju black and Hanwoo. However, only the T3 and T4 haplogroups appeared in Heugu, and most Chikso populations showed a partial of four haplogroups. These results will be useful for stable conservation and efficient management of Korean cattle breeds.
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Affiliation(s)
- Jae-Hwan Kim
- Animal Genetic Resources Research Center, NIAS, RDA, Namwon 55717, Korea
| | - Seong-Su Lee
- Animal Genetic Resources Research Center, NIAS, RDA, Namwon 55717, Korea
| | - Seung Chang Kim
- Animal Genetic Resources Research Center, NIAS, RDA, Namwon 55717, Korea
| | - Seong-Bok Choi
- Animal Genetic Resources Research Center, NIAS, RDA, Namwon 55717, Korea
| | - Su-Hyun Kim
- Gyeonggi Livestock and Veterinary Service, Suwon 16381, Korea
| | - Chang Woo Lee
- Gangwon Provincial Livestock Research Center, Hoengseong 25266, Korea
| | - Kyoung-Sub Jung
- Chungbuk Institute of Livestock and Veterinary Research, Cheongwon 28153, Korea
| | - Eun Sung Kim
- Jeonbuk Institute of Livestock and Veterinary Research, Gimje 54324, Korea
| | - Young-Sun Choi
- Jeonnam Agricultural Research and Extension Services, Gangjin 59213, Korea
| | - Sung-Bok Kim
- Chungnam Institute of Livestock Experiment Research, Cheongyang 33350, Korea
| | - Woo Hyun Kim
- Gyeongbuk Livestock Research Institute, Yeongju 36052, Korea
| | - Chang-Yeon Cho
- Animal Genetic Resources Research Center, NIAS, RDA, Namwon 55717, Korea
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18
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Hristov P, Spassov N, Iliev N, Radoslavov G. An independent event of Neolithic cattle domestication on the South-eastern Balkans: evidence from prehistoric aurochs and cattle populations. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:383-391. [PMID: 26711535 DOI: 10.3109/19401736.2015.1127361] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Neolithic/Chalcolithic livestock domestication is an important issue for understanding the mode of life and economics of ancient human communities. The Balkans appears to be a crucial point for clarifying the socio-economical interrelations between the Oldest Middle Eastern/Anatolian and newly formed cultures in Europe. Two main hypotheses regarding the early history of cattle domestication, from their ancestor - the aurochs, have been discussed: multipoint domestication centers or single point origin and subsequent worldwide dissemination. In this study, we provide molecular data about the Balkan aurochs for the first time as well as additional information for the Neolithic/Chalcolithic cattle populations in this geographic location. A total of seventeen samples from different ancient settlements were analyzed according to D-loop control region. The results did not show different genetic profile of wild and domestic populations. All haplotypes were found to belong to the basic macro-haplogroup T. The majority of specimens (n = 14) were defined to form a new Balkan-specific T6 haplogroup. Only two of the ancient samples analyzed were assigned to the T3 haplotype predominating in Europe. We attempt to throw new light on the earliest cattle domestication events in Europe, thus, the results presented are discussed in two directions: (a) The possibility of local independent domestication processes in Neolithic South-Eastern Europe; (b) The single point domestication in the Middle East and subsequent cattle dissemination in Europe. Our data does not exclude the possibility for independent domestication events followed by a second wave of parallel dissemination of cattle herds via the Mediterranean route.
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Affiliation(s)
- Peter Hristov
- a Department of Animal Diversity and Resources , Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences , Sofia 1113 , Bulgaria
| | - Nikolai Spassov
- b Palaeontology and Mineralogy Department , National Museum of Natural History, Bulgarian Academy of Sciences , 1 "Tsar Osvoboditel" Blvd , Sofia 1000 , Bulgaria
| | - Nikolai Iliev
- b Palaeontology and Mineralogy Department , National Museum of Natural History, Bulgarian Academy of Sciences , 1 "Tsar Osvoboditel" Blvd , Sofia 1000 , Bulgaria
| | - Georgi Radoslavov
- a Department of Animal Diversity and Resources , Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences , Sofia 1113 , Bulgaria
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19
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Yonesaka R, Sasazaki S, Yasue H, Niwata S, Inayoshi Y, Mukai F, Mannen H. Genetic structure and relationships of 16 Asian and European cattle populations using DigiTag2 assay. Anim Sci J 2015; 87:190-6. [PMID: 26260416 PMCID: PMC5042107 DOI: 10.1111/asj.12416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/02/2015] [Accepted: 02/04/2015] [Indexed: 11/29/2022]
Abstract
In this study, we genotyped 117 autosomal single nucleotide polymorphisms using a DigiTag2 assay to assess the genetic diversity, structure and relationships of 16 Eurasian cattle populations, including nine cattle breeds and seven native cattle. Phylogenetic and principal component analyses showed that Bos taurus and Bos indicus populations were clearly distinguished, whereas Japanese Shorthorn and Japanese Polled clustered with European populations. Furthermore, STRUCTURE analysis demonstrated the distinct separation between Bos taurus and Bos indicus (K=2), and between European and Asian populations (K=3). In addition, Japanese Holstein exhibited an admixture pattern with Asian and European cattle (K=3‐5). Mongolian (K=13‐16) and Japanese Black (K=14‐16) populations exhibited admixture patterns with different ancestries. Bos indicus populations exhibited a uniform genetic structure at K=2‐11, thereby suggesting that there are close genetic relationships among Bos indicus populations. However, the Bhutan and Bangladesh populations formed a cluster distinct from the other Bos indicus populations at K=12‐16. In conclusion, our study could sufficiently explain the genetic construction of Asian cattle populations, including: (i) the close genetic relationships among Bos indicus populations; (ii) the genetic influences of European breeds on Japanese breeds; (iii) the genetic admixture in Japanese Holstein, Mongolian and Japanese Black cattle; and (iv) the genetic subpopulations in Southeast Asia.
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Affiliation(s)
- Riku Yonesaka
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | | | | | - Yousuke Inayoshi
- Yamaguchi Prefectural Agriculture & Forestry General Technology Center, Yamaguchi, Japan
| | | | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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20
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Zhang L, Jia S, Plath M, Huang Y, Li C, Lei C, Zhao X, Chen H. Impact of Parental Bos taurus and Bos indicus Origins on Copy Number Variation in Traditional Chinese Cattle Breeds. Genome Biol Evol 2015; 7:2352-61. [PMID: 26260653 PMCID: PMC4558867 DOI: 10.1093/gbe/evv151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also in domestication. Chinese cattle were derived from Bos taurus and Bos indicus, and several breeds presumably are of hybrid origin, but the evolution of CNV regions (CNVRs) has not yet been examined in this context. Here, we of CNVRs, mtDNA D-loop sequence variation, and Y-chromosomal single nucleotide polymorphisms to assess the impact of maternal and paternal B. taurus and B. indicus origins on the distribution of CNVRs in 24 Chinese domesticated bulls. We discovered 470 genome-wide CNVRs, only 72 of which were shared by all three Y-lineages (B. taurus: Y1, Y2; B. indicus: Y3), whereas 265 were shared by inferred taurine or indicine paternal lineages, and 228 when considering their maternal taurine or indicine origins. Phylogenetic analysis uncovered eight taurine/indicine hybrids, and principal component analysis on CNVs corroborated genomic exchange during hybridization. The distribution patterns of CNVRs tended to be lineage-specific, and correlation analysis revealed significant positive or negative co-occurrences of CNVRs across lineages. Our study suggests that CNVs in Chinese cattle partly result from selective breeding during domestication, but also from hybridization and introgression.
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Affiliation(s)
- Liangzhi Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China Key laboratory of adaptation and evolution of plateau biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences
| | - Shangang Jia
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Martin Plath
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Yongzhen Huang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Congjun Li
- United States Department of Agriculture-Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, Maryland
| | - Chuzhao Lei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Xin Zhao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Hong Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
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21
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Kim JH, Byun MJ, Kim MJ, Suh SW, Ko YG, Lee CW, Jung KS, Kim ES, Yu DJ, Kim WH, Choi SB. mtDNA Diversity and Phylogenetic State of Korean Cattle Breed, Chikso. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:163-70. [PMID: 25049772 PMCID: PMC4093160 DOI: 10.5713/ajas.2012.12499] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/19/2012] [Accepted: 10/11/2012] [Indexed: 11/27/2022]
Abstract
In order to analyze the genetic diversity and phylogenetic status of the Korean Chikso breed, we determined sequences of mtDNA cytochrome b (cyt b) gene and performed phylogenetic analysis using 239 individuals from 5 Chikso populations. Five non-synonymous mutations of a total of 15 polymorphic sites were identified among 239 cyt b coding sequences. Thirteen haplotypes were defined, and haplotype diversity was 0.4709 ranging from 0.2577 to 0.6114. Thirty-five haplotypes (C1–C35) were classified among 9 Asia and 3 European breeds. C2 was a major haplotype that contained 206 sequences (64.6%) from all breeds used. C3–C13 haplotypes were Chikso-specific haplotypes. C1 and C2 haplotypes contained 80.5% of cyt b sequences of Hanwoo, Yanbian, Zaosheng and JB breeds. In phylogenetic analyses, the Chikso breed was contained into B. taurus lineage and was genetically more closely related to two Chinese breeds than to Korean brown cattle, Hanwoo. These results suggest that Chikso and Hanwoo have a genetic difference based on the mtDNA cyt b gene as well as their coat color, sufficient for classification as a separate breed.
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Affiliation(s)
- Jae-Hwan Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Mi Jeong Byun
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Myung-Jick Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Sang Won Suh
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Yeoung-Gyu Ko
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Chang Woo Lee
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Kyoung-Sub Jung
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Eun Sung Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Dae Jung Yu
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Woo Hyun Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Seong-Bok Choi
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
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22
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A new subspecies identification and population study of the Asian small-clawed otter (Aonyx cinereus) in Malay Peninsula and southern Thailand based on fecal DNA method. ScientificWorldJournal 2014; 2014:457350. [PMID: 24715812 PMCID: PMC3970038 DOI: 10.1155/2014/457350] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 12/29/2013] [Indexed: 11/17/2022] Open
Abstract
Three species of otter can be found throughout Malay Peninsula: Aonyx cinereus, Lutra sumatrana, and Lutrogale perspicillata. In this study, we focused on the A. cinereus population that ranges from the southern and the east coast to the northern regions of Malay Peninsula up to southern Thailand to review the relationships between the populations based on the mitochondrial D-loop region. Forty-eight samples from six populations were recognized as Johor, Perak, Terengganu, Kelantan, Ranong, and Thale Noi. Among the 48 samples, 33 were identified as A. cinereus, seven as L. sumatrana, and eight as L. perspicillata. Phylogenetically, two subclades formed for A. cinereus. The first subclade grouped all Malay Peninsula samples except for samples from Kelantan, and the second subclade grouped Kelantan samples with Thai sample. Genetic distance analysis supported the close relationships between Thai and Kelantan samples compared to the samples from Terengganu and the other Malaysian states. A minimum-spanning network showed that Kelantan and Thailand formed a haplogroup distinct from the other populations. Our results show that Thai subspecies A. cinereus may have migrated to Kelantan from Thai mainland. We also suggest the classification of a new subspecies from Malay Peninsula, the small-clawed otter named A. cinereus kecilensis.
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Yue X, Li R, Liu L, Zhang Y, Huang J, Chang Z, Dang R, Lan X, Chen H, Lei C. When and how did Bos indicus introgress into Mongolian cattle? Gene 2014; 537:214-9. [DOI: 10.1016/j.gene.2013.12.066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 12/31/2013] [Indexed: 11/28/2022]
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Syed-Shabthar SMF, Rosli MKA, Mohd-Zin NAA, Romaino SMN, Fazly-Ann ZA, Mahani MC, Abas-Mazni O, Zainuddin R, Yaakop S, Md-Zain BM. The molecular phylogenetic signature of Bali cattle revealed by maternal and paternal markers. Mol Biol Rep 2013; 40:5165-76. [PMID: 23686165 DOI: 10.1007/s11033-013-2619-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 04/30/2013] [Indexed: 11/28/2022]
Abstract
Bali cattle is a domestic cattle breed that can be found in Malaysia. It is a domestic cattle that was purely derived from a domestication event in Banteng (Bos javanicus) around 3,500 BC in Indonesia. This research was conducted to portray the phylogenetic relationships of the Bali cattle with other cattle species in Malaysia based on maternal and paternal lineage. We analyzed the cytochrome c oxidase I (COI) mitochondrial gene and SRY of Y chromosome obtained from five species of the Bos genus (B. javanicus, Bos gaurus, Bos indicus, Bos taurus, and Bos grunniens). The water buffalo (Bubalus bubalis) was used as an outgroup. The phylogenetic relationships were observed by employing several algorithms: Neighbor-Joining (PAUP version 4.0), Maximum parsimony (PAUP version 4.0) and Bayesian inference (MrBayes 3.1). Results from the maternal data showed that the Bali cattle formed a monophyletic clade, and together with the B. gaurus clade formed a wild cattle clade. Results were supported by high bootstrap and posterior probability values together with genetic distance data. For the paternal lineage, the sequence variation is low (with parsimony informative characters: 2/660) resulting an unresolved Neighbor-Joining tree. However, Bali cattle and other domestic cattle appear in two monophyletic clades distinct from yak, gaur and selembu. This study expresses the potential of the COI gene in portraying the phylogenetic relationships between several Bos species which is important for conservation efforts especially in decision making since cattle is highly bred and hybrid breeds are often formed. Genetic conservation for this high quality beef cattle breed is important by maintaining its genetic characters to prevent extinction or even decreased the genetic quality.
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Affiliation(s)
- S M F Syed-Shabthar
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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Prystupa JM, Hind P, Cothran EG, Plante Y. Maternal lineages in native Canadian equine populations and their relationship to the Nordic and Mountain and Moorland pony breeds. J Hered 2012; 103:380-90. [PMID: 22504109 DOI: 10.1093/jhered/ess003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A 378-bp section of the mitochondrial displacement loop was used to estimate genetic diversity in the native Canadian equine populations. The inclusion of 10 Mountain and Moorland, 3 Nordic pony breeds, 2 feral populations, and 5 horse breeds were also investigated as they may have influenced the development (or rejuvenation) of the native Canadian populations. A total of 281 samples were sequenced, which produced 75 haplotypes derived from 54 informative sites. On further investigation, 36 of these 75 haplotypes were found to be previously unreported. Overall, total diversity was lowest in the feral Sable Island population with a haplotype diversity (0.27 ± 0.12), nucleotide diversity (0.0007 ± 0.0004), and pairwise difference of 0.286 ± 0.317. This is not surprising due to the geographic isolation of this population. Haplotype diversity was highest (1.00 ± 0.13) in the New Forest population, pairwise difference was highest (8.061 ± 4.028) in the Icelandic breed, whereas nucleotide diversity was highest in the Exmoor breed (0.0209 ± 0.0025). Within the Canadian populations, haplotype diversity was highest in the Newfoundland pony (0.96 ± 0.08), whereas pairwise difference and nucleotide diversity was highest in the Canadian horse (7.090 ± 3.581 and 0.0188 ± 0.0042, respectively). Three different estimates of genetic distances were used to examine the phylogenetic relationships amongst these populations. All 3 estimates produced similar topologies. In general, the native Canadian populations were highly represented in the D clade, with particular emphasis in the D1 and D2 clades. This is an important factor when considering the phylogenetic conservation of these Canadian equine populations.
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Affiliation(s)
- Jaclyn Mercedes Prystupa
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5A8.
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